From b47500618a733eed0960df5cfd223044371ec5e9 Mon Sep 17 00:00:00 2001 From: Charles Date: Mon, 15 Jun 2015 07:07:49 +0000 Subject: [PATCH 001/165] Fixed extra_dir ('job_works') doesn't overwrite from objectstore xml. --- lib/galaxy/objectstore/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py index 123d16b846b..dd00800fc15 100644 --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -208,7 +208,7 @@ class DiskObjectStore(ObjectStore): if e.tag == 'files_dir': self.file_path = e.get('path') else: - self.extra_dirs[e.tag] = e.get('path') + self.extra_dirs[e.get('type')] = e.get('path') if extra_dirs is not None: self.extra_dirs.update( extra_dirs ) From 521b287b134691ddb50efc936b4e483351dc7b12 Mon Sep 17 00:00:00 2001 From: Charles Date: Mon, 15 Jun 2015 09:17:59 +0000 Subject: [PATCH 002/165] Add extra_dir options for S3/Swift ObjectStore. --- config/object_store_conf.xml.sample | 12 ++++++++---- lib/galaxy/objectstore/s3.py | 8 ++++++++ 2 files changed, 16 insertions(+), 4 deletions(-) diff --git a/config/object_store_conf.xml.sample b/config/object_store_conf.xml.sample index 51e1a1529d7..b373e7b5b49 100644 --- a/config/object_store_conf.xml.sample +++ b/config/object_store_conf.xml.sample @@ -23,9 +23,11 @@ @@ -34,7 +36,9 @@ - + + + --> diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py index 361c40a915a..a474fba3b0b 100644 --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -92,6 +92,14 @@ class S3ObjectStore(ObjectStore): self.conn_path = cn_xml.get('conn_path', '/') c_xml = config_xml.findall('cache')[0] self.cache_size = float(c_xml.get('size', -1)) + self.staging_path = c_xml.get('path', self.config.object_store_cache_path) + + for d_xml in config_xml.findall('extra_dir'): + self.extra_dirs[d_xml.get('type')] = d_xml.get('path') + + log.debug("Object cache dir: %s", self.staging_path) + log.debug(" job work dir: %s", self.extra_dirs['job_work']) + # for multipart upload self.s3server = {'access_key': self.access_key, 'secret_key': self.secret_key, From ea96c7142a98b53baa5d5e38b157eb8d516dcb80 Mon Sep 17 00:00:00 2001 From: Charles Date: Mon, 15 Jun 2015 18:04:27 +0000 Subject: [PATCH 003/165] Added job_work option support for S3/Swift ObjectStore. Fixed the failure when removes job script and files. --- lib/galaxy/objectstore/s3.py | 40 ++++++++++++++++++++++++++++++++++-- 1 file changed, 38 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py index a474fba3b0b..9ebe15455d3 100644 --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -208,15 +208,24 @@ class S3ObjectStore(ObjectStore): continue umask_fix_perms( path, self.config.umask, 0666, self.config.gid ) - def _construct_path(self, obj, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, **kwargs): + def _construct_path(self, obj, base_dir=None, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, **kwargs): rel_path = os.path.join(*directory_hash_id(obj.id)) if extra_dir is not None: if extra_dir_at_root: rel_path = os.path.join(extra_dir, rel_path) else: rel_path = os.path.join(rel_path, extra_dir) + + # for JOB_WORK directory + if obj_dir: + rel_path = os.path.join(rel_path, str(obj.id)) + if base_dir: + base = self.extra_dirs.get(base_dir) + return os.path.join(base, rel_path) + # S3 folders are marked by having trailing '/' so add it now rel_path = '%s/' % rel_path + if not dir_only: rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id) return rel_path @@ -382,6 +391,7 @@ class S3ObjectStore(ObjectStore): def exists(self, obj, **kwargs): in_cache = in_s3 = False rel_path = self._construct_path(obj, **kwargs) + # Check cache if self._in_cache(rel_path): in_cache = True @@ -390,11 +400,18 @@ class S3ObjectStore(ObjectStore): # log.debug("~~~~~~ File '%s' exists in cache: %s; in s3: %s" % (rel_path, in_cache, in_s3)) # dir_only does not get synced so shortcut the decision dir_only = kwargs.get('dir_only', False) + base_dir = kwargs.get('base_dir', None) if dir_only: if in_cache or in_s3: return True + # for JOB_WORK directory + elif base_dir: + if not os.path.exists(rel_path): + os.makedirs(rel_path) + return True else: return False + # TODO: Sync should probably not be done here. Add this to an async upload stack? if in_cache and not in_s3: self._push_to_os(rel_path, source_file=self._get_cache_path(rel_path)) @@ -406,11 +423,13 @@ class S3ObjectStore(ObjectStore): def create(self, obj, **kwargs): if not self.exists(obj, **kwargs): + # Pull out locally used fields extra_dir = kwargs.get('extra_dir', None) extra_dir_at_root = kwargs.get('extra_dir_at_root', False) dir_only = kwargs.get('dir_only', False) alt_name = kwargs.get('alt_name', None) + # Construct hashed path rel_path = os.path.join(*directory_hash_id(obj.id)) @@ -420,10 +439,12 @@ class S3ObjectStore(ObjectStore): rel_path = os.path.join(extra_dir, rel_path) else: rel_path = os.path.join(rel_path, extra_dir) + # Create given directory in cache cache_dir = os.path.join(self.staging_path, rel_path) if not os.path.exists(cache_dir): os.makedirs(cache_dir) + # Although not really necessary to create S3 folders (because S3 has # flat namespace), do so for consistency with the regular file system # S3 folders are marked by having trailing '/' so add it now @@ -457,7 +478,15 @@ class S3ObjectStore(ObjectStore): def delete(self, obj, entire_dir=False, **kwargs): rel_path = self._construct_path(obj, **kwargs) extra_dir = kwargs.get('extra_dir', None) + base_dir = kwargs.get('base_dir', None) + dir_only = kwargs.get('dir_only', False) + obj_dir = kwargs.get('obj_dir', False) try: + # Remove temparory data in JOB_WORK directory + if base_dir and dir_only and obj_dir: + shutil.rmtree(os.path.abspath(rel_path)) + return True + # For the case of extra_files, because we don't have a reference to # individual files/keys we need to remove the entire directory structure # with all the files in it. This is easy for the local file system, @@ -496,9 +525,16 @@ class S3ObjectStore(ObjectStore): data_file.close() return content - def get_filename(self, obj, **kwargs): + def get_filename(self, obj, **kwargs): + base_dir = kwargs.get('base_dir', None) dir_only = kwargs.get('dir_only', False) + obj_dir = kwargs.get('obj_dir', False) rel_path = self._construct_path(obj, **kwargs) + + # for JOB_WORK directory + if base_dir and dir_only and obj_dir: + return os.path.abspath(rel_path) + cache_path = self._get_cache_path(rel_path) # S3 does not recognize directories as files so cannot check if those exist. # So, if checking dir only, ensure given dir exists in cache and return From f5160f296da24e80f0fc9337e458347603358b85 Mon Sep 17 00:00:00 2001 From: Charles Date: Tue, 16 Jun 2015 09:18:01 +0000 Subject: [PATCH 004/165] Fixed pylint errors. --- lib/galaxy/objectstore/s3.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py index 9ebe15455d3..1ec6694c75d 100644 --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -93,10 +93,10 @@ class S3ObjectStore(ObjectStore): c_xml = config_xml.findall('cache')[0] self.cache_size = float(c_xml.get('size', -1)) self.staging_path = c_xml.get('path', self.config.object_store_cache_path) - + for d_xml in config_xml.findall('extra_dir'): self.extra_dirs[d_xml.get('type')] = d_xml.get('path') - + log.debug("Object cache dir: %s", self.staging_path) log.debug(" job work dir: %s", self.extra_dirs['job_work']) @@ -222,10 +222,10 @@ class S3ObjectStore(ObjectStore): if base_dir: base = self.extra_dirs.get(base_dir) return os.path.join(base, rel_path) - + # S3 folders are marked by having trailing '/' so add it now rel_path = '%s/' % rel_path - + if not dir_only: rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id) return rel_path @@ -423,7 +423,7 @@ class S3ObjectStore(ObjectStore): def create(self, obj, **kwargs): if not self.exists(obj, **kwargs): - + # Pull out locally used fields extra_dir = kwargs.get('extra_dir', None) extra_dir_at_root = kwargs.get('extra_dir_at_root', False) @@ -439,12 +439,12 @@ class S3ObjectStore(ObjectStore): rel_path = os.path.join(extra_dir, rel_path) else: rel_path = os.path.join(rel_path, extra_dir) - + # Create given directory in cache cache_dir = os.path.join(self.staging_path, rel_path) if not os.path.exists(cache_dir): os.makedirs(cache_dir) - + # Although not really necessary to create S3 folders (because S3 has # flat namespace), do so for consistency with the regular file system # S3 folders are marked by having trailing '/' so add it now @@ -525,12 +525,12 @@ class S3ObjectStore(ObjectStore): data_file.close() return content - def get_filename(self, obj, **kwargs): + def get_filename(self, obj, **kwargs): base_dir = kwargs.get('base_dir', None) dir_only = kwargs.get('dir_only', False) obj_dir = kwargs.get('obj_dir', False) rel_path = self._construct_path(obj, **kwargs) - + # for JOB_WORK directory if base_dir and dir_only and obj_dir: return os.path.abspath(rel_path) From 41e346adfe21d1d0bd023ded515e53522f192909 Mon Sep 17 00:00:00 2001 From: "y.hoogstrate@erasmusmc.nl" Date: Wed, 17 Jun 2015 11:11:14 +0200 Subject: [PATCH 005/165] Added support for DotBracket notation --- config/datatypes_conf.xml.sample | 1 + lib/galaxy/datatypes/sequence.py | 86 ++++++++++++++++++++++++++++++++ 2 files changed, 87 insertions(+) diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample index 0c21c79c018..388601fad7a 100644 --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -59,6 +59,7 @@ + diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py index e293606472c..146c803abbf 100644 --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -357,6 +357,12 @@ class Fasta( Sequence ): line = fh.readline().strip() if line == '' or line.startswith( '>' ): break + + # The third line may not contain chars like '()[].' otherwise it's most likely a DotBracket file + line = fh.readline() + if line and re.search("[\(\)\[\]\.]",line): + break + return True else: break #we found a non-empty line, but it's not a fasta header @@ -940,4 +946,84 @@ class RNADotPlotMatrix( data.Data ): pairs = True if seq and coor and pairs: return True + return False + + +class DotBracket ( Sequence ): + edam_format = "format_1457" + file_ext = "dbn" + + sequence_regexp = re.compile( "^[ACGTURYKMSWBDHVN]+$", re.I) + structure_regexp = re.compile( "^[\(\)\.\[\]]*" ) + + def set_meta( self, dataset, **kwd ): + """ + Set the number of sequences and the number of data lines + in dataset. + """ + if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize: + dataset.metadata.data_lines = None + dataset.metadata.sequences = None + dataset.metadata.seconday_structures = None + return + + data_lines = 0 + sequences = 0 + + for line in file( dataset.file_name ): + line = line.strip() + data_lines += 1 + + if line and line.startswith( '>' ): + sequences += 1 + + dataset.metadata.data_lines = data_lines + dataset.metadata.sequences = sequences + + def sniff(self, filename): + """ + The Dot-Bracket format is as follows: + + >sequenceName1 + CCCaaaGGG + (((...))) + >sequenceName2 + GGGuuuCCC + (((...))) + + Because it remains unclear whether the Dot-Bracket format may + contain multiple sequences per file, sniffing is only applied + on the first 3 lines. + """ + + i = 0 + + with open( filename, "r" ) as handle: + for line in handle: + line = line.strip() + + state = i % 3 + + #header line + if state == 0: + if(line[0] != '>'): + return False + + #sequence line + elif state == 1: + if not self.sequence_regexp.match(line): + return False + else: + sequence_size = len(line) + + #dot-bracket structure line + elif state == 2: + if (sequence_size != len(line)) or (not self.structure_regexp.match(line)) or (line.count('(') != line.count(')')) or (line.count('[') != line.count(']')): + return False + else: + return True + + i += 1 + + # Number of lines is less than 3 return False \ No newline at end of file From 4e5338d24e17f237f496b8b97e7032f63dac523e Mon Sep 17 00:00:00 2001 From: "y.hoogstrate@erasmusmc.nl" Date: Wed, 17 Jun 2015 13:31:27 +0200 Subject: [PATCH 006/165] updates to DotBracket --- config/datatypes_conf.xml.sample | 1 + lib/galaxy/datatypes/sequence.py | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample index 388601fad7a..c970956c653 100644 --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -398,6 +398,7 @@ + diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py index 146c803abbf..d03cbddf62a 100644 --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -358,9 +358,9 @@ class Fasta( Sequence ): if line == '' or line.startswith( '>' ): break - # The third line may not contain chars like '()[].' otherwise it's most likely a DotBracket file + # If there is a third line, and it isn't a header line, it may not contain chars like '()[].' otherwise it's most likely a DotBracket file line = fh.readline() - if line and re.search("[\(\)\[\]\.]",line): + if not line.startswith('>') and re.search("[\(\)\[\]\.]",line): break return True From 486899c02167c9875a02a6e0706f097af2c5cffa Mon Sep 17 00:00:00 2001 From: youri Date: Fri, 19 Jun 2015 09:19:16 +0200 Subject: [PATCH 007/165] DotBracket datatype definition is in line with Datatype description at Galaxy wiki --- config/datatypes_conf.xml.sample | 4 +- lib/galaxy/datatypes/sequence.py | 84 +++++++++++++++++--------------- 2 files changed, 48 insertions(+), 40 deletions(-) diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample index c970956c653..f0abccfa30b 100644 --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -59,7 +59,7 @@ - + @@ -398,7 +398,6 @@ - @@ -423,6 +422,7 @@ + diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py index d03cbddf62a..46c238cb430 100644 --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -954,7 +954,7 @@ class DotBracket ( Sequence ): file_ext = "dbn" sequence_regexp = re.compile( "^[ACGTURYKMSWBDHVN]+$", re.I) - structure_regexp = re.compile( "^[\(\)\.\[\]]*" ) + structure_regexp = re.compile( "^[\(\)\.\[\]{}]+$" ) def set_meta( self, dataset, **kwd ): """ @@ -982,48 +982,56 @@ class DotBracket ( Sequence ): def sniff(self, filename): """ - The Dot-Bracket format is as follows: + Galaxy Dbn (Dot-Bracket notation) rules: + + * The first non-empty line is a header line: no comment lines are allowed. + * A header line starts with a '>' symbol and continues with 0 or multiple symbols until the line ends. + * The second non-empty line is a sequence line. + * A sequence line may only include chars that match the Fasta format (https://en.wikipedia.org/wiki/FASTA_format#Sequence_representation) symbols for nucleotides: ACGTURYKMSWBDHVN, and may thus not include whitespaces. + * A sequence line has no prefix and no suffix. + * A sequence line is case insensitive. + * The third non-empty line is a structure (Dot-Bracket) line and only describes the 2D structure of the sequence above it. + * A structure line must consist of the following chars: '.{}[]()'. + * A structure line must be of the same length as the sequence line, and each char represents the structure of the nucleotide above it. + * A structure line has no prefix and no suffix. + * A nucleotide pairs with only 1 or 0 other nucleotides. + * In a structure line, the number of '(' symbols equals the number of ')' symbols, the number of '[' symbols equals the number of ']' symbols and the number of '{' symbols equals the number of '}' symbols. + * The format accepts multiple entries per file, given that each entry is provided as three lines: the header, sequence and structure line. + * Sniffing is only applied on the first entry. + * Empty lines are allowed. + """ - >sequenceName1 - CCCaaaGGG - (((...))) - >sequenceName2 - GGGuuuCCC - (((...))) - - Because it remains unclear whether the Dot-Bracket format may - contain multiple sequences per file, sniffing is only applied - on the first 3 lines. - """ - - i = 0 + state = 0 with open( filename, "r" ) as handle: for line in handle: line = line.strip() - state = i % 3 - - #header line - if state == 0: - if(line[0] != '>'): - return False - - #sequence line - elif state == 1: - if not self.sequence_regexp.match(line): - return False - else: - sequence_size = len(line) - - #dot-bracket structure line - elif state == 2: - if (sequence_size != len(line)) or (not self.structure_regexp.match(line)) or (line.count('(') != line.count(')')) or (line.count('[') != line.count(']')): - return False - else: - return True - - i += 1 + if line: + #header line + if state == 0: + if(line[0] != '>'): + return False + else: + state = 1 + + #sequence line + elif state == 1: + if not self.sequence_regexp.match(line): + return False + else: + sequence_size = len(line) + state = 2 + + #dot-bracket structure line + elif state == 2: + if sequence_size != len(line) or not self.structure_regexp.match(line) or \ + line.count('(') != line.count(')') or \ + line.count('[') != line.count(']') or \ + line.count('{') != line.count('}'): + return False + else: + return True # Number of lines is less than 3 - return False \ No newline at end of file + return False From bd868be6eb9aff76f5e0ebec801d2525d7e1b055 Mon Sep 17 00:00:00 2001 From: abretaud Date: Thu, 25 Jun 2015 12:44:12 +0200 Subject: [PATCH 008/165] fix error when displaying job params for tools containing a section --- templates/show_params.mako | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/templates/show_params.mako b/templates/show_params.mako index 9cf92a31681..a8b102c3842 100644 --- a/templates/show_params.mako +++ b/templates/show_params.mako @@ -22,6 +22,13 @@ %for i in range( len(param_values[input.name]) ): ${ inputs_recursive(input.inputs, param_values[input.name][i], depth=depth+1) } %endfor + %elif input.type == "section": + + ## + ${inputs_recursive_indent( text=input.name, depth=depth )} + + + ${ inputs_recursive( input.inputs, param_values[input.name], depth=depth+1, upgrade_messages=upgrade_messages.get( input.name ) ) } %elif input.type == "conditional": <% try: From afbadc0b0b8f4f87fd906235dca789897b953b03 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Fri, 15 May 2015 15:47:35 -0400 Subject: [PATCH 009/165] Fix function names for dynamic tool test functions. When finding methods to invoke it seems nose uses the raw function name instead of the class's attribute name (I guess this terminology makes sense), but when reporting results it uses the latter. Synchronizing these names therefore allows calling specific tool test methods from the command-line. This change is required to implement galaxyproject/planemo#145. --- test/functional/test_toolbox.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/test/functional/test_toolbox.py b/test/functional/test_toolbox.py index d707690c4c3..99d7c78d9f4 100644 --- a/test/functional/test_toolbox.py +++ b/test/functional/test_toolbox.py @@ -263,13 +263,18 @@ def build_tests( app=None, testing_shed_tools=False, master_api_key=None, user_a baseclasses = ( ToolTestCase, ) namespace = dict() for j, testdef in enumerate( tool.tests ): + test_function_name = 'test_tool_%06d' % j + def make_test_method( td ): def test_tool( self ): self.do_it( td ) + test_tool.__name__ = test_function_name + return test_tool + test_method = make_test_method( testdef ) test_method.__doc__ = "%s ( %s ) > %s" % ( tool.name, tool.id, testdef.name ) - namespace[ 'test_tool_%06d' % j ] = test_method + namespace[ test_function_name ] = test_method namespace[ 'shed_tool_id' ] = shed_tool_id namespace[ 'master_api_key' ] = master_api_key namespace[ 'user_api_key' ] = user_api_key From 03e3541cb907a72e6d1340e19f5b4e03f977d755 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Fri, 26 Jun 2015 12:27:08 -0400 Subject: [PATCH 010/165] Allow workflows executed via the API to run when Tool steps have upgrade messages, by providing allow_tool_upgrades=True within the payload. --- lib/galaxy/webapps/galaxy/api/workflows.py | 3 +++ lib/galaxy/workflow/modules.py | 9 ++++++--- lib/galaxy/workflow/run.py | 4 ++-- lib/galaxy/workflow/run_request.py | 5 ++++- 4 files changed, 15 insertions(+), 6 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py index f0e7aa9e6f5..256fed9372e 100644 --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -126,6 +126,9 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn :param workflow_name: If from_history_id is set - name of the workflow to create when extracting a workflow from history :type workflow_name: str + + :param allow_tool_upgrades: If set to True, any Tool parameter upgrades will not prevent running workflow, defaults to False + :type allow_tool_upgrades: bool """ ways_to_create = set( [ 'workflow_id', diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py index d379bab244b..f07f2ab4a3c 100644 --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -1075,7 +1075,7 @@ class WorkflowModuleInjector(object): return step_errors -def populate_module_and_state( trans, workflow, param_map ): +def populate_module_and_state( trans, workflow, param_map, allow_tool_upgrades=False ): """ Used by API but not web controller, walks through a workflow's steps and populates transient module and state attributes on each. """ @@ -1088,5 +1088,8 @@ def populate_module_and_state( trans, workflow, param_map ): message = "Workflow cannot be run because of validation errors in some steps: %s" % step_errors raise exceptions.MessageException( message ) if step.upgrade_messages: - message = "Workflow cannot be run because of step upgrade messages: %s" % step.upgrade_messages - raise exceptions.MessageException( message ) + if allow_tool_upgrades: + log.debug( 'Workflow step "%i" had upgrade messages: %s', step.id, step.upgrade_messages ) + else: + message = "Workflow cannot be run because of step upgrade messages: %s" % step.upgrade_messages + raise exceptions.MessageException( message ) diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py index 6a07fe4869b..da6f961cff4 100644 --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -58,7 +58,7 @@ def __invoke( trans, workflow, workflow_run_config, workflow_invocation=None, po """ Run the supplied workflow in the supplied target_history. """ if populate_state: - modules.populate_module_and_state( trans, workflow, workflow_run_config.param_map ) + modules.populate_module_and_state( trans, workflow, workflow_run_config.param_map, allow_tool_upgrades=workflow_run_config.allow_tool_upgrades ) invoker = WorkflowInvoker( trans, @@ -95,7 +95,7 @@ def __invoke( trans, workflow, workflow_run_config, workflow_invocation=None, po def queue_invoke( trans, workflow, workflow_run_config, request_params={}, populate_state=True ): if populate_state: - modules.populate_module_and_state( trans, workflow, workflow_run_config.param_map ) + modules.populate_module_and_state( trans, workflow, workflow_run_config.param_map, allow_tool_upgrades=workflow_run_config.allow_tool_upgrades ) workflow_invocation = workflow_run_config_to_request( trans, workflow_run_config, workflow ) workflow_invocation.workflow = workflow return trans.app.workflow_scheduling_manager.queue( diff --git a/lib/galaxy/workflow/run_request.py b/lib/galaxy/workflow/run_request.py index 1dcfae78cb9..420784eed7d 100644 --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -39,12 +39,13 @@ class WorkflowRunConfig( object ): :type param_map: dict """ - def __init__( self, target_history, replacement_dict, copy_inputs_to_history=False, inputs={}, param_map={} ): + def __init__( self, target_history, replacement_dict, copy_inputs_to_history=False, inputs={}, param_map={}, allow_tool_upgrades=False ): self.target_history = target_history self.replacement_dict = replacement_dict self.copy_inputs_to_history = copy_inputs_to_history self.inputs = inputs self.param_map = param_map + self.allow_tool_upgrades = allow_tool_upgrades def normalize_inputs(steps, inputs, inputs_by): @@ -181,6 +182,7 @@ def build_workflow_run_config( trans, workflow, payload ): add_to_history = 'no_add_to_history' not in payload history_param = payload.get('history', '') + allow_tool_upgrades = payload.get( 'allow_tool_upgrades', False ) # Sanity checks. if len( workflow.steps ) == 0: @@ -271,6 +273,7 @@ def build_workflow_run_config( trans, workflow, payload ): replacement_dict=replacement_dict, inputs=normalized_inputs, param_map=param_map, + allow_tool_upgrades=allow_tool_upgrades ) return run_config From 71b963b2d00b85cc367fae9d964dcf10373789bb Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 26 Jun 2015 17:53:56 +0100 Subject: [PATCH 011/165] Fix a few tracebacks when building docs with 'make -C doc/ html' . --- .ci/pep8_sources.txt | 1 + doc/source/conf.py | 2 +- .../bedgraph_to_array_tree_converter.py | 13 +++++++++---- .../wiggle_to_array_tree_converter.py | 9 ++++++--- .../visualization/data_providers/genome.py | 18 ++++++++++-------- 5 files changed, 27 insertions(+), 16 deletions(-) diff --git a/.ci/pep8_sources.txt b/.ci/pep8_sources.txt index aa2457c7dcc..98a13617218 100644 --- a/.ci/pep8_sources.txt +++ b/.ci/pep8_sources.txt @@ -2,6 +2,7 @@ cron/parse_builds.py lib/galaxy/auth lib/galaxy/config.py lib/galaxy/datatypes/{data,proteomics}.py +lib/galaxy/datatypes/converters/{bedgraph_to_array_tree_converter,wiggle_to_array_tree_converter}.py lib/galaxy/exceptions/error_codes.py lib/galaxy/jobs/{__init__,error_level,manager,stock_rules}.py lib/galaxy/main.py diff --git a/doc/source/conf.py b/doc/source/conf.py index 5accee30a00..2b25d7fdce2 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -274,6 +274,6 @@ class Mock(object): return Mock() # adding pbs_python, DRMAA_python, markupsafe, and drmaa here had no effect. -MOCK_MODULES = ['tables', 'decorator', 'numpy'] +MOCK_MODULES = ['tables', 'decorator'] for mod_name in MOCK_MODULES: sys.modules[mod_name] = Mock() diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py index c2bb35760a5..f66b1d8da27 100644 --- a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py +++ b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py @@ -3,13 +3,16 @@ from __future__ import division import sys + from galaxy import eggs -import pkg_resources; pkg_resources.require( "bx-python" ) -from bx.arrays.array_tree import * -# from bx.arrays.wiggle import BedReader + +eggs.require('numpy') # noqa +eggs.require('bx-python') # noqa +from bx.arrays.array_tree import array_tree_dict_from_reader, FileArrayTreeDict BLOCK_SIZE = 100 + class BedGraphReader: def __init__( self, f ): self.f = f @@ -36,6 +39,8 @@ class BedGraphReader: chrom_end = int(feature[2]) score = float(feature[3]) return chrom, chrom_start, chrom_end, None, score + + def main(): input_fname = sys.argv[1] @@ -44,7 +49,7 @@ def main(): reader = BedGraphReader( open( input_fname ) ) # Fill array from reader - d = array_tree_dict_from_reader( reader, {}, block_size = BLOCK_SIZE ) + d = array_tree_dict_from_reader( reader, {}, block_size=BLOCK_SIZE ) for array_tree in d.itervalues(): array_tree.root.build_summary() diff --git a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py index 336c0171371..6332c4ead8a 100644 --- a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py +++ b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py @@ -3,13 +3,16 @@ from __future__ import division import sys + from galaxy import eggs -import pkg_resources; pkg_resources.require( "bx-python" ) -from bx.arrays.array_tree import * +eggs.require('numpy') # noqa +eggs.require('bx-python') # noqa +from bx.arrays.array_tree import array_tree_dict_from_reader, FileArrayTreeDict from bx.arrays.wiggle import WiggleReader BLOCK_SIZE = 100 + def main(): input_fname = sys.argv[1] @@ -18,7 +21,7 @@ def main(): reader = WiggleReader( open( input_fname ) ) # Fill array from reader - d = array_tree_dict_from_reader( reader, {}, block_size = BLOCK_SIZE ) + d = array_tree_dict_from_reader( reader, {}, block_size=BLOCK_SIZE ) for array_tree in d.itervalues(): array_tree.root.build_summary() diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py index 66e102e22b8..b0f02d3e24e 100644 --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -2,25 +2,27 @@ Data providers for genome visualizations. """ -import os, sys, re -import pkg_resources import itertools -import random import math +import os +import random +import re +import sys -pkg_resources.require( "numpy" ) -pkg_resources.require( "bx-python" ) -pkg_resources.require( "pysam" ) +from galaxy import eggs +eggs.require('numpy') # noqa +eggs.require('bx-python') # noqa from bx.interval_index_file import Indexes -from bx.bbi.bigwig_file import BigWigFile from bx.bbi.bigbed_file import BigBedFile +from bx.bbi.bigwig_file import BigWigFile +eggs.require('pysam') # noqa from pysam import csamtools, ctabix +from galaxy.datatypes.interval import Bed, Gff, Gtf from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed, GFFFeature, GFFInterval, GFFReaderWrapper, parse_gff_attributes from galaxy.util.json import loads from galaxy.visualization.data_providers.basic import BaseDataProvider from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and_cigar -from galaxy.datatypes.interval import Bed, Gff, Gtf # # Utility functions. From 11e8a6c30ad174e558466ddd67b5ba70475fbac7 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Mon, 29 Jun 2015 12:06:29 +0100 Subject: [PATCH 012/165] PEP-8 and pylint fixes. --- .ci/pep8_sources.txt | 1 + .../visualization/data_providers/genome.py | 181 +++++++++--------- .../visualization/data_providers/registry.py | 1 + 3 files changed, 89 insertions(+), 94 deletions(-) diff --git a/.ci/pep8_sources.txt b/.ci/pep8_sources.txt index 98a13617218..56c81c25854 100644 --- a/.ci/pep8_sources.txt +++ b/.ci/pep8_sources.txt @@ -17,6 +17,7 @@ lib/galaxy/queue_worker.py lib/galaxy/tags lib/galaxy/tools lib/galaxy/util/{__init__,json,permutations,plugin_config,properties,simplegraph,sockets,sleeper,streamball,submodules,xml_macros}.py +lib/galaxy/visualization/data_providers/{__init__,genome,registry}.py lib/galaxy/web/{proxy,security} lib/galaxy/web/base/{__init__,interactive_environments}.py lib/galaxy/web/formatting.py diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py index b0f02d3e24e..4a36d3f26f3 100644 --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -28,15 +28,17 @@ from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and # Utility functions. # + def float_nan(n): ''' Return None instead of NaN to pass jQuery 1.4's strict JSON ''' - if n != n: # NaN != NaN + if n != n: # NaN != NaN return None else: return float(n) + def get_bounds( reads, start_pos_index, end_pos_index ): ''' Returns the minimum and maximum position for a set of reads. @@ -50,6 +52,7 @@ def get_bounds( reads, start_pos_index, end_pos_index ): max_high = read[ end_pos_index ] return max_low, max_high + def _convert_between_ucsc_and_ensemble_naming( chrom ): ''' Convert between UCSC chromosome ('chr1') naming conventions and Ensembl @@ -62,9 +65,11 @@ def _convert_between_ucsc_and_ensemble_naming( chrom ): # Convert from Ensembl to UCSC return 'chr' + chrom + def _chrom_naming_matches( chrom1, chrom2 ): return ( chrom1.startswith( 'chr' ) and chrom2.startswith( 'chr' ) ) or ( not chrom1.startswith( 'chr' ) and not chrom2.startswith( 'chr' ) ) + class FeatureLocationIndexDataProvider( BaseDataProvider ): """ Reads/writes/queries feature location index (FLI) datasets. @@ -113,6 +118,7 @@ class FeatureLocationIndexDataProvider( BaseDataProvider ): textloc_file.close() return result + class GenomeDataProvider( BaseDataProvider ): """ Base class for genome data providers. All genome providers use BED coordinate @@ -152,7 +158,7 @@ class GenomeDataProvider( BaseDataProvider ): """ Returns chroms/contigs that the dataset contains """ - return None # by default + return None # by default def has_data( self, chrom, start, end, **kwargs ): """ @@ -210,7 +216,6 @@ class GenomeDataProvider( BaseDataProvider ): 'dataset_type': self.dataset_type } - def get_filters( self ): """ Returns filters for provider's data. Return value is a list of @@ -224,7 +229,7 @@ class GenomeDataProvider( BaseDataProvider ): except AttributeError: try: column_names = range( self.original_dataset.metadata.columns ) - except: # Give up + except: # Give up return [] # Dataset must have column types; if not, cannot create filters. @@ -240,7 +245,7 @@ class GenomeDataProvider( BaseDataProvider ): # Some columns are optional, so can't assume that a filter # column is in dataset. if viz_col_index >= len( column_names ): - continue; + continue col_name = column_names[ viz_col_index ] # Make sure that column has a mapped index. If not, do not add filter. try: @@ -248,7 +253,7 @@ class GenomeDataProvider( BaseDataProvider ): except KeyError: continue filters.append( - { 'name' : attrs[ 'name' ], 'type' : column_types[viz_col_index], \ + { 'name' : attrs[ 'name' ], 'type' : column_types[viz_col_index], 'index' : attrs[ 'index' ] } ) return filters @@ -259,6 +264,7 @@ class GenomeDataProvider( BaseDataProvider ): # -- Base mixins and providers -- # + class FilterableMixin: def get_filters( self ): """ Returns a dataset's filters. """ @@ -270,13 +276,14 @@ class FilterableMixin: return True except: return False + def is_float( column_text ): try: float( column_text ) return True except: if column_text.strip().lower() == 'na': - return True #na is special cased to be a float + return True # na is special cased to be a float return False # @@ -307,27 +314,6 @@ class FilterableMixin: 'tool_id': 'gff_filter_by_attribute', 'tool_exp_name': name } ) filter_col += 1 - - ''' - # Old code: use first line in dataset to find attributes. - for i, line in enumerate( open(self.original_dataset.file_name) ): - if not line.startswith('#'): - # Look at first line for attributes and types. - attributes = parse_gff_attributes( line.split('\t')[8] ) - for attr, value in attributes.items(): - # Get attribute type. - if is_int( value ): - attr_type = 'int' - elif is_float( value ): - attr_type = 'float' - else: - attr_type = 'str' - # Add to filters. - if attr_type is not 'str': - filters.append( { 'name': attr, 'type': attr_type, 'index': filter_col } ) - filter_col += 1 - break - ''' elif isinstance( self.original_dataset.datatype, Bed ): # Can filter by score column only. filters = [ { 'name': 'Score', @@ -335,7 +321,7 @@ class FilterableMixin: 'index': filter_col, 'tool_id': 'Filter1', 'tool_exp_name': 'c5' - } ] + } ] return filters @@ -351,8 +337,8 @@ class TabixDataProvider( FilterableMixin, GenomeDataProvider ): def get_iterator( self, chrom, start, end, **kwargs ): start, end = int(start), int(end) - if end >= (2<<29): - end = (2<<29 - 1) # Tabix-enforced maximum + if end >= (2 << 29): + end = (2 << 29 - 1) # Tabix-enforced maximum bgzip_fname = self.dependencies['bgzip'].file_name @@ -371,7 +357,6 @@ class TabixDataProvider( FilterableMixin, GenomeDataProvider ): return iterator - def write_data_to_file( self, regions, filename ): out = open( filename, "w" ) @@ -390,6 +375,7 @@ class TabixDataProvider( FilterableMixin, GenomeDataProvider ): # -- Interval data providers -- # + class IntervalDataProvider( GenomeDataProvider ): dataset_type = 'interval_index' @@ -415,8 +401,11 @@ class IntervalDataProvider( GenomeDataProvider ): no_detail = ( "no_detail" in kwargs ) rval = [] message = None + # Subtract one b/c columns are 1-based but indices are 0-based. - col_fn = lambda col: None if col is None else col - 1 + def col_fn(col): + return None if col is None else col - 1 + start_col = self.original_dataset.metadata.startCol - 1 end_col = self.original_dataset.metadata.endCol - 1 strand_col = col_fn( self.original_dataset.metadata.strandCol ) @@ -424,14 +413,14 @@ class IntervalDataProvider( GenomeDataProvider ): for count, line in enumerate( iterator ): if count < start_val: continue - if max_vals and count-start_val >= max_vals: + if max_vals and count - start_val >= max_vals: message = self.error_max_vals % ( max_vals, "features" ) break feature = line.split() length = len(feature) # Unique id is just a hash of the line - payload = [ hash(line), int( feature[start_col] ), int( feature [end_col] ) ] + payload = [ hash(line), int( feature[start_col] ), int( feature[end_col] ) ] if no_detail: rval.append( payload ) @@ -442,7 +431,8 @@ class IntervalDataProvider( GenomeDataProvider ): payload.append( feature[name_col] ) if strand_col: # Put empty name as placeholder. - if not name_col: payload.append( "" ) + if not name_col: + payload.append( "" ) payload.append( feature[strand_col] ) # Score (filter data) @@ -459,6 +449,7 @@ class IntervalDataProvider( GenomeDataProvider ): def write_data_to_file( self, regions, filename ): raise Exception( "Unimplemented Function" ) + class IntervalTabixDataProvider( TabixDataProvider, IntervalDataProvider ): """ Provides data from a BED file indexed via tabix. @@ -499,7 +490,7 @@ class BedDataProvider( GenomeDataProvider ): for count, line in enumerate( iterator ): if count < start_val: continue - if max_vals and count-start_val >= max_vals: + if max_vals and count - start_val >= max_vals: message = self.error_max_vals % ( max_vals, "features" ) break # TODO: can we use column metadata to fill out payload? @@ -560,12 +551,14 @@ class BedDataProvider( GenomeDataProvider ): out.close() + class BedTabixDataProvider( TabixDataProvider, BedDataProvider ): """ Provides data from a BED file indexed via tabix. """ pass + class RawBedDataProvider( BedDataProvider ): """ Provide data from BED file. @@ -592,8 +585,8 @@ class RawBedDataProvider( BedDataProvider ): feature_start = int( feature[1] ) feature_end = int( feature[2] ) if ( chrom is not None and feature_chrom != chrom ) \ - or ( start is not None and feature_start > end ) \ - or ( end is not None and feature_end < start ): + or ( start is not None and feature_start > end ) \ + or ( end is not None and feature_end < start ): continue yield line @@ -603,6 +596,7 @@ class RawBedDataProvider( BedDataProvider ): # -- VCF data providers -- # + class VcfDataProvider( GenomeDataProvider ): """ Abstract class that processes VCF data from native format to payload format. @@ -671,7 +665,7 @@ class VcfDataProvider( GenomeDataProvider ): for count, line in enumerate( iterator ): if count < start_val: continue - if max_vals and count-start_val >= max_vals: + if max_vals and count - start_val >= max_vals: message = self.error_max_vals % ( max_vals, "features" ) break @@ -680,11 +674,9 @@ class VcfDataProvider( GenomeDataProvider ): pos, c_id, ref, alt, qual, c_filter, info = feature[ 1:8 ] # Format and samples data are optional. - format = None samples_data = [] if len( feature ) > 8: - format = feature[ 8 ] - samples_data = feature [ 9: ] + samples_data = feature[ 9: ] # VCF is 1-based but provided position is 0-based. pos = int( pos ) - 1 @@ -695,7 +687,7 @@ class VcfDataProvider( GenomeDataProvider ): continue # Set up array to track allele counts. - allele_counts = [ 0 for i in range ( alt.count( ',' ) + 1 ) ] + allele_counts = [ 0 for i in range( alt.count( ',' ) + 1 ) ] sample_gts = [] if samples_data: @@ -730,7 +722,7 @@ class VcfDataProvider( GenomeDataProvider ): # No samples, so set allele count and sample genotype manually. allele_counts = [ 1 ] sample_gts = [ '1/1' ] - + # Add locus data. locus_data = [ -1, @@ -760,6 +752,7 @@ class VcfDataProvider( GenomeDataProvider ): out.write( "%s\n" % line ) out.close() + class VcfTabixDataProvider( TabixDataProvider, VcfDataProvider ): """ Provides data from a VCF file indexed via tabix. @@ -767,6 +760,7 @@ class VcfTabixDataProvider( TabixDataProvider, VcfDataProvider ): dataset_type = 'variant' + class RawVcfDataProvider( VcfDataProvider ): """ Provide data from VCF file. @@ -779,13 +773,10 @@ class RawVcfDataProvider( VcfDataProvider ): source = open( self.original_dataset.file_name ) # Skip comments. - pos = 0 line = None for line in source: if not line.startswith("#"): break - else: - pos = source.tell() # If last line is a comment, there are no data lines. if line.startswith( "#" ): @@ -817,6 +808,7 @@ class RawVcfDataProvider( VcfDataProvider ): return line_filter_iter() + class BamDataProvider( GenomeDataProvider, FilterableMixin ): """ Provides access to intervals from a sorted indexed BAM file. Coordinate @@ -834,18 +826,17 @@ class BamDataProvider( GenomeDataProvider, FilterableMixin ): filters = [] filters.append( { 'name': 'Mapping Quality', 'type': 'number', - 'index': filter_col - } ) + 'index': filter_col } + ) return filters - def write_data_to_file( self, regions, filename ): """ Write reads in regions to file. """ # Open current BAM file using index. - bamfile = csamtools.Samfile( filename=self.original_dataset.file_name, mode='rb', \ + bamfile = csamtools.Samfile( filename=self.original_dataset.file_name, mode='rb', index_filename=self.converted_dataset.file_name ) # TODO: write headers as well? @@ -859,7 +850,7 @@ class BamDataProvider( GenomeDataProvider, FilterableMixin ): try: data = bamfile.fetch(start=start, end=end, reference=chrom) - except ValueError, e: + except ValueError: # Try alternative chrom naming. chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) try: @@ -887,7 +878,7 @@ class BamDataProvider( GenomeDataProvider, FilterableMixin ): bamfile = csamtools.Samfile( filename=orig_data_filename, mode='rb', index_filename=index_filename ) try: data = bamfile.fetch( start=start, end=end, reference=chrom ) - except ValueError, e: + except ValueError: # Try alternative chrom naming. chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) try: @@ -895,9 +886,8 @@ class BamDataProvider( GenomeDataProvider, FilterableMixin ): except ValueError: return None return data - - def process_data( self, iterator, start_val=0, max_vals=None, ref_seq=None, + def process_data( self, iterator, start_val=0, max_vals=None, ref_seq=None, iterator_type='nth', mean_depth=None, start=0, end=0, **kwargs ): """ Returns a dict with the following attributes:: @@ -932,7 +922,7 @@ class BamDataProvider( GenomeDataProvider, FilterableMixin ): def decode_strand( read_flag, mask ): """ Decode strand from read flag. """ - + strand_flag = ( read_flag & mask == 0 ) if strand_flag: return "+" @@ -956,16 +946,9 @@ class BamDataProvider( GenomeDataProvider, FilterableMixin ): """ # Convert threshold to N for stepping through iterator. - n = int( 1/threshold ) + n = int( 1 / threshold ) return itertools.islice( read_iterator, None, None, n ) - # Alternatate and much slower implementation that looks for pending pairs. - ''' - for i, e in enumerate( read_iterator ): - if e.qname in paired_pending or ( i % n ) == 0: - yield e - ''' - # -- Choose iterator. -- # Calculate threshold for non-sequential iterators based on mean_depth and read length. @@ -976,8 +959,8 @@ class BamDataProvider( GenomeDataProvider, FilterableMixin ): return { 'data': [], 'message': None, 'max_low': start, 'max_high': start } read_len = len( first_read.seq ) - num_reads = max( ( end - start ) * mean_depth / float ( read_len ), 1 ) - threshold = float( max_vals )/ num_reads + num_reads = max( ( end - start ) * mean_depth / float( read_len ), 1 ) + threshold = float( max_vals ) / num_reads iterator = itertools.chain( iter( [ first_read ] ), iterator ) # Use specified iterator type, save for when threshold is >= 1. @@ -1015,9 +998,9 @@ class BamDataProvider( GenomeDataProvider, FilterableMixin ): seq = read.seq strand = decode_strand( read.flag, 0x0010 ) if read.cigar is not None: - read_len = sum( [cig[1] for cig in read.cigar] ) # Use cigar to determine length + read_len = sum( [cig[1] for cig in read.cigar] ) # Use cigar to determine length else: - read_len = len(seq) # If no cigar, just use sequence length + read_len = len(seq) # If no cigar, just use sequence length if read.is_proper_pair: if qname in paired_pending: @@ -1030,7 +1013,7 @@ class BamDataProvider( GenomeDataProvider, FilterableMixin ): [ pair['start'], pair['end'], pair['cigar'], pair['strand'], pair['seq'] ], [ read.pos, read.pos + read_len, read.cigar, strand, seq ], None, [ pair['mapq'], read.mapq ] - ] ) + ] ) del paired_pending[qname] else: # Insert first of pair. @@ -1042,7 +1025,7 @@ class BamDataProvider( GenomeDataProvider, FilterableMixin ): read.pos, read.pos + read_len, qname, read.cigar, strand, read.seq, read.mapq ] ) count += 1 - + # Take care of reads whose mates are out of range. for qname, read in paired_pending.iteritems(): if read['mate_start'] < read['start']: @@ -1089,7 +1072,7 @@ class BamDataProvider( GenomeDataProvider, FilterableMixin ): read_cigar += '%i%s' % ( op_tuple[1], cigar_ops[ op_tuple[0] ] ) read[ cigar_field ] = read_cigar - # Choose method for processing reads. Use reference-based compression + # Choose method for processing reads. Use reference-based compression # if possible. Otherwise, convert cigar. if ref_seq: # Uppercase for easy comparison. @@ -1114,6 +1097,7 @@ class BamDataProvider( GenomeDataProvider, FilterableMixin ): return { 'data': results, 'message': message, 'max_low': max_low, 'max_high': max_high } + class SamDataProvider( BamDataProvider ): dataset_type = 'bai' @@ -1130,6 +1114,7 @@ class SamDataProvider( BamDataProvider ): self.original_dataset = converted_dataset self.converted_dataset = converted_dataset.metadata.bam_index + class BBIDataProvider( GenomeDataProvider ): """ BBI data provider for the Galaxy track browser. @@ -1144,7 +1129,7 @@ class BBIDataProvider( GenomeDataProvider ): def has_data( self, chrom ): f, bbi = self._get_dataset() all_dat = bbi.query( chrom, 0, 2147483647, 1 ) or \ - bbi.query( _convert_between_ucsc_and_ensemble_naming( chrom ), 0, 2147483647, 1 ) + bbi.query( _convert_between_ucsc_and_ensemble_naming( chrom ), 0, 2147483647, 1 ) f.close() return all_dat is not None @@ -1156,7 +1141,7 @@ class BBIDataProvider( GenomeDataProvider ): # naming convention. def _summarize_bbi( bbi, chrom, start, end, num_points ): return bbi.summarize( chrom, start, end, num_points ) or \ - bbi.summarize( _convert_between_ucsc_and_ensemble_naming( chrom ) , start, end, num_points ) + bbi.summarize( _convert_between_ucsc_and_ensemble_naming( chrom ) , start, end, num_points ) # Bigwig can be a standalone bigwig file, in which case we use # original_dataset, or coming from wig->bigwig conversion in @@ -1203,12 +1188,12 @@ class BBIDataProvider( GenomeDataProvider ): # of interval length. summary = _summarize_bbi( bbi, chrom, start, end, num_points ) if summary: - #mean = summary.sum_data / summary.valid_count + # mean = summary.sum_data / summary.valid_count - ## Standard deviation by bin, not yet used - ## var = summary.sum_squares - mean - ## var /= minimum( valid_count - 1, 1 ) - ## sd = sqrt( var ) + # Standard deviation by bin, not yet used + # var = summary.sum_squares - mean + # var /= minimum( valid_count - 1, 1 ) + # sd = sqrt( var ) pos = start step_size = (end - start) / num_points @@ -1259,12 +1244,14 @@ class BBIDataProvider( GenomeDataProvider ): 'dataset_type': self.dataset_type } + class BigBedDataProvider( BBIDataProvider ): def _get_dataset( self ): # Nothing converts to bigBed so we don't consider converted dataset f = open( self.original_dataset.file_name ) return f, BigBedFile(file=f) + class BigWigDataProvider ( BBIDataProvider ): """ Provides data from BigWig files; position data is reported in 1-based @@ -1277,6 +1264,7 @@ class BigWigDataProvider ( BBIDataProvider ): f = open( self.original_dataset.file_name ) return f, BigWigFile(file=f) + class IntervalIndexDataProvider( FilterableMixin, GenomeDataProvider ): """ Interval index files used for GFF, Pileup files. @@ -1317,7 +1305,6 @@ class IntervalIndexDataProvider( FilterableMixin, GenomeDataProvider ): provides data in the region chrom:start-end """ start, end = int(start), int(end) - source = open( self.original_dataset.file_name ) index = Indexes( self.converted_dataset.file_name ) if chrom not in index.indexes: @@ -1341,10 +1328,10 @@ class IntervalIndexDataProvider( FilterableMixin, GenomeDataProvider ): filter_cols = loads( kwargs.get( "filter_cols", "[]" ) ) no_detail = ( "no_detail" in kwargs ) for count, val in enumerate( iterator ): - start, end, offset = val[0], val[1], val[2] + offset = val[2] if count < start_val: continue - if count-start_val >= max_vals: + if count - start_val >= max_vals: message = self.error_max_vals % ( max_vals, "features" ) break source.seek( offset ) @@ -1360,6 +1347,7 @@ class IntervalIndexDataProvider( FilterableMixin, GenomeDataProvider ): return { 'data': results, 'message': message } + class RawGFFDataProvider( GenomeDataProvider ): """ Provide data from GFF file that has not been indexed. @@ -1414,7 +1402,7 @@ class RawGFFDataProvider( GenomeDataProvider ): for count, ( feature, offset ) in enumerate( iterator ): if count < start_val: continue - if count-start_val >= max_vals: + if count - start_val >= max_vals: message = self.error_max_vals % ( max_vals, "reads" ) break @@ -1422,9 +1410,9 @@ class RawGFFDataProvider( GenomeDataProvider ): payload.insert( 0, offset ) results.append( payload ) - return { 'data': results, 'dataset_type': self.dataset_type, 'message': message } + class GtfTabixDataProvider( TabixDataProvider ): """ Returns data from GTF datasets that are indexed via tabix. @@ -1456,7 +1444,7 @@ class GtfTabixDataProvider( TabixDataProvider ): for count, intervals in enumerate( features.values() ): if count < start_val: continue - if count-start_val >= max_vals: + if count - start_val >= max_vals: message = self.error_max_vals % ( max_vals, "reads" ) break @@ -1471,6 +1459,7 @@ class GtfTabixDataProvider( TabixDataProvider ): # -- ENCODE Peak data providers. # + class ENCODEPeakDataProvider( GenomeDataProvider ): """ Abstract class that processes ENCODEPeak data from native format to payload format. @@ -1486,7 +1475,7 @@ class ENCODEPeakDataProvider( GenomeDataProvider ): Provides """ - ## FIXMEs: + # FIXMEs: # (1) should be able to unify some of this code with BedDataProvider.process_data # (2) are optional number of parameters supported? @@ -1502,12 +1491,11 @@ class ENCODEPeakDataProvider( GenomeDataProvider ): for count, line in enumerate( iterator ): if count < start_val: continue - if max_vals and count-start_val >= max_vals: + if max_vals and count - start_val >= max_vals: message = self.error_max_vals % ( max_vals, "features" ) break feature = line.split() - length = len( feature ) # Feature initialization. payload = [ @@ -1516,7 +1504,7 @@ class ENCODEPeakDataProvider( GenomeDataProvider ): # Add start, end. int( feature[1] ), int( feature[2] ) - ] + ] if no_detail: rval.append( payload ) @@ -1537,12 +1525,13 @@ class ENCODEPeakDataProvider( GenomeDataProvider ): float( feature[6] ), float( feature[7] ), float( feature[8] ) - ] ) + ] ) rval.append( payload ) return { 'data': rval, 'message': message } + class ENCODEPeakTabixDataProvider( TabixDataProvider, ENCODEPeakDataProvider ): """ Provides data from an ENCODEPeak dataset indexed via tabix. @@ -1583,6 +1572,8 @@ class ENCODEPeakTabixDataProvider( TabixDataProvider, ENCODEPeakDataProvider ): # # -- ChromatinInteraction data providers -- # + + class ChromatinInteractionsDataProvider( GenomeDataProvider ): def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): """ @@ -1594,12 +1585,11 @@ class ChromatinInteractionsDataProvider( GenomeDataProvider ): for count, line in enumerate( iterator ): if count < start_val: continue - if max_vals and count-start_val >= max_vals: + if max_vals and count - start_val >= max_vals: message = self.error_max_vals % ( max_vals, "interactions" ) break feature = line.split() - length = len( feature ) s1 = int( feature[1] ) e1 = int( feature[2] ) @@ -1621,7 +1611,8 @@ class ChromatinInteractionsDataProvider( GenomeDataProvider ): return { 'data': rval, 'message': message } def get_default_max_vals( self ): - return 100000; + return 100000 + class ChromatinInteractionsTabixDataProvider( TabixDataProvider, ChromatinInteractionsDataProvider ): def get_iterator( self, chrom, start=0, end=sys.maxint, interchromosomal=False, **kwargs ): @@ -1629,7 +1620,8 @@ class ChromatinInteractionsTabixDataProvider( TabixDataProvider, ChromatinIntera """ # Modify start as needed to get earlier interactions with start region. span = int( end ) - int( start ) - filter_start = max( 0, int( start ) - span - span/2 ) + filter_start = max( 0, int( start ) - span - span / 2 ) + def filter( iter ): for line in iter: feature = line.split() @@ -1650,6 +1642,7 @@ class ChromatinInteractionsTabixDataProvider( TabixDataProvider, ChromatinIntera # -- Helper methods. -- # + def package_gff_feature( feature, no_detail=False, filter_cols=[] ): """ Package a GFF feature in an array for data providers. """ feature = convert_gff_coords_to_bed( feature ) diff --git a/lib/galaxy/visualization/data_providers/registry.py b/lib/galaxy/visualization/data_providers/registry.py index 6d159b73e04..9ab9a980356 100644 --- a/lib/galaxy/visualization/data_providers/registry.py +++ b/lib/galaxy/visualization/data_providers/registry.py @@ -7,6 +7,7 @@ from galaxy.datatypes.interval import Interval, ENCODEPeak, ChromatinInteraction from galaxy.datatypes.xml import Phyloxml from galaxy.datatypes.data import Newick, Nexus + class DataProviderRegistry( object ): """ Registry for data providers that enables listing and lookup. From 025930bfd1af074638c7ce7b2b5190a2ffe42463 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Mon, 29 Jun 2015 15:18:58 +0100 Subject: [PATCH 013/165] Move the additional API doc out of autogenerated docs. --- doc/source/api_doc.rst | 282 ++++++++++++++++++ doc/source/index.rst | 2 +- doc/source/lib/galaxy.webapps.galaxy.api.rst | 286 +------------------ 3 files changed, 285 insertions(+), 285 deletions(-) create mode 100644 doc/source/api_doc.rst diff --git a/doc/source/api_doc.rst b/doc/source/api_doc.rst new file mode 100644 index 00000000000..119b2216786 --- /dev/null +++ b/doc/source/api_doc.rst @@ -0,0 +1,282 @@ +Galaxy API Documentation +************************ + +Background +========== +In addition to being accessible through a web interface, Galaxy can also be +accessed programmatically, through shell scripts and other programs. The web +interface is appropriate for things like exploratory analysis, visualization, +construction of workflows, and rerunning workflows on new datasets. + +The web interface is less suitable for things like + - Connecting a Galaxy instance directly to your sequencer and running + workflows whenever data is ready. + - Running a workflow against multiple datasets (which can be done with the + web interface, but is tedious). + - When the analysis involves complex control, such as looping and + branching. + +The Galaxy API addresses these and other situations by exposing Galaxy +internals through an additional interface, known as an Application Programming +Interface, or API. + +Quickstart +========== + +Log in as your user, navigate to the API Keys page in the User menu, and +generate a new API key. Make a note of the API key, and then pull up a +terminal. Now we'll use the display.py script in your galaxy/scripts/api +directory for a short example:: + + % ./display.py my_key http://localhost:4096/api/histories + Collection Members + ------------------ + #1: /api/histories/8c49be448cfe29bc + name: Unnamed history + id: 8c49be448cfe29bc + #2: /api/histories/33b43b4e7093c91f + name: output test + id: 33b43b4e7093c91f + +The result is a Collection of the histories of the user specified by the API +key (you). To look at the details of a particular history, say #1 above, do +the following:: + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc + Member Information + ------------------ + state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0} + state: ok + contents_url: /api/histories/8c49be448cfe29bc/contents + id: 8c49be448cfe29bc + name: Unnamed history + +This gives detailed information about the specific member in question, in this +case the History. To view history contents, do the following:: + + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents + Collection Members + ------------------ + #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a + name: Pasted Entry + type: file + id: 6f91353f3eb0fa4a + +What we have here is another Collection of items containing all of the datasets +in this particular history. Finally, to view details of a particular dataset +in this collection, execute the following:: + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a + Member Information + ------------------ + misc_blurb: 1 line + name: Pasted Entry + data_type: txt + deleted: False + file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat + state: ok + download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt + visible: True + genome_build: ? + model_class: HistoryDatasetAssociation + file_size: 17 + metadata_data_lines: 1 + id: 6f91353f3eb0fa4a + misc_info: uploaded txt file + metadata_dbkey: ? + +And now you've successfully used the API to request and select a history, +browse the contents of that history, and then look at detailed information +about a particular dataset. + +For a more comprehensive Data Library example, set the following option in your +galaxy.ini as well, and restart galaxy again:: + + admin_users = you@example.org + library_import_dir = /path/to/some/directory + +In the directory you specified for 'library_import_dir', create some +subdirectories, and put (or symlink) files to import into Galaxy into those +subdirectories. + +In Galaxy, create an account that matches the address you put in 'admin_users', +then browse to that user's preferences and generate a new API Key. Copy the +key to your clipboard and then use these scripts:: + + % ./display.py my_key http://localhost:4096/api/libraries + Collection Members + ------------------ + + 0 elements in collection + + % ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library' + Response + -------- + /api/libraries/f3f73e481f432006 + name: api_test + id: f3f73e481f432006 + + % ./display.py my_key http://localhost:4096/api/libraries + Collection Members + ------------------ + /api/libraries/f3f73e481f432006 + name: api_test + id: f3f73e481f432006 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006 + Member Information + ------------------ + synopsis: None + contents_url: /api/libraries/f3f73e481f432006/contents + description: API Test Library + name: api_test + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents + Collection Members + ------------------ + /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 + name: / + type: folder + id: 28202595c0d2591f61ddda595d2c3670 + + % ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1' + Response + -------- + /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 + name: api_test_folder1 + id: 28202595c0d2591fa4f9089d2303fd89 + + % ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19 + Response + -------- + /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b + name: 2.bed + id: e9ef7fdb2db87d7b + /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 + name: 3.bed + id: 3b7f6a31f80a5018 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents + Collection Members + ------------------ + /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 + name: / + type: folder + id: 28202595c0d2591f61ddda595d2c3670 + /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 + name: /api_test_folder1 + type: folder + id: 28202595c0d2591fa4f9089d2303fd89 + /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b + name: /api_test_folder1/2.bed + type: file + id: e9ef7fdb2db87d7b + /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 + name: /api_test_folder1/3.bed + type: file + id: 3b7f6a31f80a5018 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b + Member Information + ------------------ + misc_blurb: 68 regions + metadata_endCol: 3 + data_type: bed + metadata_columns: 6 + metadata_nameCol: 4 + uploaded_by: nate@... + metadata_strandCol: 6 + name: 2.bed + genome_build: hg19 + metadata_comment_lines: None + metadata_startCol: 2 + metadata_chromCol: 1 + file_size: 4272 + metadata_data_lines: 68 + message: + metadata_dbkey: hg19 + misc_info: uploaded bed file + date_uploaded: 2010-06-22T17:01:51.266119 + metadata_column_types: str, int, int, str, int, str + +Other parameters are valid when uploading, they are the same parameters as are +used in the web form, like 'link_data_only' and etc. + +The request and response format should be considered alpha and are subject to change. + +API Design Guidelines +===================== + +The following section outlines guidelines related to extending and/or modifing +the Galaxy API. The Galaxy API has grown in an ad-hoc fashion over time by +many contributors and so clients SHOULD NOT expect the API will conform to +these guidelines - but developers contributing to the Galaxy API SHOULD follow +these guidelines. + + - API functionality should include docstring documentation for consumption + by readthedocs.org. + - Developers should familiarize themselves with the HTTP status code definitions + http://www.w3.org/Protocols/rfc2616/rfc2616-sec10.html. The API responses + should properly set the status code according to the result - in particular + 2XX responses should be used for successful requests, 4XX for various + kinds of client errors, and 5XX for the errors on the server side. + - If there is an error processing some part of request (one item in a list + for instance), the status code should be set to reflect the error and the + partial result may or may not be returned depending on the controller - + this behavior should be documented. + - API methods should throw a finite number of exceptions + (defined in :doc:`galaxy.exceptions`) and these should subclass + `MessageException` and not paste/wsgi HTTP exceptions. When possible, + the framework itself should be responsible catching these exceptions, + setting the status code, and building an error response. + - Error responses should not consist of plain text strings - they should be + dictionaries describing the error and containing the following:: + + { + "status_code": 400, + "err_code": 400007, + "err_msg": "Request contained invalid parameter, action could not be completed.", + "type": "error", + "extra_error_info": "Extra information." + } + + Various error conditions (once a format has been chosen and framework to + enforce it in place) should be spelled out in this document. + - Backward compatibility is important and should be maintained when possible. + If changing behavior in a non-backward compatibile way please ensure one + of the following holds - there is a strong reason to believe no consumers + depend on a behavior, the behavior is effectively broken, or the API + method being modified has not been part of a tagged dist release. + +The following bullet points represent good practices more than guidelines, please +consider them when modifying the API. + + - Functionality should not be copied and pasted between controllers - + consider refactoring functionality into associated classes or short of + that into Mixins (http://en.wikipedia.org/wiki/Composition_over_inheritance) + or into Managers (:doc:`galaxy.managers`). + - API additions are more permanent changes to Galaxy than many other potential + changes and so a second opinion on API changes should be sought. (Consider a + pull request!) + - New API functionality should include functional tests. These functional + tests should be implemented in Python and placed in + `test/functional/api`. (Once such a framework is in place - it is not + right now). + - Changes to reflect modifications to the API should be pushed upstream to + the BioBlend project if possible. + +Longer term goals/notes. + + - It would be advantageous to have a clearer separation of anonymous and + admin handling functionality. + - If at some point in the future, functionality needs to be added that + breaks backward compatibility in a significant way to a component used by + the community - a "dev" variant of the API will be established and + the community should be alerted and given a timeframe for when the old + behavior will be replaced with the new behavior. + - Consistent standards for range-based requests, batch requests, filtered + requests, etc... should be established and documented here. + + +.. include:: lib/galaxy.webapps.galaxy.api.rst diff --git a/doc/source/index.rst b/doc/source/index.rst index 02142d04c86..58450c3aaf2 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -42,7 +42,7 @@ Contents .. toctree:: :maxdepth: 5 - API Documentation + API Documentation Application Documentation diff --git a/doc/source/lib/galaxy.webapps.galaxy.api.rst b/doc/source/lib/galaxy.webapps.galaxy.api.rst index 356449d622d..8b7546bffce 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -1,287 +1,5 @@ -Galaxy API Documentation -************************ - -Background -========== -In addition to being accessible through a web interface, Galaxy can also be -accessed programmatically, through shell scripts and other programs. The web -interface is appropriate for things like exploratory analysis, visualization, -construction of workflows, and rerunning workflows on new datasets. - -The web interface is less suitable for things like - - Connecting a Galaxy instance directly to your sequencer and running - workflows whenever data is ready. - - Running a workflow against multiple datasets (which can be done with the - web interface, but is tedious). - - When the analysis involves complex control, such as looping and - branching. - -The Galaxy API addresses these and other situations by exposing Galaxy -internals through an additional interface, known as an Application Programming -Interface, or API. - -Quickstart -========== - -Log in as your user, navigate to the API Keys page in the User menu, and -generate a new API key. Make a note of the API key, and then pull up a -terminal. Now we'll use the display.py script in your galaxy/scripts/api -directory for a short example:: - - % ./display.py my_key http://localhost:4096/api/histories - Collection Members - ------------------ - #1: /api/histories/8c49be448cfe29bc - name: Unnamed history - id: 8c49be448cfe29bc - #2: /api/histories/33b43b4e7093c91f - name: output test - id: 33b43b4e7093c91f - -The result is a Collection of the histories of the user specified by the API -key (you). To look at the details of a particular history, say #1 above, do -the following:: - - % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc - Member Information - ------------------ - state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0} - state: ok - contents_url: /api/histories/8c49be448cfe29bc/contents - id: 8c49be448cfe29bc - name: Unnamed history - -This gives detailed information about the specific member in question, in this -case the History. To view history contents, do the following:: - - - % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents - Collection Members - ------------------ - #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a - name: Pasted Entry - type: file - id: 6f91353f3eb0fa4a - -What we have here is another Collection of items containing all of the datasets -in this particular history. Finally, to view details of a particular dataset -in this collection, execute the following:: - - % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a - Member Information - ------------------ - misc_blurb: 1 line - name: Pasted Entry - data_type: txt - deleted: False - file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat - state: ok - download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt - visible: True - genome_build: ? - model_class: HistoryDatasetAssociation - file_size: 17 - metadata_data_lines: 1 - id: 6f91353f3eb0fa4a - misc_info: uploaded txt file - metadata_dbkey: ? - -And now you've successfully used the API to request and select a history, -browse the contents of that history, and then look at detailed information -about a particular dataset. - -For a more comprehensive Data Library example, set the following option in your -galaxy.ini as well, and restart galaxy again:: - - admin_users = you@example.org - library_import_dir = /path/to/some/directory - -In the directory you specified for 'library_import_dir', create some -subdirectories, and put (or symlink) files to import into Galaxy into those -subdirectories. - -In Galaxy, create an account that matches the address you put in 'admin_users', -then browse to that user's preferences and generate a new API Key. Copy the -key to your clipboard and then use these scripts:: - - % ./display.py my_key http://localhost:4096/api/libraries - Collection Members - ------------------ - - 0 elements in collection - - % ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library' - Response - -------- - /api/libraries/f3f73e481f432006 - name: api_test - id: f3f73e481f432006 - - % ./display.py my_key http://localhost:4096/api/libraries - Collection Members - ------------------ - /api/libraries/f3f73e481f432006 - name: api_test - id: f3f73e481f432006 - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006 - Member Information - ------------------ - synopsis: None - contents_url: /api/libraries/f3f73e481f432006/contents - description: API Test Library - name: api_test - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents - Collection Members - ------------------ - /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 - name: / - type: folder - id: 28202595c0d2591f61ddda595d2c3670 - - % ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1' - Response - -------- - /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 - name: api_test_folder1 - id: 28202595c0d2591fa4f9089d2303fd89 - - % ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19 - Response - -------- - /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b - name: 2.bed - id: e9ef7fdb2db87d7b - /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 - name: 3.bed - id: 3b7f6a31f80a5018 - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents - Collection Members - ------------------ - /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 - name: / - type: folder - id: 28202595c0d2591f61ddda595d2c3670 - /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 - name: /api_test_folder1 - type: folder - id: 28202595c0d2591fa4f9089d2303fd89 - /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b - name: /api_test_folder1/2.bed - type: file - id: e9ef7fdb2db87d7b - /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 - name: /api_test_folder1/3.bed - type: file - id: 3b7f6a31f80a5018 - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b - Member Information - ------------------ - misc_blurb: 68 regions - metadata_endCol: 3 - data_type: bed - metadata_columns: 6 - metadata_nameCol: 4 - uploaded_by: nate@... - metadata_strandCol: 6 - name: 2.bed - genome_build: hg19 - metadata_comment_lines: None - metadata_startCol: 2 - metadata_chromCol: 1 - file_size: 4272 - metadata_data_lines: 68 - message: - metadata_dbkey: hg19 - misc_info: uploaded bed file - date_uploaded: 2010-06-22T17:01:51.266119 - metadata_column_types: str, int, int, str, int, str - -Other parameters are valid when uploading, they are the same parameters as are -used in the web form, like 'link_data_only' and etc. - -The request and response format should be considered alpha and are subject to change. - -API Design Guidelines -===================== - -The following section outlines guidelines related to extending and/or modifing -the Galaxy API. The Galaxy API has grown in an ad-hoc fashion over time by -many contributors and so clients SHOULD NOT expect the API will conform to -these guidelines - but developers contributing to the Galaxy API SHOULD follow -these guidelines. - - - API functionality should include docstring documentation for consumption - by readthedocs.org. - - Developers should familiarize themselves with the HTTP status code definitions - http://www.w3.org/Protocols/rfc2616/rfc2616-sec10.html. The API responses - should properly set the status code according to the result - in particular - 2XX responses should be used for successful requests, 4XX for various - kinds of client errors, and 5XX for the errors on the server side. - - If there is an error processing some part of request (one item in a list - for instance), the status code should be set to reflect the error and the - partial result may or may not be returned depending on the controller - - this behavior should be documented. - - API methods should throw a finite number of exceptions - (defined in :doc:`galaxy.exceptions`) and these should subclass - `MessageException` and not paste/wsgi HTTP exceptions. When possible, - the framework itself should be responsible catching these exceptions, - setting the status code, and building an error response. - - Error responses should not consist of plain text strings - they should be - dictionaries describing the error and containing the following:: - - { - "status_code": 400, - "err_code": 400007, - "err_msg": "Request contained invalid parameter, action could not be completed.", - "type": "error", - "extra_error_info": "Extra information." - } - - Various error conditions (once a format has been chosen and framework to - enforce it in place) should be spelled out in this document. - - Backward compatibility is important and should be maintained when possible. - If changing behavior in a non-backward compatibile way please ensure one - of the following holds - there is a strong reason to believe no consumers - depend on a behavior, the behavior is effectively broken, or the API - method being modified has not been part of a tagged dist release. - -The following bullet points represent good practices more than guidelines, please -consider them when modifying the API. - - - Functionality should not be copied and pasted between controllers - - consider refactoring functionality into associated classes or short of - that into Mixins (http://en.wikipedia.org/wiki/Composition_over_inheritance) - or into Managers (:doc:`galaxy.managers`). - - API additions are more permanent changes to Galaxy than many other potential - changes and so a second opinion on API changes should be sought. (Consider a - pull request!) - - New API functionality should include functional tests. These functional - tests should be implemented in Python and placed in - `test/functional/api`. (Once such a framework is in place - it is not - right now). - - Changes to reflect modifications to the API should be pushed upstream to - the BioBlend project if possible. - -Longer term goals/notes. - - - It would be advantageous to have a clearer separation of anonymous and - admin handling functionality. - - If at some point in the future, functionality needs to be added that - breaks backward compatibility in a significant way to a component used by - the community - a "dev" variant of the API will be established and - the community should be alerted and given a timeframe for when the old - behavior will be replaced with the new behavior. - - Consistent standards for range-based requests, batch requests, filtered - requests, etc... should be established and documented here. - -API Controllers -=============== - -Galaxy offers the following API controllers: +galaxy.webapps.galaxy.api package +================================= :mod:`annotations` Module ---------------------- From f339cc16313ddaeac066e2f1189c0dd09983ed59 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 26 Jun 2015 16:39:35 +0100 Subject: [PATCH 014/165] Fix doc/source/ using sphinx-apidoc v1.1.3 . --- doc/source/lib/fpconst.rst | 7 - doc/source/lib/galaxy.auth.providers.rst | 35 ++++ doc/source/lib/galaxy.auth.rst | 18 ++ doc/source/lib/galaxy.dataset_collections.rst | 58 ++++++ .../lib/galaxy.dataset_collections.types.rst | 27 +++ .../lib/galaxy.datatypes.converters.rst | 30 +-- .../lib/galaxy.datatypes.dataproviders.rst | 83 ++++++++ .../galaxy.datatypes.display_applications.rst | 8 + doc/source/lib/galaxy.datatypes.rst | 25 +++ doc/source/lib/galaxy.datatypes.util.rst | 8 + doc/source/lib/galaxy.exceptions.rst | 8 + doc/source/lib/galaxy.jobs.deferred.rst | 24 --- .../lib/galaxy.jobs.metrics.collectl.rst | 43 ++++ .../lib/galaxy.jobs.metrics.instrumenters.rst | 59 ++++++ doc/source/lib/galaxy.jobs.metrics.rst | 27 +++ doc/source/lib/galaxy.jobs.rst | 49 +++++ .../lib/galaxy.jobs.runners.cli_job.rst | 19 -- .../lib/galaxy.jobs.runners.cli_shell.rst | 19 -- .../lib/galaxy.jobs.runners.lwr_client.rst | 131 +++++++++++++ ...galaxy.jobs.runners.lwr_client.staging.rst | 27 +++ ...laxy.jobs.runners.lwr_client.transport.rst | 27 +++ doc/source/lib/galaxy.jobs.runners.rst | 28 ++- .../galaxy.jobs.runners.state_handlers.rst | 11 ++ .../lib/galaxy.jobs.runners.util.cli.job.rst | 35 ++++ .../lib/galaxy.jobs.runners.util.cli.rst | 27 +++ .../galaxy.jobs.runners.util.cli.shell.rst | 27 +++ .../lib/galaxy.jobs.runners.util.condor.rst | 11 ++ .../galaxy.jobs.runners.util.job_script.rst | 11 ++ doc/source/lib/galaxy.jobs.runners.util.rst | 44 +++++ doc/source/lib/galaxy.managers.rst | 181 ++++++++++++++--- doc/source/lib/galaxy.model.orm.ext.rst | 19 -- doc/source/lib/galaxy.model.orm.rst | 25 ++- doc/source/lib/galaxy.model.rst | 23 ++- ...alaxy.model.tool_shed_install.migrate.rst} | 2 +- .../lib/galaxy.model.tool_shed_install.rst | 26 +++ doc/source/lib/galaxy.objectstore.rst | 24 +++ doc/source/lib/galaxy.rst | 40 +++- doc/source/lib/galaxy.security.rst | 8 + doc/source/lib/galaxy.tags.rst | 8 - doc/source/lib/galaxy.tool_shed.migrate.rst | 19 -- doc/source/lib/galaxy.tool_shed.rst | 59 ------ .../galaxy.tool_shed.tool_dependencies.rst | 27 --- doc/source/lib/galaxy.tools.actions.rst | 20 +- doc/source/lib/galaxy.tools.data_manager.rst | 19 ++ .../lib/galaxy.tools.deps.resolvers.rst | 59 ++++++ doc/source/lib/galaxy.tools.deps.rst | 69 ++++++- doc/source/lib/galaxy.tools.filters.rst | 11 ++ doc/source/lib/galaxy.tools.genome_index.rst | 19 -- doc/source/lib/galaxy.tools.linters.rst | 67 +++++++ doc/source/lib/galaxy.tools.parameters.rst | 40 ++++ doc/source/lib/galaxy.tools.parser.rst | 51 +++++ doc/source/lib/galaxy.tools.rst | 62 +++++- .../lib/galaxy.tools.toolbox.filters.rst | 11 ++ .../lib/galaxy.tools.toolbox.lineages.rst | 43 ++++ doc/source/lib/galaxy.tools.toolbox.rst | 59 ++++++ doc/source/lib/galaxy.util.log.rst | 19 ++ doc/source/lib/galaxy.util.pastescript.rst | 27 +++ doc/source/lib/galaxy.util.rst | 145 ++++++++++++-- .../galaxy.visualization.data_providers.rst | 8 + .../lib/galaxy.visualization.genome.rst | 8 - .../lib/galaxy.visualization.plugins.rst | 43 ++++ doc/source/lib/galaxy.visualization.rst | 1 + .../lib/galaxy.visualization.tracks.rst | 8 - doc/source/lib/galaxy.web.base.rst | 16 ++ .../lib/galaxy.web.framework.middleware.rst | 24 +++ doc/source/lib/galaxy.web.framework.rst | 24 +++ doc/source/lib/galaxy.web.proxy.rst | 19 ++ doc/source/lib/galaxy.web.rst | 9 + .../galaxy.webapps.community.controllers.rst | 67 ------- ...webapps.community.framework.middleware.rst | 27 --- .../galaxy.webapps.community.framework.rst | 18 -- .../lib/galaxy.webapps.community.model.rst | 26 --- doc/source/lib/galaxy.webapps.community.rst | 46 ----- .../lib/galaxy.webapps.community.security.rst | 11 -- .../lib/galaxy.webapps.community.util.rst | 35 ---- doc/source/lib/galaxy.webapps.galaxy.api.rst | 184 +++++++++++++----- .../lib/galaxy.webapps.galaxy.controllers.rst | 30 ++- .../galaxy.webapps.reports.controllers.rst | 8 + doc/source/lib/galaxy.webapps.rst | 2 +- .../lib/galaxy.webapps.tool_shed.api.rst | 40 ++++ .../galaxy.webapps.tool_shed.controllers.rst | 8 + doc/source/lib/galaxy.webapps.tool_shed.rst | 1 + .../lib/galaxy.webapps.tool_shed.search.rst | 19 ++ .../lib/galaxy.webapps.tool_shed.util.rst | 24 +-- doc/source/lib/galaxy.work.rst | 11 ++ doc/source/lib/galaxy.workflow.rst | 55 ++++++ doc/source/lib/galaxy.workflow.schedulers.rst | 19 ++ doc/source/lib/galaxy_ext.metadata.rst | 19 ++ doc/source/lib/galaxy_ext.rst | 18 ++ doc/source/lib/modules.rst | 4 +- doc/source/lib/pulsar.client.rst | 131 +++++++++++++ doc/source/lib/pulsar.client.staging.rst | 27 +++ doc/source/lib/pulsar.client.transport.rst | 51 +++++ doc/source/lib/pulsar.rst | 10 + doc/source/lib/tool_shed.capsule.rst | 11 ++ .../lib/tool_shed.dependencies.repository.rst | 11 ++ doc/source/lib/tool_shed.dependencies.rst | 19 ++ .../lib/tool_shed.dependencies.tool.rst | 11 ++ .../tool_shed.galaxy_install.datatypes.rst | 11 ++ .../lib/tool_shed.galaxy_install.metadata.rst | 11 ++ ...galaxy_install.repository_dependencies.rst | 11 ++ doc/source/lib/tool_shed.galaxy_install.rst | 39 +++- ...alaxy_install.tool_dependencies.recipe.rst | 51 +++++ ..._shed.galaxy_install.tool_dependencies.rst | 21 +- .../lib/tool_shed.galaxy_install.tools.rst | 19 ++ ...shed.galaxy_install.utility_containers.rst | 11 ++ doc/source/lib/tool_shed.grids.rst | 8 + doc/source/lib/tool_shed.managers.rst | 19 ++ doc/source/lib/tool_shed.metadata.rst | 19 ++ doc/source/lib/tool_shed.repository_types.rst | 51 +++++ doc/source/lib/tool_shed.rst | 15 ++ doc/source/lib/tool_shed.tools.rst | 27 +++ doc/source/lib/tool_shed.util.rst | 74 +++++-- .../lib/tool_shed.utility_containers.rst | 19 ++ doc/source/releases/15.05.rst | 2 - 115 files changed, 2954 insertions(+), 665 deletions(-) delete mode 100644 doc/source/lib/fpconst.rst create mode 100644 doc/source/lib/galaxy.auth.providers.rst create mode 100644 doc/source/lib/galaxy.auth.rst create mode 100644 doc/source/lib/galaxy.dataset_collections.rst create mode 100644 doc/source/lib/galaxy.dataset_collections.types.rst create mode 100644 doc/source/lib/galaxy.datatypes.dataproviders.rst create mode 100644 doc/source/lib/galaxy.jobs.metrics.collectl.rst create mode 100644 doc/source/lib/galaxy.jobs.metrics.instrumenters.rst create mode 100644 doc/source/lib/galaxy.jobs.metrics.rst delete mode 100644 doc/source/lib/galaxy.jobs.runners.cli_job.rst delete mode 100644 doc/source/lib/galaxy.jobs.runners.cli_shell.rst create mode 100644 doc/source/lib/galaxy.jobs.runners.lwr_client.rst create mode 100644 doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst create mode 100644 doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst create mode 100644 doc/source/lib/galaxy.jobs.runners.state_handlers.rst create mode 100644 doc/source/lib/galaxy.jobs.runners.util.cli.job.rst create mode 100644 doc/source/lib/galaxy.jobs.runners.util.cli.rst create mode 100644 doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst create mode 100644 doc/source/lib/galaxy.jobs.runners.util.condor.rst create mode 100644 doc/source/lib/galaxy.jobs.runners.util.job_script.rst create mode 100644 doc/source/lib/galaxy.jobs.runners.util.rst delete mode 100644 doc/source/lib/galaxy.model.orm.ext.rst rename doc/source/lib/{galaxy.webapps.community.model.migrate.rst => galaxy.model.tool_shed_install.migrate.rst} (68%) create mode 100644 doc/source/lib/galaxy.model.tool_shed_install.rst delete mode 100644 doc/source/lib/galaxy.tool_shed.migrate.rst delete mode 100644 doc/source/lib/galaxy.tool_shed.rst delete mode 100644 doc/source/lib/galaxy.tool_shed.tool_dependencies.rst create mode 100644 doc/source/lib/galaxy.tools.data_manager.rst create mode 100644 doc/source/lib/galaxy.tools.deps.resolvers.rst create mode 100644 doc/source/lib/galaxy.tools.filters.rst delete mode 100644 doc/source/lib/galaxy.tools.genome_index.rst create mode 100644 doc/source/lib/galaxy.tools.linters.rst create mode 100644 doc/source/lib/galaxy.tools.parser.rst create mode 100644 doc/source/lib/galaxy.tools.toolbox.filters.rst create mode 100644 doc/source/lib/galaxy.tools.toolbox.lineages.rst create mode 100644 doc/source/lib/galaxy.tools.toolbox.rst create mode 100644 doc/source/lib/galaxy.util.log.rst create mode 100644 doc/source/lib/galaxy.util.pastescript.rst create mode 100644 doc/source/lib/galaxy.visualization.plugins.rst create mode 100644 doc/source/lib/galaxy.web.proxy.rst delete mode 100644 doc/source/lib/galaxy.webapps.community.controllers.rst delete mode 100644 doc/source/lib/galaxy.webapps.community.framework.middleware.rst delete mode 100644 doc/source/lib/galaxy.webapps.community.framework.rst delete mode 100644 doc/source/lib/galaxy.webapps.community.model.rst delete mode 100644 doc/source/lib/galaxy.webapps.community.rst delete mode 100644 doc/source/lib/galaxy.webapps.community.security.rst delete mode 100644 doc/source/lib/galaxy.webapps.community.util.rst create mode 100644 doc/source/lib/galaxy.webapps.tool_shed.search.rst create mode 100644 doc/source/lib/galaxy.work.rst create mode 100644 doc/source/lib/galaxy.workflow.schedulers.rst create mode 100644 doc/source/lib/galaxy_ext.metadata.rst create mode 100644 doc/source/lib/galaxy_ext.rst create mode 100644 doc/source/lib/pulsar.client.rst create mode 100644 doc/source/lib/pulsar.client.staging.rst create mode 100644 doc/source/lib/pulsar.client.transport.rst create mode 100644 doc/source/lib/pulsar.rst create mode 100644 doc/source/lib/tool_shed.capsule.rst create mode 100644 doc/source/lib/tool_shed.dependencies.repository.rst create mode 100644 doc/source/lib/tool_shed.dependencies.rst create mode 100644 doc/source/lib/tool_shed.dependencies.tool.rst create mode 100644 doc/source/lib/tool_shed.galaxy_install.datatypes.rst create mode 100644 doc/source/lib/tool_shed.galaxy_install.metadata.rst create mode 100644 doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst create mode 100644 doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst create mode 100644 doc/source/lib/tool_shed.galaxy_install.tools.rst create mode 100644 doc/source/lib/tool_shed.galaxy_install.utility_containers.rst create mode 100644 doc/source/lib/tool_shed.managers.rst create mode 100644 doc/source/lib/tool_shed.metadata.rst create mode 100644 doc/source/lib/tool_shed.repository_types.rst create mode 100644 doc/source/lib/tool_shed.tools.rst create mode 100644 doc/source/lib/tool_shed.utility_containers.rst diff --git a/doc/source/lib/fpconst.rst b/doc/source/lib/fpconst.rst deleted file mode 100644 index 842351fad4b..00000000000 --- a/doc/source/lib/fpconst.rst +++ /dev/null @@ -1,7 +0,0 @@ -fpconst Module -============== - -.. automodule:: fpconst - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/lib/galaxy.auth.providers.rst b/doc/source/lib/galaxy.auth.providers.rst new file mode 100644 index 00000000000..aff6f57976d --- /dev/null +++ b/doc/source/lib/galaxy.auth.providers.rst @@ -0,0 +1,35 @@ +providers Package +================= + +:mod:`providers` Package +------------------------ + +.. automodule:: galaxy.auth.providers + :members: + :undoc-members: + :show-inheritance: + +:mod:`alwaysreject` Module +-------------------------- + +.. automodule:: galaxy.auth.providers.alwaysreject + :members: + :undoc-members: + :show-inheritance: + +:mod:`ldap_ad` Module +--------------------- + +.. automodule:: galaxy.auth.providers.ldap_ad + :members: + :undoc-members: + :show-inheritance: + +:mod:`localdb` Module +--------------------- + +.. automodule:: galaxy.auth.providers.localdb + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.auth.rst b/doc/source/lib/galaxy.auth.rst new file mode 100644 index 00000000000..885330d32ec --- /dev/null +++ b/doc/source/lib/galaxy.auth.rst @@ -0,0 +1,18 @@ +auth Package +============ + +:mod:`auth` Package +------------------- + +.. automodule:: galaxy.auth + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.auth.providers + diff --git a/doc/source/lib/galaxy.dataset_collections.rst b/doc/source/lib/galaxy.dataset_collections.rst new file mode 100644 index 00000000000..a507225613f --- /dev/null +++ b/doc/source/lib/galaxy.dataset_collections.rst @@ -0,0 +1,58 @@ +dataset_collections Package +=========================== + +:mod:`builder` Module +--------------------- + +.. automodule:: galaxy.dataset_collections.builder + :members: + :undoc-members: + :show-inheritance: + +:mod:`matching` Module +---------------------- + +.. automodule:: galaxy.dataset_collections.matching + :members: + :undoc-members: + :show-inheritance: + +:mod:`registry` Module +---------------------- + +.. automodule:: galaxy.dataset_collections.registry + :members: + :undoc-members: + :show-inheritance: + +:mod:`structure` Module +----------------------- + +.. automodule:: galaxy.dataset_collections.structure + :members: + :undoc-members: + :show-inheritance: + +:mod:`subcollections` Module +---------------------------- + +.. automodule:: galaxy.dataset_collections.subcollections + :members: + :undoc-members: + :show-inheritance: + +:mod:`type_description` Module +------------------------------ + +.. automodule:: galaxy.dataset_collections.type_description + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.dataset_collections.types + diff --git a/doc/source/lib/galaxy.dataset_collections.types.rst b/doc/source/lib/galaxy.dataset_collections.types.rst new file mode 100644 index 00000000000..83352f729b1 --- /dev/null +++ b/doc/source/lib/galaxy.dataset_collections.types.rst @@ -0,0 +1,27 @@ +types Package +============= + +:mod:`types` Package +-------------------- + +.. automodule:: galaxy.dataset_collections.types + :members: + :undoc-members: + :show-inheritance: + +:mod:`list` Module +------------------ + +.. automodule:: galaxy.dataset_collections.types.list + :members: + :undoc-members: + :show-inheritance: + +:mod:`paired` Module +-------------------- + +.. automodule:: galaxy.dataset_collections.types.paired + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.datatypes.converters.rst b/doc/source/lib/galaxy.datatypes.converters.rst index 99565bdfd81..342ba17312a 100644 --- a/doc/source/lib/galaxy.datatypes.converters.rst +++ b/doc/source/lib/galaxy.datatypes.converters.rst @@ -1,14 +1,6 @@ converters Package ================== -:mod:`bed_to_genetrack_converter` Module ----------------------------------------- - -.. automodule:: galaxy.datatypes.converters.bed_to_genetrack_converter - :members: - :undoc-members: - :show-inheritance: - :mod:`bed_to_gff_converter` Module ---------------------------------- @@ -129,14 +121,6 @@ converters Package :undoc-members: :show-inheritance: -:mod:`interval_to_summary_tree_converter` Module ------------------------------------------------- - -.. automodule:: galaxy.datatypes.converters.interval_to_summary_tree_converter - :members: - :undoc-members: - :show-inheritance: - :mod:`interval_to_tabix_converter` Module ----------------------------------------- @@ -201,10 +185,10 @@ converters Package :undoc-members: :show-inheritance: -:mod:`sam_or_bam_to_summary_tree_converter` Module --------------------------------------------------- +:mod:`pileup_to_interval_index_converter` Module +------------------------------------------------ -.. automodule:: galaxy.datatypes.converters.sam_or_bam_to_summary_tree_converter +.. automodule:: galaxy.datatypes.converters.pileup_to_interval_index_converter :members: :undoc-members: :show-inheritance: @@ -225,14 +209,6 @@ converters Package :undoc-members: :show-inheritance: -:mod:`vcf_to_summary_tree_converter` Module -------------------------------------------- - -.. automodule:: galaxy.datatypes.converters.vcf_to_summary_tree_converter - :members: - :undoc-members: - :show-inheritance: - :mod:`vcf_to_vcf_bgzip` Module ------------------------------ diff --git a/doc/source/lib/galaxy.datatypes.dataproviders.rst b/doc/source/lib/galaxy.datatypes.dataproviders.rst new file mode 100644 index 00000000000..a804265f0df --- /dev/null +++ b/doc/source/lib/galaxy.datatypes.dataproviders.rst @@ -0,0 +1,83 @@ +dataproviders Package +===================== + +:mod:`dataproviders` Package +---------------------------- + +.. automodule:: galaxy.datatypes.dataproviders + :members: + :undoc-members: + :show-inheritance: + +:mod:`base` Module +------------------ + +.. automodule:: galaxy.datatypes.dataproviders.base + :members: + :undoc-members: + :show-inheritance: + +:mod:`chunk` Module +------------------- + +.. automodule:: galaxy.datatypes.dataproviders.chunk + :members: + :undoc-members: + :show-inheritance: + +:mod:`column` Module +-------------------- + +.. automodule:: galaxy.datatypes.dataproviders.column + :members: + :undoc-members: + :show-inheritance: + +:mod:`dataset` Module +--------------------- + +.. automodule:: galaxy.datatypes.dataproviders.dataset + :members: + :undoc-members: + :show-inheritance: + +:mod:`decorators` Module +------------------------ + +.. automodule:: galaxy.datatypes.dataproviders.decorators + :members: + :undoc-members: + :show-inheritance: + +:mod:`exceptions` Module +------------------------ + +.. automodule:: galaxy.datatypes.dataproviders.exceptions + :members: + :undoc-members: + :show-inheritance: + +:mod:`external` Module +---------------------- + +.. automodule:: galaxy.datatypes.dataproviders.external + :members: + :undoc-members: + :show-inheritance: + +:mod:`hierarchy` Module +----------------------- + +.. automodule:: galaxy.datatypes.dataproviders.hierarchy + :members: + :undoc-members: + :show-inheritance: + +:mod:`line` Module +------------------ + +.. automodule:: galaxy.datatypes.dataproviders.line + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.datatypes.display_applications.rst b/doc/source/lib/galaxy.datatypes.display_applications.rst index 371a9eb619d..11300857cf8 100644 --- a/doc/source/lib/galaxy.datatypes.display_applications.rst +++ b/doc/source/lib/galaxy.datatypes.display_applications.rst @@ -1,6 +1,14 @@ display_applications Package ============================ +:mod:`display_applications` Package +----------------------------------- + +.. automodule:: galaxy.datatypes.display_applications + :members: + :undoc-members: + :show-inheritance: + :mod:`application` Module ------------------------- diff --git a/doc/source/lib/galaxy.datatypes.rst b/doc/source/lib/galaxy.datatypes.rst index 6479be38551..c85f459d43f 100644 --- a/doc/source/lib/galaxy.datatypes.rst +++ b/doc/source/lib/galaxy.datatypes.rst @@ -57,6 +57,14 @@ datatypes Package :undoc-members: :show-inheritance: +:mod:`graph` Module +------------------- + +.. automodule:: galaxy.datatypes.graph + :members: + :undoc-members: + :show-inheritance: + :mod:`images` Module -------------------- @@ -81,6 +89,14 @@ datatypes Package :undoc-members: :show-inheritance: +:mod:`msa` Module +----------------- + +.. automodule:: galaxy.datatypes.msa + :members: + :undoc-members: + :show-inheritance: + :mod:`ngsindex` Module ---------------------- @@ -129,6 +145,14 @@ datatypes Package :undoc-members: :show-inheritance: +:mod:`text` Module +------------------ + +.. automodule:: galaxy.datatypes.text + :members: + :undoc-members: + :show-inheritance: + :mod:`tracks` Module -------------------- @@ -151,6 +175,7 @@ Subpackages .. toctree:: galaxy.datatypes.converters + galaxy.datatypes.dataproviders galaxy.datatypes.display_applications galaxy.datatypes.util diff --git a/doc/source/lib/galaxy.datatypes.util.rst b/doc/source/lib/galaxy.datatypes.util.rst index c6eab95c0a9..59705cc70e8 100644 --- a/doc/source/lib/galaxy.datatypes.util.rst +++ b/doc/source/lib/galaxy.datatypes.util.rst @@ -9,6 +9,14 @@ util Package :undoc-members: :show-inheritance: +:mod:`generic_util` Module +-------------------------- + +.. automodule:: galaxy.datatypes.util.generic_util + :members: + :undoc-members: + :show-inheritance: + :mod:`gff_util` Module ---------------------- diff --git a/doc/source/lib/galaxy.exceptions.rst b/doc/source/lib/galaxy.exceptions.rst index a164ff81f86..8b62b21bf8c 100644 --- a/doc/source/lib/galaxy.exceptions.rst +++ b/doc/source/lib/galaxy.exceptions.rst @@ -9,3 +9,11 @@ exceptions Package :undoc-members: :show-inheritance: +:mod:`error_codes` Module +------------------------- + +.. automodule:: galaxy.exceptions.error_codes + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.deferred.rst b/doc/source/lib/galaxy.jobs.deferred.rst index 19b967685c0..81709bb1124 100644 --- a/doc/source/lib/galaxy.jobs.deferred.rst +++ b/doc/source/lib/galaxy.jobs.deferred.rst @@ -17,30 +17,6 @@ deferred Package :undoc-members: :show-inheritance: -:mod:`genome_index` Module --------------------------- - -.. automodule:: galaxy.jobs.deferred.genome_index - :members: - :undoc-members: - :show-inheritance: - -:mod:`genome_transfer` Module ------------------------------ - -.. automodule:: galaxy.jobs.deferred.genome_transfer - :members: - :undoc-members: - :show-inheritance: - -:mod:`liftover_transfer` Module -------------------------------- - -.. automodule:: galaxy.jobs.deferred.liftover_transfer - :members: - :undoc-members: - :show-inheritance: - :mod:`manual_data_transfer` Module ---------------------------------- diff --git a/doc/source/lib/galaxy.jobs.metrics.collectl.rst b/doc/source/lib/galaxy.jobs.metrics.collectl.rst new file mode 100644 index 00000000000..ebd0f3bb2f5 --- /dev/null +++ b/doc/source/lib/galaxy.jobs.metrics.collectl.rst @@ -0,0 +1,43 @@ +collectl Package +================ + +:mod:`collectl` Package +----------------------- + +.. automodule:: galaxy.jobs.metrics.collectl + :members: + :undoc-members: + :show-inheritance: + +:mod:`cli` Module +----------------- + +.. automodule:: galaxy.jobs.metrics.collectl.cli + :members: + :undoc-members: + :show-inheritance: + +:mod:`processes` Module +----------------------- + +.. automodule:: galaxy.jobs.metrics.collectl.processes + :members: + :undoc-members: + :show-inheritance: + +:mod:`stats` Module +------------------- + +.. automodule:: galaxy.jobs.metrics.collectl.stats + :members: + :undoc-members: + :show-inheritance: + +:mod:`subsystems` Module +------------------------ + +.. automodule:: galaxy.jobs.metrics.collectl.subsystems + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst b/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst new file mode 100644 index 00000000000..94b790d72ce --- /dev/null +++ b/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst @@ -0,0 +1,59 @@ +instrumenters Package +===================== + +:mod:`instrumenters` Package +---------------------------- + +.. automodule:: galaxy.jobs.metrics.instrumenters + :members: + :undoc-members: + :show-inheritance: + +:mod:`collectl` Module +---------------------- + +.. automodule:: galaxy.jobs.metrics.instrumenters.collectl + :members: + :undoc-members: + :show-inheritance: + +:mod:`core` Module +------------------ + +.. automodule:: galaxy.jobs.metrics.instrumenters.core + :members: + :undoc-members: + :show-inheritance: + +:mod:`cpuinfo` Module +--------------------- + +.. automodule:: galaxy.jobs.metrics.instrumenters.cpuinfo + :members: + :undoc-members: + :show-inheritance: + +:mod:`env` Module +----------------- + +.. automodule:: galaxy.jobs.metrics.instrumenters.env + :members: + :undoc-members: + :show-inheritance: + +:mod:`meminfo` Module +--------------------- + +.. automodule:: galaxy.jobs.metrics.instrumenters.meminfo + :members: + :undoc-members: + :show-inheritance: + +:mod:`uname` Module +------------------- + +.. automodule:: galaxy.jobs.metrics.instrumenters.uname + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.metrics.rst b/doc/source/lib/galaxy.jobs.metrics.rst new file mode 100644 index 00000000000..a9f3de2d925 --- /dev/null +++ b/doc/source/lib/galaxy.jobs.metrics.rst @@ -0,0 +1,27 @@ +metrics Package +=============== + +:mod:`metrics` Package +---------------------- + +.. automodule:: galaxy.jobs.metrics + :members: + :undoc-members: + :show-inheritance: + +:mod:`formatting` Module +------------------------ + +.. automodule:: galaxy.jobs.metrics.formatting + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.jobs.metrics.collectl + galaxy.jobs.metrics.instrumenters + diff --git a/doc/source/lib/galaxy.jobs.rst b/doc/source/lib/galaxy.jobs.rst index 587dff8f124..be174b5e8d4 100644 --- a/doc/source/lib/galaxy.jobs.rst +++ b/doc/source/lib/galaxy.jobs.rst @@ -9,6 +9,30 @@ jobs Package :undoc-members: :show-inheritance: +:mod:`command_factory` Module +----------------------------- + +.. automodule:: galaxy.jobs.command_factory + :members: + :undoc-members: + :show-inheritance: + +:mod:`datasets` Module +---------------------- + +.. automodule:: galaxy.jobs.datasets + :members: + :undoc-members: + :show-inheritance: + +:mod:`error_level` Module +------------------------- + +.. automodule:: galaxy.jobs.error_level + :members: + :undoc-members: + :show-inheritance: + :mod:`handler` Module --------------------- @@ -33,6 +57,30 @@ jobs Package :undoc-members: :show-inheritance: +:mod:`output_checker` Module +---------------------------- + +.. automodule:: galaxy.jobs.output_checker + :members: + :undoc-members: + :show-inheritance: + +:mod:`rule_helper` Module +------------------------- + +.. automodule:: galaxy.jobs.rule_helper + :members: + :undoc-members: + :show-inheritance: + +:mod:`stock_rules` Module +------------------------- + +.. automodule:: galaxy.jobs.stock_rules + :members: + :undoc-members: + :show-inheritance: + :mod:`transfer_manager` Module ------------------------------ @@ -48,6 +96,7 @@ Subpackages galaxy.jobs.actions galaxy.jobs.deferred + galaxy.jobs.metrics galaxy.jobs.rules galaxy.jobs.runners galaxy.jobs.splitters diff --git a/doc/source/lib/galaxy.jobs.runners.cli_job.rst b/doc/source/lib/galaxy.jobs.runners.cli_job.rst deleted file mode 100644 index b373a06ae3c..00000000000 --- a/doc/source/lib/galaxy.jobs.runners.cli_job.rst +++ /dev/null @@ -1,19 +0,0 @@ -cli_job Package -=============== - -:mod:`cli_job` Package ----------------------- - -.. automodule:: galaxy.jobs.runners.cli_job - :members: - :undoc-members: - :show-inheritance: - -:mod:`torque` Module --------------------- - -.. automodule:: galaxy.jobs.runners.cli_job.torque - :members: - :undoc-members: - :show-inheritance: - diff --git a/doc/source/lib/galaxy.jobs.runners.cli_shell.rst b/doc/source/lib/galaxy.jobs.runners.cli_shell.rst deleted file mode 100644 index 9b96bbcfc52..00000000000 --- a/doc/source/lib/galaxy.jobs.runners.cli_shell.rst +++ /dev/null @@ -1,19 +0,0 @@ -cli_shell Package -================= - -:mod:`cli_shell` Package ------------------------- - -.. automodule:: galaxy.jobs.runners.cli_shell - :members: - :undoc-members: - :show-inheritance: - -:mod:`rsh` Module ------------------ - -.. automodule:: galaxy.jobs.runners.cli_shell.rsh - :members: - :undoc-members: - :show-inheritance: - diff --git a/doc/source/lib/galaxy.jobs.runners.lwr_client.rst b/doc/source/lib/galaxy.jobs.runners.lwr_client.rst new file mode 100644 index 00000000000..74f2efa3f9e --- /dev/null +++ b/doc/source/lib/galaxy.jobs.runners.lwr_client.rst @@ -0,0 +1,131 @@ +lwr_client Package +================== + +:mod:`lwr_client` Package +------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client + :members: + :undoc-members: + :show-inheritance: + +:mod:`action_mapper` Module +--------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.action_mapper + :members: + :undoc-members: + :show-inheritance: + +:mod:`amqp_exchange` Module +--------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.amqp_exchange + :members: + :undoc-members: + :show-inheritance: + +:mod:`amqp_exchange_factory` Module +----------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.amqp_exchange_factory + :members: + :undoc-members: + :show-inheritance: + +:mod:`client` Module +-------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.client + :members: + :undoc-members: + :show-inheritance: + +:mod:`config_util` Module +------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.config_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`decorators` Module +------------------------ + +.. automodule:: galaxy.jobs.runners.lwr_client.decorators + :members: + :undoc-members: + :show-inheritance: + +:mod:`destination` Module +------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.destination + :members: + :undoc-members: + :show-inheritance: + +:mod:`interface` Module +----------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.interface + :members: + :undoc-members: + :show-inheritance: + +:mod:`job_directory` Module +--------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.job_directory + :members: + :undoc-members: + :show-inheritance: + +:mod:`manager` Module +--------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.manager + :members: + :undoc-members: + :show-inheritance: + +:mod:`object_client` Module +--------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.object_client + :members: + :undoc-members: + :show-inheritance: + +:mod:`path_mapper` Module +------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.path_mapper + :members: + :undoc-members: + :show-inheritance: + +:mod:`setup_handler` Module +--------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.setup_handler + :members: + :undoc-members: + :show-inheritance: + +:mod:`util` Module +------------------ + +.. automodule:: galaxy.jobs.runners.lwr_client.util + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.jobs.runners.lwr_client.staging + galaxy.jobs.runners.lwr_client.transport + diff --git a/doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst b/doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst new file mode 100644 index 00000000000..62feff29ae9 --- /dev/null +++ b/doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst @@ -0,0 +1,27 @@ +staging Package +=============== + +:mod:`staging` Package +---------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.staging + :members: + :undoc-members: + :show-inheritance: + +:mod:`down` Module +------------------ + +.. automodule:: galaxy.jobs.runners.lwr_client.staging.down + :members: + :undoc-members: + :show-inheritance: + +:mod:`up` Module +---------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.staging.up + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst b/doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst new file mode 100644 index 00000000000..427b43e96d1 --- /dev/null +++ b/doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst @@ -0,0 +1,27 @@ +transport Package +================= + +:mod:`transport` Package +------------------------ + +.. automodule:: galaxy.jobs.runners.lwr_client.transport + :members: + :undoc-members: + :show-inheritance: + +:mod:`curl` Module +------------------ + +.. automodule:: galaxy.jobs.runners.lwr_client.transport.curl + :members: + :undoc-members: + :show-inheritance: + +:mod:`standard` Module +---------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.transport.standard + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.rst b/doc/source/lib/galaxy.jobs.runners.rst index 01c244c7f8a..83cf3a5a41e 100644 --- a/doc/source/lib/galaxy.jobs.runners.rst +++ b/doc/source/lib/galaxy.jobs.runners.rst @@ -57,6 +57,30 @@ runners Package :undoc-members: :show-inheritance: +:mod:`pulsar` Module +-------------------- + +.. automodule:: galaxy.jobs.runners.pulsar + :members: + :undoc-members: + :show-inheritance: + +:mod:`slurm` Module +------------------- + +.. automodule:: galaxy.jobs.runners.slurm + :members: + :undoc-members: + :show-inheritance: + +:mod:`state_handler_factory` Module +----------------------------------- + +.. automodule:: galaxy.jobs.runners.state_handler_factory + :members: + :undoc-members: + :show-inheritance: + :mod:`tasks` Module ------------------- @@ -70,7 +94,7 @@ Subpackages .. toctree:: - galaxy.jobs.runners.cli_job - galaxy.jobs.runners.cli_shell galaxy.jobs.runners.lwr_client + galaxy.jobs.runners.state_handlers + galaxy.jobs.runners.util diff --git a/doc/source/lib/galaxy.jobs.runners.state_handlers.rst b/doc/source/lib/galaxy.jobs.runners.state_handlers.rst new file mode 100644 index 00000000000..bbf8577287a --- /dev/null +++ b/doc/source/lib/galaxy.jobs.runners.state_handlers.rst @@ -0,0 +1,11 @@ +state_handlers Package +====================== + +:mod:`resubmit` Module +---------------------- + +.. automodule:: galaxy.jobs.runners.state_handlers.resubmit + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst new file mode 100644 index 00000000000..f98c1cb988a --- /dev/null +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst @@ -0,0 +1,35 @@ +job Package +=========== + +:mod:`job` Package +------------------ + +.. automodule:: galaxy.jobs.runners.util.cli.job + :members: + :undoc-members: + :show-inheritance: + +:mod:`slurm` Module +------------------- + +.. automodule:: galaxy.jobs.runners.util.cli.job.slurm + :members: + :undoc-members: + :show-inheritance: + +:mod:`slurm_torque` Module +-------------------------- + +.. automodule:: galaxy.jobs.runners.util.cli.job.slurm_torque + :members: + :undoc-members: + :show-inheritance: + +:mod:`torque` Module +-------------------- + +.. automodule:: galaxy.jobs.runners.util.cli.job.torque + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.rst new file mode 100644 index 00000000000..b3426fc78f8 --- /dev/null +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.rst @@ -0,0 +1,27 @@ +cli Package +=========== + +:mod:`cli` Package +------------------ + +.. automodule:: galaxy.jobs.runners.util.cli + :members: + :undoc-members: + :show-inheritance: + +:mod:`factory` Module +--------------------- + +.. automodule:: galaxy.jobs.runners.util.cli.factory + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.jobs.runners.util.cli.job + galaxy.jobs.runners.util.cli.shell + diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst new file mode 100644 index 00000000000..115c1cfc0dd --- /dev/null +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst @@ -0,0 +1,27 @@ +shell Package +============= + +:mod:`shell` Package +-------------------- + +.. automodule:: galaxy.jobs.runners.util.cli.shell + :members: + :undoc-members: + :show-inheritance: + +:mod:`local` Module +------------------- + +.. automodule:: galaxy.jobs.runners.util.cli.shell.local + :members: + :undoc-members: + :show-inheritance: + +:mod:`rsh` Module +----------------- + +.. automodule:: galaxy.jobs.runners.util.cli.shell.rsh + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.util.condor.rst b/doc/source/lib/galaxy.jobs.runners.util.condor.rst new file mode 100644 index 00000000000..8678f6a98a7 --- /dev/null +++ b/doc/source/lib/galaxy.jobs.runners.util.condor.rst @@ -0,0 +1,11 @@ +condor Package +============== + +:mod:`condor` Package +--------------------- + +.. automodule:: galaxy.jobs.runners.util.condor + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.util.job_script.rst b/doc/source/lib/galaxy.jobs.runners.util.job_script.rst new file mode 100644 index 00000000000..7599d9a1f64 --- /dev/null +++ b/doc/source/lib/galaxy.jobs.runners.util.job_script.rst @@ -0,0 +1,11 @@ +job_script Package +================== + +:mod:`job_script` Package +------------------------- + +.. automodule:: galaxy.jobs.runners.util.job_script + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.util.rst b/doc/source/lib/galaxy.jobs.runners.util.rst new file mode 100644 index 00000000000..410034390c9 --- /dev/null +++ b/doc/source/lib/galaxy.jobs.runners.util.rst @@ -0,0 +1,44 @@ +util Package +============ + +:mod:`util` Package +------------------- + +.. automodule:: galaxy.jobs.runners.util + :members: + :undoc-members: + :show-inheritance: + +:mod:`env` Module +----------------- + +.. automodule:: galaxy.jobs.runners.util.env + :members: + :undoc-members: + :show-inheritance: + +:mod:`external` Module +---------------------- + +.. automodule:: galaxy.jobs.runners.util.external + :members: + :undoc-members: + :show-inheritance: + +:mod:`kill` Module +------------------ + +.. automodule:: galaxy.jobs.runners.util.kill + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.jobs.runners.util.cli + galaxy.jobs.runners.util.condor + galaxy.jobs.runners.util.job_script + diff --git a/doc/source/lib/galaxy.managers.rst b/doc/source/lib/galaxy.managers.rst index ba29bf24565..ae0ab647d05 100644 --- a/doc/source/lib/galaxy.managers.rst +++ b/doc/source/lib/galaxy.managers.rst @@ -1,92 +1,227 @@ managers Package -================== +================ :mod:`managers` Package -------------------------- +----------------------- .. automodule:: galaxy.managers + :members: + :undoc-members: + :show-inheritance: +:mod:`annotatable` Module +------------------------- + +.. automodule:: galaxy.managers.annotatable + :members: + :undoc-members: + :show-inheritance: :mod:`api_keys` Module ------------------------------- +---------------------- .. automodule:: galaxy.managers.api_keys - + :members: + :undoc-members: + :show-inheritance: :mod:`base` Module ------------------------------- +------------------ .. automodule:: galaxy.managers.base - + :members: + :undoc-members: + :show-inheritance: :mod:`citations` Module ------------------------------- +----------------------- .. automodule:: galaxy.managers.citations - + :members: + :undoc-members: + :show-inheritance: :mod:`collections` Module ------------------------------- +------------------------- .. automodule:: galaxy.managers.collections - + :members: + :undoc-members: + :show-inheritance: :mod:`collections_util` Module ------------------------------ .. automodule:: galaxy.managers.collections_util + :members: + :undoc-members: + :show-inheritance: +:mod:`configuration` Module +--------------------------- + +.. automodule:: galaxy.managers.configuration + :members: + :undoc-members: + :show-inheritance: + +:mod:`containers` Module +------------------------ + +.. automodule:: galaxy.managers.containers + :members: + :undoc-members: + :show-inheritance: :mod:`context` Module ------------------------------- +--------------------- .. automodule:: galaxy.managers.context + :members: + :undoc-members: + :show-inheritance: +:mod:`datasets` Module +---------------------- + +.. automodule:: galaxy.managers.datasets + :members: + :undoc-members: + :show-inheritance: + +:mod:`deletable` Module +----------------------- + +.. automodule:: galaxy.managers.deletable + :members: + :undoc-members: + :show-inheritance: :mod:`folders` Module ------------------------------- +--------------------- .. automodule:: galaxy.managers.folders - + :members: + :undoc-members: + :show-inheritance: :mod:`hdas` Module ------------------------------- +------------------ .. automodule:: galaxy.managers.hdas - + :members: + :undoc-members: + :show-inheritance: :mod:`histories` Module ------------------------------- +----------------------- .. automodule:: galaxy.managers.histories - + :members: + :undoc-members: + :show-inheritance: :mod:`lddas` Module ------------------------------- +------------------- .. automodule:: galaxy.managers.lddas - + :members: + :undoc-members: + :show-inheritance: :mod:`libraries` Module ------------------------------- +----------------------- .. automodule:: galaxy.managers.libraries + :members: + :undoc-members: + :show-inheritance: +:mod:`pages` Module +------------------- + +.. automodule:: galaxy.managers.pages + :members: + :undoc-members: + :show-inheritance: + +:mod:`ratable` Module +--------------------- + +.. automodule:: galaxy.managers.ratable + :members: + :undoc-members: + :show-inheritance: + +:mod:`rbac_secured` Module +-------------------------- + +.. automodule:: galaxy.managers.rbac_secured + :members: + :undoc-members: + :show-inheritance: :mod:`roles` Module ------------------------------- +------------------- .. automodule:: galaxy.managers.roles + :members: + :undoc-members: + :show-inheritance: +:mod:`secured` Module +--------------------- + +.. automodule:: galaxy.managers.secured + :members: + :undoc-members: + :show-inheritance: + +:mod:`sharable` Module +---------------------- + +.. automodule:: galaxy.managers.sharable + :members: + :undoc-members: + :show-inheritance: + +:mod:`taggable` Module +---------------------- + +.. automodule:: galaxy.managers.taggable + :members: + :undoc-members: + :show-inheritance: :mod:`tags` Module ------------------------------- +------------------ .. automodule:: galaxy.managers.tags + :members: + :undoc-members: + :show-inheritance: +:mod:`users` Module +------------------- + +.. automodule:: galaxy.managers.users + :members: + :undoc-members: + :show-inheritance: + +:mod:`visualizations` Module +---------------------------- + +.. automodule:: galaxy.managers.visualizations + :members: + :undoc-members: + :show-inheritance: :mod:`workflows` Module ------------------------------- +----------------------- .. automodule:: galaxy.managers.workflows + :members: :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.model.orm.ext.rst b/doc/source/lib/galaxy.model.orm.ext.rst deleted file mode 100644 index 5794c198b03..00000000000 --- a/doc/source/lib/galaxy.model.orm.ext.rst +++ /dev/null @@ -1,19 +0,0 @@ -ext Package -=========== - -:mod:`ext` Package ------------------- - -.. automodule:: galaxy.model.orm.ext - :members: - :undoc-members: - :show-inheritance: - -:mod:`assignmapper` Module --------------------------- - -.. automodule:: galaxy.model.orm.ext.assignmapper - :members: - :undoc-members: - :show-inheritance: - diff --git a/doc/source/lib/galaxy.model.orm.rst b/doc/source/lib/galaxy.model.orm.rst index 827ad79aa31..379141b94ed 100644 --- a/doc/source/lib/galaxy.model.orm.rst +++ b/doc/source/lib/galaxy.model.orm.rst @@ -9,6 +9,14 @@ orm Package :undoc-members: :show-inheritance: +:mod:`engine_factory` Module +---------------------------- + +.. automodule:: galaxy.model.orm.engine_factory + :members: + :undoc-members: + :show-inheritance: + :mod:`logging_connection_proxy` Module -------------------------------------- @@ -17,10 +25,19 @@ orm Package :undoc-members: :show-inheritance: -Subpackages ------------ +:mod:`now` Module +----------------- -.. toctree:: +.. automodule:: galaxy.model.orm.now + :members: + :undoc-members: + :show-inheritance: - galaxy.model.orm.ext +:mod:`scripts` Module +--------------------- + +.. automodule:: galaxy.model.orm.scripts + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.model.rst b/doc/source/lib/galaxy.model.rst index e9eed834062..e063ff3d456 100644 --- a/doc/source/lib/galaxy.model.rst +++ b/doc/source/lib/galaxy.model.rst @@ -9,6 +9,14 @@ model Package :undoc-members: :show-inheritance: +:mod:`base` Module +------------------ + +.. automodule:: galaxy.model.base + :members: + :undoc-members: + :show-inheritance: + :mod:`custom_types` Module -------------------------- @@ -33,10 +41,18 @@ model Package :undoc-members: :show-inheritance: -:mod:`mapping_tests` Module ---------------------------- +:mod:`search` Module +-------------------- -.. automodule:: galaxy.model.mapping_tests +.. automodule:: galaxy.model.search + :members: + :undoc-members: + :show-inheritance: + +:mod:`util` Module +------------------ + +.. automodule:: galaxy.model.util :members: :undoc-members: :show-inheritance: @@ -48,4 +64,5 @@ Subpackages galaxy.model.migrate galaxy.model.orm + galaxy.model.tool_shed_install diff --git a/doc/source/lib/galaxy.webapps.community.model.migrate.rst b/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst similarity index 68% rename from doc/source/lib/galaxy.webapps.community.model.migrate.rst rename to doc/source/lib/galaxy.model.tool_shed_install.migrate.rst index cfd09107747..f117f24a115 100644 --- a/doc/source/lib/galaxy.webapps.community.model.migrate.rst +++ b/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst @@ -4,7 +4,7 @@ migrate Package :mod:`check` Module ------------------- -.. automodule:: galaxy.webapps.community.model.migrate.check +.. automodule:: galaxy.model.tool_shed_install.migrate.check :members: :undoc-members: :show-inheritance: diff --git a/doc/source/lib/galaxy.model.tool_shed_install.rst b/doc/source/lib/galaxy.model.tool_shed_install.rst new file mode 100644 index 00000000000..3d311847ab5 --- /dev/null +++ b/doc/source/lib/galaxy.model.tool_shed_install.rst @@ -0,0 +1,26 @@ +tool_shed_install Package +========================= + +:mod:`tool_shed_install` Package +-------------------------------- + +.. automodule:: galaxy.model.tool_shed_install + :members: + :undoc-members: + :show-inheritance: + +:mod:`mapping` Module +--------------------- + +.. automodule:: galaxy.model.tool_shed_install.mapping + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.model.tool_shed_install.migrate + diff --git a/doc/source/lib/galaxy.objectstore.rst b/doc/source/lib/galaxy.objectstore.rst index 42999958bd2..19343f88e39 100644 --- a/doc/source/lib/galaxy.objectstore.rst +++ b/doc/source/lib/galaxy.objectstore.rst @@ -9,6 +9,30 @@ objectstore Package :undoc-members: :show-inheritance: +:mod:`pulsar` Module +-------------------- + +.. automodule:: galaxy.objectstore.pulsar + :members: + :undoc-members: + :show-inheritance: + +:mod:`rods` Module +------------------ + +.. automodule:: galaxy.objectstore.rods + :members: + :undoc-members: + :show-inheritance: + +:mod:`s3` Module +---------------- + +.. automodule:: galaxy.objectstore.s3 + :members: + :undoc-members: + :show-inheritance: + :mod:`s3_multipart_upload` Module --------------------------------- diff --git a/doc/source/lib/galaxy.rst b/doc/source/lib/galaxy.rst index b9a9027d131..a1a42e221e4 100644 --- a/doc/source/lib/galaxy.rst +++ b/doc/source/lib/galaxy.rst @@ -25,30 +25,66 @@ galaxy Package :undoc-members: :show-inheritance: +:mod:`main` Module +------------------ + +.. automodule:: galaxy.main + :members: + :undoc-members: + :show-inheritance: + +:mod:`queue_worker` Module +-------------------------- + +.. automodule:: galaxy.queue_worker + :members: + :undoc-members: + :show-inheritance: + +:mod:`queues` Module +-------------------- + +.. automodule:: galaxy.queues + :members: + :undoc-members: + :show-inheritance: + +:mod:`version` Module +--------------------- + +.. automodule:: galaxy.version + :members: + :undoc-members: + :show-inheritance: + Subpackages ----------- .. toctree:: galaxy.actions + galaxy.auth + galaxy.dataset_collections galaxy.datatypes galaxy.eggs galaxy.exceptions galaxy.external_services galaxy.forms galaxy.jobs - galaxy.model galaxy.managers + galaxy.metadata + galaxy.model galaxy.objectstore galaxy.openid galaxy.quota galaxy.sample_tracking galaxy.security galaxy.tags - galaxy.tool_shed galaxy.tools galaxy.util galaxy.visualization galaxy.web galaxy.webapps + galaxy.work galaxy.workflow + diff --git a/doc/source/lib/galaxy.security.rst b/doc/source/lib/galaxy.security.rst index 9bba56c7e12..ff90ef6e6e2 100644 --- a/doc/source/lib/galaxy.security.rst +++ b/doc/source/lib/galaxy.security.rst @@ -9,6 +9,14 @@ security Package :undoc-members: :show-inheritance: +:mod:`passwords` Module +----------------------- + +.. automodule:: galaxy.security.passwords + :members: + :undoc-members: + :show-inheritance: + :mod:`validate_user_input` Module --------------------------------- diff --git a/doc/source/lib/galaxy.tags.rst b/doc/source/lib/galaxy.tags.rst index eff268d5dc4..38d5152b8e7 100644 --- a/doc/source/lib/galaxy.tags.rst +++ b/doc/source/lib/galaxy.tags.rst @@ -9,11 +9,3 @@ tags Package :undoc-members: :show-inheritance: -:mod:`tag_handler` Module -------------------------- - -.. automodule:: galaxy.tags.tag_handler - :members: - :undoc-members: - :show-inheritance: - diff --git a/doc/source/lib/galaxy.tool_shed.migrate.rst b/doc/source/lib/galaxy.tool_shed.migrate.rst deleted file mode 100644 index 095f79a99d7..00000000000 --- a/doc/source/lib/galaxy.tool_shed.migrate.rst +++ /dev/null @@ -1,19 +0,0 @@ -migrate Package -=============== - -:mod:`check` Module -------------------- - -.. automodule:: galaxy.tool_shed.migrate.check - :members: - :undoc-members: - :show-inheritance: - -:mod:`common` Module --------------------- - -.. automodule:: galaxy.tool_shed.migrate.common - :members: - :undoc-members: - :show-inheritance: - diff --git a/doc/source/lib/galaxy.tool_shed.rst b/doc/source/lib/galaxy.tool_shed.rst deleted file mode 100644 index d1cb451fd7b..00000000000 --- a/doc/source/lib/galaxy.tool_shed.rst +++ /dev/null @@ -1,59 +0,0 @@ -tool_shed Package -================= - -:mod:`tool_shed` Package ------------------------- - -.. automodule:: galaxy.tool_shed - :members: - :undoc-members: - :show-inheritance: - -:mod:`common_util` Module -------------------------- - -.. automodule:: galaxy.tool_shed.common_util - :members: - :undoc-members: - :show-inheritance: - -:mod:`encoding_util` Module ---------------------------- - -.. automodule:: galaxy.tool_shed.encoding_util - :members: - :undoc-members: - :show-inheritance: - -:mod:`install_manager` Module ------------------------------ - -.. automodule:: galaxy.tool_shed.install_manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`tool_shed_registry` Module --------------------------------- - -.. automodule:: galaxy.tool_shed.tool_shed_registry - :members: - :undoc-members: - :show-inheritance: - -:mod:`update_manager` Module ----------------------------- - -.. automodule:: galaxy.tool_shed.update_manager - :members: - :undoc-members: - :show-inheritance: - -Subpackages ------------ - -.. toctree:: - - galaxy.tool_shed.migrate - galaxy.tool_shed.tool_dependencies - diff --git a/doc/source/lib/galaxy.tool_shed.tool_dependencies.rst b/doc/source/lib/galaxy.tool_shed.tool_dependencies.rst deleted file mode 100644 index 8115eb4d62a..00000000000 --- a/doc/source/lib/galaxy.tool_shed.tool_dependencies.rst +++ /dev/null @@ -1,27 +0,0 @@ -tool_dependencies Package -========================= - -:mod:`common_util` Module -------------------------- - -.. automodule:: galaxy.tool_shed.tool_dependencies.common_util - :members: - :undoc-members: - :show-inheritance: - -:mod:`fabric_util` Module -------------------------- - -.. automodule:: galaxy.tool_shed.tool_dependencies.fabric_util - :members: - :undoc-members: - :show-inheritance: - -:mod:`install_util` Module --------------------------- - -.. automodule:: galaxy.tool_shed.tool_dependencies.install_util - :members: - :undoc-members: - :show-inheritance: - diff --git a/doc/source/lib/galaxy.tools.actions.rst b/doc/source/lib/galaxy.tools.actions.rst index 6bc274bd4b0..870cc2ca31b 100644 --- a/doc/source/lib/galaxy.tools.actions.rst +++ b/doc/source/lib/galaxy.tools.actions.rst @@ -9,18 +9,26 @@ actions Package :undoc-members: :show-inheritance: -:mod:`history_imp_exp` Module ------------------------------ +:mod:`data_manager` Module +-------------------------- -.. automodule:: galaxy.tools.actions.history_imp_exp +.. automodule:: galaxy.tools.actions.data_manager :members: :undoc-members: :show-inheritance: -:mod:`index_genome` Module --------------------------- +:mod:`data_source` Module +------------------------- -.. automodule:: galaxy.tools.actions.index_genome +.. automodule:: galaxy.tools.actions.data_source + :members: + :undoc-members: + :show-inheritance: + +:mod:`history_imp_exp` Module +----------------------------- + +.. automodule:: galaxy.tools.actions.history_imp_exp :members: :undoc-members: :show-inheritance: diff --git a/doc/source/lib/galaxy.tools.data_manager.rst b/doc/source/lib/galaxy.tools.data_manager.rst new file mode 100644 index 00000000000..bbf07acd662 --- /dev/null +++ b/doc/source/lib/galaxy.tools.data_manager.rst @@ -0,0 +1,19 @@ +data_manager Package +==================== + +:mod:`data_manager` Package +--------------------------- + +.. automodule:: galaxy.tools.data_manager + :members: + :undoc-members: + :show-inheritance: + +:mod:`manager` Module +--------------------- + +.. automodule:: galaxy.tools.data_manager.manager + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.deps.resolvers.rst b/doc/source/lib/galaxy.tools.deps.resolvers.rst new file mode 100644 index 00000000000..5890b4eed38 --- /dev/null +++ b/doc/source/lib/galaxy.tools.deps.resolvers.rst @@ -0,0 +1,59 @@ +resolvers Package +================= + +:mod:`resolvers` Package +------------------------ + +.. automodule:: galaxy.tools.deps.resolvers + :members: + :undoc-members: + :show-inheritance: + +:mod:`brewed_tool_shed_packages` Module +--------------------------------------- + +.. automodule:: galaxy.tools.deps.resolvers.brewed_tool_shed_packages + :members: + :undoc-members: + :show-inheritance: + +:mod:`galaxy_packages` Module +----------------------------- + +.. automodule:: galaxy.tools.deps.resolvers.galaxy_packages + :members: + :undoc-members: + :show-inheritance: + +:mod:`homebrew` Module +---------------------- + +.. automodule:: galaxy.tools.deps.resolvers.homebrew + :members: + :undoc-members: + :show-inheritance: + +:mod:`modules` Module +--------------------- + +.. automodule:: galaxy.tools.deps.resolvers.modules + :members: + :undoc-members: + :show-inheritance: + +:mod:`resolver_mixins` Module +----------------------------- + +.. automodule:: galaxy.tools.deps.resolvers.resolver_mixins + :members: + :undoc-members: + :show-inheritance: + +:mod:`tool_shed_packages` Module +-------------------------------- + +.. automodule:: galaxy.tools.deps.resolvers.tool_shed_packages + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.deps.rst b/doc/source/lib/galaxy.tools.deps.rst index ef6e24cbf8b..404d660628e 100644 --- a/doc/source/lib/galaxy.tools.deps.rst +++ b/doc/source/lib/galaxy.tools.deps.rst @@ -9,11 +9,74 @@ deps Package :undoc-members: :show-inheritance: -:mod:`tests` Module -------------------- +:mod:`brew_exts` Module +----------------------- -.. automodule:: galaxy.tools.deps.tests +.. automodule:: galaxy.tools.deps.brew_exts :members: :undoc-members: :show-inheritance: +:mod:`brew_util` Module +----------------------- + +.. automodule:: galaxy.tools.deps.brew_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`commands` Module +---------------------- + +.. automodule:: galaxy.tools.deps.commands + :members: + :undoc-members: + :show-inheritance: + +:mod:`containers` Module +------------------------ + +.. automodule:: galaxy.tools.deps.containers + :members: + :undoc-members: + :show-inheritance: + +:mod:`dependencies` Module +-------------------------- + +.. automodule:: galaxy.tools.deps.dependencies + :members: + :undoc-members: + :show-inheritance: + +:mod:`docker_util` Module +------------------------- + +.. automodule:: galaxy.tools.deps.docker_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`dockerfiles` Module +------------------------- + +.. automodule:: galaxy.tools.deps.dockerfiles + :members: + :undoc-members: + :show-inheritance: + +:mod:`requirements` Module +-------------------------- + +.. automodule:: galaxy.tools.deps.requirements + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.tools.deps.resolvers + diff --git a/doc/source/lib/galaxy.tools.filters.rst b/doc/source/lib/galaxy.tools.filters.rst new file mode 100644 index 00000000000..e31664e9cd3 --- /dev/null +++ b/doc/source/lib/galaxy.tools.filters.rst @@ -0,0 +1,11 @@ +filters Package +=============== + +:mod:`filters` Package +---------------------- + +.. automodule:: galaxy.tools.filters + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.genome_index.rst b/doc/source/lib/galaxy.tools.genome_index.rst deleted file mode 100644 index 4849080849a..00000000000 --- a/doc/source/lib/galaxy.tools.genome_index.rst +++ /dev/null @@ -1,19 +0,0 @@ -genome_index Package -==================== - -:mod:`genome_index` Package ---------------------------- - -.. automodule:: galaxy.tools.genome_index - :members: - :undoc-members: - :show-inheritance: - -:mod:`index_genome` Module --------------------------- - -.. automodule:: galaxy.tools.genome_index.index_genome - :members: - :undoc-members: - :show-inheritance: - diff --git a/doc/source/lib/galaxy.tools.linters.rst b/doc/source/lib/galaxy.tools.linters.rst new file mode 100644 index 00000000000..e8e91a60b88 --- /dev/null +++ b/doc/source/lib/galaxy.tools.linters.rst @@ -0,0 +1,67 @@ +linters Package +=============== + +:mod:`linters` Package +---------------------- + +.. automodule:: galaxy.tools.linters + :members: + :undoc-members: + :show-inheritance: + +:mod:`citations` Module +----------------------- + +.. automodule:: galaxy.tools.linters.citations + :members: + :undoc-members: + :show-inheritance: + +:mod:`command` Module +--------------------- + +.. automodule:: galaxy.tools.linters.command + :members: + :undoc-members: + :show-inheritance: + +:mod:`help` Module +------------------ + +.. automodule:: galaxy.tools.linters.help + :members: + :undoc-members: + :show-inheritance: + +:mod:`inputs` Module +-------------------- + +.. automodule:: galaxy.tools.linters.inputs + :members: + :undoc-members: + :show-inheritance: + +:mod:`outputs` Module +--------------------- + +.. automodule:: galaxy.tools.linters.outputs + :members: + :undoc-members: + :show-inheritance: + +:mod:`tests` Module +------------------- + +.. automodule:: galaxy.tools.linters.tests + :members: + :undoc-members: + :show-inheritance: + +:mod:`top_level` Module +----------------------- + +.. automodule:: galaxy.tools.linters.top_level + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.parameters.rst b/doc/source/lib/galaxy.tools.parameters.rst index 72cd3447e17..183d17cb295 100644 --- a/doc/source/lib/galaxy.tools.parameters.rst +++ b/doc/source/lib/galaxy.tools.parameters.rst @@ -17,6 +17,14 @@ parameters Package :undoc-members: :show-inheritance: +:mod:`dataset_matcher` Module +----------------------------- + +.. automodule:: galaxy.tools.parameters.dataset_matcher + :members: + :undoc-members: + :show-inheritance: + :mod:`dynamic_options` Module ----------------------------- @@ -33,6 +41,14 @@ parameters Package :undoc-members: :show-inheritance: +:mod:`history_query` Module +--------------------------- + +.. automodule:: galaxy.tools.parameters.history_query + :members: + :undoc-members: + :show-inheritance: + :mod:`input_translation` Module ------------------------------- @@ -41,6 +57,14 @@ parameters Package :undoc-members: :show-inheritance: +:mod:`meta` Module +------------------ + +.. automodule:: galaxy.tools.parameters.meta + :members: + :undoc-members: + :show-inheritance: + :mod:`output` Module -------------------- @@ -49,6 +73,14 @@ parameters Package :undoc-members: :show-inheritance: +:mod:`output_collect` Module +---------------------------- + +.. automodule:: galaxy.tools.parameters.output_collect + :members: + :undoc-members: + :show-inheritance: + :mod:`sanitize` Module ---------------------- @@ -65,3 +97,11 @@ parameters Package :undoc-members: :show-inheritance: +:mod:`wrapped` Module +--------------------- + +.. automodule:: galaxy.tools.parameters.wrapped + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.parser.rst b/doc/source/lib/galaxy.tools.parser.rst new file mode 100644 index 00000000000..8c316098d72 --- /dev/null +++ b/doc/source/lib/galaxy.tools.parser.rst @@ -0,0 +1,51 @@ +parser Package +============== + +:mod:`parser` Package +--------------------- + +.. automodule:: galaxy.tools.parser + :members: + :undoc-members: + :show-inheritance: + +:mod:`factory` Module +--------------------- + +.. automodule:: galaxy.tools.parser.factory + :members: + :undoc-members: + :show-inheritance: + +:mod:`interface` Module +----------------------- + +.. automodule:: galaxy.tools.parser.interface + :members: + :undoc-members: + :show-inheritance: + +:mod:`util` Module +------------------ + +.. automodule:: galaxy.tools.parser.util + :members: + :undoc-members: + :show-inheritance: + +:mod:`xml` Module +----------------- + +.. automodule:: galaxy.tools.parser.xml + :members: + :undoc-members: + :show-inheritance: + +:mod:`yaml` Module +------------------ + +.. automodule:: galaxy.tools.parser.yaml + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.rst b/doc/source/lib/galaxy.tools.rst index 4b57fd3b731..90bb129cbd4 100644 --- a/doc/source/lib/galaxy.tools.rst +++ b/doc/source/lib/galaxy.tools.rst @@ -9,6 +9,22 @@ tools Package :undoc-members: :show-inheritance: +:mod:`errors` Module +-------------------- + +.. automodule:: galaxy.tools.errors + :members: + :undoc-members: + :show-inheritance: + +:mod:`evaluation` Module +------------------------ + +.. automodule:: galaxy.tools.evaluation + :members: + :undoc-members: + :show-inheritance: + :mod:`exception_handling` Module -------------------------------- @@ -17,6 +33,38 @@ tools Package :undoc-members: :show-inheritance: +:mod:`execute` Module +--------------------- + +.. automodule:: galaxy.tools.execute + :members: + :undoc-members: + :show-inheritance: + +:mod:`lint` Module +------------------ + +.. automodule:: galaxy.tools.lint + :members: + :undoc-members: + :show-inheritance: + +:mod:`loader` Module +-------------------- + +.. automodule:: galaxy.tools.loader + :members: + :undoc-members: + :show-inheritance: + +:mod:`loader_directory` Module +------------------------------ + +.. automodule:: galaxy.tools.loader_directory + :members: + :undoc-members: + :show-inheritance: + :mod:`test` Module ------------------ @@ -25,6 +73,14 @@ tools Package :undoc-members: :show-inheritance: +:mod:`wrappers` Module +---------------------- + +.. automodule:: galaxy.tools.wrappers + :members: + :undoc-members: + :show-inheritance: + Subpackages ----------- @@ -32,10 +88,14 @@ Subpackages galaxy.tools.actions galaxy.tools.data + galaxy.tools.data_manager galaxy.tools.deps - galaxy.tools.genome_index + galaxy.tools.filters galaxy.tools.imp_exp + galaxy.tools.linters galaxy.tools.parameters + galaxy.tools.parser galaxy.tools.search + galaxy.tools.toolbox galaxy.tools.util diff --git a/doc/source/lib/galaxy.tools.toolbox.filters.rst b/doc/source/lib/galaxy.tools.toolbox.filters.rst new file mode 100644 index 00000000000..d168b000a9e --- /dev/null +++ b/doc/source/lib/galaxy.tools.toolbox.filters.rst @@ -0,0 +1,11 @@ +filters Package +=============== + +:mod:`filters` Package +---------------------- + +.. automodule:: galaxy.tools.toolbox.filters + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.toolbox.lineages.rst b/doc/source/lib/galaxy.tools.toolbox.lineages.rst new file mode 100644 index 00000000000..bd3811cdb1e --- /dev/null +++ b/doc/source/lib/galaxy.tools.toolbox.lineages.rst @@ -0,0 +1,43 @@ +lineages Package +================ + +:mod:`lineages` Package +----------------------- + +.. automodule:: galaxy.tools.toolbox.lineages + :members: + :undoc-members: + :show-inheritance: + +:mod:`factory` Module +--------------------- + +.. automodule:: galaxy.tools.toolbox.lineages.factory + :members: + :undoc-members: + :show-inheritance: + +:mod:`interface` Module +----------------------- + +.. automodule:: galaxy.tools.toolbox.lineages.interface + :members: + :undoc-members: + :show-inheritance: + +:mod:`stock` Module +------------------- + +.. automodule:: galaxy.tools.toolbox.lineages.stock + :members: + :undoc-members: + :show-inheritance: + +:mod:`tool_shed` Module +----------------------- + +.. automodule:: galaxy.tools.toolbox.lineages.tool_shed + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.toolbox.rst b/doc/source/lib/galaxy.tools.toolbox.rst new file mode 100644 index 00000000000..8739d4fb201 --- /dev/null +++ b/doc/source/lib/galaxy.tools.toolbox.rst @@ -0,0 +1,59 @@ +toolbox Package +=============== + +:mod:`toolbox` Package +---------------------- + +.. automodule:: galaxy.tools.toolbox + :members: + :undoc-members: + :show-inheritance: + +:mod:`base` Module +------------------ + +.. automodule:: galaxy.tools.toolbox.base + :members: + :undoc-members: + :show-inheritance: + +:mod:`integrated_panel` Module +------------------------------ + +.. automodule:: galaxy.tools.toolbox.integrated_panel + :members: + :undoc-members: + :show-inheritance: + +:mod:`panel` Module +------------------- + +.. automodule:: galaxy.tools.toolbox.panel + :members: + :undoc-members: + :show-inheritance: + +:mod:`tags` Module +------------------ + +.. automodule:: galaxy.tools.toolbox.tags + :members: + :undoc-members: + :show-inheritance: + +:mod:`watcher` Module +--------------------- + +.. automodule:: galaxy.tools.toolbox.watcher + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.tools.toolbox.filters + galaxy.tools.toolbox.lineages + diff --git a/doc/source/lib/galaxy.util.log.rst b/doc/source/lib/galaxy.util.log.rst new file mode 100644 index 00000000000..c3aa8056511 --- /dev/null +++ b/doc/source/lib/galaxy.util.log.rst @@ -0,0 +1,19 @@ +log Package +=========== + +:mod:`log` Package +------------------ + +.. automodule:: galaxy.util.log + :members: + :undoc-members: + :show-inheritance: + +:mod:`fluent_log` Module +------------------------ + +.. automodule:: galaxy.util.log.fluent_log + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.util.pastescript.rst b/doc/source/lib/galaxy.util.pastescript.rst new file mode 100644 index 00000000000..beb1f826ebe --- /dev/null +++ b/doc/source/lib/galaxy.util.pastescript.rst @@ -0,0 +1,27 @@ +pastescript Package +=================== + +:mod:`pastescript` Package +-------------------------- + +.. automodule:: galaxy.util.pastescript + :members: + :undoc-members: + :show-inheritance: + +:mod:`loadwsgi` Module +---------------------- + +.. automodule:: galaxy.util.pastescript.loadwsgi + :members: + :undoc-members: + :show-inheritance: + +:mod:`serve` Module +------------------- + +.. automodule:: galaxy.util.pastescript.serve + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.util.rst b/doc/source/lib/galaxy.util.rst index 6866a5f0fb6..e37346a6b6b 100644 --- a/doc/source/lib/galaxy.util.rst +++ b/doc/source/lib/galaxy.util.rst @@ -17,6 +17,14 @@ util Package :undoc-members: :show-inheritance: +:mod:`biostar` Module +--------------------- + +.. automodule:: galaxy.util.biostar + :members: + :undoc-members: + :show-inheritance: + :mod:`bunch` Module ------------------- @@ -25,6 +33,14 @@ util Package :undoc-members: :show-inheritance: +:mod:`dbkeys` Module +-------------------- + +.. automodule:: galaxy.util.dbkeys + :members: + :undoc-members: + :show-inheritance: + :mod:`debugging` Module ----------------------- @@ -33,6 +49,22 @@ util Package :undoc-members: :show-inheritance: +:mod:`dictobj` Module +--------------------- + +.. automodule:: galaxy.util.dictobj + :members: + :undoc-members: + :show-inheritance: + +:mod:`directory_hash` Module +---------------------------- + +.. automodule:: galaxy.util.directory_hash + :members: + :undoc-members: + :show-inheritance: + :mod:`expressions` Module ------------------------- @@ -73,18 +105,26 @@ util Package :undoc-members: :show-inheritance: -:mod:`lrucache` Module ----------------------- +:mod:`jstree` Module +-------------------- -.. automodule:: galaxy.util.lrucache +.. automodule:: galaxy.util.jstree :members: :undoc-members: :show-inheritance: -:mod:`memdump` Module ---------------------- +:mod:`lazy_process` Module +-------------------------- -.. automodule:: galaxy.util.memdump +.. automodule:: galaxy.util.lazy_process + :members: + :undoc-members: + :show-inheritance: + +:mod:`lrucache` Module +---------------------- + +.. automodule:: galaxy.util.lrucache :members: :undoc-members: :show-inheritance: @@ -97,6 +137,14 @@ util Package :undoc-members: :show-inheritance: +:mod:`object_wrapper` Module +---------------------------- + +.. automodule:: galaxy.util.object_wrapper + :members: + :undoc-members: + :show-inheritance: + :mod:`odict` Module ------------------- @@ -105,6 +153,30 @@ util Package :undoc-members: :show-inheritance: +:mod:`permutations` Module +-------------------------- + +.. automodule:: galaxy.util.permutations + :members: + :undoc-members: + :show-inheritance: + +:mod:`plugin_config` Module +--------------------------- + +.. automodule:: galaxy.util.plugin_config + :members: + :undoc-members: + :show-inheritance: + +:mod:`properties` Module +------------------------ + +.. automodule:: galaxy.util.properties + :members: + :undoc-members: + :show-inheritance: + :mod:`sanitize_html` Module --------------------------- @@ -113,18 +185,42 @@ util Package :undoc-members: :show-inheritance: -:mod:`shed_util` Module ------------------------ +:mod:`simplegraph` Module +------------------------- -.. automodule:: galaxy.util.shed_util +.. automodule:: galaxy.util.simplegraph :members: :undoc-members: :show-inheritance: -:mod:`shed_util_common` Module ------------------------------- +:mod:`sleeper` Module +--------------------- -.. automodule:: galaxy.util.shed_util_common +.. automodule:: galaxy.util.sleeper + :members: + :undoc-members: + :show-inheritance: + +:mod:`sockets` Module +--------------------- + +.. automodule:: galaxy.util.sockets + :members: + :undoc-members: + :show-inheritance: + +:mod:`specs` Module +------------------- + +.. automodule:: galaxy.util.specs + :members: + :undoc-members: + :show-inheritance: + +:mod:`sqlite` Module +-------------------- + +.. automodule:: galaxy.util.sqlite :members: :undoc-members: :show-inheritance: @@ -137,6 +233,14 @@ util Package :undoc-members: :show-inheritance: +:mod:`submodules` Module +------------------------ + +.. automodule:: galaxy.util.submodules + :members: + :undoc-members: + :show-inheritance: + :mod:`template` Module ---------------------- @@ -153,6 +257,22 @@ util Package :undoc-members: :show-inheritance: +:mod:`validation` Module +------------------------ + +.. automodule:: galaxy.util.validation + :members: + :undoc-members: + :show-inheritance: + +:mod:`xml_macros` Module +------------------------ + +.. automodule:: galaxy.util.xml_macros + :members: + :undoc-members: + :show-inheritance: + Subpackages ----------- @@ -160,4 +280,5 @@ Subpackages galaxy.util.backports galaxy.util.log + galaxy.util.pastescript diff --git a/doc/source/lib/galaxy.visualization.data_providers.rst b/doc/source/lib/galaxy.visualization.data_providers.rst index a7561325011..ba55a961528 100644 --- a/doc/source/lib/galaxy.visualization.data_providers.rst +++ b/doc/source/lib/galaxy.visualization.data_providers.rst @@ -17,6 +17,14 @@ data_providers Package :undoc-members: :show-inheritance: +:mod:`cigar` Module +------------------- + +.. automodule:: galaxy.visualization.data_providers.cigar + :members: + :undoc-members: + :show-inheritance: + :mod:`genome` Module -------------------- diff --git a/doc/source/lib/galaxy.visualization.genome.rst b/doc/source/lib/galaxy.visualization.genome.rst index 1605b712107..8e880dd6b5f 100644 --- a/doc/source/lib/galaxy.visualization.genome.rst +++ b/doc/source/lib/galaxy.visualization.genome.rst @@ -9,11 +9,3 @@ genome Package :undoc-members: :show-inheritance: -:mod:`visual_analytics` Module ------------------------------- - -.. automodule:: galaxy.visualization.genome.visual_analytics - :members: - :undoc-members: - :show-inheritance: - diff --git a/doc/source/lib/galaxy.visualization.plugins.rst b/doc/source/lib/galaxy.visualization.plugins.rst new file mode 100644 index 00000000000..d276f6d2c32 --- /dev/null +++ b/doc/source/lib/galaxy.visualization.plugins.rst @@ -0,0 +1,43 @@ +plugins Package +=============== + +:mod:`config_parser` Module +--------------------------- + +.. automodule:: galaxy.visualization.plugins.config_parser + :members: + :undoc-members: + :show-inheritance: + +:mod:`plugin` Module +-------------------- + +.. automodule:: galaxy.visualization.plugins.plugin + :members: + :undoc-members: + :show-inheritance: + +:mod:`registry` Module +---------------------- + +.. automodule:: galaxy.visualization.plugins.registry + :members: + :undoc-members: + :show-inheritance: + +:mod:`resource_parser` Module +----------------------------- + +.. automodule:: galaxy.visualization.plugins.resource_parser + :members: + :undoc-members: + :show-inheritance: + +:mod:`utils` Module +------------------- + +.. automodule:: galaxy.visualization.plugins.utils + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.visualization.rst b/doc/source/lib/galaxy.visualization.rst index 3d85a78ba4e..ba80d9719ce 100644 --- a/doc/source/lib/galaxy.visualization.rst +++ b/doc/source/lib/galaxy.visualization.rst @@ -24,5 +24,6 @@ Subpackages galaxy.visualization.data_providers galaxy.visualization.genome + galaxy.visualization.plugins galaxy.visualization.tracks diff --git a/doc/source/lib/galaxy.visualization.tracks.rst b/doc/source/lib/galaxy.visualization.tracks.rst index 8242d51dff2..9823b4191df 100644 --- a/doc/source/lib/galaxy.visualization.tracks.rst +++ b/doc/source/lib/galaxy.visualization.tracks.rst @@ -9,11 +9,3 @@ tracks Package :undoc-members: :show-inheritance: -:mod:`summary` Module ---------------------- - -.. automodule:: galaxy.visualization.tracks.summary - :members: - :undoc-members: - :show-inheritance: - diff --git a/doc/source/lib/galaxy.web.base.rst b/doc/source/lib/galaxy.web.base.rst index 3f1078c6b3a..8b12d23d8c2 100644 --- a/doc/source/lib/galaxy.web.base.rst +++ b/doc/source/lib/galaxy.web.base.rst @@ -9,6 +9,22 @@ base Package :undoc-members: :show-inheritance: +:mod:`interactive_environments` Module +-------------------------------------- + +.. automodule:: galaxy.web.base.interactive_environments + :members: + :undoc-members: + :show-inheritance: + +:mod:`pluginframework` Module +----------------------------- + +.. automodule:: galaxy.web.base.pluginframework + :members: + :undoc-members: + :show-inheritance: + Subpackages ----------- diff --git a/doc/source/lib/galaxy.web.framework.middleware.rst b/doc/source/lib/galaxy.web.framework.middleware.rst index 1ce4b89f9ba..ddaff84b275 100644 --- a/doc/source/lib/galaxy.web.framework.middleware.rst +++ b/doc/source/lib/galaxy.web.framework.middleware.rst @@ -9,6 +9,14 @@ middleware Package :undoc-members: :show-inheritance: +:mod:`error` Module +------------------- + +.. automodule:: galaxy.web.framework.middleware.error + :members: + :undoc-members: + :show-inheritance: + :mod:`profile` Module --------------------- @@ -25,6 +33,22 @@ middleware Package :undoc-members: :show-inheritance: +:mod:`request_id` Module +------------------------ + +.. automodule:: galaxy.web.framework.middleware.request_id + :members: + :undoc-members: + :show-inheritance: + +:mod:`sentry` Module +-------------------- + +.. automodule:: galaxy.web.framework.middleware.sentry + :members: + :undoc-members: + :show-inheritance: + :mod:`static` Module -------------------- diff --git a/doc/source/lib/galaxy.web.framework.rst b/doc/source/lib/galaxy.web.framework.rst index 5391c910912..7e02bd99e5b 100644 --- a/doc/source/lib/galaxy.web.framework.rst +++ b/doc/source/lib/galaxy.web.framework.rst @@ -17,6 +17,22 @@ framework Package :undoc-members: :show-inheritance: +:mod:`decorators` Module +------------------------ + +.. automodule:: galaxy.web.framework.decorators + :members: + :undoc-members: + :show-inheritance: + +:mod:`formbuilder` Module +------------------------- + +.. automodule:: galaxy.web.framework.formbuilder + :members: + :undoc-members: + :show-inheritance: + :mod:`openid_manager` Module ---------------------------- @@ -25,6 +41,14 @@ framework Package :undoc-members: :show-inheritance: +:mod:`webapp` Module +-------------------- + +.. automodule:: galaxy.web.framework.webapp + :members: + :undoc-members: + :show-inheritance: + Subpackages ----------- diff --git a/doc/source/lib/galaxy.web.proxy.rst b/doc/source/lib/galaxy.web.proxy.rst new file mode 100644 index 00000000000..a9f49e364e8 --- /dev/null +++ b/doc/source/lib/galaxy.web.proxy.rst @@ -0,0 +1,19 @@ +proxy Package +============= + +:mod:`proxy` Package +-------------------- + +.. automodule:: galaxy.web.proxy + :members: + :undoc-members: + :show-inheritance: + +:mod:`filelock` Module +---------------------- + +.. automodule:: galaxy.web.proxy.filelock + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.web.rst b/doc/source/lib/galaxy.web.rst index c929ad6a40e..5d721616340 100644 --- a/doc/source/lib/galaxy.web.rst +++ b/doc/source/lib/galaxy.web.rst @@ -25,6 +25,14 @@ web Package :undoc-members: :show-inheritance: +:mod:`formatting` Module +------------------------ + +.. automodule:: galaxy.web.formatting + :members: + :undoc-members: + :show-inheritance: + :mod:`params` Module -------------------- @@ -40,5 +48,6 @@ Subpackages galaxy.web.base galaxy.web.framework + galaxy.web.proxy galaxy.web.security diff --git a/doc/source/lib/galaxy.webapps.community.controllers.rst b/doc/source/lib/galaxy.webapps.community.controllers.rst deleted file mode 100644 index d2a1f217603..00000000000 --- a/doc/source/lib/galaxy.webapps.community.controllers.rst +++ /dev/null @@ -1,67 +0,0 @@ -controllers Package -=================== - -:mod:`controllers` Package --------------------------- - -.. automodule:: galaxy.webapps.community.controllers - :members: - :undoc-members: - :show-inheritance: - -:mod:`admin` Module -------------------- - -.. automodule:: galaxy.webapps.community.controllers.admin - :members: - :undoc-members: - :show-inheritance: - -:mod:`common` Module --------------------- - -.. automodule:: galaxy.webapps.community.controllers.common - :members: - :undoc-members: - :show-inheritance: - -:mod:`hg` Module ----------------- - -.. automodule:: galaxy.webapps.community.controllers.hg - :members: - :undoc-members: - :show-inheritance: - -:mod:`repository` Module ------------------------- - -.. automodule:: galaxy.webapps.community.controllers.repository - :members: - :undoc-members: - :show-inheritance: - -:mod:`repository_review` Module -------------------------------- - -.. automodule:: galaxy.webapps.community.controllers.repository_review - :members: - :undoc-members: - :show-inheritance: - -:mod:`upload` Module --------------------- - -.. automodule:: galaxy.webapps.community.controllers.upload - :members: - :undoc-members: - :show-inheritance: - -:mod:`user` Module ------------------- - -.. automodule:: galaxy.webapps.community.controllers.user - :members: - :undoc-members: - :show-inheritance: - diff --git a/doc/source/lib/galaxy.webapps.community.framework.middleware.rst b/doc/source/lib/galaxy.webapps.community.framework.middleware.rst deleted file mode 100644 index 5bb9965acf6..00000000000 --- a/doc/source/lib/galaxy.webapps.community.framework.middleware.rst +++ /dev/null @@ -1,27 +0,0 @@ -middleware Package -================== - -:mod:`middleware` Package -------------------------- - -.. automodule:: galaxy.webapps.community.framework.middleware - :members: - :undoc-members: - :show-inheritance: - -:mod:`hg` Module ----------------- - -.. automodule:: galaxy.webapps.community.framework.middleware.hg - :members: - :undoc-members: - :show-inheritance: - -:mod:`remoteuser` Module ------------------------- - -.. automodule:: galaxy.webapps.community.framework.middleware.remoteuser - :members: - :undoc-members: - :show-inheritance: - diff --git a/doc/source/lib/galaxy.webapps.community.framework.rst b/doc/source/lib/galaxy.webapps.community.framework.rst deleted file mode 100644 index b428492d31a..00000000000 --- a/doc/source/lib/galaxy.webapps.community.framework.rst +++ /dev/null @@ -1,18 +0,0 @@ -framework Package -================= - -:mod:`framework` Package ------------------------- - -.. automodule:: galaxy.webapps.community.framework - :members: - :undoc-members: - :show-inheritance: - -Subpackages ------------ - -.. toctree:: - - galaxy.webapps.community.framework.middleware - diff --git a/doc/source/lib/galaxy.webapps.community.model.rst b/doc/source/lib/galaxy.webapps.community.model.rst deleted file mode 100644 index 1c8583259c0..00000000000 --- a/doc/source/lib/galaxy.webapps.community.model.rst +++ /dev/null @@ -1,26 +0,0 @@ -model Package -============= - -:mod:`model` Package --------------------- - -.. automodule:: galaxy.webapps.community.model - :members: - :undoc-members: - :show-inheritance: - -:mod:`mapping` Module ---------------------- - -.. automodule:: galaxy.webapps.community.model.mapping - :members: - :undoc-members: - :show-inheritance: - -Subpackages ------------ - -.. toctree:: - - galaxy.webapps.community.model.migrate - diff --git a/doc/source/lib/galaxy.webapps.community.rst b/doc/source/lib/galaxy.webapps.community.rst deleted file mode 100644 index 904044beea8..00000000000 --- a/doc/source/lib/galaxy.webapps.community.rst +++ /dev/null @@ -1,46 +0,0 @@ -community Package -================= - -:mod:`community` Package ------------------------- - -.. automodule:: galaxy.webapps.community - :members: - :undoc-members: - :show-inheritance: - -:mod:`app` Module ------------------ - -.. automodule:: galaxy.webapps.community.app - :members: - :undoc-members: - :show-inheritance: - -:mod:`buildapp` Module ----------------------- - -.. automodule:: galaxy.webapps.community.buildapp - :members: - :undoc-members: - :show-inheritance: - -:mod:`config` Module --------------------- - -.. automodule:: galaxy.webapps.community.config - :members: - :undoc-members: - :show-inheritance: - -Subpackages ------------ - -.. toctree:: - - galaxy.webapps.community.controllers - galaxy.webapps.community.framework - galaxy.webapps.community.model - galaxy.webapps.community.security - galaxy.webapps.community.util - diff --git a/doc/source/lib/galaxy.webapps.community.security.rst b/doc/source/lib/galaxy.webapps.community.security.rst deleted file mode 100644 index d4c92a8daf9..00000000000 --- a/doc/source/lib/galaxy.webapps.community.security.rst +++ /dev/null @@ -1,11 +0,0 @@ -security Package -================ - -:mod:`security` Package ------------------------ - -.. automodule:: galaxy.webapps.community.security - :members: - :undoc-members: - :show-inheritance: - diff --git a/doc/source/lib/galaxy.webapps.community.util.rst b/doc/source/lib/galaxy.webapps.community.util.rst deleted file mode 100644 index aa8e5fee8dd..00000000000 --- a/doc/source/lib/galaxy.webapps.community.util.rst +++ /dev/null @@ -1,35 +0,0 @@ -util Package -============ - -:mod:`container_util` Module ----------------------------- - -.. automodule:: galaxy.webapps.community.util.container_util - :members: - :undoc-members: - :show-inheritance: - -:mod:`hgweb_config` Module --------------------------- - -.. automodule:: galaxy.webapps.community.util.hgweb_config - :members: - :undoc-members: - :show-inheritance: - -:mod:`shed_statistics` Module ------------------------------ - -.. automodule:: galaxy.webapps.community.util.shed_statistics - :members: - :undoc-members: - :show-inheritance: - -:mod:`workflow_util` Module ---------------------------- - -.. automodule:: galaxy.webapps.community.util.workflow_util - :members: - :undoc-members: - :show-inheritance: - diff --git a/doc/source/lib/galaxy.webapps.galaxy.api.rst b/doc/source/lib/galaxy.webapps.galaxy.api.rst index 8b7546bffce..5ff9d716e45 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -2,232 +2,314 @@ galaxy.webapps.galaxy.api package ================================= :mod:`annotations` Module ----------------------- +------------------------- .. automodule:: galaxy.webapps.galaxy.api.annotations + :members: + :undoc-members: + :show-inheritance: :mod:`authenticate` Module ----------------------- +-------------------------- .. automodule:: galaxy.webapps.galaxy.api.authenticate + :members: + :undoc-members: + :show-inheritance: :mod:`configuration` Module ----------------------- +--------------------------- .. automodule:: galaxy.webapps.galaxy.api.configuration + :members: + :undoc-members: + :show-inheritance: :mod:`dataset_collections` Module ----------------------- +--------------------------------- .. automodule:: galaxy.webapps.galaxy.api.dataset_collections - + :members: + :undoc-members: + :show-inheritance: :mod:`datasets` Module ---------------------- .. automodule:: galaxy.webapps.galaxy.api.datasets - + :members: + :undoc-members: + :show-inheritance: :mod:`datatypes` Module ----------------------- +----------------------- .. automodule:: galaxy.webapps.galaxy.api.datatypes - + :members: + :undoc-members: + :show-inheritance: :mod:`extended_metadata` Module ----------------------- +------------------------------- .. automodule:: galaxy.webapps.galaxy.api.extended_metadata - + :members: + :undoc-members: + :show-inheritance: :mod:`folder_contents` Module ----------------------------- .. automodule:: galaxy.webapps.galaxy.api.folder_contents - + :members: + :undoc-members: + :show-inheritance: :mod:`folders` Module --------------------- .. automodule:: galaxy.webapps.galaxy.api.folders - + :members: + :undoc-members: + :show-inheritance: :mod:`forms` Module ------------------- .. automodule:: galaxy.webapps.galaxy.api.forms - + :members: + :undoc-members: + :show-inheritance: :mod:`genomes` Module --------------------- .. automodule:: galaxy.webapps.galaxy.api.genomes - + :members: + :undoc-members: + :show-inheritance: :mod:`group_roles` Module ------------------------- .. automodule:: galaxy.webapps.galaxy.api.group_roles - + :members: + :undoc-members: + :show-inheritance: :mod:`group_users` Module ------------------------- .. automodule:: galaxy.webapps.galaxy.api.group_users - + :members: + :undoc-members: + :show-inheritance: :mod:`groups` Module -------------------- .. automodule:: galaxy.webapps.galaxy.api.groups - + :members: + :undoc-members: + :show-inheritance: :mod:`histories` Module ----------------------- .. automodule:: galaxy.webapps.galaxy.api.histories - + :members: + :undoc-members: + :show-inheritance: :mod:`history_contents` Module ------------------------------ .. automodule:: galaxy.webapps.galaxy.api.history_contents - + :members: + :undoc-members: + :show-inheritance: :mod:`item_tags` Module ----------------------- .. automodule:: galaxy.webapps.galaxy.api.item_tags - + :members: + :undoc-members: + :show-inheritance: :mod:`job_files` Module ----------------------- +----------------------- .. automodule:: galaxy.webapps.galaxy.api.job_files - + :members: + :undoc-members: + :show-inheritance: :mod:`jobs` Module ----------------------- +------------------ .. automodule:: galaxy.webapps.galaxy.api.jobs - + :members: + :undoc-members: + :show-inheritance: :mod:`lda_datasets` Module -------------------------- .. automodule:: galaxy.webapps.galaxy.api.lda_datasets - + :members: + :undoc-members: + :show-inheritance: :mod:`libraries` Module ----------------------- .. automodule:: galaxy.webapps.galaxy.api.libraries - + :members: + :undoc-members: + :show-inheritance: :mod:`library_contents` Module ------------------------------ .. automodule:: galaxy.webapps.galaxy.api.library_contents - + :members: + :undoc-members: + :show-inheritance: :mod:`metrics` Module ----------------------- +--------------------- .. automodule:: galaxy.webapps.galaxy.api.metrics - + :members: + :undoc-members: + :show-inheritance: :mod:`page_revisions` Module ----------------------- +---------------------------- .. automodule:: galaxy.webapps.galaxy.api.page_revisions - + :members: + :undoc-members: + :show-inheritance: :mod:`pages` Module ----------------------- +------------------- .. automodule:: galaxy.webapps.galaxy.api.pages - + :members: + :undoc-members: + :show-inheritance: :mod:`provenance` Module ----------------------- +------------------------ .. automodule:: galaxy.webapps.galaxy.api.provenance - + :members: + :undoc-members: + :show-inheritance: :mod:`quotas` Module -------------------- .. automodule:: galaxy.webapps.galaxy.api.quotas - + :members: + :undoc-members: + :show-inheritance: :mod:`remote_files` Module ----------------------- +-------------------------- .. automodule:: galaxy.webapps.galaxy.api.remote_files - + :members: + :undoc-members: + :show-inheritance: :mod:`request_types` Module --------------------------- .. automodule:: galaxy.webapps.galaxy.api.request_types - + :members: + :undoc-members: + :show-inheritance: :mod:`requests` Module ---------------------- .. automodule:: galaxy.webapps.galaxy.api.requests - + :members: + :undoc-members: + :show-inheritance: :mod:`roles` Module ------------------- .. automodule:: galaxy.webapps.galaxy.api.roles - + :members: + :undoc-members: + :show-inheritance: :mod:`samples` Module --------------------- .. automodule:: galaxy.webapps.galaxy.api.samples - + :members: + :undoc-members: + :show-inheritance: :mod:`search` Module ----------------------- +-------------------- .. automodule:: galaxy.webapps.galaxy.api.search - + :members: + :undoc-members: + :show-inheritance: :mod:`tool_data` Module ----------------------- +----------------------- .. automodule:: galaxy.webapps.galaxy.api.tool_data - + :members: + :undoc-members: + :show-inheritance: :mod:`tool_shed_repositories` Module ----------------------- +------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.tool_shed_repositories - + :members: + :undoc-members: + :show-inheritance: :mod:`tools` Module ------------------- .. automodule:: galaxy.webapps.galaxy.api.tools - + :members: + :undoc-members: + :show-inheritance: :mod:`users` Module ------------------- .. automodule:: galaxy.webapps.galaxy.api.users - + :members: + :undoc-members: + :show-inheritance: :mod:`visualizations` Module ---------------------------- .. automodule:: galaxy.webapps.galaxy.api.visualizations - + :members: + :undoc-members: + :show-inheritance: :mod:`workflows` Module ----------------------- .. automodule:: galaxy.webapps.galaxy.api.workflows + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst index 4517fc2ba37..3b870bf2092 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst @@ -33,6 +33,14 @@ controllers Package :undoc-members: :show-inheritance: +:mod:`biostar` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.biostar + :members: + :undoc-members: + :show-inheritance: + :mod:`cloudlaunch` Module ------------------------- @@ -41,10 +49,10 @@ controllers Package :undoc-members: :show-inheritance: -:mod:`data_admin` Module ------------------------- +:mod:`data_manager` Module +-------------------------- -.. automodule:: galaxy.webapps.galaxy.controllers.data_admin +.. automodule:: galaxy.webapps.galaxy.controllers.data_manager :members: :undoc-members: :show-inheritance: @@ -177,6 +185,14 @@ controllers Package :undoc-members: :show-inheritance: +:mod:`search` Module +-------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.search + :members: + :undoc-members: + :show-inheritance: + :mod:`tag` Module ----------------- @@ -209,6 +225,14 @@ controllers Package :undoc-members: :show-inheritance: +:mod:`userskeys` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.userskeys + :members: + :undoc-members: + :show-inheritance: + :mod:`visualization` Module --------------------------- diff --git a/doc/source/lib/galaxy.webapps.reports.controllers.rst b/doc/source/lib/galaxy.webapps.reports.controllers.rst index fceead9e86c..72e2b6da340 100644 --- a/doc/source/lib/galaxy.webapps.reports.controllers.rst +++ b/doc/source/lib/galaxy.webapps.reports.controllers.rst @@ -17,6 +17,14 @@ controllers Package :undoc-members: :show-inheritance: +:mod:`query` Module +------------------- + +.. automodule:: galaxy.webapps.reports.controllers.query + :members: + :undoc-members: + :show-inheritance: + :mod:`root` Module ------------------ diff --git a/doc/source/lib/galaxy.webapps.rst b/doc/source/lib/galaxy.webapps.rst index 4f45cdbc4b6..7b0597ba68c 100644 --- a/doc/source/lib/galaxy.webapps.rst +++ b/doc/source/lib/galaxy.webapps.rst @@ -14,7 +14,7 @@ Subpackages .. toctree:: - galaxy.webapps.community galaxy.webapps.galaxy galaxy.webapps.reports + galaxy.webapps.tool_shed diff --git a/doc/source/lib/galaxy.webapps.tool_shed.api.rst b/doc/source/lib/galaxy.webapps.tool_shed.api.rst index 854f99f3e03..98dae6f2fd8 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.api.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.api.rst @@ -1,6 +1,30 @@ api Package =========== +:mod:`authenticate` Module +-------------------------- + +.. automodule:: galaxy.webapps.tool_shed.api.authenticate + :members: + :undoc-members: + :show-inheritance: + +:mod:`categories` Module +------------------------ + +.. automodule:: galaxy.webapps.tool_shed.api.categories + :members: + :undoc-members: + :show-inheritance: + +:mod:`groups` Module +-------------------- + +.. automodule:: galaxy.webapps.tool_shed.api.groups + :members: + :undoc-members: + :show-inheritance: + :mod:`repositories` Module -------------------------- @@ -17,3 +41,19 @@ api Package :undoc-members: :show-inheritance: +:mod:`tools` Module +------------------- + +.. automodule:: galaxy.webapps.tool_shed.api.tools + :members: + :undoc-members: + :show-inheritance: + +:mod:`users` Module +------------------- + +.. automodule:: galaxy.webapps.tool_shed.api.users + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst b/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst index 01163fcd545..986d7fe3f57 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst @@ -17,6 +17,14 @@ controllers Package :undoc-members: :show-inheritance: +:mod:`groups` Module +-------------------- + +.. automodule:: galaxy.webapps.tool_shed.controllers.groups + :members: + :undoc-members: + :show-inheritance: + :mod:`hg` Module ---------------- diff --git a/doc/source/lib/galaxy.webapps.tool_shed.rst b/doc/source/lib/galaxy.webapps.tool_shed.rst index 1590f2988c1..e358e871712 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.rst @@ -42,6 +42,7 @@ Subpackages galaxy.webapps.tool_shed.controllers galaxy.webapps.tool_shed.framework galaxy.webapps.tool_shed.model + galaxy.webapps.tool_shed.search galaxy.webapps.tool_shed.security galaxy.webapps.tool_shed.util diff --git a/doc/source/lib/galaxy.webapps.tool_shed.search.rst b/doc/source/lib/galaxy.webapps.tool_shed.search.rst new file mode 100644 index 00000000000..78ccaa6cffb --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.search.rst @@ -0,0 +1,19 @@ +search Package +============== + +:mod:`repo_search` Module +------------------------- + +.. automodule:: galaxy.webapps.tool_shed.search.repo_search + :members: + :undoc-members: + :show-inheritance: + +:mod:`tool_search` Module +------------------------- + +.. automodule:: galaxy.webapps.tool_shed.search.tool_search + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.webapps.tool_shed.util.rst b/doc/source/lib/galaxy.webapps.tool_shed.util.rst index a8623852afa..8eff5d41834 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.util.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.util.rst @@ -1,22 +1,6 @@ util Package ============ -:mod:`common_util` Module -------------------------- - -.. automodule:: galaxy.webapps.tool_shed.util.common_util - :members: - :undoc-members: - :show-inheritance: - -:mod:`container_util` Module ----------------------------- - -.. automodule:: galaxy.webapps.tool_shed.util.container_util - :members: - :undoc-members: - :show-inheritance: - :mod:`hgweb_config` Module -------------------------- @@ -25,6 +9,14 @@ util Package :undoc-members: :show-inheritance: +:mod:`ratings_util` Module +-------------------------- + +.. automodule:: galaxy.webapps.tool_shed.util.ratings_util + :members: + :undoc-members: + :show-inheritance: + :mod:`shed_statistics` Module ----------------------------- diff --git a/doc/source/lib/galaxy.work.rst b/doc/source/lib/galaxy.work.rst new file mode 100644 index 00000000000..00f74832bc8 --- /dev/null +++ b/doc/source/lib/galaxy.work.rst @@ -0,0 +1,11 @@ +work Package +============ + +:mod:`context` Module +--------------------- + +.. automodule:: galaxy.work.context + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.workflow.rst b/doc/source/lib/galaxy.workflow.rst index 52fd8e5fb0a..7f41691fc77 100644 --- a/doc/source/lib/galaxy.workflow.rst +++ b/doc/source/lib/galaxy.workflow.rst @@ -1,6 +1,14 @@ workflow Package ================ +:mod:`extract` Module +--------------------- + +.. automodule:: galaxy.workflow.extract + :members: + :undoc-members: + :show-inheritance: + :mod:`modules` Module --------------------- @@ -9,3 +17,50 @@ workflow Package :undoc-members: :show-inheritance: +:mod:`render` Module +-------------------- + +.. automodule:: galaxy.workflow.render + :members: + :undoc-members: + :show-inheritance: + +:mod:`run` Module +----------------- + +.. automodule:: galaxy.workflow.run + :members: + :undoc-members: + :show-inheritance: + +:mod:`run_request` Module +------------------------- + +.. automodule:: galaxy.workflow.run_request + :members: + :undoc-members: + :show-inheritance: + +:mod:`scheduling_manager` Module +-------------------------------- + +.. automodule:: galaxy.workflow.scheduling_manager + :members: + :undoc-members: + :show-inheritance: + +:mod:`steps` Module +------------------- + +.. automodule:: galaxy.workflow.steps + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.workflow.schedulers + diff --git a/doc/source/lib/galaxy.workflow.schedulers.rst b/doc/source/lib/galaxy.workflow.schedulers.rst new file mode 100644 index 00000000000..792b5f500ea --- /dev/null +++ b/doc/source/lib/galaxy.workflow.schedulers.rst @@ -0,0 +1,19 @@ +schedulers Package +================== + +:mod:`schedulers` Package +------------------------- + +.. automodule:: galaxy.workflow.schedulers + :members: + :undoc-members: + :show-inheritance: + +:mod:`core` Module +------------------ + +.. automodule:: galaxy.workflow.schedulers.core + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy_ext.metadata.rst b/doc/source/lib/galaxy_ext.metadata.rst new file mode 100644 index 00000000000..c475fafca7c --- /dev/null +++ b/doc/source/lib/galaxy_ext.metadata.rst @@ -0,0 +1,19 @@ +metadata Package +================ + +:mod:`metadata` Package +----------------------- + +.. automodule:: galaxy_ext.metadata + :members: + :undoc-members: + :show-inheritance: + +:mod:`set_metadata` Module +-------------------------- + +.. automodule:: galaxy_ext.metadata.set_metadata + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy_ext.rst b/doc/source/lib/galaxy_ext.rst new file mode 100644 index 00000000000..1c13d00470b --- /dev/null +++ b/doc/source/lib/galaxy_ext.rst @@ -0,0 +1,18 @@ +galaxy_ext Package +================== + +:mod:`galaxy_ext` Package +------------------------- + +.. automodule:: galaxy_ext + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy_ext.metadata + diff --git a/doc/source/lib/modules.rst b/doc/source/lib/modules.rst index c6255ce98fd..bb4749bc352 100644 --- a/doc/source/lib/modules.rst +++ b/doc/source/lib/modules.rst @@ -4,10 +4,12 @@ lib .. toctree:: :maxdepth: 4 - fpconst galaxy + galaxy_ext galaxy_utils log_tempfile mimeparse pkg_resources psyco_full + pulsar + tool_shed diff --git a/doc/source/lib/pulsar.client.rst b/doc/source/lib/pulsar.client.rst new file mode 100644 index 00000000000..6458d71332f --- /dev/null +++ b/doc/source/lib/pulsar.client.rst @@ -0,0 +1,131 @@ +client Package +============== + +:mod:`client` Package +--------------------- + +.. automodule:: pulsar.client + :members: + :undoc-members: + :show-inheritance: + +:mod:`action_mapper` Module +--------------------------- + +.. automodule:: pulsar.client.action_mapper + :members: + :undoc-members: + :show-inheritance: + +:mod:`amqp_exchange` Module +--------------------------- + +.. automodule:: pulsar.client.amqp_exchange + :members: + :undoc-members: + :show-inheritance: + +:mod:`amqp_exchange_factory` Module +----------------------------------- + +.. automodule:: pulsar.client.amqp_exchange_factory + :members: + :undoc-members: + :show-inheritance: + +:mod:`client` Module +-------------------- + +.. automodule:: pulsar.client.client + :members: + :undoc-members: + :show-inheritance: + +:mod:`config_util` Module +------------------------- + +.. automodule:: pulsar.client.config_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`decorators` Module +------------------------ + +.. automodule:: pulsar.client.decorators + :members: + :undoc-members: + :show-inheritance: + +:mod:`destination` Module +------------------------- + +.. automodule:: pulsar.client.destination + :members: + :undoc-members: + :show-inheritance: + +:mod:`interface` Module +----------------------- + +.. automodule:: pulsar.client.interface + :members: + :undoc-members: + :show-inheritance: + +:mod:`job_directory` Module +--------------------------- + +.. automodule:: pulsar.client.job_directory + :members: + :undoc-members: + :show-inheritance: + +:mod:`manager` Module +--------------------- + +.. automodule:: pulsar.client.manager + :members: + :undoc-members: + :show-inheritance: + +:mod:`object_client` Module +--------------------------- + +.. automodule:: pulsar.client.object_client + :members: + :undoc-members: + :show-inheritance: + +:mod:`path_mapper` Module +------------------------- + +.. automodule:: pulsar.client.path_mapper + :members: + :undoc-members: + :show-inheritance: + +:mod:`setup_handler` Module +--------------------------- + +.. automodule:: pulsar.client.setup_handler + :members: + :undoc-members: + :show-inheritance: + +:mod:`util` Module +------------------ + +.. automodule:: pulsar.client.util + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + pulsar.client.staging + pulsar.client.transport + diff --git a/doc/source/lib/pulsar.client.staging.rst b/doc/source/lib/pulsar.client.staging.rst new file mode 100644 index 00000000000..6731bc362b3 --- /dev/null +++ b/doc/source/lib/pulsar.client.staging.rst @@ -0,0 +1,27 @@ +staging Package +=============== + +:mod:`staging` Package +---------------------- + +.. automodule:: pulsar.client.staging + :members: + :undoc-members: + :show-inheritance: + +:mod:`down` Module +------------------ + +.. automodule:: pulsar.client.staging.down + :members: + :undoc-members: + :show-inheritance: + +:mod:`up` Module +---------------- + +.. automodule:: pulsar.client.staging.up + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/pulsar.client.transport.rst b/doc/source/lib/pulsar.client.transport.rst new file mode 100644 index 00000000000..afeb8f24a3b --- /dev/null +++ b/doc/source/lib/pulsar.client.transport.rst @@ -0,0 +1,51 @@ +transport Package +================= + +:mod:`transport` Package +------------------------ + +.. automodule:: pulsar.client.transport + :members: + :undoc-members: + :show-inheritance: + +:mod:`curl` Module +------------------ + +.. automodule:: pulsar.client.transport.curl + :members: + :undoc-members: + :show-inheritance: + +:mod:`poster` Module +-------------------- + +.. automodule:: pulsar.client.transport.poster + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests` Module +---------------------- + +.. automodule:: pulsar.client.transport.requests + :members: + :undoc-members: + :show-inheritance: + +:mod:`ssh` Module +----------------- + +.. automodule:: pulsar.client.transport.ssh + :members: + :undoc-members: + :show-inheritance: + +:mod:`standard` Module +---------------------- + +.. automodule:: pulsar.client.transport.standard + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/pulsar.rst b/doc/source/lib/pulsar.rst new file mode 100644 index 00000000000..754078e9094 --- /dev/null +++ b/doc/source/lib/pulsar.rst @@ -0,0 +1,10 @@ +pulsar Package +============== + +Subpackages +----------- + +.. toctree:: + + pulsar.client + diff --git a/doc/source/lib/tool_shed.capsule.rst b/doc/source/lib/tool_shed.capsule.rst new file mode 100644 index 00000000000..9496653d044 --- /dev/null +++ b/doc/source/lib/tool_shed.capsule.rst @@ -0,0 +1,11 @@ +capsule Package +=============== + +:mod:`capsule_manager` Module +----------------------------- + +.. automodule:: tool_shed.capsule.capsule_manager + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/tool_shed.dependencies.repository.rst b/doc/source/lib/tool_shed.dependencies.repository.rst new file mode 100644 index 00000000000..5382a5ba40a --- /dev/null +++ b/doc/source/lib/tool_shed.dependencies.repository.rst @@ -0,0 +1,11 @@ +repository Package +================== + +:mod:`relation_builder` Module +------------------------------ + +.. automodule:: tool_shed.dependencies.repository.relation_builder + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/tool_shed.dependencies.rst b/doc/source/lib/tool_shed.dependencies.rst new file mode 100644 index 00000000000..e7b62a50159 --- /dev/null +++ b/doc/source/lib/tool_shed.dependencies.rst @@ -0,0 +1,19 @@ +dependencies Package +==================== + +:mod:`attribute_handlers` Module +-------------------------------- + +.. automodule:: tool_shed.dependencies.attribute_handlers + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + tool_shed.dependencies.repository + tool_shed.dependencies.tool + diff --git a/doc/source/lib/tool_shed.dependencies.tool.rst b/doc/source/lib/tool_shed.dependencies.tool.rst new file mode 100644 index 00000000000..9ba9c8b2472 --- /dev/null +++ b/doc/source/lib/tool_shed.dependencies.tool.rst @@ -0,0 +1,11 @@ +tool Package +============ + +:mod:`tag_attribute_handler` Module +----------------------------------- + +.. automodule:: tool_shed.dependencies.tool.tag_attribute_handler + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.datatypes.rst b/doc/source/lib/tool_shed.galaxy_install.datatypes.rst new file mode 100644 index 00000000000..e5021e079c6 --- /dev/null +++ b/doc/source/lib/tool_shed.galaxy_install.datatypes.rst @@ -0,0 +1,11 @@ +datatypes Package +================= + +:mod:`custom_datatype_manager` Module +------------------------------------- + +.. automodule:: tool_shed.galaxy_install.datatypes.custom_datatype_manager + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.metadata.rst b/doc/source/lib/tool_shed.galaxy_install.metadata.rst new file mode 100644 index 00000000000..a710cc6ad1b --- /dev/null +++ b/doc/source/lib/tool_shed.galaxy_install.metadata.rst @@ -0,0 +1,11 @@ +metadata Package +================ + +:mod:`installed_repository_metadata_manager` Module +--------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.metadata.installed_repository_metadata_manager + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst b/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst new file mode 100644 index 00000000000..ac2c06dad4d --- /dev/null +++ b/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst @@ -0,0 +1,11 @@ +repository_dependencies Package +=============================== + +:mod:`repository_dependency_manager` Module +------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.rst b/doc/source/lib/tool_shed.galaxy_install.rst index 28e61519afe..c2da4ac3c55 100644 --- a/doc/source/lib/tool_shed.galaxy_install.rst +++ b/doc/source/lib/tool_shed.galaxy_install.rst @@ -1,10 +1,10 @@ galaxy_install Package ====================== -:mod:`galaxy_install` Package ------------------------------ +:mod:`dependency_display` Module +-------------------------------- -.. automodule:: tool_shed.galaxy_install +.. automodule:: tool_shed.galaxy_install.dependency_display :members: :undoc-members: :show-inheritance: @@ -17,18 +17,34 @@ galaxy_install Package :undoc-members: :show-inheritance: -:mod:`repository_util` Module ------------------------------ +:mod:`installed_repository_manager` Module +------------------------------------------ -.. automodule:: tool_shed.galaxy_install.repository_util +.. automodule:: tool_shed.galaxy_install.installed_repository_manager :members: :undoc-members: :show-inheritance: -:mod:`update_manager` Module ----------------------------- +:mod:`repair_repository_manager` Module +--------------------------------------- -.. automodule:: tool_shed.galaxy_install.update_manager +.. automodule:: tool_shed.galaxy_install.repair_repository_manager + :members: + :undoc-members: + :show-inheritance: + +:mod:`tool_migration_manager` Module +------------------------------------ + +.. automodule:: tool_shed.galaxy_install.tool_migration_manager + :members: + :undoc-members: + :show-inheritance: + +:mod:`update_repository_manager` Module +--------------------------------------- + +.. automodule:: tool_shed.galaxy_install.update_repository_manager :members: :undoc-members: :show-inheritance: @@ -38,7 +54,12 @@ Subpackages .. toctree:: + tool_shed.galaxy_install.datatypes tool_shed.galaxy_install.grids + tool_shed.galaxy_install.metadata tool_shed.galaxy_install.migrate + tool_shed.galaxy_install.repository_dependencies tool_shed.galaxy_install.tool_dependencies + tool_shed.galaxy_install.tools + tool_shed.galaxy_install.utility_containers diff --git a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst new file mode 100644 index 00000000000..6a7abd723fb --- /dev/null +++ b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst @@ -0,0 +1,51 @@ +recipe Package +============== + +:mod:`asynchronous_reader` Module +--------------------------------- + +.. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader + :members: + :undoc-members: + :show-inheritance: + +:mod:`env_file_builder` Module +------------------------------ + +.. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder + :members: + :undoc-members: + :show-inheritance: + +:mod:`install_environment` Module +--------------------------------- + +.. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment + :members: + :undoc-members: + :show-inheritance: + +:mod:`recipe_manager` Module +---------------------------- + +.. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager + :members: + :undoc-members: + :show-inheritance: + +:mod:`step_handler` Module +-------------------------- + +.. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.step_handler + :members: + :undoc-members: + :show-inheritance: + +:mod:`tag_handler` Module +------------------------- + +.. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst index 4871c0b1f58..c5b6ee4091f 100644 --- a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst +++ b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst @@ -1,27 +1,18 @@ tool_dependencies Package ========================= -:mod:`common_util` Module +:mod:`env_manager` Module ------------------------- -.. automodule:: tool_shed.galaxy_install.tool_dependencies.common_util +.. automodule:: tool_shed.galaxy_install.tool_dependencies.env_manager :members: :undoc-members: :show-inheritance: -:mod:`fabric_util` Module -------------------------- +Subpackages +----------- -.. automodule:: tool_shed.galaxy_install.tool_dependencies.fabric_util - :members: - :undoc-members: - :show-inheritance: +.. toctree:: -:mod:`install_util` Module --------------------------- - -.. automodule:: tool_shed.galaxy_install.tool_dependencies.install_util - :members: - :undoc-members: - :show-inheritance: + tool_shed.galaxy_install.tool_dependencies.recipe diff --git a/doc/source/lib/tool_shed.galaxy_install.tools.rst b/doc/source/lib/tool_shed.galaxy_install.tools.rst new file mode 100644 index 00000000000..922667d523c --- /dev/null +++ b/doc/source/lib/tool_shed.galaxy_install.tools.rst @@ -0,0 +1,19 @@ +tools Package +============= + +:mod:`data_manager` Module +-------------------------- + +.. automodule:: tool_shed.galaxy_install.tools.data_manager + :members: + :undoc-members: + :show-inheritance: + +:mod:`tool_panel_manager` Module +-------------------------------- + +.. automodule:: tool_shed.galaxy_install.tools.tool_panel_manager + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst b/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst new file mode 100644 index 00000000000..60dd22914fc --- /dev/null +++ b/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst @@ -0,0 +1,11 @@ +utility_containers Package +========================== + +:mod:`utility_containers` Package +--------------------------------- + +.. automodule:: tool_shed.galaxy_install.utility_containers + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/tool_shed.grids.rst b/doc/source/lib/tool_shed.grids.rst index 154f92b8369..86c0bf2ee70 100644 --- a/doc/source/lib/tool_shed.grids.rst +++ b/doc/source/lib/tool_shed.grids.rst @@ -9,6 +9,14 @@ grids Package :undoc-members: :show-inheritance: +:mod:`repository_grid_filter_manager` Module +-------------------------------------------- + +.. automodule:: tool_shed.grids.repository_grid_filter_manager + :members: + :undoc-members: + :show-inheritance: + :mod:`repository_grids` Module ------------------------------ diff --git a/doc/source/lib/tool_shed.managers.rst b/doc/source/lib/tool_shed.managers.rst new file mode 100644 index 00000000000..f400d8d767e --- /dev/null +++ b/doc/source/lib/tool_shed.managers.rst @@ -0,0 +1,19 @@ +managers Package +================ + +:mod:`groups` Module +-------------------- + +.. automodule:: tool_shed.managers.groups + :members: + :undoc-members: + :show-inheritance: + +:mod:`repositories` Module +-------------------------- + +.. automodule:: tool_shed.managers.repositories + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/tool_shed.metadata.rst b/doc/source/lib/tool_shed.metadata.rst new file mode 100644 index 00000000000..735acfd5e9d --- /dev/null +++ b/doc/source/lib/tool_shed.metadata.rst @@ -0,0 +1,19 @@ +metadata Package +================ + +:mod:`metadata_generator` Module +-------------------------------- + +.. automodule:: tool_shed.metadata.metadata_generator + :members: + :undoc-members: + :show-inheritance: + +:mod:`repository_metadata_manager` Module +----------------------------------------- + +.. automodule:: tool_shed.metadata.repository_metadata_manager + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/tool_shed.repository_types.rst b/doc/source/lib/tool_shed.repository_types.rst new file mode 100644 index 00000000000..b64e85a7a18 --- /dev/null +++ b/doc/source/lib/tool_shed.repository_types.rst @@ -0,0 +1,51 @@ +repository_types Package +======================== + +:mod:`metadata` Module +---------------------- + +.. automodule:: tool_shed.repository_types.metadata + :members: + :undoc-members: + :show-inheritance: + +:mod:`registry` Module +---------------------- + +.. automodule:: tool_shed.repository_types.registry + :members: + :undoc-members: + :show-inheritance: + +:mod:`repository_suite_definition` Module +----------------------------------------- + +.. automodule:: tool_shed.repository_types.repository_suite_definition + :members: + :undoc-members: + :show-inheritance: + +:mod:`tool_dependency_definition` Module +---------------------------------------- + +.. automodule:: tool_shed.repository_types.tool_dependency_definition + :members: + :undoc-members: + :show-inheritance: + +:mod:`unrestricted` Module +-------------------------- + +.. automodule:: tool_shed.repository_types.unrestricted + :members: + :undoc-members: + :show-inheritance: + +:mod:`util` Module +------------------ + +.. automodule:: tool_shed.repository_types.util + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/tool_shed.rst b/doc/source/lib/tool_shed.rst index 76794397c1c..4bf54d75b21 100644 --- a/doc/source/lib/tool_shed.rst +++ b/doc/source/lib/tool_shed.rst @@ -1,6 +1,14 @@ tool_shed Package ================= +:mod:`repository_registry` Module +--------------------------------- + +.. automodule:: tool_shed.repository_registry + :members: + :undoc-members: + :show-inheritance: + :mod:`tool_shed_registry` Module -------------------------------- @@ -14,7 +22,14 @@ Subpackages .. toctree:: + tool_shed.capsule + tool_shed.dependencies tool_shed.galaxy_install tool_shed.grids + tool_shed.managers + tool_shed.metadata + tool_shed.repository_types + tool_shed.tools tool_shed.util + tool_shed.utility_containers diff --git a/doc/source/lib/tool_shed.tools.rst b/doc/source/lib/tool_shed.tools.rst new file mode 100644 index 00000000000..a734ba26f96 --- /dev/null +++ b/doc/source/lib/tool_shed.tools.rst @@ -0,0 +1,27 @@ +tools Package +============= + +:mod:`data_table_manager` Module +-------------------------------- + +.. automodule:: tool_shed.tools.data_table_manager + :members: + :undoc-members: + :show-inheritance: + +:mod:`tool_validator` Module +---------------------------- + +.. automodule:: tool_shed.tools.tool_validator + :members: + :undoc-members: + :show-inheritance: + +:mod:`tool_version_manager` Module +---------------------------------- + +.. automodule:: tool_shed.tools.tool_version_manager + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/tool_shed.util.rst b/doc/source/lib/tool_shed.util.rst index 17d6e4c490d..add05826aee 100644 --- a/doc/source/lib/tool_shed.util.rst +++ b/doc/source/lib/tool_shed.util.rst @@ -1,10 +1,18 @@ util Package ============ -:mod:`common_install_util` Module ---------------------------------- +:mod:`basic_util` Module +------------------------ -.. automodule:: tool_shed.util.common_install_util +.. automodule:: tool_shed.util.basic_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`commit_util` Module +------------------------- + +.. automodule:: tool_shed.util.commit_util :members: :undoc-members: :show-inheritance: @@ -17,18 +25,10 @@ util Package :undoc-members: :show-inheritance: -:mod:`data_manager_util` Module -------------------------------- +:mod:`container_util` Module +---------------------------- -.. automodule:: tool_shed.util.data_manager_util - :members: - :undoc-members: - :show-inheritance: - -:mod:`datatype_util` Module ---------------------------- - -.. automodule:: tool_shed.util.datatype_util +.. automodule:: tool_shed.util.container_util :members: :undoc-members: :show-inheritance: @@ -41,6 +41,14 @@ util Package :undoc-members: :show-inheritance: +:mod:`hg_util` Module +--------------------- + +.. automodule:: tool_shed.util.hg_util + :members: + :undoc-members: + :show-inheritance: + :mod:`metadata_util` Module --------------------------- @@ -57,10 +65,18 @@ util Package :undoc-members: :show-inheritance: -:mod:`repository_dependency_util` Module ----------------------------------------- +:mod:`repository_content_util` Module +------------------------------------- -.. automodule:: tool_shed.util.repository_dependency_util +.. automodule:: tool_shed.util.repository_content_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`repository_util` Module +----------------------------- + +.. automodule:: tool_shed.util.repository_util :members: :undoc-members: :show-inheritance: @@ -73,6 +89,14 @@ util Package :undoc-members: :show-inheritance: +:mod:`search_util` Module +------------------------- + +.. automodule:: tool_shed.util.search_util + :members: + :undoc-members: + :show-inheritance: + :mod:`shed_util_common` Module ------------------------------ @@ -97,6 +121,14 @@ util Package :undoc-members: :show-inheritance: +:mod:`web_util` Module +---------------------- + +.. automodule:: tool_shed.util.web_util + :members: + :undoc-members: + :show-inheritance: + :mod:`workflow_util` Module --------------------------- @@ -105,3 +137,11 @@ util Package :undoc-members: :show-inheritance: +:mod:`xml_util` Module +---------------------- + +.. automodule:: tool_shed.util.xml_util + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/tool_shed.utility_containers.rst b/doc/source/lib/tool_shed.utility_containers.rst new file mode 100644 index 00000000000..d5b2f756591 --- /dev/null +++ b/doc/source/lib/tool_shed.utility_containers.rst @@ -0,0 +1,19 @@ +utility_containers Package +========================== + +:mod:`utility_containers` Package +--------------------------------- + +.. automodule:: tool_shed.utility_containers + :members: + :undoc-members: + :show-inheritance: + +:mod:`utility_container_manager` Module +--------------------------------------- + +.. automodule:: tool_shed.utility_containers.utility_container_manager + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/releases/15.05.rst b/doc/source/releases/15.05.rst index 7e5aea7fbdb..8e68f3f1989 100644 --- a/doc/source/releases/15.05.rst +++ b/doc/source/releases/15.05.rst @@ -9,7 +9,6 @@ Enhancements ------------------------------- -.. starthighlight * Pluggable framework to custom authentication (including new LDAP/Active Directory integration). Thanks to many including Andrew Robinson, Nicola Soranzo, and David Trudgian. `Pull Request 1`_, `Pull Request 33`_, @@ -20,7 +19,6 @@ Enhancements * New UI widgets allowing much more flexibility when creating simple dataset pair and list collections. `Pull Request 134`_, `Trello `__ -.. endhighlight * Improved JavaScript build system for client code and libraries (now using uglify_ and featuring `Source Maps`_). 72c876c_, 9a7f5fc_, 648a623_, 22f280f_, `Trello `__ From ee0ce040cebd043bbb76930ac55cf4f5e11dd40c Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 26 Jun 2015 18:05:12 +0100 Subject: [PATCH 015/165] Update to sphinx-apidoc v1.3.1 . sphinx-apidoc -M -o doc/source/lib/ lib/ --- doc/source/conf.py | 4 +- doc/source/lib/galaxy.actions.rst | 17 +- doc/source/lib/galaxy.auth.providers.rst | 23 +- doc/source/lib/galaxy.auth.rst | 7 +- doc/source/lib/galaxy.dataset_collections.rst | 101 ++-- .../lib/galaxy.dataset_collections.types.rst | 19 +- .../lib/galaxy.datatypes.converters.rst | 129 +++-- .../lib/galaxy.datatypes.dataproviders.rst | 47 +- .../galaxy.datatypes.display_applications.rst | 23 +- doc/source/lib/galaxy.datatypes.rst | 349 ++++++------ doc/source/lib/galaxy.datatypes.util.rst | 23 +- doc/source/lib/galaxy.eggs.rst | 19 +- doc/source/lib/galaxy.exceptions.rst | 15 +- ...laxy.external_services.result_handlers.rst | 17 +- doc/source/lib/galaxy.external_services.rst | 53 +- doc/source/lib/galaxy.forms.rst | 17 +- doc/source/lib/galaxy.jobs.actions.rst | 15 +- doc/source/lib/galaxy.jobs.deferred.rst | 23 +- .../lib/galaxy.jobs.metrics.collectl.rst | 27 +- .../lib/galaxy.jobs.metrics.instrumenters.rst | 35 +- doc/source/lib/galaxy.jobs.metrics.rst | 27 +- doc/source/lib/galaxy.jobs.rst | 171 +++--- .../lib/galaxy.jobs.runners.lwr_client.rst | 235 ++++---- ...galaxy.jobs.runners.lwr_client.staging.rst | 19 +- ...laxy.jobs.runners.lwr_client.transport.rst | 19 +- doc/source/lib/galaxy.jobs.runners.rst | 171 +++--- .../galaxy.jobs.runners.state_handlers.rst | 17 +- .../lib/galaxy.jobs.runners.util.cli.job.rst | 23 +- .../lib/galaxy.jobs.runners.util.cli.rst | 27 +- .../galaxy.jobs.runners.util.cli.shell.rst | 19 +- .../lib/galaxy.jobs.runners.util.condor.rst | 7 +- .../galaxy.jobs.runners.util.job_script.rst | 7 +- doc/source/lib/galaxy.jobs.runners.util.rst | 59 +- doc/source/lib/galaxy.jobs.splitters.rst | 21 +- doc/source/lib/galaxy.managers.rst | 119 ++-- doc/source/lib/galaxy.model.migrate.rst | 17 +- doc/source/lib/galaxy.model.orm.rst | 27 +- doc/source/lib/galaxy.model.rst | 107 ++-- ...galaxy.model.tool_shed_install.migrate.rst | 17 +- .../lib/galaxy.model.tool_shed_install.rst | 27 +- doc/source/lib/galaxy.objectstore.rst | 27 +- doc/source/lib/galaxy.openid.rst | 15 +- doc/source/lib/galaxy.quota.rst | 7 +- doc/source/lib/galaxy.rst | 105 ++-- doc/source/lib/galaxy.sample_tracking.rst | 29 +- doc/source/lib/galaxy.security.rst | 19 +- doc/source/lib/galaxy.tags.rst | 7 +- doc/source/lib/galaxy.tools.actions.rst | 35 +- doc/source/lib/galaxy.tools.data.rst | 7 +- doc/source/lib/galaxy.tools.data_manager.rst | 15 +- .../lib/galaxy.tools.deps.resolvers.rst | 35 +- doc/source/lib/galaxy.tools.deps.rst | 139 ++--- doc/source/lib/galaxy.tools.filters.rst | 7 +- doc/source/lib/galaxy.tools.imp_exp.rst | 19 +- doc/source/lib/galaxy.tools.linters.rst | 39 +- doc/source/lib/galaxy.tools.parameters.rst | 59 +- doc/source/lib/galaxy.tools.parser.rst | 31 +- doc/source/lib/galaxy.tools.rst | 155 ++--- doc/source/lib/galaxy.tools.search.rst | 7 +- .../lib/galaxy.tools.toolbox.filters.rst | 7 +- .../lib/galaxy.tools.toolbox.lineages.rst | 27 +- doc/source/lib/galaxy.tools.toolbox.rst | 91 +-- .../lib/galaxy.tools.util.galaxyops.rst | 7 +- doc/source/lib/galaxy.tools.util.rst | 27 +- .../lib/galaxy.util.backports.importlib.rst | 7 +- doc/source/lib/galaxy.util.backports.rst | 7 +- doc/source/lib/galaxy.util.log.rst | 15 +- doc/source/lib/galaxy.util.pastescript.rst | 19 +- doc/source/lib/galaxy.util.rst | 539 +++++++++--------- ....visualization.data_providers.phyloviz.rst | 27 +- .../galaxy.visualization.data_providers.rst | 75 +-- .../lib/galaxy.visualization.genome.rst | 7 +- .../lib/galaxy.visualization.plugins.rst | 33 +- doc/source/lib/galaxy.visualization.rst | 27 +- .../lib/galaxy.visualization.tracks.rst | 7 +- .../lib/galaxy.web.base.controllers.rst | 17 +- doc/source/lib/galaxy.web.base.rst | 53 +- .../lib/galaxy.web.framework.helpers.rst | 15 +- .../lib/galaxy.web.framework.middleware.rst | 43 +- doc/source/lib/galaxy.web.framework.rst | 91 +-- doc/source/lib/galaxy.web.proxy.rst | 15 +- doc/source/lib/galaxy.web.rst | 75 +-- doc/source/lib/galaxy.web.security.rst | 7 +- doc/source/lib/galaxy.webapps.galaxy.api.rst | 165 +++--- .../lib/galaxy.webapps.galaxy.controllers.rst | 131 ++--- doc/source/lib/galaxy.webapps.galaxy.rst | 21 +- .../galaxy.webapps.reports.controllers.rst | 39 +- doc/source/lib/galaxy.webapps.reports.rst | 59 +- doc/source/lib/galaxy.webapps.rst | 7 +- .../lib/galaxy.webapps.tool_shed.api.rst | 41 +- .../galaxy.webapps.tool_shed.controllers.rst | 39 +- ...webapps.tool_shed.framework.middleware.rst | 19 +- .../galaxy.webapps.tool_shed.framework.rst | 7 +- ...galaxy.webapps.tool_shed.model.migrate.rst | 17 +- .../lib/galaxy.webapps.tool_shed.model.rst | 27 +- doc/source/lib/galaxy.webapps.tool_shed.rst | 59 +- .../lib/galaxy.webapps.tool_shed.search.rst | 21 +- .../lib/galaxy.webapps.tool_shed.security.rst | 7 +- .../lib/galaxy.webapps.tool_shed.util.rst | 25 +- doc/source/lib/galaxy.work.rst | 17 +- doc/source/lib/galaxy.workflow.rst | 117 ++-- doc/source/lib/galaxy.workflow.schedulers.rst | 15 +- doc/source/lib/galaxy_ext.metadata.rst | 15 +- doc/source/lib/galaxy_ext.rst | 5 +- doc/source/lib/galaxy_utils.rst | 7 +- doc/source/lib/galaxy_utils.sequence.rst | 33 +- doc/source/lib/log_tempfile.rst | 2 +- doc/source/lib/mimeparse.rst | 2 +- doc/source/lib/pkg_resources.rst | 2 +- doc/source/lib/psyco_full.rst | 2 +- doc/source/lib/pulsar.client.rst | 235 ++++---- doc/source/lib/pulsar.client.staging.rst | 19 +- doc/source/lib/pulsar.client.transport.rst | 31 +- doc/source/lib/pulsar.rst | 7 +- doc/source/lib/tool_shed.capsule.rst | 17 +- .../lib/tool_shed.dependencies.repository.rst | 17 +- doc/source/lib/tool_shed.dependencies.rst | 21 +- .../lib/tool_shed.dependencies.tool.rst | 17 +- .../tool_shed.galaxy_install.datatypes.rst | 17 +- .../lib/tool_shed.galaxy_install.grids.rst | 17 +- .../lib/tool_shed.galaxy_install.metadata.rst | 17 +- .../lib/tool_shed.galaxy_install.migrate.rst | 21 +- ...galaxy_install.repository_dependencies.rst | 17 +- doc/source/lib/tool_shed.galaxy_install.rst | 101 ++-- ...alaxy_install.tool_dependencies.recipe.rst | 37 +- ..._shed.galaxy_install.tool_dependencies.rst | 21 +- .../lib/tool_shed.galaxy_install.tools.rst | 21 +- ...shed.galaxy_install.utility_containers.rst | 7 +- doc/source/lib/tool_shed.grids.rst | 33 +- doc/source/lib/tool_shed.managers.rst | 21 +- doc/source/lib/tool_shed.metadata.rst | 21 +- doc/source/lib/tool_shed.repository_types.rst | 37 +- doc/source/lib/tool_shed.rst | 35 +- doc/source/lib/tool_shed.tools.rst | 25 +- doc/source/lib/tool_shed.util.rst | 85 +-- .../lib/tool_shed.utility_containers.rst | 15 +- 136 files changed, 3162 insertions(+), 2745 deletions(-) diff --git a/doc/source/conf.py b/doc/source/conf.py index 2b25d7fdce2..9e8ae5b0f70 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -17,8 +17,6 @@ import sys, os, datetime ####### REQUIRED GALAXY INCLUDES sys.path.append(os.path.join(os.getcwd(), '../../lib')) -import galaxy -from galaxy import eggs ####### @@ -103,7 +101,7 @@ pygments_style = 'sphinx' # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. -html_theme = 'default' +html_theme = 'classic' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the diff --git a/doc/source/lib/galaxy.actions.rst b/doc/source/lib/galaxy.actions.rst index d022b96ef2b..bd4c48070b6 100644 --- a/doc/source/lib/galaxy.actions.rst +++ b/doc/source/lib/galaxy.actions.rst @@ -1,11 +1,20 @@ -actions Package -=============== +galaxy.actions package +====================== -:mod:`admin` Module -------------------- +.. automodule:: galaxy.actions + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.actions.admin module +--------------------------- .. automodule:: galaxy.actions.admin :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.auth.providers.rst b/doc/source/lib/galaxy.auth.providers.rst index aff6f57976d..1c5c1945329 100644 --- a/doc/source/lib/galaxy.auth.providers.rst +++ b/doc/source/lib/galaxy.auth.providers.rst @@ -1,35 +1,36 @@ -providers Package -================= - -:mod:`providers` Package ------------------------- +galaxy.auth.providers package +============================= .. automodule:: galaxy.auth.providers :members: :undoc-members: :show-inheritance: -:mod:`alwaysreject` Module --------------------------- +Submodules +---------- + +galaxy.auth.providers.alwaysreject module +----------------------------------------- .. automodule:: galaxy.auth.providers.alwaysreject :members: :undoc-members: :show-inheritance: -:mod:`ldap_ad` Module ---------------------- +galaxy.auth.providers.ldap_ad module +------------------------------------ .. automodule:: galaxy.auth.providers.ldap_ad :members: :undoc-members: :show-inheritance: -:mod:`localdb` Module ---------------------- +galaxy.auth.providers.localdb module +------------------------------------ .. automodule:: galaxy.auth.providers.localdb :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.auth.rst b/doc/source/lib/galaxy.auth.rst index 885330d32ec..eefcbc6f87d 100644 --- a/doc/source/lib/galaxy.auth.rst +++ b/doc/source/lib/galaxy.auth.rst @@ -1,8 +1,5 @@ -auth Package -============ - -:mod:`auth` Package -------------------- +galaxy.auth package +=================== .. automodule:: galaxy.auth :members: diff --git a/doc/source/lib/galaxy.dataset_collections.rst b/doc/source/lib/galaxy.dataset_collections.rst index a507225613f..e065d302c50 100644 --- a/doc/source/lib/galaxy.dataset_collections.rst +++ b/doc/source/lib/galaxy.dataset_collections.rst @@ -1,50 +1,7 @@ -dataset_collections Package -=========================== +galaxy.dataset_collections package +================================== -:mod:`builder` Module ---------------------- - -.. automodule:: galaxy.dataset_collections.builder - :members: - :undoc-members: - :show-inheritance: - -:mod:`matching` Module ----------------------- - -.. automodule:: galaxy.dataset_collections.matching - :members: - :undoc-members: - :show-inheritance: - -:mod:`registry` Module ----------------------- - -.. automodule:: galaxy.dataset_collections.registry - :members: - :undoc-members: - :show-inheritance: - -:mod:`structure` Module ------------------------ - -.. automodule:: galaxy.dataset_collections.structure - :members: - :undoc-members: - :show-inheritance: - -:mod:`subcollections` Module ----------------------------- - -.. automodule:: galaxy.dataset_collections.subcollections - :members: - :undoc-members: - :show-inheritance: - -:mod:`type_description` Module ------------------------------- - -.. automodule:: galaxy.dataset_collections.type_description +.. automodule:: galaxy.dataset_collections :members: :undoc-members: :show-inheritance: @@ -56,3 +13,55 @@ Subpackages galaxy.dataset_collections.types +Submodules +---------- + +galaxy.dataset_collections.builder module +----------------------------------------- + +.. automodule:: galaxy.dataset_collections.builder + :members: + :undoc-members: + :show-inheritance: + +galaxy.dataset_collections.matching module +------------------------------------------ + +.. automodule:: galaxy.dataset_collections.matching + :members: + :undoc-members: + :show-inheritance: + +galaxy.dataset_collections.registry module +------------------------------------------ + +.. automodule:: galaxy.dataset_collections.registry + :members: + :undoc-members: + :show-inheritance: + +galaxy.dataset_collections.structure module +------------------------------------------- + +.. automodule:: galaxy.dataset_collections.structure + :members: + :undoc-members: + :show-inheritance: + +galaxy.dataset_collections.subcollections module +------------------------------------------------ + +.. automodule:: galaxy.dataset_collections.subcollections + :members: + :undoc-members: + :show-inheritance: + +galaxy.dataset_collections.type_description module +-------------------------------------------------- + +.. automodule:: galaxy.dataset_collections.type_description + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.dataset_collections.types.rst b/doc/source/lib/galaxy.dataset_collections.types.rst index 83352f729b1..639fbf2b5c5 100644 --- a/doc/source/lib/galaxy.dataset_collections.types.rst +++ b/doc/source/lib/galaxy.dataset_collections.types.rst @@ -1,27 +1,28 @@ -types Package -============= - -:mod:`types` Package --------------------- +galaxy.dataset_collections.types package +======================================== .. automodule:: galaxy.dataset_collections.types :members: :undoc-members: :show-inheritance: -:mod:`list` Module ------------------- +Submodules +---------- + +galaxy.dataset_collections.types.list module +-------------------------------------------- .. automodule:: galaxy.dataset_collections.types.list :members: :undoc-members: :show-inheritance: -:mod:`paired` Module --------------------- +galaxy.dataset_collections.types.paired module +---------------------------------------------- .. automodule:: galaxy.dataset_collections.types.paired :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.datatypes.converters.rst b/doc/source/lib/galaxy.datatypes.converters.rst index 342ba17312a..7435e980ab5 100644 --- a/doc/source/lib/galaxy.datatypes.converters.rst +++ b/doc/source/lib/galaxy.datatypes.converters.rst @@ -1,235 +1,244 @@ -converters Package -================== +galaxy.datatypes.converters package +=================================== -:mod:`bed_to_gff_converter` Module ----------------------------------- +.. automodule:: galaxy.datatypes.converters + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.datatypes.converters.bed_to_gff_converter module +------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.bed_to_gff_converter :members: :undoc-members: :show-inheritance: -:mod:`bedgraph_to_array_tree_converter` Module ----------------------------------------------- +galaxy.datatypes.converters.bedgraph_to_array_tree_converter module +------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.bedgraph_to_array_tree_converter :members: :undoc-members: :show-inheritance: -:mod:`bgzip` Module -------------------- +galaxy.datatypes.converters.bgzip module +---------------------------------------- .. automodule:: galaxy.datatypes.converters.bgzip :members: :undoc-members: :show-inheritance: -:mod:`fasta_to_len` Module --------------------------- +galaxy.datatypes.converters.fasta_to_len module +----------------------------------------------- .. automodule:: galaxy.datatypes.converters.fasta_to_len :members: :undoc-members: :show-inheritance: -:mod:`fasta_to_tabular_converter` Module ----------------------------------------- +galaxy.datatypes.converters.fasta_to_tabular_converter module +------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fasta_to_tabular_converter :members: :undoc-members: :show-inheritance: -:mod:`fastq_to_fqtoc` Module ----------------------------- +galaxy.datatypes.converters.fastq_to_fqtoc module +------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fastq_to_fqtoc :members: :undoc-members: :show-inheritance: -:mod:`fastqsolexa_to_fasta_converter` Module --------------------------------------------- +galaxy.datatypes.converters.fastqsolexa_to_fasta_converter module +----------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fastqsolexa_to_fasta_converter :members: :undoc-members: :show-inheritance: -:mod:`fastqsolexa_to_qual_converter` Module -------------------------------------------- +galaxy.datatypes.converters.fastqsolexa_to_qual_converter module +---------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fastqsolexa_to_qual_converter :members: :undoc-members: :show-inheritance: -:mod:`gff_to_bed_converter` Module ----------------------------------- +galaxy.datatypes.converters.gff_to_bed_converter module +------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.gff_to_bed_converter :members: :undoc-members: :show-inheritance: -:mod:`gff_to_interval_index_converter` Module ---------------------------------------------- +galaxy.datatypes.converters.gff_to_interval_index_converter module +------------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.gff_to_interval_index_converter :members: :undoc-members: :show-inheritance: -:mod:`interval_to_bed_converter` Module ---------------------------------------- +galaxy.datatypes.converters.interval_to_bed_converter module +------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.interval_to_bed_converter :members: :undoc-members: :show-inheritance: -:mod:`interval_to_bedstrict_converter` Module ---------------------------------------------- +galaxy.datatypes.converters.interval_to_bedstrict_converter module +------------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.interval_to_bedstrict_converter :members: :undoc-members: :show-inheritance: -:mod:`interval_to_coverage` Module ----------------------------------- +galaxy.datatypes.converters.interval_to_coverage module +------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_coverage :members: :undoc-members: :show-inheritance: -:mod:`interval_to_fli` Module ------------------------------ +galaxy.datatypes.converters.interval_to_fli module +-------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_fli :members: :undoc-members: :show-inheritance: -:mod:`interval_to_interval_index_converter` Module --------------------------------------------------- +galaxy.datatypes.converters.interval_to_interval_index_converter module +----------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_interval_index_converter :members: :undoc-members: :show-inheritance: -:mod:`interval_to_tabix_converter` Module ------------------------------------------ +galaxy.datatypes.converters.interval_to_tabix_converter module +-------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_tabix_converter :members: :undoc-members: :show-inheritance: -:mod:`lped_to_fped_converter` Module ------------------------------------- +galaxy.datatypes.converters.lped_to_fped_converter module +--------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.lped_to_fped_converter :members: :undoc-members: :show-inheritance: -:mod:`lped_to_pbed_converter` Module ------------------------------------- +galaxy.datatypes.converters.lped_to_pbed_converter module +--------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.lped_to_pbed_converter :members: :undoc-members: :show-inheritance: -:mod:`maf_to_fasta_converter` Module ------------------------------------- +galaxy.datatypes.converters.maf_to_fasta_converter module +--------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.maf_to_fasta_converter :members: :undoc-members: :show-inheritance: -:mod:`maf_to_interval_converter` Module ---------------------------------------- +galaxy.datatypes.converters.maf_to_interval_converter module +------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.maf_to_interval_converter :members: :undoc-members: :show-inheritance: -:mod:`pbed_ldreduced_converter` Module --------------------------------------- +galaxy.datatypes.converters.pbed_ldreduced_converter module +----------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.pbed_ldreduced_converter :members: :undoc-members: :show-inheritance: -:mod:`pbed_to_lped_converter` Module ------------------------------------- +galaxy.datatypes.converters.pbed_to_lped_converter module +--------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.pbed_to_lped_converter :members: :undoc-members: :show-inheritance: -:mod:`picard_interval_list_to_bed6_converter` Module ----------------------------------------------------- +galaxy.datatypes.converters.picard_interval_list_to_bed6_converter module +------------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.picard_interval_list_to_bed6_converter :members: :undoc-members: :show-inheritance: -:mod:`pileup_to_interval_index_converter` Module ------------------------------------------------- +galaxy.datatypes.converters.pileup_to_interval_index_converter module +--------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.pileup_to_interval_index_converter :members: :undoc-members: :show-inheritance: -:mod:`sam_to_bam` Module ------------------------- +galaxy.datatypes.converters.sam_to_bam module +--------------------------------------------- .. automodule:: galaxy.datatypes.converters.sam_to_bam :members: :undoc-members: :show-inheritance: -:mod:`vcf_to_interval_index_converter` Module ---------------------------------------------- +galaxy.datatypes.converters.vcf_to_interval_index_converter module +------------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.vcf_to_interval_index_converter :members: :undoc-members: :show-inheritance: -:mod:`vcf_to_vcf_bgzip` Module ------------------------------- +galaxy.datatypes.converters.vcf_to_vcf_bgzip module +--------------------------------------------------- .. automodule:: galaxy.datatypes.converters.vcf_to_vcf_bgzip :members: :undoc-members: :show-inheritance: -:mod:`wiggle_to_array_tree_converter` Module --------------------------------------------- +galaxy.datatypes.converters.wiggle_to_array_tree_converter module +----------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.wiggle_to_array_tree_converter :members: :undoc-members: :show-inheritance: -:mod:`wiggle_to_simple_converter` Module ----------------------------------------- +galaxy.datatypes.converters.wiggle_to_simple_converter module +------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.wiggle_to_simple_converter :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.datatypes.dataproviders.rst b/doc/source/lib/galaxy.datatypes.dataproviders.rst index a804265f0df..cd85ef190df 100644 --- a/doc/source/lib/galaxy.datatypes.dataproviders.rst +++ b/doc/source/lib/galaxy.datatypes.dataproviders.rst @@ -1,83 +1,84 @@ -dataproviders Package -===================== - -:mod:`dataproviders` Package ----------------------------- +galaxy.datatypes.dataproviders package +====================================== .. automodule:: galaxy.datatypes.dataproviders :members: :undoc-members: :show-inheritance: -:mod:`base` Module ------------------- +Submodules +---------- + +galaxy.datatypes.dataproviders.base module +------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.base :members: :undoc-members: :show-inheritance: -:mod:`chunk` Module -------------------- +galaxy.datatypes.dataproviders.chunk module +------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.chunk :members: :undoc-members: :show-inheritance: -:mod:`column` Module --------------------- +galaxy.datatypes.dataproviders.column module +-------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.column :members: :undoc-members: :show-inheritance: -:mod:`dataset` Module ---------------------- +galaxy.datatypes.dataproviders.dataset module +--------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.dataset :members: :undoc-members: :show-inheritance: -:mod:`decorators` Module ------------------------- +galaxy.datatypes.dataproviders.decorators module +------------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.decorators :members: :undoc-members: :show-inheritance: -:mod:`exceptions` Module ------------------------- +galaxy.datatypes.dataproviders.exceptions module +------------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.exceptions :members: :undoc-members: :show-inheritance: -:mod:`external` Module ----------------------- +galaxy.datatypes.dataproviders.external module +---------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.external :members: :undoc-members: :show-inheritance: -:mod:`hierarchy` Module ------------------------ +galaxy.datatypes.dataproviders.hierarchy module +----------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.hierarchy :members: :undoc-members: :show-inheritance: -:mod:`line` Module ------------------- +galaxy.datatypes.dataproviders.line module +------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.line :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.datatypes.display_applications.rst b/doc/source/lib/galaxy.datatypes.display_applications.rst index 11300857cf8..a6f3e5e53a2 100644 --- a/doc/source/lib/galaxy.datatypes.display_applications.rst +++ b/doc/source/lib/galaxy.datatypes.display_applications.rst @@ -1,35 +1,36 @@ -display_applications Package -============================ - -:mod:`display_applications` Package ------------------------------------ +galaxy.datatypes.display_applications package +============================================= .. automodule:: galaxy.datatypes.display_applications :members: :undoc-members: :show-inheritance: -:mod:`application` Module -------------------------- +Submodules +---------- + +galaxy.datatypes.display_applications.application module +-------------------------------------------------------- .. automodule:: galaxy.datatypes.display_applications.application :members: :undoc-members: :show-inheritance: -:mod:`parameters` Module ------------------------- +galaxy.datatypes.display_applications.parameters module +------------------------------------------------------- .. automodule:: galaxy.datatypes.display_applications.parameters :members: :undoc-members: :show-inheritance: -:mod:`util` Module ------------------- +galaxy.datatypes.display_applications.util module +------------------------------------------------- .. automodule:: galaxy.datatypes.display_applications.util :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.datatypes.rst b/doc/source/lib/galaxy.datatypes.rst index c85f459d43f..e660f27b6e5 100644 --- a/doc/source/lib/galaxy.datatypes.rst +++ b/doc/source/lib/galaxy.datatypes.rst @@ -1,170 +1,7 @@ -datatypes Package -================= +galaxy.datatypes package +======================== -:mod:`assembly` Module ----------------------- - -.. automodule:: galaxy.datatypes.assembly - :members: - :undoc-members: - :show-inheritance: - -:mod:`binary` Module --------------------- - -.. automodule:: galaxy.datatypes.binary - :members: - :undoc-members: - :show-inheritance: - -:mod:`checkers` Module ----------------------- - -.. automodule:: galaxy.datatypes.checkers - :members: - :undoc-members: - :show-inheritance: - -:mod:`chrominfo` Module ------------------------ - -.. automodule:: galaxy.datatypes.chrominfo - :members: - :undoc-members: - :show-inheritance: - -:mod:`coverage` Module ----------------------- - -.. automodule:: galaxy.datatypes.coverage - :members: - :undoc-members: - :show-inheritance: - -:mod:`data` Module ------------------- - -.. automodule:: galaxy.datatypes.data - :members: - :undoc-members: - :show-inheritance: - -:mod:`genetics` Module ----------------------- - -.. automodule:: galaxy.datatypes.genetics - :members: - :undoc-members: - :show-inheritance: - -:mod:`graph` Module -------------------- - -.. automodule:: galaxy.datatypes.graph - :members: - :undoc-members: - :show-inheritance: - -:mod:`images` Module --------------------- - -.. automodule:: galaxy.datatypes.images - :members: - :undoc-members: - :show-inheritance: - -:mod:`interval` Module ----------------------- - -.. automodule:: galaxy.datatypes.interval - :members: - :undoc-members: - :show-inheritance: - -:mod:`metadata` Module ----------------------- - -.. automodule:: galaxy.datatypes.metadata - :members: - :undoc-members: - :show-inheritance: - -:mod:`msa` Module ------------------ - -.. automodule:: galaxy.datatypes.msa - :members: - :undoc-members: - :show-inheritance: - -:mod:`ngsindex` Module ----------------------- - -.. automodule:: galaxy.datatypes.ngsindex - :members: - :undoc-members: - :show-inheritance: - -:mod:`qualityscore` Module --------------------------- - -.. automodule:: galaxy.datatypes.qualityscore - :members: - :undoc-members: - :show-inheritance: - -:mod:`registry` Module ----------------------- - -.. automodule:: galaxy.datatypes.registry - :members: - :undoc-members: - :show-inheritance: - -:mod:`sequence` Module ----------------------- - -.. automodule:: galaxy.datatypes.sequence - :members: - :undoc-members: - :show-inheritance: - -:mod:`sniff` Module -------------------- - -.. automodule:: galaxy.datatypes.sniff - :members: - :undoc-members: - :show-inheritance: - -:mod:`tabular` Module ---------------------- - -.. automodule:: galaxy.datatypes.tabular - :members: - :undoc-members: - :show-inheritance: - -:mod:`text` Module ------------------- - -.. automodule:: galaxy.datatypes.text - :members: - :undoc-members: - :show-inheritance: - -:mod:`tracks` Module --------------------- - -.. automodule:: galaxy.datatypes.tracks - :members: - :undoc-members: - :show-inheritance: - -:mod:`xml` Module ------------------ - -.. automodule:: galaxy.datatypes.xml +.. automodule:: galaxy.datatypes :members: :undoc-members: :show-inheritance: @@ -179,3 +16,183 @@ Subpackages galaxy.datatypes.display_applications galaxy.datatypes.util +Submodules +---------- + +galaxy.datatypes.assembly module +-------------------------------- + +.. automodule:: galaxy.datatypes.assembly + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.binary module +------------------------------ + +.. automodule:: galaxy.datatypes.binary + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.checkers module +-------------------------------- + +.. automodule:: galaxy.datatypes.checkers + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.chrominfo module +--------------------------------- + +.. automodule:: galaxy.datatypes.chrominfo + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.coverage module +-------------------------------- + +.. automodule:: galaxy.datatypes.coverage + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.data module +---------------------------- + +.. automodule:: galaxy.datatypes.data + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.genetics module +-------------------------------- + +.. automodule:: galaxy.datatypes.genetics + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.graph module +----------------------------- + +.. automodule:: galaxy.datatypes.graph + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.images module +------------------------------ + +.. automodule:: galaxy.datatypes.images + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.interval module +-------------------------------- + +.. automodule:: galaxy.datatypes.interval + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.metadata module +-------------------------------- + +.. automodule:: galaxy.datatypes.metadata + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.msa module +--------------------------- + +.. automodule:: galaxy.datatypes.msa + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.ngsindex module +-------------------------------- + +.. automodule:: galaxy.datatypes.ngsindex + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.proteomics module +---------------------------------- + +.. automodule:: galaxy.datatypes.proteomics + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.qualityscore module +------------------------------------ + +.. automodule:: galaxy.datatypes.qualityscore + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.registry module +-------------------------------- + +.. automodule:: galaxy.datatypes.registry + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.sequence module +-------------------------------- + +.. automodule:: galaxy.datatypes.sequence + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.sniff module +----------------------------- + +.. automodule:: galaxy.datatypes.sniff + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.tabular module +------------------------------- + +.. automodule:: galaxy.datatypes.tabular + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.text module +---------------------------- + +.. automodule:: galaxy.datatypes.text + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.tracks module +------------------------------ + +.. automodule:: galaxy.datatypes.tracks + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.xml module +--------------------------- + +.. automodule:: galaxy.datatypes.xml + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.datatypes.util.rst b/doc/source/lib/galaxy.datatypes.util.rst index 59705cc70e8..6b9466b202d 100644 --- a/doc/source/lib/galaxy.datatypes.util.rst +++ b/doc/source/lib/galaxy.datatypes.util.rst @@ -1,35 +1,36 @@ -util Package -============ - -:mod:`util` Package -------------------- +galaxy.datatypes.util package +============================= .. automodule:: galaxy.datatypes.util :members: :undoc-members: :show-inheritance: -:mod:`generic_util` Module --------------------------- +Submodules +---------- + +galaxy.datatypes.util.generic_util module +----------------------------------------- .. automodule:: galaxy.datatypes.util.generic_util :members: :undoc-members: :show-inheritance: -:mod:`gff_util` Module ----------------------- +galaxy.datatypes.util.gff_util module +------------------------------------- .. automodule:: galaxy.datatypes.util.gff_util :members: :undoc-members: :show-inheritance: -:mod:`image_util` Module ------------------------- +galaxy.datatypes.util.image_util module +--------------------------------------- .. automodule:: galaxy.datatypes.util.image_util :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.eggs.rst b/doc/source/lib/galaxy.eggs.rst index 948d631b6d7..52a243b3272 100644 --- a/doc/source/lib/galaxy.eggs.rst +++ b/doc/source/lib/galaxy.eggs.rst @@ -1,27 +1,28 @@ -eggs Package -============ - -:mod:`eggs` Package -------------------- +galaxy.eggs package +=================== .. automodule:: galaxy.eggs :members: :undoc-members: :show-inheritance: -:mod:`dist` Module ------------------- +Submodules +---------- + +galaxy.eggs.dist module +----------------------- .. automodule:: galaxy.eggs.dist :members: :undoc-members: :show-inheritance: -:mod:`scramble` Module ----------------------- +galaxy.eggs.scramble module +--------------------------- .. automodule:: galaxy.eggs.scramble :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.exceptions.rst b/doc/source/lib/galaxy.exceptions.rst index 8b62b21bf8c..dd83fb808b1 100644 --- a/doc/source/lib/galaxy.exceptions.rst +++ b/doc/source/lib/galaxy.exceptions.rst @@ -1,19 +1,20 @@ -exceptions Package -================== - -:mod:`exceptions` Package -------------------------- +galaxy.exceptions package +========================= .. automodule:: galaxy.exceptions :members: :undoc-members: :show-inheritance: -:mod:`error_codes` Module -------------------------- +Submodules +---------- + +galaxy.exceptions.error_codes module +------------------------------------ .. automodule:: galaxy.exceptions.error_codes :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.external_services.result_handlers.rst b/doc/source/lib/galaxy.external_services.result_handlers.rst index c8946b14b99..749bfb7c25c 100644 --- a/doc/source/lib/galaxy.external_services.result_handlers.rst +++ b/doc/source/lib/galaxy.external_services.result_handlers.rst @@ -1,11 +1,20 @@ -result_handlers Package -======================= +galaxy.external_services.result_handlers package +================================================ -:mod:`basic` Module -------------------- +.. automodule:: galaxy.external_services.result_handlers + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.external_services.result_handlers.basic module +----------------------------------------------------- .. automodule:: galaxy.external_services.result_handlers.basic :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.external_services.rst b/doc/source/lib/galaxy.external_services.rst index 955f82eeb7f..b08913dc425 100644 --- a/doc/source/lib/galaxy.external_services.rst +++ b/doc/source/lib/galaxy.external_services.rst @@ -1,26 +1,7 @@ -external_services Package -========================= +galaxy.external_services package +================================ -:mod:`actions` Module ---------------------- - -.. automodule:: galaxy.external_services.actions - :members: - :undoc-members: - :show-inheritance: - -:mod:`parameters` Module ------------------------- - -.. automodule:: galaxy.external_services.parameters - :members: - :undoc-members: - :show-inheritance: - -:mod:`service` Module ---------------------- - -.. automodule:: galaxy.external_services.service +.. automodule:: galaxy.external_services :members: :undoc-members: :show-inheritance: @@ -32,3 +13,31 @@ Subpackages galaxy.external_services.result_handlers +Submodules +---------- + +galaxy.external_services.actions module +--------------------------------------- + +.. automodule:: galaxy.external_services.actions + :members: + :undoc-members: + :show-inheritance: + +galaxy.external_services.parameters module +------------------------------------------ + +.. automodule:: galaxy.external_services.parameters + :members: + :undoc-members: + :show-inheritance: + +galaxy.external_services.service module +--------------------------------------- + +.. automodule:: galaxy.external_services.service + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.forms.rst b/doc/source/lib/galaxy.forms.rst index 004bffe09df..088d52bcb9c 100644 --- a/doc/source/lib/galaxy.forms.rst +++ b/doc/source/lib/galaxy.forms.rst @@ -1,11 +1,20 @@ -forms Package -============= +galaxy.forms package +==================== -:mod:`forms` Module -------------------- +.. automodule:: galaxy.forms + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.forms.forms module +------------------------- .. automodule:: galaxy.forms.forms :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.actions.rst b/doc/source/lib/galaxy.jobs.actions.rst index c3f69a190c9..7ec9a937d81 100644 --- a/doc/source/lib/galaxy.jobs.actions.rst +++ b/doc/source/lib/galaxy.jobs.actions.rst @@ -1,19 +1,20 @@ -actions Package -=============== - -:mod:`actions` Package ----------------------- +galaxy.jobs.actions package +=========================== .. automodule:: galaxy.jobs.actions :members: :undoc-members: :show-inheritance: -:mod:`post` Module ------------------- +Submodules +---------- + +galaxy.jobs.actions.post module +------------------------------- .. automodule:: galaxy.jobs.actions.post :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.deferred.rst b/doc/source/lib/galaxy.jobs.deferred.rst index 81709bb1124..371a1721bb7 100644 --- a/doc/source/lib/galaxy.jobs.deferred.rst +++ b/doc/source/lib/galaxy.jobs.deferred.rst @@ -1,35 +1,36 @@ -deferred Package -================ - -:mod:`deferred` Package ------------------------ +galaxy.jobs.deferred package +============================ .. automodule:: galaxy.jobs.deferred :members: :undoc-members: :show-inheritance: -:mod:`data_transfer` Module ---------------------------- +Submodules +---------- + +galaxy.jobs.deferred.data_transfer module +----------------------------------------- .. automodule:: galaxy.jobs.deferred.data_transfer :members: :undoc-members: :show-inheritance: -:mod:`manual_data_transfer` Module ----------------------------------- +galaxy.jobs.deferred.manual_data_transfer module +------------------------------------------------ .. automodule:: galaxy.jobs.deferred.manual_data_transfer :members: :undoc-members: :show-inheritance: -:mod:`pacific_biosciences_smrt_portal` Module ---------------------------------------------- +galaxy.jobs.deferred.pacific_biosciences_smrt_portal module +----------------------------------------------------------- .. automodule:: galaxy.jobs.deferred.pacific_biosciences_smrt_portal :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.metrics.collectl.rst b/doc/source/lib/galaxy.jobs.metrics.collectl.rst index ebd0f3bb2f5..01120a3705a 100644 --- a/doc/source/lib/galaxy.jobs.metrics.collectl.rst +++ b/doc/source/lib/galaxy.jobs.metrics.collectl.rst @@ -1,43 +1,44 @@ -collectl Package -================ - -:mod:`collectl` Package ------------------------ +galaxy.jobs.metrics.collectl package +==================================== .. automodule:: galaxy.jobs.metrics.collectl :members: :undoc-members: :show-inheritance: -:mod:`cli` Module ------------------ +Submodules +---------- + +galaxy.jobs.metrics.collectl.cli module +--------------------------------------- .. automodule:: galaxy.jobs.metrics.collectl.cli :members: :undoc-members: :show-inheritance: -:mod:`processes` Module ------------------------ +galaxy.jobs.metrics.collectl.processes module +--------------------------------------------- .. automodule:: galaxy.jobs.metrics.collectl.processes :members: :undoc-members: :show-inheritance: -:mod:`stats` Module -------------------- +galaxy.jobs.metrics.collectl.stats module +----------------------------------------- .. automodule:: galaxy.jobs.metrics.collectl.stats :members: :undoc-members: :show-inheritance: -:mod:`subsystems` Module ------------------------- +galaxy.jobs.metrics.collectl.subsystems module +---------------------------------------------- .. automodule:: galaxy.jobs.metrics.collectl.subsystems :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst b/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst index 94b790d72ce..71b1a865ccb 100644 --- a/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst +++ b/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst @@ -1,59 +1,60 @@ -instrumenters Package -===================== - -:mod:`instrumenters` Package ----------------------------- +galaxy.jobs.metrics.instrumenters package +========================================= .. automodule:: galaxy.jobs.metrics.instrumenters :members: :undoc-members: :show-inheritance: -:mod:`collectl` Module ----------------------- +Submodules +---------- + +galaxy.jobs.metrics.instrumenters.collectl module +------------------------------------------------- .. automodule:: galaxy.jobs.metrics.instrumenters.collectl :members: :undoc-members: :show-inheritance: -:mod:`core` Module ------------------- +galaxy.jobs.metrics.instrumenters.core module +--------------------------------------------- .. automodule:: galaxy.jobs.metrics.instrumenters.core :members: :undoc-members: :show-inheritance: -:mod:`cpuinfo` Module ---------------------- +galaxy.jobs.metrics.instrumenters.cpuinfo module +------------------------------------------------ .. automodule:: galaxy.jobs.metrics.instrumenters.cpuinfo :members: :undoc-members: :show-inheritance: -:mod:`env` Module ------------------ +galaxy.jobs.metrics.instrumenters.env module +-------------------------------------------- .. automodule:: galaxy.jobs.metrics.instrumenters.env :members: :undoc-members: :show-inheritance: -:mod:`meminfo` Module ---------------------- +galaxy.jobs.metrics.instrumenters.meminfo module +------------------------------------------------ .. automodule:: galaxy.jobs.metrics.instrumenters.meminfo :members: :undoc-members: :show-inheritance: -:mod:`uname` Module -------------------- +galaxy.jobs.metrics.instrumenters.uname module +---------------------------------------------- .. automodule:: galaxy.jobs.metrics.instrumenters.uname :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.metrics.rst b/doc/source/lib/galaxy.jobs.metrics.rst index a9f3de2d925..b050d0f523f 100644 --- a/doc/source/lib/galaxy.jobs.metrics.rst +++ b/doc/source/lib/galaxy.jobs.metrics.rst @@ -1,22 +1,11 @@ -metrics Package -=============== - -:mod:`metrics` Package ----------------------- +galaxy.jobs.metrics package +=========================== .. automodule:: galaxy.jobs.metrics :members: :undoc-members: :show-inheritance: -:mod:`formatting` Module ------------------------- - -.. automodule:: galaxy.jobs.metrics.formatting - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -25,3 +14,15 @@ Subpackages galaxy.jobs.metrics.collectl galaxy.jobs.metrics.instrumenters +Submodules +---------- + +galaxy.jobs.metrics.formatting module +------------------------------------- + +.. automodule:: galaxy.jobs.metrics.formatting + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.jobs.rst b/doc/source/lib/galaxy.jobs.rst index be174b5e8d4..86c56ad5c51 100644 --- a/doc/source/lib/galaxy.jobs.rst +++ b/doc/source/lib/galaxy.jobs.rst @@ -1,94 +1,11 @@ -jobs Package -============ - -:mod:`jobs` Package -------------------- +galaxy.jobs package +=================== .. automodule:: galaxy.jobs :members: :undoc-members: :show-inheritance: -:mod:`command_factory` Module ------------------------------ - -.. automodule:: galaxy.jobs.command_factory - :members: - :undoc-members: - :show-inheritance: - -:mod:`datasets` Module ----------------------- - -.. automodule:: galaxy.jobs.datasets - :members: - :undoc-members: - :show-inheritance: - -:mod:`error_level` Module -------------------------- - -.. automodule:: galaxy.jobs.error_level - :members: - :undoc-members: - :show-inheritance: - -:mod:`handler` Module ---------------------- - -.. automodule:: galaxy.jobs.handler - :members: - :undoc-members: - :show-inheritance: - -:mod:`manager` Module ---------------------- - -.. automodule:: galaxy.jobs.manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`mapper` Module --------------------- - -.. automodule:: galaxy.jobs.mapper - :members: - :undoc-members: - :show-inheritance: - -:mod:`output_checker` Module ----------------------------- - -.. automodule:: galaxy.jobs.output_checker - :members: - :undoc-members: - :show-inheritance: - -:mod:`rule_helper` Module -------------------------- - -.. automodule:: galaxy.jobs.rule_helper - :members: - :undoc-members: - :show-inheritance: - -:mod:`stock_rules` Module -------------------------- - -.. automodule:: galaxy.jobs.stock_rules - :members: - :undoc-members: - :show-inheritance: - -:mod:`transfer_manager` Module ------------------------------- - -.. automodule:: galaxy.jobs.transfer_manager - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -101,3 +18,87 @@ Subpackages galaxy.jobs.runners galaxy.jobs.splitters +Submodules +---------- + +galaxy.jobs.command_factory module +---------------------------------- + +.. automodule:: galaxy.jobs.command_factory + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.datasets module +--------------------------- + +.. automodule:: galaxy.jobs.datasets + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.error_level module +------------------------------ + +.. automodule:: galaxy.jobs.error_level + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.handler module +-------------------------- + +.. automodule:: galaxy.jobs.handler + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.manager module +-------------------------- + +.. automodule:: galaxy.jobs.manager + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.mapper module +------------------------- + +.. automodule:: galaxy.jobs.mapper + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.output_checker module +--------------------------------- + +.. automodule:: galaxy.jobs.output_checker + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.rule_helper module +------------------------------ + +.. automodule:: galaxy.jobs.rule_helper + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.stock_rules module +------------------------------ + +.. automodule:: galaxy.jobs.stock_rules + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.transfer_manager module +----------------------------------- + +.. automodule:: galaxy.jobs.transfer_manager + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.jobs.runners.lwr_client.rst b/doc/source/lib/galaxy.jobs.runners.lwr_client.rst index 74f2efa3f9e..1c0be4e8fac 100644 --- a/doc/source/lib/galaxy.jobs.runners.lwr_client.rst +++ b/doc/source/lib/galaxy.jobs.runners.lwr_client.rst @@ -1,126 +1,11 @@ -lwr_client Package -================== - -:mod:`lwr_client` Package -------------------------- +galaxy.jobs.runners.lwr_client package +====================================== .. automodule:: galaxy.jobs.runners.lwr_client :members: :undoc-members: :show-inheritance: -:mod:`action_mapper` Module ---------------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.action_mapper - :members: - :undoc-members: - :show-inheritance: - -:mod:`amqp_exchange` Module ---------------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.amqp_exchange - :members: - :undoc-members: - :show-inheritance: - -:mod:`amqp_exchange_factory` Module ------------------------------------ - -.. automodule:: galaxy.jobs.runners.lwr_client.amqp_exchange_factory - :members: - :undoc-members: - :show-inheritance: - -:mod:`client` Module --------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.client - :members: - :undoc-members: - :show-inheritance: - -:mod:`config_util` Module -------------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.config_util - :members: - :undoc-members: - :show-inheritance: - -:mod:`decorators` Module ------------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.decorators - :members: - :undoc-members: - :show-inheritance: - -:mod:`destination` Module -------------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.destination - :members: - :undoc-members: - :show-inheritance: - -:mod:`interface` Module ------------------------ - -.. automodule:: galaxy.jobs.runners.lwr_client.interface - :members: - :undoc-members: - :show-inheritance: - -:mod:`job_directory` Module ---------------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.job_directory - :members: - :undoc-members: - :show-inheritance: - -:mod:`manager` Module ---------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`object_client` Module ---------------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.object_client - :members: - :undoc-members: - :show-inheritance: - -:mod:`path_mapper` Module -------------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.path_mapper - :members: - :undoc-members: - :show-inheritance: - -:mod:`setup_handler` Module ---------------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.setup_handler - :members: - :undoc-members: - :show-inheritance: - -:mod:`util` Module ------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.util - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -129,3 +14,119 @@ Subpackages galaxy.jobs.runners.lwr_client.staging galaxy.jobs.runners.lwr_client.transport +Submodules +---------- + +galaxy.jobs.runners.lwr_client.action_mapper module +--------------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.action_mapper + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.amqp_exchange module +--------------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.amqp_exchange + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.amqp_exchange_factory module +----------------------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.amqp_exchange_factory + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.client module +-------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.client + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.config_util module +------------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.config_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.decorators module +------------------------------------------------ + +.. automodule:: galaxy.jobs.runners.lwr_client.decorators + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.destination module +------------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.destination + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.interface module +----------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.interface + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.job_directory module +--------------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.job_directory + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.manager module +--------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.manager + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.object_client module +--------------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.object_client + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.path_mapper module +------------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.path_mapper + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.setup_handler module +--------------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.setup_handler + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.util module +------------------------------------------ + +.. automodule:: galaxy.jobs.runners.lwr_client.util + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst b/doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst index 62feff29ae9..7ae6a269d3a 100644 --- a/doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst +++ b/doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst @@ -1,27 +1,28 @@ -staging Package -=============== - -:mod:`staging` Package ----------------------- +galaxy.jobs.runners.lwr_client.staging package +============================================== .. automodule:: galaxy.jobs.runners.lwr_client.staging :members: :undoc-members: :show-inheritance: -:mod:`down` Module ------------------- +Submodules +---------- + +galaxy.jobs.runners.lwr_client.staging.down module +-------------------------------------------------- .. automodule:: galaxy.jobs.runners.lwr_client.staging.down :members: :undoc-members: :show-inheritance: -:mod:`up` Module ----------------- +galaxy.jobs.runners.lwr_client.staging.up module +------------------------------------------------ .. automodule:: galaxy.jobs.runners.lwr_client.staging.up :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst b/doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst index 427b43e96d1..f884599ba2d 100644 --- a/doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst +++ b/doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst @@ -1,27 +1,28 @@ -transport Package -================= - -:mod:`transport` Package ------------------------- +galaxy.jobs.runners.lwr_client.transport package +================================================ .. automodule:: galaxy.jobs.runners.lwr_client.transport :members: :undoc-members: :show-inheritance: -:mod:`curl` Module ------------------- +Submodules +---------- + +galaxy.jobs.runners.lwr_client.transport.curl module +---------------------------------------------------- .. automodule:: galaxy.jobs.runners.lwr_client.transport.curl :members: :undoc-members: :show-inheritance: -:mod:`standard` Module ----------------------- +galaxy.jobs.runners.lwr_client.transport.standard module +-------------------------------------------------------- .. automodule:: galaxy.jobs.runners.lwr_client.transport.standard :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.rst b/doc/source/lib/galaxy.jobs.runners.rst index 83cf3a5a41e..30c2f598717 100644 --- a/doc/source/lib/galaxy.jobs.runners.rst +++ b/doc/source/lib/galaxy.jobs.runners.rst @@ -1,94 +1,11 @@ -runners Package -=============== - -:mod:`runners` Package ----------------------- +galaxy.jobs.runners package +=========================== .. automodule:: galaxy.jobs.runners :members: :undoc-members: :show-inheritance: -:mod:`cli` Module ------------------ - -.. automodule:: galaxy.jobs.runners.cli - :members: - :undoc-members: - :show-inheritance: - -:mod:`condor` Module --------------------- - -.. automodule:: galaxy.jobs.runners.condor - :members: - :undoc-members: - :show-inheritance: - -:mod:`drmaa` Module -------------------- - -.. automodule:: galaxy.jobs.runners.drmaa - :members: - :undoc-members: - :show-inheritance: - -:mod:`local` Module -------------------- - -.. automodule:: galaxy.jobs.runners.local - :members: - :undoc-members: - :show-inheritance: - -:mod:`lwr` Module ------------------ - -.. automodule:: galaxy.jobs.runners.lwr - :members: - :undoc-members: - :show-inheritance: - -:mod:`pbs` Module ------------------ - -.. automodule:: galaxy.jobs.runners.pbs - :members: - :undoc-members: - :show-inheritance: - -:mod:`pulsar` Module --------------------- - -.. automodule:: galaxy.jobs.runners.pulsar - :members: - :undoc-members: - :show-inheritance: - -:mod:`slurm` Module -------------------- - -.. automodule:: galaxy.jobs.runners.slurm - :members: - :undoc-members: - :show-inheritance: - -:mod:`state_handler_factory` Module ------------------------------------ - -.. automodule:: galaxy.jobs.runners.state_handler_factory - :members: - :undoc-members: - :show-inheritance: - -:mod:`tasks` Module -------------------- - -.. automodule:: galaxy.jobs.runners.tasks - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -98,3 +15,87 @@ Subpackages galaxy.jobs.runners.state_handlers galaxy.jobs.runners.util +Submodules +---------- + +galaxy.jobs.runners.cli module +------------------------------ + +.. automodule:: galaxy.jobs.runners.cli + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.condor module +--------------------------------- + +.. automodule:: galaxy.jobs.runners.condor + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.drmaa module +-------------------------------- + +.. automodule:: galaxy.jobs.runners.drmaa + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.local module +-------------------------------- + +.. automodule:: galaxy.jobs.runners.local + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr module +------------------------------ + +.. automodule:: galaxy.jobs.runners.lwr + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.pbs module +------------------------------ + +.. automodule:: galaxy.jobs.runners.pbs + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.pulsar module +--------------------------------- + +.. automodule:: galaxy.jobs.runners.pulsar + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.slurm module +-------------------------------- + +.. automodule:: galaxy.jobs.runners.slurm + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.state_handler_factory module +------------------------------------------------ + +.. automodule:: galaxy.jobs.runners.state_handler_factory + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.tasks module +-------------------------------- + +.. automodule:: galaxy.jobs.runners.tasks + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.jobs.runners.state_handlers.rst b/doc/source/lib/galaxy.jobs.runners.state_handlers.rst index bbf8577287a..06b15dd3f54 100644 --- a/doc/source/lib/galaxy.jobs.runners.state_handlers.rst +++ b/doc/source/lib/galaxy.jobs.runners.state_handlers.rst @@ -1,11 +1,20 @@ -state_handlers Package -====================== +galaxy.jobs.runners.state_handlers package +========================================== -:mod:`resubmit` Module ----------------------- +.. automodule:: galaxy.jobs.runners.state_handlers + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.jobs.runners.state_handlers.resubmit module +-------------------------------------------------- .. automodule:: galaxy.jobs.runners.state_handlers.resubmit :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst index f98c1cb988a..ec1149a0d87 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst @@ -1,35 +1,36 @@ -job Package -=========== - -:mod:`job` Package ------------------- +galaxy.jobs.runners.util.cli.job package +======================================== .. automodule:: galaxy.jobs.runners.util.cli.job :members: :undoc-members: :show-inheritance: -:mod:`slurm` Module -------------------- +Submodules +---------- + +galaxy.jobs.runners.util.cli.job.slurm module +--------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.job.slurm :members: :undoc-members: :show-inheritance: -:mod:`slurm_torque` Module --------------------------- +galaxy.jobs.runners.util.cli.job.slurm_torque module +---------------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.job.slurm_torque :members: :undoc-members: :show-inheritance: -:mod:`torque` Module --------------------- +galaxy.jobs.runners.util.cli.job.torque module +---------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.job.torque :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.rst index b3426fc78f8..dadd626718b 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.cli.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.rst @@ -1,22 +1,11 @@ -cli Package -=========== - -:mod:`cli` Package ------------------- +galaxy.jobs.runners.util.cli package +==================================== .. automodule:: galaxy.jobs.runners.util.cli :members: :undoc-members: :show-inheritance: -:mod:`factory` Module ---------------------- - -.. automodule:: galaxy.jobs.runners.util.cli.factory - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -25,3 +14,15 @@ Subpackages galaxy.jobs.runners.util.cli.job galaxy.jobs.runners.util.cli.shell +Submodules +---------- + +galaxy.jobs.runners.util.cli.factory module +------------------------------------------- + +.. automodule:: galaxy.jobs.runners.util.cli.factory + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst index 115c1cfc0dd..42e5c7ffe73 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst @@ -1,27 +1,28 @@ -shell Package -============= - -:mod:`shell` Package --------------------- +galaxy.jobs.runners.util.cli.shell package +========================================== .. automodule:: galaxy.jobs.runners.util.cli.shell :members: :undoc-members: :show-inheritance: -:mod:`local` Module -------------------- +Submodules +---------- + +galaxy.jobs.runners.util.cli.shell.local module +----------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.shell.local :members: :undoc-members: :show-inheritance: -:mod:`rsh` Module ------------------ +galaxy.jobs.runners.util.cli.shell.rsh module +--------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.shell.rsh :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.util.condor.rst b/doc/source/lib/galaxy.jobs.runners.util.condor.rst index 8678f6a98a7..823ea51ac3e 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.condor.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.condor.rst @@ -1,8 +1,5 @@ -condor Package -============== - -:mod:`condor` Package ---------------------- +galaxy.jobs.runners.util.condor package +======================================= .. automodule:: galaxy.jobs.runners.util.condor :members: diff --git a/doc/source/lib/galaxy.jobs.runners.util.job_script.rst b/doc/source/lib/galaxy.jobs.runners.util.job_script.rst index 7599d9a1f64..bcc2b16e9eb 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.job_script.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.job_script.rst @@ -1,8 +1,5 @@ -job_script Package -================== - -:mod:`job_script` Package -------------------------- +galaxy.jobs.runners.util.job_script package +=========================================== .. automodule:: galaxy.jobs.runners.util.job_script :members: diff --git a/doc/source/lib/galaxy.jobs.runners.util.rst b/doc/source/lib/galaxy.jobs.runners.util.rst index 410034390c9..8bdd25fc7b4 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.rst @@ -1,38 +1,11 @@ -util Package -============ - -:mod:`util` Package -------------------- +galaxy.jobs.runners.util package +================================ .. automodule:: galaxy.jobs.runners.util :members: :undoc-members: :show-inheritance: -:mod:`env` Module ------------------ - -.. automodule:: galaxy.jobs.runners.util.env - :members: - :undoc-members: - :show-inheritance: - -:mod:`external` Module ----------------------- - -.. automodule:: galaxy.jobs.runners.util.external - :members: - :undoc-members: - :show-inheritance: - -:mod:`kill` Module ------------------- - -.. automodule:: galaxy.jobs.runners.util.kill - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -42,3 +15,31 @@ Subpackages galaxy.jobs.runners.util.condor galaxy.jobs.runners.util.job_script +Submodules +---------- + +galaxy.jobs.runners.util.env module +----------------------------------- + +.. automodule:: galaxy.jobs.runners.util.env + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.util.external module +---------------------------------------- + +.. automodule:: galaxy.jobs.runners.util.external + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.util.kill module +------------------------------------ + +.. automodule:: galaxy.jobs.runners.util.kill + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.jobs.splitters.rst b/doc/source/lib/galaxy.jobs.splitters.rst index 66545414b2e..d8af934e1be 100644 --- a/doc/source/lib/galaxy.jobs.splitters.rst +++ b/doc/source/lib/galaxy.jobs.splitters.rst @@ -1,19 +1,28 @@ -splitters Package -================= +galaxy.jobs.splitters package +============================= -:mod:`basic` Module -------------------- +.. automodule:: galaxy.jobs.splitters + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.jobs.splitters.basic module +---------------------------------- .. automodule:: galaxy.jobs.splitters.basic :members: :undoc-members: :show-inheritance: -:mod:`multi` Module -------------------- +galaxy.jobs.splitters.multi module +---------------------------------- .. automodule:: galaxy.jobs.splitters.multi :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.managers.rst b/doc/source/lib/galaxy.managers.rst index ae0ab647d05..5fab9245342 100644 --- a/doc/source/lib/galaxy.managers.rst +++ b/doc/source/lib/galaxy.managers.rst @@ -1,227 +1,228 @@ -managers Package -================ - -:mod:`managers` Package ------------------------ +galaxy.managers package +======================= .. automodule:: galaxy.managers :members: :undoc-members: :show-inheritance: -:mod:`annotatable` Module -------------------------- +Submodules +---------- + +galaxy.managers.annotatable module +---------------------------------- .. automodule:: galaxy.managers.annotatable :members: :undoc-members: :show-inheritance: -:mod:`api_keys` Module ----------------------- +galaxy.managers.api_keys module +------------------------------- .. automodule:: galaxy.managers.api_keys :members: :undoc-members: :show-inheritance: -:mod:`base` Module ------------------- +galaxy.managers.base module +--------------------------- .. automodule:: galaxy.managers.base :members: :undoc-members: :show-inheritance: -:mod:`citations` Module ------------------------ +galaxy.managers.citations module +-------------------------------- .. automodule:: galaxy.managers.citations :members: :undoc-members: :show-inheritance: -:mod:`collections` Module -------------------------- +galaxy.managers.collections module +---------------------------------- .. automodule:: galaxy.managers.collections :members: :undoc-members: :show-inheritance: -:mod:`collections_util` Module ------------------------------- +galaxy.managers.collections_util module +--------------------------------------- .. automodule:: galaxy.managers.collections_util :members: :undoc-members: :show-inheritance: -:mod:`configuration` Module ---------------------------- +galaxy.managers.configuration module +------------------------------------ .. automodule:: galaxy.managers.configuration :members: :undoc-members: :show-inheritance: -:mod:`containers` Module ------------------------- +galaxy.managers.containers module +--------------------------------- .. automodule:: galaxy.managers.containers :members: :undoc-members: :show-inheritance: -:mod:`context` Module ---------------------- +galaxy.managers.context module +------------------------------ .. automodule:: galaxy.managers.context :members: :undoc-members: :show-inheritance: -:mod:`datasets` Module ----------------------- +galaxy.managers.datasets module +------------------------------- .. automodule:: galaxy.managers.datasets :members: :undoc-members: :show-inheritance: -:mod:`deletable` Module ------------------------ +galaxy.managers.deletable module +-------------------------------- .. automodule:: galaxy.managers.deletable :members: :undoc-members: :show-inheritance: -:mod:`folders` Module ---------------------- +galaxy.managers.folders module +------------------------------ .. automodule:: galaxy.managers.folders :members: :undoc-members: :show-inheritance: -:mod:`hdas` Module ------------------- +galaxy.managers.hdas module +--------------------------- .. automodule:: galaxy.managers.hdas :members: :undoc-members: :show-inheritance: -:mod:`histories` Module ------------------------ +galaxy.managers.histories module +-------------------------------- .. automodule:: galaxy.managers.histories :members: :undoc-members: :show-inheritance: -:mod:`lddas` Module -------------------- +galaxy.managers.lddas module +---------------------------- .. automodule:: galaxy.managers.lddas :members: :undoc-members: :show-inheritance: -:mod:`libraries` Module ------------------------ +galaxy.managers.libraries module +-------------------------------- .. automodule:: galaxy.managers.libraries :members: :undoc-members: :show-inheritance: -:mod:`pages` Module -------------------- +galaxy.managers.pages module +---------------------------- .. automodule:: galaxy.managers.pages :members: :undoc-members: :show-inheritance: -:mod:`ratable` Module ---------------------- +galaxy.managers.ratable module +------------------------------ .. automodule:: galaxy.managers.ratable :members: :undoc-members: :show-inheritance: -:mod:`rbac_secured` Module --------------------------- +galaxy.managers.rbac_secured module +----------------------------------- .. automodule:: galaxy.managers.rbac_secured :members: :undoc-members: :show-inheritance: -:mod:`roles` Module -------------------- +galaxy.managers.roles module +---------------------------- .. automodule:: galaxy.managers.roles :members: :undoc-members: :show-inheritance: -:mod:`secured` Module ---------------------- +galaxy.managers.secured module +------------------------------ .. automodule:: galaxy.managers.secured :members: :undoc-members: :show-inheritance: -:mod:`sharable` Module ----------------------- +galaxy.managers.sharable module +------------------------------- .. automodule:: galaxy.managers.sharable :members: :undoc-members: :show-inheritance: -:mod:`taggable` Module ----------------------- +galaxy.managers.taggable module +------------------------------- .. automodule:: galaxy.managers.taggable :members: :undoc-members: :show-inheritance: -:mod:`tags` Module ------------------- +galaxy.managers.tags module +--------------------------- .. automodule:: galaxy.managers.tags :members: :undoc-members: :show-inheritance: -:mod:`users` Module -------------------- +galaxy.managers.users module +---------------------------- .. automodule:: galaxy.managers.users :members: :undoc-members: :show-inheritance: -:mod:`visualizations` Module ----------------------------- +galaxy.managers.visualizations module +------------------------------------- .. automodule:: galaxy.managers.visualizations :members: :undoc-members: :show-inheritance: -:mod:`workflows` Module ------------------------ +galaxy.managers.workflows module +-------------------------------- .. automodule:: galaxy.managers.workflows :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.model.migrate.rst b/doc/source/lib/galaxy.model.migrate.rst index 7218eff3296..60857c84097 100644 --- a/doc/source/lib/galaxy.model.migrate.rst +++ b/doc/source/lib/galaxy.model.migrate.rst @@ -1,11 +1,20 @@ -migrate Package -=============== +galaxy.model.migrate package +============================ -:mod:`check` Module -------------------- +.. automodule:: galaxy.model.migrate + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.model.migrate.check module +--------------------------------- .. automodule:: galaxy.model.migrate.check :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.model.orm.rst b/doc/source/lib/galaxy.model.orm.rst index 379141b94ed..b6896869c00 100644 --- a/doc/source/lib/galaxy.model.orm.rst +++ b/doc/source/lib/galaxy.model.orm.rst @@ -1,43 +1,44 @@ -orm Package -=========== - -:mod:`orm` Package ------------------- +galaxy.model.orm package +======================== .. automodule:: galaxy.model.orm :members: :undoc-members: :show-inheritance: -:mod:`engine_factory` Module ----------------------------- +Submodules +---------- + +galaxy.model.orm.engine_factory module +-------------------------------------- .. automodule:: galaxy.model.orm.engine_factory :members: :undoc-members: :show-inheritance: -:mod:`logging_connection_proxy` Module --------------------------------------- +galaxy.model.orm.logging_connection_proxy module +------------------------------------------------ .. automodule:: galaxy.model.orm.logging_connection_proxy :members: :undoc-members: :show-inheritance: -:mod:`now` Module ------------------ +galaxy.model.orm.now module +--------------------------- .. automodule:: galaxy.model.orm.now :members: :undoc-members: :show-inheritance: -:mod:`scripts` Module ---------------------- +galaxy.model.orm.scripts module +------------------------------- .. automodule:: galaxy.model.orm.scripts :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.model.rst b/doc/source/lib/galaxy.model.rst index e063ff3d456..748a7ba7710 100644 --- a/doc/source/lib/galaxy.model.rst +++ b/doc/source/lib/galaxy.model.rst @@ -1,62 +1,11 @@ -model Package -============= - -:mod:`model` Package --------------------- +galaxy.model package +==================== .. automodule:: galaxy.model :members: :undoc-members: :show-inheritance: -:mod:`base` Module ------------------- - -.. automodule:: galaxy.model.base - :members: - :undoc-members: - :show-inheritance: - -:mod:`custom_types` Module --------------------------- - -.. automodule:: galaxy.model.custom_types - :members: - :undoc-members: - :show-inheritance: - -:mod:`item_attrs` Module ------------------------- - -.. automodule:: galaxy.model.item_attrs - :members: - :undoc-members: - :show-inheritance: - -:mod:`mapping` Module ---------------------- - -.. automodule:: galaxy.model.mapping - :members: - :undoc-members: - :show-inheritance: - -:mod:`search` Module --------------------- - -.. automodule:: galaxy.model.search - :members: - :undoc-members: - :show-inheritance: - -:mod:`util` Module ------------------- - -.. automodule:: galaxy.model.util - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -66,3 +15,55 @@ Subpackages galaxy.model.orm galaxy.model.tool_shed_install +Submodules +---------- + +galaxy.model.base module +------------------------ + +.. automodule:: galaxy.model.base + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.custom_types module +-------------------------------- + +.. automodule:: galaxy.model.custom_types + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.item_attrs module +------------------------------ + +.. automodule:: galaxy.model.item_attrs + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.mapping module +--------------------------- + +.. automodule:: galaxy.model.mapping + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.search module +-------------------------- + +.. automodule:: galaxy.model.search + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.util module +------------------------ + +.. automodule:: galaxy.model.util + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst b/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst index f117f24a115..56b44de4bc7 100644 --- a/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst +++ b/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst @@ -1,11 +1,20 @@ -migrate Package -=============== +galaxy.model.tool_shed_install.migrate package +============================================== -:mod:`check` Module -------------------- +.. automodule:: galaxy.model.tool_shed_install.migrate + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.model.tool_shed_install.migrate.check module +--------------------------------------------------- .. automodule:: galaxy.model.tool_shed_install.migrate.check :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.model.tool_shed_install.rst b/doc/source/lib/galaxy.model.tool_shed_install.rst index 3d311847ab5..24e6b47e45b 100644 --- a/doc/source/lib/galaxy.model.tool_shed_install.rst +++ b/doc/source/lib/galaxy.model.tool_shed_install.rst @@ -1,22 +1,11 @@ -tool_shed_install Package -========================= - -:mod:`tool_shed_install` Package --------------------------------- +galaxy.model.tool_shed_install package +====================================== .. automodule:: galaxy.model.tool_shed_install :members: :undoc-members: :show-inheritance: -:mod:`mapping` Module ---------------------- - -.. automodule:: galaxy.model.tool_shed_install.mapping - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -24,3 +13,15 @@ Subpackages galaxy.model.tool_shed_install.migrate +Submodules +---------- + +galaxy.model.tool_shed_install.mapping module +--------------------------------------------- + +.. automodule:: galaxy.model.tool_shed_install.mapping + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.objectstore.rst b/doc/source/lib/galaxy.objectstore.rst index 19343f88e39..71457af109e 100644 --- a/doc/source/lib/galaxy.objectstore.rst +++ b/doc/source/lib/galaxy.objectstore.rst @@ -1,43 +1,44 @@ -objectstore Package -=================== - -:mod:`objectstore` Package --------------------------- +galaxy.objectstore package +========================== .. automodule:: galaxy.objectstore :members: :undoc-members: :show-inheritance: -:mod:`pulsar` Module --------------------- +Submodules +---------- + +galaxy.objectstore.pulsar module +-------------------------------- .. automodule:: galaxy.objectstore.pulsar :members: :undoc-members: :show-inheritance: -:mod:`rods` Module ------------------- +galaxy.objectstore.rods module +------------------------------ .. automodule:: galaxy.objectstore.rods :members: :undoc-members: :show-inheritance: -:mod:`s3` Module ----------------- +galaxy.objectstore.s3 module +---------------------------- .. automodule:: galaxy.objectstore.s3 :members: :undoc-members: :show-inheritance: -:mod:`s3_multipart_upload` Module ---------------------------------- +galaxy.objectstore.s3_multipart_upload module +--------------------------------------------- .. automodule:: galaxy.objectstore.s3_multipart_upload :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.openid.rst b/doc/source/lib/galaxy.openid.rst index d5dd49a08d3..ccd8057cfce 100644 --- a/doc/source/lib/galaxy.openid.rst +++ b/doc/source/lib/galaxy.openid.rst @@ -1,19 +1,20 @@ -openid Package -============== - -:mod:`openid` Package ---------------------- +galaxy.openid package +===================== .. automodule:: galaxy.openid :members: :undoc-members: :show-inheritance: -:mod:`providers` Module ------------------------ +Submodules +---------- + +galaxy.openid.providers module +------------------------------ .. automodule:: galaxy.openid.providers :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.quota.rst b/doc/source/lib/galaxy.quota.rst index b06c6ba33d3..36802033ce1 100644 --- a/doc/source/lib/galaxy.quota.rst +++ b/doc/source/lib/galaxy.quota.rst @@ -1,8 +1,5 @@ -quota Package -============= - -:mod:`quota` Package --------------------- +galaxy.quota package +==================== .. automodule:: galaxy.quota :members: diff --git a/doc/source/lib/galaxy.rst b/doc/source/lib/galaxy.rst index a1a42e221e4..b811fd86a1a 100644 --- a/doc/source/lib/galaxy.rst +++ b/doc/source/lib/galaxy.rst @@ -1,62 +1,11 @@ -galaxy Package +galaxy package ============== -:mod:`galaxy` Package ---------------------- - .. automodule:: galaxy :members: :undoc-members: :show-inheritance: -:mod:`app` Module ------------------ - -.. automodule:: galaxy.app - :members: - :undoc-members: - :show-inheritance: - -:mod:`config` Module --------------------- - -.. automodule:: galaxy.config - :members: - :undoc-members: - :show-inheritance: - -:mod:`main` Module ------------------- - -.. automodule:: galaxy.main - :members: - :undoc-members: - :show-inheritance: - -:mod:`queue_worker` Module --------------------------- - -.. automodule:: galaxy.queue_worker - :members: - :undoc-members: - :show-inheritance: - -:mod:`queues` Module --------------------- - -.. automodule:: galaxy.queues - :members: - :undoc-members: - :show-inheritance: - -:mod:`version` Module ---------------------- - -.. automodule:: galaxy.version - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -88,3 +37,55 @@ Subpackages galaxy.work galaxy.workflow +Submodules +---------- + +galaxy.app module +----------------- + +.. automodule:: galaxy.app + :members: + :undoc-members: + :show-inheritance: + +galaxy.config module +-------------------- + +.. automodule:: galaxy.config + :members: + :undoc-members: + :show-inheritance: + +galaxy.main module +------------------ + +.. automodule:: galaxy.main + :members: + :undoc-members: + :show-inheritance: + +galaxy.queue_worker module +-------------------------- + +.. automodule:: galaxy.queue_worker + :members: + :undoc-members: + :show-inheritance: + +galaxy.queues module +-------------------- + +.. automodule:: galaxy.queues + :members: + :undoc-members: + :show-inheritance: + +galaxy.version module +--------------------- + +.. automodule:: galaxy.version + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.sample_tracking.rst b/doc/source/lib/galaxy.sample_tracking.rst index 52dd1e6c7f6..dbef4b76139 100644 --- a/doc/source/lib/galaxy.sample_tracking.rst +++ b/doc/source/lib/galaxy.sample_tracking.rst @@ -1,35 +1,44 @@ -sample_tracking Package -======================= +galaxy.sample_tracking package +============================== -:mod:`data_transfer` Module ---------------------------- +.. automodule:: galaxy.sample_tracking + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.sample_tracking.data_transfer module +------------------------------------------- .. automodule:: galaxy.sample_tracking.data_transfer :members: :undoc-members: :show-inheritance: -:mod:`external_service_types` Module ------------------------------------- +galaxy.sample_tracking.external_service_types module +---------------------------------------------------- .. automodule:: galaxy.sample_tracking.external_service_types :members: :undoc-members: :show-inheritance: -:mod:`request_types` Module ---------------------------- +galaxy.sample_tracking.request_types module +------------------------------------------- .. automodule:: galaxy.sample_tracking.request_types :members: :undoc-members: :show-inheritance: -:mod:`sample` Module --------------------- +galaxy.sample_tracking.sample module +------------------------------------ .. automodule:: galaxy.sample_tracking.sample :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.security.rst b/doc/source/lib/galaxy.security.rst index ff90ef6e6e2..5f1ab5fe123 100644 --- a/doc/source/lib/galaxy.security.rst +++ b/doc/source/lib/galaxy.security.rst @@ -1,27 +1,28 @@ -security Package -================ - -:mod:`security` Package ------------------------ +galaxy.security package +======================= .. automodule:: galaxy.security :members: :undoc-members: :show-inheritance: -:mod:`passwords` Module ------------------------ +Submodules +---------- + +galaxy.security.passwords module +-------------------------------- .. automodule:: galaxy.security.passwords :members: :undoc-members: :show-inheritance: -:mod:`validate_user_input` Module ---------------------------------- +galaxy.security.validate_user_input module +------------------------------------------ .. automodule:: galaxy.security.validate_user_input :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.tags.rst b/doc/source/lib/galaxy.tags.rst index 38d5152b8e7..d61869f22bd 100644 --- a/doc/source/lib/galaxy.tags.rst +++ b/doc/source/lib/galaxy.tags.rst @@ -1,8 +1,5 @@ -tags Package -============ - -:mod:`tags` Package -------------------- +galaxy.tags package +=================== .. automodule:: galaxy.tags :members: diff --git a/doc/source/lib/galaxy.tools.actions.rst b/doc/source/lib/galaxy.tools.actions.rst index 870cc2ca31b..1cf4863c217 100644 --- a/doc/source/lib/galaxy.tools.actions.rst +++ b/doc/source/lib/galaxy.tools.actions.rst @@ -1,59 +1,60 @@ -actions Package -=============== - -:mod:`actions` Package ----------------------- +galaxy.tools.actions package +============================ .. automodule:: galaxy.tools.actions :members: :undoc-members: :show-inheritance: -:mod:`data_manager` Module --------------------------- +Submodules +---------- + +galaxy.tools.actions.data_manager module +---------------------------------------- .. automodule:: galaxy.tools.actions.data_manager :members: :undoc-members: :show-inheritance: -:mod:`data_source` Module -------------------------- +galaxy.tools.actions.data_source module +--------------------------------------- .. automodule:: galaxy.tools.actions.data_source :members: :undoc-members: :show-inheritance: -:mod:`history_imp_exp` Module ------------------------------ +galaxy.tools.actions.history_imp_exp module +------------------------------------------- .. automodule:: galaxy.tools.actions.history_imp_exp :members: :undoc-members: :show-inheritance: -:mod:`metadata` Module ----------------------- +galaxy.tools.actions.metadata module +------------------------------------ .. automodule:: galaxy.tools.actions.metadata :members: :undoc-members: :show-inheritance: -:mod:`upload` Module --------------------- +galaxy.tools.actions.upload module +---------------------------------- .. automodule:: galaxy.tools.actions.upload :members: :undoc-members: :show-inheritance: -:mod:`upload_common` Module ---------------------------- +galaxy.tools.actions.upload_common module +----------------------------------------- .. automodule:: galaxy.tools.actions.upload_common :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.data.rst b/doc/source/lib/galaxy.tools.data.rst index 92641efedcb..4435ba549f8 100644 --- a/doc/source/lib/galaxy.tools.data.rst +++ b/doc/source/lib/galaxy.tools.data.rst @@ -1,8 +1,5 @@ -data Package -============ - -:mod:`data` Package -------------------- +galaxy.tools.data package +========================= .. automodule:: galaxy.tools.data :members: diff --git a/doc/source/lib/galaxy.tools.data_manager.rst b/doc/source/lib/galaxy.tools.data_manager.rst index bbf07acd662..02c75fa28ad 100644 --- a/doc/source/lib/galaxy.tools.data_manager.rst +++ b/doc/source/lib/galaxy.tools.data_manager.rst @@ -1,19 +1,20 @@ -data_manager Package -==================== - -:mod:`data_manager` Package ---------------------------- +galaxy.tools.data_manager package +================================= .. automodule:: galaxy.tools.data_manager :members: :undoc-members: :show-inheritance: -:mod:`manager` Module ---------------------- +Submodules +---------- + +galaxy.tools.data_manager.manager module +---------------------------------------- .. automodule:: galaxy.tools.data_manager.manager :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.deps.resolvers.rst b/doc/source/lib/galaxy.tools.deps.resolvers.rst index 5890b4eed38..ef2282bb8d3 100644 --- a/doc/source/lib/galaxy.tools.deps.resolvers.rst +++ b/doc/source/lib/galaxy.tools.deps.resolvers.rst @@ -1,59 +1,60 @@ -resolvers Package -================= - -:mod:`resolvers` Package ------------------------- +galaxy.tools.deps.resolvers package +=================================== .. automodule:: galaxy.tools.deps.resolvers :members: :undoc-members: :show-inheritance: -:mod:`brewed_tool_shed_packages` Module ---------------------------------------- +Submodules +---------- + +galaxy.tools.deps.resolvers.brewed_tool_shed_packages module +------------------------------------------------------------ .. automodule:: galaxy.tools.deps.resolvers.brewed_tool_shed_packages :members: :undoc-members: :show-inheritance: -:mod:`galaxy_packages` Module ------------------------------ +galaxy.tools.deps.resolvers.galaxy_packages module +-------------------------------------------------- .. automodule:: galaxy.tools.deps.resolvers.galaxy_packages :members: :undoc-members: :show-inheritance: -:mod:`homebrew` Module ----------------------- +galaxy.tools.deps.resolvers.homebrew module +------------------------------------------- .. automodule:: galaxy.tools.deps.resolvers.homebrew :members: :undoc-members: :show-inheritance: -:mod:`modules` Module ---------------------- +galaxy.tools.deps.resolvers.modules module +------------------------------------------ .. automodule:: galaxy.tools.deps.resolvers.modules :members: :undoc-members: :show-inheritance: -:mod:`resolver_mixins` Module ------------------------------ +galaxy.tools.deps.resolvers.resolver_mixins module +-------------------------------------------------- .. automodule:: galaxy.tools.deps.resolvers.resolver_mixins :members: :undoc-members: :show-inheritance: -:mod:`tool_shed_packages` Module --------------------------------- +galaxy.tools.deps.resolvers.tool_shed_packages module +----------------------------------------------------- .. automodule:: galaxy.tools.deps.resolvers.tool_shed_packages :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.deps.rst b/doc/source/lib/galaxy.tools.deps.rst index 404d660628e..f64c423dc22 100644 --- a/doc/source/lib/galaxy.tools.deps.rst +++ b/doc/source/lib/galaxy.tools.deps.rst @@ -1,78 +1,11 @@ -deps Package -============ - -:mod:`deps` Package -------------------- +galaxy.tools.deps package +========================= .. automodule:: galaxy.tools.deps :members: :undoc-members: :show-inheritance: -:mod:`brew_exts` Module ------------------------ - -.. automodule:: galaxy.tools.deps.brew_exts - :members: - :undoc-members: - :show-inheritance: - -:mod:`brew_util` Module ------------------------ - -.. automodule:: galaxy.tools.deps.brew_util - :members: - :undoc-members: - :show-inheritance: - -:mod:`commands` Module ----------------------- - -.. automodule:: galaxy.tools.deps.commands - :members: - :undoc-members: - :show-inheritance: - -:mod:`containers` Module ------------------------- - -.. automodule:: galaxy.tools.deps.containers - :members: - :undoc-members: - :show-inheritance: - -:mod:`dependencies` Module --------------------------- - -.. automodule:: galaxy.tools.deps.dependencies - :members: - :undoc-members: - :show-inheritance: - -:mod:`docker_util` Module -------------------------- - -.. automodule:: galaxy.tools.deps.docker_util - :members: - :undoc-members: - :show-inheritance: - -:mod:`dockerfiles` Module -------------------------- - -.. automodule:: galaxy.tools.deps.dockerfiles - :members: - :undoc-members: - :show-inheritance: - -:mod:`requirements` Module --------------------------- - -.. automodule:: galaxy.tools.deps.requirements - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -80,3 +13,71 @@ Subpackages galaxy.tools.deps.resolvers +Submodules +---------- + +galaxy.tools.deps.brew_exts module +---------------------------------- + +.. automodule:: galaxy.tools.deps.brew_exts + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.deps.brew_util module +---------------------------------- + +.. automodule:: galaxy.tools.deps.brew_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.deps.commands module +--------------------------------- + +.. automodule:: galaxy.tools.deps.commands + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.deps.containers module +----------------------------------- + +.. automodule:: galaxy.tools.deps.containers + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.deps.dependencies module +------------------------------------- + +.. automodule:: galaxy.tools.deps.dependencies + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.deps.docker_util module +------------------------------------ + +.. automodule:: galaxy.tools.deps.docker_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.deps.dockerfiles module +------------------------------------ + +.. automodule:: galaxy.tools.deps.dockerfiles + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.deps.requirements module +------------------------------------- + +.. automodule:: galaxy.tools.deps.requirements + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tools.filters.rst b/doc/source/lib/galaxy.tools.filters.rst index e31664e9cd3..bbea7ec45e4 100644 --- a/doc/source/lib/galaxy.tools.filters.rst +++ b/doc/source/lib/galaxy.tools.filters.rst @@ -1,8 +1,5 @@ -filters Package -=============== - -:mod:`filters` Package ----------------------- +galaxy.tools.filters package +============================ .. automodule:: galaxy.tools.filters :members: diff --git a/doc/source/lib/galaxy.tools.imp_exp.rst b/doc/source/lib/galaxy.tools.imp_exp.rst index 2801da055dd..e466f86b0a4 100644 --- a/doc/source/lib/galaxy.tools.imp_exp.rst +++ b/doc/source/lib/galaxy.tools.imp_exp.rst @@ -1,27 +1,28 @@ -imp_exp Package -=============== - -:mod:`imp_exp` Package ----------------------- +galaxy.tools.imp_exp package +============================ .. automodule:: galaxy.tools.imp_exp :members: :undoc-members: :show-inheritance: -:mod:`export_history` Module ----------------------------- +Submodules +---------- + +galaxy.tools.imp_exp.export_history module +------------------------------------------ .. automodule:: galaxy.tools.imp_exp.export_history :members: :undoc-members: :show-inheritance: -:mod:`unpack_tar_gz_archive` Module ------------------------------------ +galaxy.tools.imp_exp.unpack_tar_gz_archive module +------------------------------------------------- .. automodule:: galaxy.tools.imp_exp.unpack_tar_gz_archive :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.linters.rst b/doc/source/lib/galaxy.tools.linters.rst index e8e91a60b88..a27e6bf42bd 100644 --- a/doc/source/lib/galaxy.tools.linters.rst +++ b/doc/source/lib/galaxy.tools.linters.rst @@ -1,67 +1,68 @@ -linters Package -=============== - -:mod:`linters` Package ----------------------- +galaxy.tools.linters package +============================ .. automodule:: galaxy.tools.linters :members: :undoc-members: :show-inheritance: -:mod:`citations` Module ------------------------ +Submodules +---------- + +galaxy.tools.linters.citations module +------------------------------------- .. automodule:: galaxy.tools.linters.citations :members: :undoc-members: :show-inheritance: -:mod:`command` Module ---------------------- +galaxy.tools.linters.command module +----------------------------------- .. automodule:: galaxy.tools.linters.command :members: :undoc-members: :show-inheritance: -:mod:`help` Module ------------------- +galaxy.tools.linters.help module +-------------------------------- .. automodule:: galaxy.tools.linters.help :members: :undoc-members: :show-inheritance: -:mod:`inputs` Module --------------------- +galaxy.tools.linters.inputs module +---------------------------------- .. automodule:: galaxy.tools.linters.inputs :members: :undoc-members: :show-inheritance: -:mod:`outputs` Module ---------------------- +galaxy.tools.linters.outputs module +----------------------------------- .. automodule:: galaxy.tools.linters.outputs :members: :undoc-members: :show-inheritance: -:mod:`tests` Module -------------------- +galaxy.tools.linters.tests module +--------------------------------- .. automodule:: galaxy.tools.linters.tests :members: :undoc-members: :show-inheritance: -:mod:`top_level` Module ------------------------ +galaxy.tools.linters.top_level module +------------------------------------- .. automodule:: galaxy.tools.linters.top_level :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.parameters.rst b/doc/source/lib/galaxy.tools.parameters.rst index 183d17cb295..28309e13f58 100644 --- a/doc/source/lib/galaxy.tools.parameters.rst +++ b/doc/source/lib/galaxy.tools.parameters.rst @@ -1,107 +1,108 @@ -parameters Package -================== - -:mod:`parameters` Package -------------------------- +galaxy.tools.parameters package +=============================== .. automodule:: galaxy.tools.parameters :members: :undoc-members: :show-inheritance: -:mod:`basic` Module -------------------- +Submodules +---------- + +galaxy.tools.parameters.basic module +------------------------------------ .. automodule:: galaxy.tools.parameters.basic :members: :undoc-members: :show-inheritance: -:mod:`dataset_matcher` Module ------------------------------ +galaxy.tools.parameters.dataset_matcher module +---------------------------------------------- .. automodule:: galaxy.tools.parameters.dataset_matcher :members: :undoc-members: :show-inheritance: -:mod:`dynamic_options` Module ------------------------------ +galaxy.tools.parameters.dynamic_options module +---------------------------------------------- .. automodule:: galaxy.tools.parameters.dynamic_options :members: :undoc-members: :show-inheritance: -:mod:`grouping` Module ----------------------- +galaxy.tools.parameters.grouping module +--------------------------------------- .. automodule:: galaxy.tools.parameters.grouping :members: :undoc-members: :show-inheritance: -:mod:`history_query` Module ---------------------------- +galaxy.tools.parameters.history_query module +-------------------------------------------- .. automodule:: galaxy.tools.parameters.history_query :members: :undoc-members: :show-inheritance: -:mod:`input_translation` Module -------------------------------- +galaxy.tools.parameters.input_translation module +------------------------------------------------ .. automodule:: galaxy.tools.parameters.input_translation :members: :undoc-members: :show-inheritance: -:mod:`meta` Module ------------------- +galaxy.tools.parameters.meta module +----------------------------------- .. automodule:: galaxy.tools.parameters.meta :members: :undoc-members: :show-inheritance: -:mod:`output` Module --------------------- +galaxy.tools.parameters.output module +------------------------------------- .. automodule:: galaxy.tools.parameters.output :members: :undoc-members: :show-inheritance: -:mod:`output_collect` Module ----------------------------- +galaxy.tools.parameters.output_collect module +--------------------------------------------- .. automodule:: galaxy.tools.parameters.output_collect :members: :undoc-members: :show-inheritance: -:mod:`sanitize` Module ----------------------- +galaxy.tools.parameters.sanitize module +--------------------------------------- .. automodule:: galaxy.tools.parameters.sanitize :members: :undoc-members: :show-inheritance: -:mod:`validation` Module ------------------------- +galaxy.tools.parameters.validation module +----------------------------------------- .. automodule:: galaxy.tools.parameters.validation :members: :undoc-members: :show-inheritance: -:mod:`wrapped` Module ---------------------- +galaxy.tools.parameters.wrapped module +-------------------------------------- .. automodule:: galaxy.tools.parameters.wrapped :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.parser.rst b/doc/source/lib/galaxy.tools.parser.rst index 8c316098d72..ecdc2b15feb 100644 --- a/doc/source/lib/galaxy.tools.parser.rst +++ b/doc/source/lib/galaxy.tools.parser.rst @@ -1,51 +1,52 @@ -parser Package -============== - -:mod:`parser` Package ---------------------- +galaxy.tools.parser package +=========================== .. automodule:: galaxy.tools.parser :members: :undoc-members: :show-inheritance: -:mod:`factory` Module ---------------------- +Submodules +---------- + +galaxy.tools.parser.factory module +---------------------------------- .. automodule:: galaxy.tools.parser.factory :members: :undoc-members: :show-inheritance: -:mod:`interface` Module ------------------------ +galaxy.tools.parser.interface module +------------------------------------ .. automodule:: galaxy.tools.parser.interface :members: :undoc-members: :show-inheritance: -:mod:`util` Module ------------------- +galaxy.tools.parser.util module +------------------------------- .. automodule:: galaxy.tools.parser.util :members: :undoc-members: :show-inheritance: -:mod:`xml` Module ------------------ +galaxy.tools.parser.xml module +------------------------------ .. automodule:: galaxy.tools.parser.xml :members: :undoc-members: :show-inheritance: -:mod:`yaml` Module ------------------- +galaxy.tools.parser.yaml module +------------------------------- .. automodule:: galaxy.tools.parser.yaml :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.rst b/doc/source/lib/galaxy.tools.rst index 90bb129cbd4..01add8d971c 100644 --- a/doc/source/lib/galaxy.tools.rst +++ b/doc/source/lib/galaxy.tools.rst @@ -1,86 +1,11 @@ -tools Package -============= - -:mod:`tools` Package --------------------- +galaxy.tools package +==================== .. automodule:: galaxy.tools :members: :undoc-members: :show-inheritance: -:mod:`errors` Module --------------------- - -.. automodule:: galaxy.tools.errors - :members: - :undoc-members: - :show-inheritance: - -:mod:`evaluation` Module ------------------------- - -.. automodule:: galaxy.tools.evaluation - :members: - :undoc-members: - :show-inheritance: - -:mod:`exception_handling` Module --------------------------------- - -.. automodule:: galaxy.tools.exception_handling - :members: - :undoc-members: - :show-inheritance: - -:mod:`execute` Module ---------------------- - -.. automodule:: galaxy.tools.execute - :members: - :undoc-members: - :show-inheritance: - -:mod:`lint` Module ------------------- - -.. automodule:: galaxy.tools.lint - :members: - :undoc-members: - :show-inheritance: - -:mod:`loader` Module --------------------- - -.. automodule:: galaxy.tools.loader - :members: - :undoc-members: - :show-inheritance: - -:mod:`loader_directory` Module ------------------------------- - -.. automodule:: galaxy.tools.loader_directory - :members: - :undoc-members: - :show-inheritance: - -:mod:`test` Module ------------------- - -.. automodule:: galaxy.tools.test - :members: - :undoc-members: - :show-inheritance: - -:mod:`wrappers` Module ----------------------- - -.. automodule:: galaxy.tools.wrappers - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -99,3 +24,79 @@ Subpackages galaxy.tools.toolbox galaxy.tools.util +Submodules +---------- + +galaxy.tools.errors module +-------------------------- + +.. automodule:: galaxy.tools.errors + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.evaluation module +------------------------------ + +.. automodule:: galaxy.tools.evaluation + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.exception_handling module +-------------------------------------- + +.. automodule:: galaxy.tools.exception_handling + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.execute module +--------------------------- + +.. automodule:: galaxy.tools.execute + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.lint module +------------------------ + +.. automodule:: galaxy.tools.lint + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.loader module +-------------------------- + +.. automodule:: galaxy.tools.loader + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.loader_directory module +------------------------------------ + +.. automodule:: galaxy.tools.loader_directory + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.test module +------------------------ + +.. automodule:: galaxy.tools.test + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.wrappers module +---------------------------- + +.. automodule:: galaxy.tools.wrappers + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tools.search.rst b/doc/source/lib/galaxy.tools.search.rst index 616079f69b7..edbb5bf3c79 100644 --- a/doc/source/lib/galaxy.tools.search.rst +++ b/doc/source/lib/galaxy.tools.search.rst @@ -1,8 +1,5 @@ -search Package -============== - -:mod:`search` Package ---------------------- +galaxy.tools.search package +=========================== .. automodule:: galaxy.tools.search :members: diff --git a/doc/source/lib/galaxy.tools.toolbox.filters.rst b/doc/source/lib/galaxy.tools.toolbox.filters.rst index d168b000a9e..a5a81d279fb 100644 --- a/doc/source/lib/galaxy.tools.toolbox.filters.rst +++ b/doc/source/lib/galaxy.tools.toolbox.filters.rst @@ -1,8 +1,5 @@ -filters Package -=============== - -:mod:`filters` Package ----------------------- +galaxy.tools.toolbox.filters package +==================================== .. automodule:: galaxy.tools.toolbox.filters :members: diff --git a/doc/source/lib/galaxy.tools.toolbox.lineages.rst b/doc/source/lib/galaxy.tools.toolbox.lineages.rst index bd3811cdb1e..3159c8d248d 100644 --- a/doc/source/lib/galaxy.tools.toolbox.lineages.rst +++ b/doc/source/lib/galaxy.tools.toolbox.lineages.rst @@ -1,43 +1,44 @@ -lineages Package -================ - -:mod:`lineages` Package ------------------------ +galaxy.tools.toolbox.lineages package +===================================== .. automodule:: galaxy.tools.toolbox.lineages :members: :undoc-members: :show-inheritance: -:mod:`factory` Module ---------------------- +Submodules +---------- + +galaxy.tools.toolbox.lineages.factory module +-------------------------------------------- .. automodule:: galaxy.tools.toolbox.lineages.factory :members: :undoc-members: :show-inheritance: -:mod:`interface` Module ------------------------ +galaxy.tools.toolbox.lineages.interface module +---------------------------------------------- .. automodule:: galaxy.tools.toolbox.lineages.interface :members: :undoc-members: :show-inheritance: -:mod:`stock` Module -------------------- +galaxy.tools.toolbox.lineages.stock module +------------------------------------------ .. automodule:: galaxy.tools.toolbox.lineages.stock :members: :undoc-members: :show-inheritance: -:mod:`tool_shed` Module ------------------------ +galaxy.tools.toolbox.lineages.tool_shed module +---------------------------------------------- .. automodule:: galaxy.tools.toolbox.lineages.tool_shed :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.toolbox.rst b/doc/source/lib/galaxy.tools.toolbox.rst index 8739d4fb201..7528cb77e08 100644 --- a/doc/source/lib/galaxy.tools.toolbox.rst +++ b/doc/source/lib/galaxy.tools.toolbox.rst @@ -1,54 +1,11 @@ -toolbox Package -=============== - -:mod:`toolbox` Package ----------------------- +galaxy.tools.toolbox package +============================ .. automodule:: galaxy.tools.toolbox :members: :undoc-members: :show-inheritance: -:mod:`base` Module ------------------- - -.. automodule:: galaxy.tools.toolbox.base - :members: - :undoc-members: - :show-inheritance: - -:mod:`integrated_panel` Module ------------------------------- - -.. automodule:: galaxy.tools.toolbox.integrated_panel - :members: - :undoc-members: - :show-inheritance: - -:mod:`panel` Module -------------------- - -.. automodule:: galaxy.tools.toolbox.panel - :members: - :undoc-members: - :show-inheritance: - -:mod:`tags` Module ------------------- - -.. automodule:: galaxy.tools.toolbox.tags - :members: - :undoc-members: - :show-inheritance: - -:mod:`watcher` Module ---------------------- - -.. automodule:: galaxy.tools.toolbox.watcher - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -57,3 +14,47 @@ Subpackages galaxy.tools.toolbox.filters galaxy.tools.toolbox.lineages +Submodules +---------- + +galaxy.tools.toolbox.base module +-------------------------------- + +.. automodule:: galaxy.tools.toolbox.base + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.toolbox.integrated_panel module +-------------------------------------------- + +.. automodule:: galaxy.tools.toolbox.integrated_panel + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.toolbox.panel module +--------------------------------- + +.. automodule:: galaxy.tools.toolbox.panel + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.toolbox.tags module +-------------------------------- + +.. automodule:: galaxy.tools.toolbox.tags + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.toolbox.watcher module +----------------------------------- + +.. automodule:: galaxy.tools.toolbox.watcher + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tools.util.galaxyops.rst b/doc/source/lib/galaxy.tools.util.galaxyops.rst index 2e749eefb13..4ea949a2fac 100644 --- a/doc/source/lib/galaxy.tools.util.galaxyops.rst +++ b/doc/source/lib/galaxy.tools.util.galaxyops.rst @@ -1,8 +1,5 @@ -galaxyops Package -================= - -:mod:`galaxyops` Package ------------------------- +galaxy.tools.util.galaxyops package +=================================== .. automodule:: galaxy.tools.util.galaxyops :members: diff --git a/doc/source/lib/galaxy.tools.util.rst b/doc/source/lib/galaxy.tools.util.rst index 04efb192a74..f7b6b6f32d0 100644 --- a/doc/source/lib/galaxy.tools.util.rst +++ b/doc/source/lib/galaxy.tools.util.rst @@ -1,22 +1,11 @@ -util Package -============ - -:mod:`util` Package -------------------- +galaxy.tools.util package +========================= .. automodule:: galaxy.tools.util :members: :undoc-members: :show-inheritance: -:mod:`maf_utilities` Module ---------------------------- - -.. automodule:: galaxy.tools.util.maf_utilities - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -24,3 +13,15 @@ Subpackages galaxy.tools.util.galaxyops +Submodules +---------- + +galaxy.tools.util.maf_utilities module +-------------------------------------- + +.. automodule:: galaxy.tools.util.maf_utilities + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.util.backports.importlib.rst b/doc/source/lib/galaxy.util.backports.importlib.rst index 765830ac0bc..974cf47f98d 100644 --- a/doc/source/lib/galaxy.util.backports.importlib.rst +++ b/doc/source/lib/galaxy.util.backports.importlib.rst @@ -1,8 +1,5 @@ -importlib Package -================= - -:mod:`importlib` Package ------------------------- +galaxy.util.backports.importlib package +======================================= .. automodule:: galaxy.util.backports.importlib :members: diff --git a/doc/source/lib/galaxy.util.backports.rst b/doc/source/lib/galaxy.util.backports.rst index ead946d6eca..69356d80fcd 100644 --- a/doc/source/lib/galaxy.util.backports.rst +++ b/doc/source/lib/galaxy.util.backports.rst @@ -1,8 +1,5 @@ -backports Package -================= - -:mod:`backports` Package ------------------------- +galaxy.util.backports package +============================= .. automodule:: galaxy.util.backports :members: diff --git a/doc/source/lib/galaxy.util.log.rst b/doc/source/lib/galaxy.util.log.rst index c3aa8056511..0f81bc0115c 100644 --- a/doc/source/lib/galaxy.util.log.rst +++ b/doc/source/lib/galaxy.util.log.rst @@ -1,19 +1,20 @@ -log Package -=========== - -:mod:`log` Package ------------------- +galaxy.util.log package +======================= .. automodule:: galaxy.util.log :members: :undoc-members: :show-inheritance: -:mod:`fluent_log` Module ------------------------- +Submodules +---------- + +galaxy.util.log.fluent_log module +--------------------------------- .. automodule:: galaxy.util.log.fluent_log :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.util.pastescript.rst b/doc/source/lib/galaxy.util.pastescript.rst index beb1f826ebe..0a861eb5a4f 100644 --- a/doc/source/lib/galaxy.util.pastescript.rst +++ b/doc/source/lib/galaxy.util.pastescript.rst @@ -1,27 +1,28 @@ -pastescript Package -=================== - -:mod:`pastescript` Package --------------------------- +galaxy.util.pastescript package +=============================== .. automodule:: galaxy.util.pastescript :members: :undoc-members: :show-inheritance: -:mod:`loadwsgi` Module ----------------------- +Submodules +---------- + +galaxy.util.pastescript.loadwsgi module +--------------------------------------- .. automodule:: galaxy.util.pastescript.loadwsgi :members: :undoc-members: :show-inheritance: -:mod:`serve` Module -------------------- +galaxy.util.pastescript.serve module +------------------------------------ .. automodule:: galaxy.util.pastescript.serve :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.util.rst b/doc/source/lib/galaxy.util.rst index e37346a6b6b..dd2eca1c66b 100644 --- a/doc/source/lib/galaxy.util.rst +++ b/doc/source/lib/galaxy.util.rst @@ -1,278 +1,11 @@ -util Package -============ - -:mod:`util` Package -------------------- +galaxy.util package +=================== .. automodule:: galaxy.util :members: :undoc-members: :show-inheritance: -:mod:`aliaspickler` Module --------------------------- - -.. automodule:: galaxy.util.aliaspickler - :members: - :undoc-members: - :show-inheritance: - -:mod:`biostar` Module ---------------------- - -.. automodule:: galaxy.util.biostar - :members: - :undoc-members: - :show-inheritance: - -:mod:`bunch` Module -------------------- - -.. automodule:: galaxy.util.bunch - :members: - :undoc-members: - :show-inheritance: - -:mod:`dbkeys` Module --------------------- - -.. automodule:: galaxy.util.dbkeys - :members: - :undoc-members: - :show-inheritance: - -:mod:`debugging` Module ------------------------ - -.. automodule:: galaxy.util.debugging - :members: - :undoc-members: - :show-inheritance: - -:mod:`dictobj` Module ---------------------- - -.. automodule:: galaxy.util.dictobj - :members: - :undoc-members: - :show-inheritance: - -:mod:`directory_hash` Module ----------------------------- - -.. automodule:: galaxy.util.directory_hash - :members: - :undoc-members: - :show-inheritance: - -:mod:`expressions` Module -------------------------- - -.. automodule:: galaxy.util.expressions - :members: - :undoc-members: - :show-inheritance: - -:mod:`hash_util` Module ------------------------ - -.. automodule:: galaxy.util.hash_util - :members: - :undoc-members: - :show-inheritance: - -:mod:`heartbeat` Module ------------------------ - -.. automodule:: galaxy.util.heartbeat - :members: - :undoc-members: - :show-inheritance: - -:mod:`inflection` Module ------------------------- - -.. automodule:: galaxy.util.inflection - :members: - :undoc-members: - :show-inheritance: - -:mod:`json` Module ------------------- - -.. automodule:: galaxy.util.json - :members: - :undoc-members: - :show-inheritance: - -:mod:`jstree` Module --------------------- - -.. automodule:: galaxy.util.jstree - :members: - :undoc-members: - :show-inheritance: - -:mod:`lazy_process` Module --------------------------- - -.. automodule:: galaxy.util.lazy_process - :members: - :undoc-members: - :show-inheritance: - -:mod:`lrucache` Module ----------------------- - -.. automodule:: galaxy.util.lrucache - :members: - :undoc-members: - :show-inheritance: - -:mod:`none_like` Module ------------------------ - -.. automodule:: galaxy.util.none_like - :members: - :undoc-members: - :show-inheritance: - -:mod:`object_wrapper` Module ----------------------------- - -.. automodule:: galaxy.util.object_wrapper - :members: - :undoc-members: - :show-inheritance: - -:mod:`odict` Module -------------------- - -.. automodule:: galaxy.util.odict - :members: - :undoc-members: - :show-inheritance: - -:mod:`permutations` Module --------------------------- - -.. automodule:: galaxy.util.permutations - :members: - :undoc-members: - :show-inheritance: - -:mod:`plugin_config` Module ---------------------------- - -.. automodule:: galaxy.util.plugin_config - :members: - :undoc-members: - :show-inheritance: - -:mod:`properties` Module ------------------------- - -.. automodule:: galaxy.util.properties - :members: - :undoc-members: - :show-inheritance: - -:mod:`sanitize_html` Module ---------------------------- - -.. automodule:: galaxy.util.sanitize_html - :members: - :undoc-members: - :show-inheritance: - -:mod:`simplegraph` Module -------------------------- - -.. automodule:: galaxy.util.simplegraph - :members: - :undoc-members: - :show-inheritance: - -:mod:`sleeper` Module ---------------------- - -.. automodule:: galaxy.util.sleeper - :members: - :undoc-members: - :show-inheritance: - -:mod:`sockets` Module ---------------------- - -.. automodule:: galaxy.util.sockets - :members: - :undoc-members: - :show-inheritance: - -:mod:`specs` Module -------------------- - -.. automodule:: galaxy.util.specs - :members: - :undoc-members: - :show-inheritance: - -:mod:`sqlite` Module --------------------- - -.. automodule:: galaxy.util.sqlite - :members: - :undoc-members: - :show-inheritance: - -:mod:`streamball` Module ------------------------- - -.. automodule:: galaxy.util.streamball - :members: - :undoc-members: - :show-inheritance: - -:mod:`submodules` Module ------------------------- - -.. automodule:: galaxy.util.submodules - :members: - :undoc-members: - :show-inheritance: - -:mod:`template` Module ----------------------- - -.. automodule:: galaxy.util.template - :members: - :undoc-members: - :show-inheritance: - -:mod:`topsort` Module ---------------------- - -.. automodule:: galaxy.util.topsort - :members: - :undoc-members: - :show-inheritance: - -:mod:`validation` Module ------------------------- - -.. automodule:: galaxy.util.validation - :members: - :undoc-members: - :show-inheritance: - -:mod:`xml_macros` Module ------------------------- - -.. automodule:: galaxy.util.xml_macros - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -282,3 +15,271 @@ Subpackages galaxy.util.log galaxy.util.pastescript +Submodules +---------- + +galaxy.util.aliaspickler module +------------------------------- + +.. automodule:: galaxy.util.aliaspickler + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.biostar module +-------------------------- + +.. automodule:: galaxy.util.biostar + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.bunch module +------------------------ + +.. automodule:: galaxy.util.bunch + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.dbkeys module +------------------------- + +.. automodule:: galaxy.util.dbkeys + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.debugging module +---------------------------- + +.. automodule:: galaxy.util.debugging + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.dictobj module +-------------------------- + +.. automodule:: galaxy.util.dictobj + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.directory_hash module +--------------------------------- + +.. automodule:: galaxy.util.directory_hash + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.expressions module +------------------------------ + +.. automodule:: galaxy.util.expressions + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.hash_util module +---------------------------- + +.. automodule:: galaxy.util.hash_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.heartbeat module +---------------------------- + +.. automodule:: galaxy.util.heartbeat + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.inflection module +----------------------------- + +.. automodule:: galaxy.util.inflection + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.json module +----------------------- + +.. automodule:: galaxy.util.json + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.jstree module +------------------------- + +.. automodule:: galaxy.util.jstree + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.lazy_process module +------------------------------- + +.. automodule:: galaxy.util.lazy_process + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.lrucache module +--------------------------- + +.. automodule:: galaxy.util.lrucache + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.none_like module +---------------------------- + +.. automodule:: galaxy.util.none_like + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.object_wrapper module +--------------------------------- + +.. automodule:: galaxy.util.object_wrapper + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.odict module +------------------------ + +.. automodule:: galaxy.util.odict + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.permutations module +------------------------------- + +.. automodule:: galaxy.util.permutations + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.plugin_config module +-------------------------------- + +.. automodule:: galaxy.util.plugin_config + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.properties module +----------------------------- + +.. automodule:: galaxy.util.properties + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.sanitize_html module +-------------------------------- + +.. automodule:: galaxy.util.sanitize_html + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.simplegraph module +------------------------------ + +.. automodule:: galaxy.util.simplegraph + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.sleeper module +-------------------------- + +.. automodule:: galaxy.util.sleeper + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.sockets module +-------------------------- + +.. automodule:: galaxy.util.sockets + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.specs module +------------------------ + +.. automodule:: galaxy.util.specs + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.sqlite module +------------------------- + +.. automodule:: galaxy.util.sqlite + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.streamball module +----------------------------- + +.. automodule:: galaxy.util.streamball + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.submodules module +----------------------------- + +.. automodule:: galaxy.util.submodules + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.template module +--------------------------- + +.. automodule:: galaxy.util.template + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.topsort module +-------------------------- + +.. automodule:: galaxy.util.topsort + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.validation module +----------------------------- + +.. automodule:: galaxy.util.validation + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.xml_macros module +----------------------------- + +.. automodule:: galaxy.util.xml_macros + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst b/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst index 7d51bfb4f84..26b7cb913ca 100644 --- a/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst +++ b/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst @@ -1,43 +1,44 @@ -phyloviz Package -================ - -:mod:`phyloviz` Package ------------------------ +galaxy.visualization.data_providers.phyloviz package +==================================================== .. automodule:: galaxy.visualization.data_providers.phyloviz :members: :undoc-members: :show-inheritance: -:mod:`baseparser` Module ------------------------- +Submodules +---------- + +galaxy.visualization.data_providers.phyloviz.baseparser module +-------------------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.phyloviz.baseparser :members: :undoc-members: :show-inheritance: -:mod:`newickparser` Module --------------------------- +galaxy.visualization.data_providers.phyloviz.newickparser module +---------------------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.phyloviz.newickparser :members: :undoc-members: :show-inheritance: -:mod:`nexusparser` Module -------------------------- +galaxy.visualization.data_providers.phyloviz.nexusparser module +--------------------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.phyloviz.nexusparser :members: :undoc-members: :show-inheritance: -:mod:`phyloxmlparser` Module ----------------------------- +galaxy.visualization.data_providers.phyloviz.phyloxmlparser module +------------------------------------------------------------------ .. automodule:: galaxy.visualization.data_providers.phyloviz.phyloxmlparser :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.visualization.data_providers.rst b/doc/source/lib/galaxy.visualization.data_providers.rst index ba55a961528..3180ac79181 100644 --- a/doc/source/lib/galaxy.visualization.data_providers.rst +++ b/doc/source/lib/galaxy.visualization.data_providers.rst @@ -1,46 +1,11 @@ -data_providers Package -====================== - -:mod:`data_providers` Package ------------------------------ +galaxy.visualization.data_providers package +=========================================== .. automodule:: galaxy.visualization.data_providers :members: :undoc-members: :show-inheritance: -:mod:`basic` Module -------------------- - -.. automodule:: galaxy.visualization.data_providers.basic - :members: - :undoc-members: - :show-inheritance: - -:mod:`cigar` Module -------------------- - -.. automodule:: galaxy.visualization.data_providers.cigar - :members: - :undoc-members: - :show-inheritance: - -:mod:`genome` Module --------------------- - -.. automodule:: galaxy.visualization.data_providers.genome - :members: - :undoc-members: - :show-inheritance: - -:mod:`registry` Module ----------------------- - -.. automodule:: galaxy.visualization.data_providers.registry - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -48,3 +13,39 @@ Subpackages galaxy.visualization.data_providers.phyloviz +Submodules +---------- + +galaxy.visualization.data_providers.basic module +------------------------------------------------ + +.. automodule:: galaxy.visualization.data_providers.basic + :members: + :undoc-members: + :show-inheritance: + +galaxy.visualization.data_providers.cigar module +------------------------------------------------ + +.. automodule:: galaxy.visualization.data_providers.cigar + :members: + :undoc-members: + :show-inheritance: + +galaxy.visualization.data_providers.genome module +------------------------------------------------- + +.. automodule:: galaxy.visualization.data_providers.genome + :members: + :undoc-members: + :show-inheritance: + +galaxy.visualization.data_providers.registry module +--------------------------------------------------- + +.. automodule:: galaxy.visualization.data_providers.registry + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.visualization.genome.rst b/doc/source/lib/galaxy.visualization.genome.rst index 8e880dd6b5f..9097529321c 100644 --- a/doc/source/lib/galaxy.visualization.genome.rst +++ b/doc/source/lib/galaxy.visualization.genome.rst @@ -1,8 +1,5 @@ -genome Package -============== - -:mod:`genome` Package ---------------------- +galaxy.visualization.genome package +=================================== .. automodule:: galaxy.visualization.genome :members: diff --git a/doc/source/lib/galaxy.visualization.plugins.rst b/doc/source/lib/galaxy.visualization.plugins.rst index d276f6d2c32..b8ded7d9b6d 100644 --- a/doc/source/lib/galaxy.visualization.plugins.rst +++ b/doc/source/lib/galaxy.visualization.plugins.rst @@ -1,43 +1,52 @@ -plugins Package -=============== +galaxy.visualization.plugins package +==================================== -:mod:`config_parser` Module ---------------------------- +.. automodule:: galaxy.visualization.plugins + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.visualization.plugins.config_parser module +------------------------------------------------- .. automodule:: galaxy.visualization.plugins.config_parser :members: :undoc-members: :show-inheritance: -:mod:`plugin` Module --------------------- +galaxy.visualization.plugins.plugin module +------------------------------------------ .. automodule:: galaxy.visualization.plugins.plugin :members: :undoc-members: :show-inheritance: -:mod:`registry` Module ----------------------- +galaxy.visualization.plugins.registry module +-------------------------------------------- .. automodule:: galaxy.visualization.plugins.registry :members: :undoc-members: :show-inheritance: -:mod:`resource_parser` Module ------------------------------ +galaxy.visualization.plugins.resource_parser module +--------------------------------------------------- .. automodule:: galaxy.visualization.plugins.resource_parser :members: :undoc-members: :show-inheritance: -:mod:`utils` Module -------------------- +galaxy.visualization.plugins.utils module +----------------------------------------- .. automodule:: galaxy.visualization.plugins.utils :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.visualization.rst b/doc/source/lib/galaxy.visualization.rst index ba80d9719ce..1f334499e29 100644 --- a/doc/source/lib/galaxy.visualization.rst +++ b/doc/source/lib/galaxy.visualization.rst @@ -1,22 +1,11 @@ -visualization Package -===================== - -:mod:`visualization` Package ----------------------------- +galaxy.visualization package +============================ .. automodule:: galaxy.visualization :members: :undoc-members: :show-inheritance: -:mod:`genomes` Module ---------------------- - -.. automodule:: galaxy.visualization.genomes - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -27,3 +16,15 @@ Subpackages galaxy.visualization.plugins galaxy.visualization.tracks +Submodules +---------- + +galaxy.visualization.genomes module +----------------------------------- + +.. automodule:: galaxy.visualization.genomes + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.visualization.tracks.rst b/doc/source/lib/galaxy.visualization.tracks.rst index 9823b4191df..2d279399ef6 100644 --- a/doc/source/lib/galaxy.visualization.tracks.rst +++ b/doc/source/lib/galaxy.visualization.tracks.rst @@ -1,8 +1,5 @@ -tracks Package -============== - -:mod:`tracks` Package ---------------------- +galaxy.visualization.tracks package +=================================== .. automodule:: galaxy.visualization.tracks :members: diff --git a/doc/source/lib/galaxy.web.base.controllers.rst b/doc/source/lib/galaxy.web.base.controllers.rst index a37900b0aa5..6c153a18d4d 100644 --- a/doc/source/lib/galaxy.web.base.controllers.rst +++ b/doc/source/lib/galaxy.web.base.controllers.rst @@ -1,11 +1,20 @@ -controllers Package -=================== +galaxy.web.base.controllers package +=================================== -:mod:`admin` Module -------------------- +.. automodule:: galaxy.web.base.controllers + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.web.base.controllers.admin module +---------------------------------------- .. automodule:: galaxy.web.base.controllers.admin :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.web.base.rst b/doc/source/lib/galaxy.web.base.rst index 8b12d23d8c2..3ac90729275 100644 --- a/doc/source/lib/galaxy.web.base.rst +++ b/doc/source/lib/galaxy.web.base.rst @@ -1,26 +1,7 @@ -base Package -============ +galaxy.web.base package +======================= -:mod:`controller` Module ------------------------- - -.. automodule:: galaxy.web.base.controller - :members: - :undoc-members: - :show-inheritance: - -:mod:`interactive_environments` Module --------------------------------------- - -.. automodule:: galaxy.web.base.interactive_environments - :members: - :undoc-members: - :show-inheritance: - -:mod:`pluginframework` Module ------------------------------ - -.. automodule:: galaxy.web.base.pluginframework +.. automodule:: galaxy.web.base :members: :undoc-members: :show-inheritance: @@ -32,3 +13,31 @@ Subpackages galaxy.web.base.controllers +Submodules +---------- + +galaxy.web.base.controller module +--------------------------------- + +.. automodule:: galaxy.web.base.controller + :members: + :undoc-members: + :show-inheritance: + +galaxy.web.base.interactive_environments module +----------------------------------------------- + +.. automodule:: galaxy.web.base.interactive_environments + :members: + :undoc-members: + :show-inheritance: + +galaxy.web.base.pluginframework module +-------------------------------------- + +.. automodule:: galaxy.web.base.pluginframework + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.web.framework.helpers.rst b/doc/source/lib/galaxy.web.framework.helpers.rst index 690122ac045..d1916931133 100644 --- a/doc/source/lib/galaxy.web.framework.helpers.rst +++ b/doc/source/lib/galaxy.web.framework.helpers.rst @@ -1,19 +1,20 @@ -helpers Package -=============== - -:mod:`helpers` Package ----------------------- +galaxy.web.framework.helpers package +==================================== .. automodule:: galaxy.web.framework.helpers :members: :undoc-members: :show-inheritance: -:mod:`grids` Module -------------------- +Submodules +---------- + +galaxy.web.framework.helpers.grids module +----------------------------------------- .. automodule:: galaxy.web.framework.helpers.grids :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.web.framework.middleware.rst b/doc/source/lib/galaxy.web.framework.middleware.rst index ddaff84b275..3eb2cbe0ed2 100644 --- a/doc/source/lib/galaxy.web.framework.middleware.rst +++ b/doc/source/lib/galaxy.web.framework.middleware.rst @@ -1,75 +1,76 @@ -middleware Package -================== - -:mod:`middleware` Package -------------------------- +galaxy.web.framework.middleware package +======================================= .. automodule:: galaxy.web.framework.middleware :members: :undoc-members: :show-inheritance: -:mod:`error` Module -------------------- +Submodules +---------- + +galaxy.web.framework.middleware.error module +-------------------------------------------- .. automodule:: galaxy.web.framework.middleware.error :members: :undoc-members: :show-inheritance: -:mod:`profile` Module ---------------------- +galaxy.web.framework.middleware.profile module +---------------------------------------------- .. automodule:: galaxy.web.framework.middleware.profile :members: :undoc-members: :show-inheritance: -:mod:`remoteuser` Module ------------------------- +galaxy.web.framework.middleware.remoteuser module +------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.remoteuser :members: :undoc-members: :show-inheritance: -:mod:`request_id` Module ------------------------- +galaxy.web.framework.middleware.request_id module +------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.request_id :members: :undoc-members: :show-inheritance: -:mod:`sentry` Module --------------------- +galaxy.web.framework.middleware.sentry module +--------------------------------------------- .. automodule:: galaxy.web.framework.middleware.sentry :members: :undoc-members: :show-inheritance: -:mod:`static` Module --------------------- +galaxy.web.framework.middleware.static module +--------------------------------------------- .. automodule:: galaxy.web.framework.middleware.static :members: :undoc-members: :show-inheritance: -:mod:`translogger` Module -------------------------- +galaxy.web.framework.middleware.translogger module +-------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.translogger :members: :undoc-members: :show-inheritance: -:mod:`xforwardedhost` Module ----------------------------- +galaxy.web.framework.middleware.xforwardedhost module +----------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.xforwardedhost :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.web.framework.rst b/doc/source/lib/galaxy.web.framework.rst index 7e02bd99e5b..f6357d01eb2 100644 --- a/doc/source/lib/galaxy.web.framework.rst +++ b/doc/source/lib/galaxy.web.framework.rst @@ -1,54 +1,11 @@ -framework Package -================= - -:mod:`framework` Package ------------------------- +galaxy.web.framework package +============================ .. automodule:: galaxy.web.framework :members: :undoc-members: :show-inheritance: -:mod:`base` Module ------------------- - -.. automodule:: galaxy.web.framework.base - :members: - :undoc-members: - :show-inheritance: - -:mod:`decorators` Module ------------------------- - -.. automodule:: galaxy.web.framework.decorators - :members: - :undoc-members: - :show-inheritance: - -:mod:`formbuilder` Module -------------------------- - -.. automodule:: galaxy.web.framework.formbuilder - :members: - :undoc-members: - :show-inheritance: - -:mod:`openid_manager` Module ----------------------------- - -.. automodule:: galaxy.web.framework.openid_manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`webapp` Module --------------------- - -.. automodule:: galaxy.web.framework.webapp - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -57,3 +14,47 @@ Subpackages galaxy.web.framework.helpers galaxy.web.framework.middleware +Submodules +---------- + +galaxy.web.framework.base module +-------------------------------- + +.. automodule:: galaxy.web.framework.base + :members: + :undoc-members: + :show-inheritance: + +galaxy.web.framework.decorators module +-------------------------------------- + +.. automodule:: galaxy.web.framework.decorators + :members: + :undoc-members: + :show-inheritance: + +galaxy.web.framework.formbuilder module +--------------------------------------- + +.. automodule:: galaxy.web.framework.formbuilder + :members: + :undoc-members: + :show-inheritance: + +galaxy.web.framework.openid_manager module +------------------------------------------ + +.. automodule:: galaxy.web.framework.openid_manager + :members: + :undoc-members: + :show-inheritance: + +galaxy.web.framework.webapp module +---------------------------------- + +.. automodule:: galaxy.web.framework.webapp + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.web.proxy.rst b/doc/source/lib/galaxy.web.proxy.rst index a9f49e364e8..53c7c4bbca7 100644 --- a/doc/source/lib/galaxy.web.proxy.rst +++ b/doc/source/lib/galaxy.web.proxy.rst @@ -1,19 +1,20 @@ -proxy Package -============= - -:mod:`proxy` Package --------------------- +galaxy.web.proxy package +======================== .. automodule:: galaxy.web.proxy :members: :undoc-members: :show-inheritance: -:mod:`filelock` Module ----------------------- +Submodules +---------- + +galaxy.web.proxy.filelock module +-------------------------------- .. automodule:: galaxy.web.proxy.filelock :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.web.rst b/doc/source/lib/galaxy.web.rst index 5d721616340..762db65e65b 100644 --- a/doc/source/lib/galaxy.web.rst +++ b/doc/source/lib/galaxy.web.rst @@ -1,46 +1,11 @@ -web Package -=========== - -:mod:`web` Package ------------------- +galaxy.web package +================== .. automodule:: galaxy.web :members: :undoc-members: :show-inheritance: -:mod:`buildapp` Module ----------------------- - -.. automodule:: galaxy.web.buildapp - :members: - :undoc-members: - :show-inheritance: - -:mod:`form_builder` Module --------------------------- - -.. automodule:: galaxy.web.form_builder - :members: - :undoc-members: - :show-inheritance: - -:mod:`formatting` Module ------------------------- - -.. automodule:: galaxy.web.formatting - :members: - :undoc-members: - :show-inheritance: - -:mod:`params` Module --------------------- - -.. automodule:: galaxy.web.params - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -51,3 +16,39 @@ Subpackages galaxy.web.proxy galaxy.web.security +Submodules +---------- + +galaxy.web.buildapp module +-------------------------- + +.. automodule:: galaxy.web.buildapp + :members: + :undoc-members: + :show-inheritance: + +galaxy.web.form_builder module +------------------------------ + +.. automodule:: galaxy.web.form_builder + :members: + :undoc-members: + :show-inheritance: + +galaxy.web.formatting module +---------------------------- + +.. automodule:: galaxy.web.formatting + :members: + :undoc-members: + :show-inheritance: + +galaxy.web.params module +------------------------ + +.. automodule:: galaxy.web.params + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.web.security.rst b/doc/source/lib/galaxy.web.security.rst index 2904ea1e5cb..276b543abb7 100644 --- a/doc/source/lib/galaxy.web.security.rst +++ b/doc/source/lib/galaxy.web.security.rst @@ -1,8 +1,5 @@ -security Package -================ - -:mod:`security` Package ------------------------ +galaxy.web.security package +=========================== .. automodule:: galaxy.web.security :members: diff --git a/doc/source/lib/galaxy.webapps.galaxy.api.rst b/doc/source/lib/galaxy.webapps.galaxy.api.rst index 5ff9d716e45..657035ef368 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -1,315 +1,324 @@ galaxy.webapps.galaxy.api package ================================= -:mod:`annotations` Module -------------------------- +.. automodule:: galaxy.webapps.galaxy.api + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.webapps.galaxy.api.annotations module +-------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.annotations :members: :undoc-members: :show-inheritance: -:mod:`authenticate` Module --------------------------- +galaxy.webapps.galaxy.api.authenticate module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.authenticate :members: :undoc-members: :show-inheritance: -:mod:`configuration` Module ---------------------------- +galaxy.webapps.galaxy.api.configuration module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.configuration :members: :undoc-members: :show-inheritance: -:mod:`dataset_collections` Module ---------------------------------- +galaxy.webapps.galaxy.api.dataset_collections module +---------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.dataset_collections :members: :undoc-members: :show-inheritance: -:mod:`datasets` Module ----------------------- +galaxy.webapps.galaxy.api.datasets module +----------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.datasets :members: :undoc-members: :show-inheritance: -:mod:`datatypes` Module ------------------------ +galaxy.webapps.galaxy.api.datatypes module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.datatypes :members: :undoc-members: :show-inheritance: -:mod:`extended_metadata` Module -------------------------------- +galaxy.webapps.galaxy.api.extended_metadata module +-------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.extended_metadata :members: :undoc-members: :show-inheritance: -:mod:`folder_contents` Module ------------------------------ +galaxy.webapps.galaxy.api.folder_contents module +------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.folder_contents :members: :undoc-members: :show-inheritance: -:mod:`folders` Module ---------------------- +galaxy.webapps.galaxy.api.folders module +---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.folders :members: :undoc-members: :show-inheritance: -:mod:`forms` Module -------------------- +galaxy.webapps.galaxy.api.forms module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.forms :members: :undoc-members: :show-inheritance: -:mod:`genomes` Module ---------------------- +galaxy.webapps.galaxy.api.genomes module +---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.genomes :members: :undoc-members: :show-inheritance: -:mod:`group_roles` Module -------------------------- +galaxy.webapps.galaxy.api.group_roles module +-------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.group_roles :members: :undoc-members: :show-inheritance: -:mod:`group_users` Module -------------------------- +galaxy.webapps.galaxy.api.group_users module +-------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.group_users :members: :undoc-members: :show-inheritance: -:mod:`groups` Module --------------------- +galaxy.webapps.galaxy.api.groups module +--------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.groups :members: :undoc-members: :show-inheritance: -:mod:`histories` Module ------------------------ +galaxy.webapps.galaxy.api.histories module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.histories :members: :undoc-members: :show-inheritance: -:mod:`history_contents` Module ------------------------------- +galaxy.webapps.galaxy.api.history_contents module +------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.history_contents :members: :undoc-members: :show-inheritance: -:mod:`item_tags` Module ------------------------ +galaxy.webapps.galaxy.api.item_tags module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.item_tags :members: :undoc-members: :show-inheritance: -:mod:`job_files` Module ------------------------ +galaxy.webapps.galaxy.api.job_files module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.job_files :members: :undoc-members: :show-inheritance: -:mod:`jobs` Module ------------------- +galaxy.webapps.galaxy.api.jobs module +------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.jobs :members: :undoc-members: :show-inheritance: -:mod:`lda_datasets` Module --------------------------- +galaxy.webapps.galaxy.api.lda_datasets module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.lda_datasets :members: :undoc-members: :show-inheritance: -:mod:`libraries` Module ------------------------ +galaxy.webapps.galaxy.api.libraries module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.libraries :members: :undoc-members: :show-inheritance: -:mod:`library_contents` Module ------------------------------- +galaxy.webapps.galaxy.api.library_contents module +------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.library_contents :members: :undoc-members: :show-inheritance: -:mod:`metrics` Module ---------------------- +galaxy.webapps.galaxy.api.metrics module +---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.metrics :members: :undoc-members: :show-inheritance: -:mod:`page_revisions` Module ----------------------------- +galaxy.webapps.galaxy.api.page_revisions module +----------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.page_revisions :members: :undoc-members: :show-inheritance: -:mod:`pages` Module -------------------- +galaxy.webapps.galaxy.api.pages module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.pages :members: :undoc-members: :show-inheritance: -:mod:`provenance` Module ------------------------- +galaxy.webapps.galaxy.api.provenance module +------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.provenance :members: :undoc-members: :show-inheritance: -:mod:`quotas` Module --------------------- +galaxy.webapps.galaxy.api.quotas module +--------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.quotas :members: :undoc-members: :show-inheritance: -:mod:`remote_files` Module --------------------------- +galaxy.webapps.galaxy.api.remote_files module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.remote_files :members: :undoc-members: :show-inheritance: -:mod:`request_types` Module ---------------------------- +galaxy.webapps.galaxy.api.request_types module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.request_types :members: :undoc-members: :show-inheritance: -:mod:`requests` Module ----------------------- +galaxy.webapps.galaxy.api.requests module +----------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.requests :members: :undoc-members: :show-inheritance: -:mod:`roles` Module -------------------- +galaxy.webapps.galaxy.api.roles module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.roles :members: :undoc-members: :show-inheritance: -:mod:`samples` Module ---------------------- +galaxy.webapps.galaxy.api.samples module +---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.samples :members: :undoc-members: :show-inheritance: -:mod:`search` Module --------------------- +galaxy.webapps.galaxy.api.search module +--------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.search :members: :undoc-members: :show-inheritance: -:mod:`tool_data` Module ------------------------ +galaxy.webapps.galaxy.api.tool_data module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.tool_data :members: :undoc-members: :show-inheritance: -:mod:`tool_shed_repositories` Module ------------------------------------- +galaxy.webapps.galaxy.api.tool_shed_repositories module +------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tool_shed_repositories :members: :undoc-members: :show-inheritance: -:mod:`tools` Module -------------------- +galaxy.webapps.galaxy.api.tools module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tools :members: :undoc-members: :show-inheritance: -:mod:`users` Module -------------------- +galaxy.webapps.galaxy.api.users module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.users :members: :undoc-members: :show-inheritance: -:mod:`visualizations` Module ----------------------------- +galaxy.webapps.galaxy.api.visualizations module +----------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.visualizations :members: :undoc-members: :show-inheritance: -:mod:`workflows` Module ------------------------ +galaxy.webapps.galaxy.api.workflows module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.workflows :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst index 3b870bf2092..5a59cc4af81 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst @@ -1,251 +1,252 @@ -controllers Package -=================== - -:mod:`controllers` Package --------------------------- +galaxy.webapps.galaxy.controllers package +========================================= .. automodule:: galaxy.webapps.galaxy.controllers :members: :undoc-members: :show-inheritance: -:mod:`admin` Module -------------------- +Submodules +---------- + +galaxy.webapps.galaxy.controllers.admin module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.admin :members: :undoc-members: :show-inheritance: -:mod:`admin_toolshed` Module ----------------------------- +galaxy.webapps.galaxy.controllers.admin_toolshed module +------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.admin_toolshed :members: :undoc-members: :show-inheritance: -:mod:`async` Module -------------------- +galaxy.webapps.galaxy.controllers.async module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.async :members: :undoc-members: :show-inheritance: -:mod:`biostar` Module ---------------------- +galaxy.webapps.galaxy.controllers.biostar module +------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.biostar :members: :undoc-members: :show-inheritance: -:mod:`cloudlaunch` Module -------------------------- +galaxy.webapps.galaxy.controllers.cloudlaunch module +---------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.cloudlaunch :members: :undoc-members: :show-inheritance: -:mod:`data_manager` Module --------------------------- +galaxy.webapps.galaxy.controllers.data_manager module +----------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.data_manager :members: :undoc-members: :show-inheritance: -:mod:`dataset` Module ---------------------- +galaxy.webapps.galaxy.controllers.dataset module +------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.dataset :members: :undoc-members: :show-inheritance: -:mod:`error` Module -------------------- +galaxy.webapps.galaxy.controllers.error module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.error :members: :undoc-members: :show-inheritance: -:mod:`external_service` Module ------------------------------- +galaxy.webapps.galaxy.controllers.external_service module +--------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.external_service :members: :undoc-members: :show-inheritance: -:mod:`external_services` Module -------------------------------- +galaxy.webapps.galaxy.controllers.external_services module +---------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.external_services :members: :undoc-members: :show-inheritance: -:mod:`forms` Module -------------------- +galaxy.webapps.galaxy.controllers.forms module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.forms :members: :undoc-members: :show-inheritance: -:mod:`history` Module ---------------------- +galaxy.webapps.galaxy.controllers.history module +------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.history :members: :undoc-members: :show-inheritance: -:mod:`library` Module ---------------------- +galaxy.webapps.galaxy.controllers.library module +------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.library :members: :undoc-members: :show-inheritance: -:mod:`library_admin` Module ---------------------------- +galaxy.webapps.galaxy.controllers.library_admin module +------------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.library_admin :members: :undoc-members: :show-inheritance: -:mod:`library_common` Module ----------------------------- +galaxy.webapps.galaxy.controllers.library_common module +------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.library_common :members: :undoc-members: :show-inheritance: -:mod:`mobile` Module --------------------- +galaxy.webapps.galaxy.controllers.mobile module +----------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.mobile :members: :undoc-members: :show-inheritance: -:mod:`page` Module ------------------- +galaxy.webapps.galaxy.controllers.page module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.page :members: :undoc-members: :show-inheritance: -:mod:`request_type` Module --------------------------- +galaxy.webapps.galaxy.controllers.request_type module +----------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.request_type :members: :undoc-members: :show-inheritance: -:mod:`requests` Module ----------------------- +galaxy.webapps.galaxy.controllers.requests module +------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.requests :members: :undoc-members: :show-inheritance: -:mod:`requests_admin` Module ----------------------------- +galaxy.webapps.galaxy.controllers.requests_admin module +------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.requests_admin :members: :undoc-members: :show-inheritance: -:mod:`requests_common` Module ------------------------------ +galaxy.webapps.galaxy.controllers.requests_common module +-------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.requests_common :members: :undoc-members: :show-inheritance: -:mod:`root` Module ------------------- +galaxy.webapps.galaxy.controllers.root module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.root :members: :undoc-members: :show-inheritance: -:mod:`search` Module --------------------- +galaxy.webapps.galaxy.controllers.search module +----------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.search :members: :undoc-members: :show-inheritance: -:mod:`tag` Module ------------------ +galaxy.webapps.galaxy.controllers.tag module +-------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.tag :members: :undoc-members: :show-inheritance: -:mod:`tool_runner` Module -------------------------- +galaxy.webapps.galaxy.controllers.tool_runner module +---------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.tool_runner :members: :undoc-members: :show-inheritance: -:mod:`ucsc_proxy` Module ------------------------- +galaxy.webapps.galaxy.controllers.ucsc_proxy module +--------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.ucsc_proxy :members: :undoc-members: :show-inheritance: -:mod:`user` Module ------------------- +galaxy.webapps.galaxy.controllers.user module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.user :members: :undoc-members: :show-inheritance: -:mod:`userskeys` Module ------------------------ +galaxy.webapps.galaxy.controllers.userskeys module +-------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.userskeys :members: :undoc-members: :show-inheritance: -:mod:`visualization` Module ---------------------------- +galaxy.webapps.galaxy.controllers.visualization module +------------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.visualization :members: :undoc-members: :show-inheritance: -:mod:`workflow` Module ----------------------- +galaxy.webapps.galaxy.controllers.workflow module +------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.workflow :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.webapps.galaxy.rst b/doc/source/lib/galaxy.webapps.galaxy.rst index 42642bec26c..5256155b1ed 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.rst @@ -1,10 +1,7 @@ -galaxy Package -============== +galaxy.webapps.galaxy package +============================= -:mod:`buildapp` Module ----------------------- - -.. automodule:: galaxy.webapps.galaxy.buildapp +.. automodule:: galaxy.webapps.galaxy :members: :undoc-members: :show-inheritance: @@ -17,3 +14,15 @@ Subpackages galaxy.webapps.galaxy.api galaxy.webapps.galaxy.controllers +Submodules +---------- + +galaxy.webapps.galaxy.buildapp module +------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.buildapp + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.webapps.reports.controllers.rst b/doc/source/lib/galaxy.webapps.reports.controllers.rst index 72e2b6da340..122b8e286ba 100644 --- a/doc/source/lib/galaxy.webapps.reports.controllers.rst +++ b/doc/source/lib/galaxy.webapps.reports.controllers.rst @@ -1,67 +1,68 @@ -controllers Package -=================== - -:mod:`controllers` Package --------------------------- +galaxy.webapps.reports.controllers package +========================================== .. automodule:: galaxy.webapps.reports.controllers :members: :undoc-members: :show-inheritance: -:mod:`jobs` Module ------------------- +Submodules +---------- + +galaxy.webapps.reports.controllers.jobs module +---------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.jobs :members: :undoc-members: :show-inheritance: -:mod:`query` Module -------------------- +galaxy.webapps.reports.controllers.query module +----------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.query :members: :undoc-members: :show-inheritance: -:mod:`root` Module ------------------- +galaxy.webapps.reports.controllers.root module +---------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.root :members: :undoc-members: :show-inheritance: -:mod:`sample_tracking` Module ------------------------------ +galaxy.webapps.reports.controllers.sample_tracking module +--------------------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.sample_tracking :members: :undoc-members: :show-inheritance: -:mod:`system` Module --------------------- +galaxy.webapps.reports.controllers.system module +------------------------------------------------ .. automodule:: galaxy.webapps.reports.controllers.system :members: :undoc-members: :show-inheritance: -:mod:`users` Module -------------------- +galaxy.webapps.reports.controllers.users module +----------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.users :members: :undoc-members: :show-inheritance: -:mod:`workflows` Module ------------------------ +galaxy.webapps.reports.controllers.workflows module +--------------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.workflows :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.webapps.reports.rst b/doc/source/lib/galaxy.webapps.reports.rst index 59231f71951..8e9fff62be8 100644 --- a/doc/source/lib/galaxy.webapps.reports.rst +++ b/doc/source/lib/galaxy.webapps.reports.rst @@ -1,38 +1,11 @@ -reports Package -=============== - -:mod:`reports` Package ----------------------- +galaxy.webapps.reports package +============================== .. automodule:: galaxy.webapps.reports :members: :undoc-members: :show-inheritance: -:mod:`app` Module ------------------ - -.. automodule:: galaxy.webapps.reports.app - :members: - :undoc-members: - :show-inheritance: - -:mod:`buildapp` Module ----------------------- - -.. automodule:: galaxy.webapps.reports.buildapp - :members: - :undoc-members: - :show-inheritance: - -:mod:`config` Module --------------------- - -.. automodule:: galaxy.webapps.reports.config - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -40,3 +13,31 @@ Subpackages galaxy.webapps.reports.controllers +Submodules +---------- + +galaxy.webapps.reports.app module +--------------------------------- + +.. automodule:: galaxy.webapps.reports.app + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.reports.buildapp module +-------------------------------------- + +.. automodule:: galaxy.webapps.reports.buildapp + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.reports.config module +------------------------------------ + +.. automodule:: galaxy.webapps.reports.config + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.webapps.rst b/doc/source/lib/galaxy.webapps.rst index 7b0597ba68c..2e301191c77 100644 --- a/doc/source/lib/galaxy.webapps.rst +++ b/doc/source/lib/galaxy.webapps.rst @@ -1,8 +1,5 @@ -webapps Package -=============== - -:mod:`webapps` Package ----------------------- +galaxy.webapps package +====================== .. automodule:: galaxy.webapps :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.api.rst b/doc/source/lib/galaxy.webapps.tool_shed.api.rst index 98dae6f2fd8..ae4c3b45f24 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.api.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.api.rst @@ -1,59 +1,68 @@ -api Package -=========== +galaxy.webapps.tool_shed.api package +==================================== -:mod:`authenticate` Module --------------------------- +.. automodule:: galaxy.webapps.tool_shed.api + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.webapps.tool_shed.api.authenticate module +------------------------------------------------ .. automodule:: galaxy.webapps.tool_shed.api.authenticate :members: :undoc-members: :show-inheritance: -:mod:`categories` Module ------------------------- +galaxy.webapps.tool_shed.api.categories module +---------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.categories :members: :undoc-members: :show-inheritance: -:mod:`groups` Module --------------------- +galaxy.webapps.tool_shed.api.groups module +------------------------------------------ .. automodule:: galaxy.webapps.tool_shed.api.groups :members: :undoc-members: :show-inheritance: -:mod:`repositories` Module --------------------------- +galaxy.webapps.tool_shed.api.repositories module +------------------------------------------------ .. automodule:: galaxy.webapps.tool_shed.api.repositories :members: :undoc-members: :show-inheritance: -:mod:`repository_revisions` Module ----------------------------------- +galaxy.webapps.tool_shed.api.repository_revisions module +-------------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.repository_revisions :members: :undoc-members: :show-inheritance: -:mod:`tools` Module -------------------- +galaxy.webapps.tool_shed.api.tools module +----------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.tools :members: :undoc-members: :show-inheritance: -:mod:`users` Module -------------------- +galaxy.webapps.tool_shed.api.users module +----------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.users :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst b/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst index 986d7fe3f57..6e9e7914c46 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst @@ -1,67 +1,68 @@ -controllers Package -=================== - -:mod:`controllers` Package --------------------------- +galaxy.webapps.tool_shed.controllers package +============================================ .. automodule:: galaxy.webapps.tool_shed.controllers :members: :undoc-members: :show-inheritance: -:mod:`admin` Module -------------------- +Submodules +---------- + +galaxy.webapps.tool_shed.controllers.admin module +------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.admin :members: :undoc-members: :show-inheritance: -:mod:`groups` Module --------------------- +galaxy.webapps.tool_shed.controllers.groups module +-------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.groups :members: :undoc-members: :show-inheritance: -:mod:`hg` Module ----------------- +galaxy.webapps.tool_shed.controllers.hg module +---------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.hg :members: :undoc-members: :show-inheritance: -:mod:`repository` Module ------------------------- +galaxy.webapps.tool_shed.controllers.repository module +------------------------------------------------------ .. automodule:: galaxy.webapps.tool_shed.controllers.repository :members: :undoc-members: :show-inheritance: -:mod:`repository_review` Module -------------------------------- +galaxy.webapps.tool_shed.controllers.repository_review module +------------------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.repository_review :members: :undoc-members: :show-inheritance: -:mod:`upload` Module --------------------- +galaxy.webapps.tool_shed.controllers.upload module +-------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.upload :members: :undoc-members: :show-inheritance: -:mod:`user` Module ------------------- +galaxy.webapps.tool_shed.controllers.user module +------------------------------------------------ .. automodule:: galaxy.webapps.tool_shed.controllers.user :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst b/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst index 4de7ea427c2..361baef5268 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst @@ -1,27 +1,28 @@ -middleware Package -================== - -:mod:`middleware` Package -------------------------- +galaxy.webapps.tool_shed.framework.middleware package +===================================================== .. automodule:: galaxy.webapps.tool_shed.framework.middleware :members: :undoc-members: :show-inheritance: -:mod:`hg` Module ----------------- +Submodules +---------- + +galaxy.webapps.tool_shed.framework.middleware.hg module +------------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.framework.middleware.hg :members: :undoc-members: :show-inheritance: -:mod:`remoteuser` Module ------------------------- +galaxy.webapps.tool_shed.framework.middleware.remoteuser module +--------------------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.framework.middleware.remoteuser :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.webapps.tool_shed.framework.rst b/doc/source/lib/galaxy.webapps.tool_shed.framework.rst index d0f4b8abdf8..0276dcbd1c4 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.framework.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.framework.rst @@ -1,8 +1,5 @@ -framework Package -================= - -:mod:`framework` Package ------------------------- +galaxy.webapps.tool_shed.framework package +========================================== .. automodule:: galaxy.webapps.tool_shed.framework :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst b/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst index 2d4197c30a3..9fd4bd531e8 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst @@ -1,11 +1,20 @@ -migrate Package -=============== +galaxy.webapps.tool_shed.model.migrate package +============================================== -:mod:`check` Module -------------------- +.. automodule:: galaxy.webapps.tool_shed.model.migrate + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.webapps.tool_shed.model.migrate.check module +--------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.model.migrate.check :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.webapps.tool_shed.model.rst b/doc/source/lib/galaxy.webapps.tool_shed.model.rst index 429f0d57917..bc60bd734c3 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.model.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.model.rst @@ -1,22 +1,11 @@ -model Package -============= - -:mod:`model` Package --------------------- +galaxy.webapps.tool_shed.model package +====================================== .. automodule:: galaxy.webapps.tool_shed.model :members: :undoc-members: :show-inheritance: -:mod:`mapping` Module ---------------------- - -.. automodule:: galaxy.webapps.tool_shed.model.mapping - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -24,3 +13,15 @@ Subpackages galaxy.webapps.tool_shed.model.migrate +Submodules +---------- + +galaxy.webapps.tool_shed.model.mapping module +--------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.mapping + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.webapps.tool_shed.rst b/doc/source/lib/galaxy.webapps.tool_shed.rst index e358e871712..836aa571014 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.rst @@ -1,38 +1,11 @@ -tool_shed Package -================= - -:mod:`tool_shed` Package ------------------------- +galaxy.webapps.tool_shed package +================================ .. automodule:: galaxy.webapps.tool_shed :members: :undoc-members: :show-inheritance: -:mod:`app` Module ------------------ - -.. automodule:: galaxy.webapps.tool_shed.app - :members: - :undoc-members: - :show-inheritance: - -:mod:`buildapp` Module ----------------------- - -.. automodule:: galaxy.webapps.tool_shed.buildapp - :members: - :undoc-members: - :show-inheritance: - -:mod:`config` Module --------------------- - -.. automodule:: galaxy.webapps.tool_shed.config - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -46,3 +19,31 @@ Subpackages galaxy.webapps.tool_shed.security galaxy.webapps.tool_shed.util +Submodules +---------- + +galaxy.webapps.tool_shed.app module +----------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.app + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool_shed.buildapp module +---------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.buildapp + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool_shed.config module +-------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.config + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.webapps.tool_shed.search.rst b/doc/source/lib/galaxy.webapps.tool_shed.search.rst index 78ccaa6cffb..9daeff111f0 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.search.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.search.rst @@ -1,19 +1,28 @@ -search Package -============== +galaxy.webapps.tool_shed.search package +======================================= -:mod:`repo_search` Module -------------------------- +.. automodule:: galaxy.webapps.tool_shed.search + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.webapps.tool_shed.search.repo_search module +-------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.search.repo_search :members: :undoc-members: :show-inheritance: -:mod:`tool_search` Module -------------------------- +galaxy.webapps.tool_shed.search.tool_search module +-------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.search.tool_search :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.webapps.tool_shed.security.rst b/doc/source/lib/galaxy.webapps.tool_shed.security.rst index ac3f17fb38d..4e39d99210a 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.security.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.security.rst @@ -1,8 +1,5 @@ -security Package -================ - -:mod:`security` Package ------------------------ +galaxy.webapps.tool_shed.security package +========================================= .. automodule:: galaxy.webapps.tool_shed.security :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.util.rst b/doc/source/lib/galaxy.webapps.tool_shed.util.rst index 8eff5d41834..6ee1d6c7a9f 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.util.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.util.rst @@ -1,27 +1,36 @@ -util Package -============ +galaxy.webapps.tool_shed.util package +===================================== -:mod:`hgweb_config` Module --------------------------- +.. automodule:: galaxy.webapps.tool_shed.util + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.webapps.tool_shed.util.hgweb_config module +------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.util.hgweb_config :members: :undoc-members: :show-inheritance: -:mod:`ratings_util` Module --------------------------- +galaxy.webapps.tool_shed.util.ratings_util module +------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.util.ratings_util :members: :undoc-members: :show-inheritance: -:mod:`shed_statistics` Module ------------------------------ +galaxy.webapps.tool_shed.util.shed_statistics module +---------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.util.shed_statistics :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.work.rst b/doc/source/lib/galaxy.work.rst index 00f74832bc8..415a5b881c8 100644 --- a/doc/source/lib/galaxy.work.rst +++ b/doc/source/lib/galaxy.work.rst @@ -1,11 +1,20 @@ -work Package -============ +galaxy.work package +=================== -:mod:`context` Module ---------------------- +.. automodule:: galaxy.work + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.work.context module +-------------------------- .. automodule:: galaxy.work.context :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.workflow.rst b/doc/source/lib/galaxy.workflow.rst index 7f41691fc77..8d0a2c4dfb6 100644 --- a/doc/source/lib/galaxy.workflow.rst +++ b/doc/source/lib/galaxy.workflow.rst @@ -1,58 +1,7 @@ -workflow Package -================ +galaxy.workflow package +======================= -:mod:`extract` Module ---------------------- - -.. automodule:: galaxy.workflow.extract - :members: - :undoc-members: - :show-inheritance: - -:mod:`modules` Module ---------------------- - -.. automodule:: galaxy.workflow.modules - :members: - :undoc-members: - :show-inheritance: - -:mod:`render` Module --------------------- - -.. automodule:: galaxy.workflow.render - :members: - :undoc-members: - :show-inheritance: - -:mod:`run` Module ------------------ - -.. automodule:: galaxy.workflow.run - :members: - :undoc-members: - :show-inheritance: - -:mod:`run_request` Module -------------------------- - -.. automodule:: galaxy.workflow.run_request - :members: - :undoc-members: - :show-inheritance: - -:mod:`scheduling_manager` Module --------------------------------- - -.. automodule:: galaxy.workflow.scheduling_manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`steps` Module -------------------- - -.. automodule:: galaxy.workflow.steps +.. automodule:: galaxy.workflow :members: :undoc-members: :show-inheritance: @@ -64,3 +13,63 @@ Subpackages galaxy.workflow.schedulers +Submodules +---------- + +galaxy.workflow.extract module +------------------------------ + +.. automodule:: galaxy.workflow.extract + :members: + :undoc-members: + :show-inheritance: + +galaxy.workflow.modules module +------------------------------ + +.. automodule:: galaxy.workflow.modules + :members: + :undoc-members: + :show-inheritance: + +galaxy.workflow.render module +----------------------------- + +.. automodule:: galaxy.workflow.render + :members: + :undoc-members: + :show-inheritance: + +galaxy.workflow.run module +-------------------------- + +.. automodule:: galaxy.workflow.run + :members: + :undoc-members: + :show-inheritance: + +galaxy.workflow.run_request module +---------------------------------- + +.. automodule:: galaxy.workflow.run_request + :members: + :undoc-members: + :show-inheritance: + +galaxy.workflow.scheduling_manager module +----------------------------------------- + +.. automodule:: galaxy.workflow.scheduling_manager + :members: + :undoc-members: + :show-inheritance: + +galaxy.workflow.steps module +---------------------------- + +.. automodule:: galaxy.workflow.steps + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.workflow.schedulers.rst b/doc/source/lib/galaxy.workflow.schedulers.rst index 792b5f500ea..43801194aa8 100644 --- a/doc/source/lib/galaxy.workflow.schedulers.rst +++ b/doc/source/lib/galaxy.workflow.schedulers.rst @@ -1,19 +1,20 @@ -schedulers Package -================== - -:mod:`schedulers` Package -------------------------- +galaxy.workflow.schedulers package +================================== .. automodule:: galaxy.workflow.schedulers :members: :undoc-members: :show-inheritance: -:mod:`core` Module ------------------- +Submodules +---------- + +galaxy.workflow.schedulers.core module +-------------------------------------- .. automodule:: galaxy.workflow.schedulers.core :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy_ext.metadata.rst b/doc/source/lib/galaxy_ext.metadata.rst index c475fafca7c..489f529521f 100644 --- a/doc/source/lib/galaxy_ext.metadata.rst +++ b/doc/source/lib/galaxy_ext.metadata.rst @@ -1,19 +1,20 @@ -metadata Package -================ - -:mod:`metadata` Package ------------------------ +galaxy_ext.metadata package +=========================== .. automodule:: galaxy_ext.metadata :members: :undoc-members: :show-inheritance: -:mod:`set_metadata` Module --------------------------- +Submodules +---------- + +galaxy_ext.metadata.set_metadata module +--------------------------------------- .. automodule:: galaxy_ext.metadata.set_metadata :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy_ext.rst b/doc/source/lib/galaxy_ext.rst index 1c13d00470b..040ba0b19c6 100644 --- a/doc/source/lib/galaxy_ext.rst +++ b/doc/source/lib/galaxy_ext.rst @@ -1,9 +1,6 @@ -galaxy_ext Package +galaxy_ext package ================== -:mod:`galaxy_ext` Package -------------------------- - .. automodule:: galaxy_ext :members: :undoc-members: diff --git a/doc/source/lib/galaxy_utils.rst b/doc/source/lib/galaxy_utils.rst index 3ed28649f1b..c17a7199d73 100644 --- a/doc/source/lib/galaxy_utils.rst +++ b/doc/source/lib/galaxy_utils.rst @@ -1,6 +1,11 @@ -galaxy_utils Package +galaxy_utils package ==================== +.. automodule:: galaxy_utils + :members: + :undoc-members: + :show-inheritance: + Subpackages ----------- diff --git a/doc/source/lib/galaxy_utils.sequence.rst b/doc/source/lib/galaxy_utils.sequence.rst index b1900d7421f..f047ab6e219 100644 --- a/doc/source/lib/galaxy_utils.sequence.rst +++ b/doc/source/lib/galaxy_utils.sequence.rst @@ -1,43 +1,52 @@ -sequence Package -================ +galaxy_utils.sequence package +============================= -:mod:`fasta` Module -------------------- +.. automodule:: galaxy_utils.sequence + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy_utils.sequence.fasta module +---------------------------------- .. automodule:: galaxy_utils.sequence.fasta :members: :undoc-members: :show-inheritance: -:mod:`fastq` Module -------------------- +galaxy_utils.sequence.fastq module +---------------------------------- .. automodule:: galaxy_utils.sequence.fastq :members: :undoc-members: :show-inheritance: -:mod:`sequence` Module ----------------------- +galaxy_utils.sequence.sequence module +------------------------------------- .. automodule:: galaxy_utils.sequence.sequence :members: :undoc-members: :show-inheritance: -:mod:`transform` Module ------------------------ +galaxy_utils.sequence.transform module +-------------------------------------- .. automodule:: galaxy_utils.sequence.transform :members: :undoc-members: :show-inheritance: -:mod:`vcf` Module ------------------ +galaxy_utils.sequence.vcf module +-------------------------------- .. automodule:: galaxy_utils.sequence.vcf :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/log_tempfile.rst b/doc/source/lib/log_tempfile.rst index a5ca8f23b82..51b904985f8 100644 --- a/doc/source/lib/log_tempfile.rst +++ b/doc/source/lib/log_tempfile.rst @@ -1,4 +1,4 @@ -log_tempfile Module +log_tempfile module =================== .. automodule:: log_tempfile diff --git a/doc/source/lib/mimeparse.rst b/doc/source/lib/mimeparse.rst index 0490cfdc8b3..afcdfa0c86b 100644 --- a/doc/source/lib/mimeparse.rst +++ b/doc/source/lib/mimeparse.rst @@ -1,4 +1,4 @@ -mimeparse Module +mimeparse module ================ .. automodule:: mimeparse diff --git a/doc/source/lib/pkg_resources.rst b/doc/source/lib/pkg_resources.rst index ef99aca6efc..e3082f69603 100644 --- a/doc/source/lib/pkg_resources.rst +++ b/doc/source/lib/pkg_resources.rst @@ -1,4 +1,4 @@ -pkg_resources Module +pkg_resources module ==================== .. automodule:: pkg_resources diff --git a/doc/source/lib/psyco_full.rst b/doc/source/lib/psyco_full.rst index 9e75f1b0955..370be05776f 100644 --- a/doc/source/lib/psyco_full.rst +++ b/doc/source/lib/psyco_full.rst @@ -1,4 +1,4 @@ -psyco_full Module +psyco_full module ================= .. automodule:: psyco_full diff --git a/doc/source/lib/pulsar.client.rst b/doc/source/lib/pulsar.client.rst index 6458d71332f..3a29f55ffae 100644 --- a/doc/source/lib/pulsar.client.rst +++ b/doc/source/lib/pulsar.client.rst @@ -1,126 +1,11 @@ -client Package -============== - -:mod:`client` Package ---------------------- +pulsar.client package +===================== .. automodule:: pulsar.client :members: :undoc-members: :show-inheritance: -:mod:`action_mapper` Module ---------------------------- - -.. automodule:: pulsar.client.action_mapper - :members: - :undoc-members: - :show-inheritance: - -:mod:`amqp_exchange` Module ---------------------------- - -.. automodule:: pulsar.client.amqp_exchange - :members: - :undoc-members: - :show-inheritance: - -:mod:`amqp_exchange_factory` Module ------------------------------------ - -.. automodule:: pulsar.client.amqp_exchange_factory - :members: - :undoc-members: - :show-inheritance: - -:mod:`client` Module --------------------- - -.. automodule:: pulsar.client.client - :members: - :undoc-members: - :show-inheritance: - -:mod:`config_util` Module -------------------------- - -.. automodule:: pulsar.client.config_util - :members: - :undoc-members: - :show-inheritance: - -:mod:`decorators` Module ------------------------- - -.. automodule:: pulsar.client.decorators - :members: - :undoc-members: - :show-inheritance: - -:mod:`destination` Module -------------------------- - -.. automodule:: pulsar.client.destination - :members: - :undoc-members: - :show-inheritance: - -:mod:`interface` Module ------------------------ - -.. automodule:: pulsar.client.interface - :members: - :undoc-members: - :show-inheritance: - -:mod:`job_directory` Module ---------------------------- - -.. automodule:: pulsar.client.job_directory - :members: - :undoc-members: - :show-inheritance: - -:mod:`manager` Module ---------------------- - -.. automodule:: pulsar.client.manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`object_client` Module ---------------------------- - -.. automodule:: pulsar.client.object_client - :members: - :undoc-members: - :show-inheritance: - -:mod:`path_mapper` Module -------------------------- - -.. automodule:: pulsar.client.path_mapper - :members: - :undoc-members: - :show-inheritance: - -:mod:`setup_handler` Module ---------------------------- - -.. automodule:: pulsar.client.setup_handler - :members: - :undoc-members: - :show-inheritance: - -:mod:`util` Module ------------------- - -.. automodule:: pulsar.client.util - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -129,3 +14,119 @@ Subpackages pulsar.client.staging pulsar.client.transport +Submodules +---------- + +pulsar.client.action_mapper module +---------------------------------- + +.. automodule:: pulsar.client.action_mapper + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.amqp_exchange module +---------------------------------- + +.. automodule:: pulsar.client.amqp_exchange + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.amqp_exchange_factory module +------------------------------------------ + +.. automodule:: pulsar.client.amqp_exchange_factory + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.client module +--------------------------- + +.. automodule:: pulsar.client.client + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.config_util module +-------------------------------- + +.. automodule:: pulsar.client.config_util + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.decorators module +------------------------------- + +.. automodule:: pulsar.client.decorators + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.destination module +-------------------------------- + +.. automodule:: pulsar.client.destination + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.interface module +------------------------------ + +.. automodule:: pulsar.client.interface + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.job_directory module +---------------------------------- + +.. automodule:: pulsar.client.job_directory + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.manager module +---------------------------- + +.. automodule:: pulsar.client.manager + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.object_client module +---------------------------------- + +.. automodule:: pulsar.client.object_client + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.path_mapper module +-------------------------------- + +.. automodule:: pulsar.client.path_mapper + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.setup_handler module +---------------------------------- + +.. automodule:: pulsar.client.setup_handler + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.util module +------------------------- + +.. automodule:: pulsar.client.util + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/pulsar.client.staging.rst b/doc/source/lib/pulsar.client.staging.rst index 6731bc362b3..4d33f6676b8 100644 --- a/doc/source/lib/pulsar.client.staging.rst +++ b/doc/source/lib/pulsar.client.staging.rst @@ -1,27 +1,28 @@ -staging Package -=============== - -:mod:`staging` Package ----------------------- +pulsar.client.staging package +============================= .. automodule:: pulsar.client.staging :members: :undoc-members: :show-inheritance: -:mod:`down` Module ------------------- +Submodules +---------- + +pulsar.client.staging.down module +--------------------------------- .. automodule:: pulsar.client.staging.down :members: :undoc-members: :show-inheritance: -:mod:`up` Module ----------------- +pulsar.client.staging.up module +------------------------------- .. automodule:: pulsar.client.staging.up :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/pulsar.client.transport.rst b/doc/source/lib/pulsar.client.transport.rst index afeb8f24a3b..8b68dbb15a5 100644 --- a/doc/source/lib/pulsar.client.transport.rst +++ b/doc/source/lib/pulsar.client.transport.rst @@ -1,51 +1,52 @@ -transport Package -================= - -:mod:`transport` Package ------------------------- +pulsar.client.transport package +=============================== .. automodule:: pulsar.client.transport :members: :undoc-members: :show-inheritance: -:mod:`curl` Module ------------------- +Submodules +---------- + +pulsar.client.transport.curl module +----------------------------------- .. automodule:: pulsar.client.transport.curl :members: :undoc-members: :show-inheritance: -:mod:`poster` Module --------------------- +pulsar.client.transport.poster module +------------------------------------- .. automodule:: pulsar.client.transport.poster :members: :undoc-members: :show-inheritance: -:mod:`requests` Module ----------------------- +pulsar.client.transport.requests module +--------------------------------------- .. automodule:: pulsar.client.transport.requests :members: :undoc-members: :show-inheritance: -:mod:`ssh` Module ------------------ +pulsar.client.transport.ssh module +---------------------------------- .. automodule:: pulsar.client.transport.ssh :members: :undoc-members: :show-inheritance: -:mod:`standard` Module ----------------------- +pulsar.client.transport.standard module +--------------------------------------- .. automodule:: pulsar.client.transport.standard :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/pulsar.rst b/doc/source/lib/pulsar.rst index 754078e9094..c22c0a95bdb 100644 --- a/doc/source/lib/pulsar.rst +++ b/doc/source/lib/pulsar.rst @@ -1,6 +1,11 @@ -pulsar Package +pulsar package ============== +.. automodule:: pulsar + :members: + :undoc-members: + :show-inheritance: + Subpackages ----------- diff --git a/doc/source/lib/tool_shed.capsule.rst b/doc/source/lib/tool_shed.capsule.rst index 9496653d044..3865f875806 100644 --- a/doc/source/lib/tool_shed.capsule.rst +++ b/doc/source/lib/tool_shed.capsule.rst @@ -1,11 +1,20 @@ -capsule Package -=============== +tool_shed.capsule package +========================= -:mod:`capsule_manager` Module ------------------------------ +.. automodule:: tool_shed.capsule + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.capsule.capsule_manager module +---------------------------------------- .. automodule:: tool_shed.capsule.capsule_manager :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.dependencies.repository.rst b/doc/source/lib/tool_shed.dependencies.repository.rst index 5382a5ba40a..bd6356b7531 100644 --- a/doc/source/lib/tool_shed.dependencies.repository.rst +++ b/doc/source/lib/tool_shed.dependencies.repository.rst @@ -1,11 +1,20 @@ -repository Package -================== +tool_shed.dependencies.repository package +========================================= -:mod:`relation_builder` Module ------------------------------- +.. automodule:: tool_shed.dependencies.repository + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.dependencies.repository.relation_builder module +--------------------------------------------------------- .. automodule:: tool_shed.dependencies.repository.relation_builder :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.dependencies.rst b/doc/source/lib/tool_shed.dependencies.rst index e7b62a50159..563583e596f 100644 --- a/doc/source/lib/tool_shed.dependencies.rst +++ b/doc/source/lib/tool_shed.dependencies.rst @@ -1,10 +1,7 @@ -dependencies Package -==================== +tool_shed.dependencies package +============================== -:mod:`attribute_handlers` Module --------------------------------- - -.. automodule:: tool_shed.dependencies.attribute_handlers +.. automodule:: tool_shed.dependencies :members: :undoc-members: :show-inheritance: @@ -17,3 +14,15 @@ Subpackages tool_shed.dependencies.repository tool_shed.dependencies.tool +Submodules +---------- + +tool_shed.dependencies.attribute_handlers module +------------------------------------------------ + +.. automodule:: tool_shed.dependencies.attribute_handlers + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/tool_shed.dependencies.tool.rst b/doc/source/lib/tool_shed.dependencies.tool.rst index 9ba9c8b2472..3062aa20041 100644 --- a/doc/source/lib/tool_shed.dependencies.tool.rst +++ b/doc/source/lib/tool_shed.dependencies.tool.rst @@ -1,11 +1,20 @@ -tool Package -============ +tool_shed.dependencies.tool package +=================================== -:mod:`tag_attribute_handler` Module ------------------------------------ +.. automodule:: tool_shed.dependencies.tool + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.dependencies.tool.tag_attribute_handler module +-------------------------------------------------------- .. automodule:: tool_shed.dependencies.tool.tag_attribute_handler :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.datatypes.rst b/doc/source/lib/tool_shed.galaxy_install.datatypes.rst index e5021e079c6..bab6f246f76 100644 --- a/doc/source/lib/tool_shed.galaxy_install.datatypes.rst +++ b/doc/source/lib/tool_shed.galaxy_install.datatypes.rst @@ -1,11 +1,20 @@ -datatypes Package -================= +tool_shed.galaxy_install.datatypes package +========================================== -:mod:`custom_datatype_manager` Module -------------------------------------- +.. automodule:: tool_shed.galaxy_install.datatypes + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.galaxy_install.datatypes.custom_datatype_manager module +----------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.datatypes.custom_datatype_manager :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.grids.rst b/doc/source/lib/tool_shed.galaxy_install.grids.rst index c75c5c716ea..b01741c0d70 100644 --- a/doc/source/lib/tool_shed.galaxy_install.grids.rst +++ b/doc/source/lib/tool_shed.galaxy_install.grids.rst @@ -1,11 +1,20 @@ -grids Package -============= +tool_shed.galaxy_install.grids package +====================================== -:mod:`admin_toolshed_grids` Module ----------------------------------- +.. automodule:: tool_shed.galaxy_install.grids + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.galaxy_install.grids.admin_toolshed_grids module +---------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.grids.admin_toolshed_grids :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.metadata.rst b/doc/source/lib/tool_shed.galaxy_install.metadata.rst index a710cc6ad1b..8a63d06e5d0 100644 --- a/doc/source/lib/tool_shed.galaxy_install.metadata.rst +++ b/doc/source/lib/tool_shed.galaxy_install.metadata.rst @@ -1,11 +1,20 @@ -metadata Package -================ +tool_shed.galaxy_install.metadata package +========================================= -:mod:`installed_repository_metadata_manager` Module ---------------------------------------------------- +.. automodule:: tool_shed.galaxy_install.metadata + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.galaxy_install.metadata.installed_repository_metadata_manager module +------------------------------------------------------------------------------ .. automodule:: tool_shed.galaxy_install.metadata.installed_repository_metadata_manager :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.migrate.rst b/doc/source/lib/tool_shed.galaxy_install.migrate.rst index 5d553b446d1..4e3291da76b 100644 --- a/doc/source/lib/tool_shed.galaxy_install.migrate.rst +++ b/doc/source/lib/tool_shed.galaxy_install.migrate.rst @@ -1,19 +1,28 @@ -migrate Package -=============== +tool_shed.galaxy_install.migrate package +======================================== -:mod:`check` Module -------------------- +.. automodule:: tool_shed.galaxy_install.migrate + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.galaxy_install.migrate.check module +--------------------------------------------- .. automodule:: tool_shed.galaxy_install.migrate.check :members: :undoc-members: :show-inheritance: -:mod:`common` Module --------------------- +tool_shed.galaxy_install.migrate.common module +---------------------------------------------- .. automodule:: tool_shed.galaxy_install.migrate.common :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst b/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst index ac2c06dad4d..5110d9fb105 100644 --- a/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst +++ b/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst @@ -1,11 +1,20 @@ -repository_dependencies Package -=============================== +tool_shed.galaxy_install.repository_dependencies package +======================================================== -:mod:`repository_dependency_manager` Module -------------------------------------------- +.. automodule:: tool_shed.galaxy_install.repository_dependencies + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager module +------------------------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.rst b/doc/source/lib/tool_shed.galaxy_install.rst index c2da4ac3c55..f4510a24c13 100644 --- a/doc/source/lib/tool_shed.galaxy_install.rst +++ b/doc/source/lib/tool_shed.galaxy_install.rst @@ -1,50 +1,7 @@ -galaxy_install Package -====================== +tool_shed.galaxy_install package +================================ -:mod:`dependency_display` Module --------------------------------- - -.. automodule:: tool_shed.galaxy_install.dependency_display - :members: - :undoc-members: - :show-inheritance: - -:mod:`install_manager` Module ------------------------------ - -.. automodule:: tool_shed.galaxy_install.install_manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`installed_repository_manager` Module ------------------------------------------- - -.. automodule:: tool_shed.galaxy_install.installed_repository_manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`repair_repository_manager` Module ---------------------------------------- - -.. automodule:: tool_shed.galaxy_install.repair_repository_manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`tool_migration_manager` Module ------------------------------------- - -.. automodule:: tool_shed.galaxy_install.tool_migration_manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`update_repository_manager` Module ---------------------------------------- - -.. automodule:: tool_shed.galaxy_install.update_repository_manager +.. automodule:: tool_shed.galaxy_install :members: :undoc-members: :show-inheritance: @@ -63,3 +20,55 @@ Subpackages tool_shed.galaxy_install.tools tool_shed.galaxy_install.utility_containers +Submodules +---------- + +tool_shed.galaxy_install.dependency_display module +-------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.dependency_display + :members: + :undoc-members: + :show-inheritance: + +tool_shed.galaxy_install.install_manager module +----------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.install_manager + :members: + :undoc-members: + :show-inheritance: + +tool_shed.galaxy_install.installed_repository_manager module +------------------------------------------------------------ + +.. automodule:: tool_shed.galaxy_install.installed_repository_manager + :members: + :undoc-members: + :show-inheritance: + +tool_shed.galaxy_install.repair_repository_manager module +--------------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.repair_repository_manager + :members: + :undoc-members: + :show-inheritance: + +tool_shed.galaxy_install.tool_migration_manager module +------------------------------------------------------ + +.. automodule:: tool_shed.galaxy_install.tool_migration_manager + :members: + :undoc-members: + :show-inheritance: + +tool_shed.galaxy_install.update_repository_manager module +--------------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.update_repository_manager + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst index 6a7abd723fb..29d76529234 100644 --- a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst +++ b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst @@ -1,51 +1,60 @@ -recipe Package -============== +tool_shed.galaxy_install.tool_dependencies.recipe package +========================================================= -:mod:`asynchronous_reader` Module ---------------------------------- +.. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader module +---------------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader :members: :undoc-members: :show-inheritance: -:mod:`env_file_builder` Module ------------------------------- +tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder module +------------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder :members: :undoc-members: :show-inheritance: -:mod:`install_environment` Module ---------------------------------- +tool_shed.galaxy_install.tool_dependencies.recipe.install_environment module +---------------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment :members: :undoc-members: :show-inheritance: -:mod:`recipe_manager` Module ----------------------------- +tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager module +----------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager :members: :undoc-members: :show-inheritance: -:mod:`step_handler` Module --------------------------- +tool_shed.galaxy_install.tool_dependencies.recipe.step_handler module +--------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.step_handler :members: :undoc-members: :show-inheritance: -:mod:`tag_handler` Module -------------------------- +tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler module +-------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst index c5b6ee4091f..5f67bad6c1e 100644 --- a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst +++ b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst @@ -1,10 +1,7 @@ -tool_dependencies Package -========================= +tool_shed.galaxy_install.tool_dependencies package +================================================== -:mod:`env_manager` Module -------------------------- - -.. automodule:: tool_shed.galaxy_install.tool_dependencies.env_manager +.. automodule:: tool_shed.galaxy_install.tool_dependencies :members: :undoc-members: :show-inheritance: @@ -16,3 +13,15 @@ Subpackages tool_shed.galaxy_install.tool_dependencies.recipe +Submodules +---------- + +tool_shed.galaxy_install.tool_dependencies.env_manager module +------------------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.tool_dependencies.env_manager + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/tool_shed.galaxy_install.tools.rst b/doc/source/lib/tool_shed.galaxy_install.tools.rst index 922667d523c..1d1d0f37243 100644 --- a/doc/source/lib/tool_shed.galaxy_install.tools.rst +++ b/doc/source/lib/tool_shed.galaxy_install.tools.rst @@ -1,19 +1,28 @@ -tools Package -============= +tool_shed.galaxy_install.tools package +====================================== -:mod:`data_manager` Module --------------------------- +.. automodule:: tool_shed.galaxy_install.tools + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.galaxy_install.tools.data_manager module +-------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tools.data_manager :members: :undoc-members: :show-inheritance: -:mod:`tool_panel_manager` Module --------------------------------- +tool_shed.galaxy_install.tools.tool_panel_manager module +-------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tools.tool_panel_manager :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst b/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst index 60dd22914fc..347d7317fc2 100644 --- a/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst +++ b/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst @@ -1,8 +1,5 @@ -utility_containers Package -========================== - -:mod:`utility_containers` Package ---------------------------------- +tool_shed.galaxy_install.utility_containers package +=================================================== .. automodule:: tool_shed.galaxy_install.utility_containers :members: diff --git a/doc/source/lib/tool_shed.grids.rst b/doc/source/lib/tool_shed.grids.rst index 86c0bf2ee70..7ee5fb07ce8 100644 --- a/doc/source/lib/tool_shed.grids.rst +++ b/doc/source/lib/tool_shed.grids.rst @@ -1,43 +1,52 @@ -grids Package -============= +tool_shed.grids package +======================= -:mod:`admin_grids` Module -------------------------- +.. automodule:: tool_shed.grids + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.grids.admin_grids module +---------------------------------- .. automodule:: tool_shed.grids.admin_grids :members: :undoc-members: :show-inheritance: -:mod:`repository_grid_filter_manager` Module --------------------------------------------- +tool_shed.grids.repository_grid_filter_manager module +----------------------------------------------------- .. automodule:: tool_shed.grids.repository_grid_filter_manager :members: :undoc-members: :show-inheritance: -:mod:`repository_grids` Module ------------------------------- +tool_shed.grids.repository_grids module +--------------------------------------- .. automodule:: tool_shed.grids.repository_grids :members: :undoc-members: :show-inheritance: -:mod:`repository_review_grids` Module -------------------------------------- +tool_shed.grids.repository_review_grids module +---------------------------------------------- .. automodule:: tool_shed.grids.repository_review_grids :members: :undoc-members: :show-inheritance: -:mod:`util` Module ------------------- +tool_shed.grids.util module +--------------------------- .. automodule:: tool_shed.grids.util :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.managers.rst b/doc/source/lib/tool_shed.managers.rst index f400d8d767e..04de3ce0371 100644 --- a/doc/source/lib/tool_shed.managers.rst +++ b/doc/source/lib/tool_shed.managers.rst @@ -1,19 +1,28 @@ -managers Package -================ +tool_shed.managers package +========================== -:mod:`groups` Module --------------------- +.. automodule:: tool_shed.managers + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.managers.groups module +-------------------------------- .. automodule:: tool_shed.managers.groups :members: :undoc-members: :show-inheritance: -:mod:`repositories` Module --------------------------- +tool_shed.managers.repositories module +-------------------------------------- .. automodule:: tool_shed.managers.repositories :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.metadata.rst b/doc/source/lib/tool_shed.metadata.rst index 735acfd5e9d..7e2ba80941d 100644 --- a/doc/source/lib/tool_shed.metadata.rst +++ b/doc/source/lib/tool_shed.metadata.rst @@ -1,19 +1,28 @@ -metadata Package -================ +tool_shed.metadata package +========================== -:mod:`metadata_generator` Module --------------------------------- +.. automodule:: tool_shed.metadata + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.metadata.metadata_generator module +-------------------------------------------- .. automodule:: tool_shed.metadata.metadata_generator :members: :undoc-members: :show-inheritance: -:mod:`repository_metadata_manager` Module ------------------------------------------ +tool_shed.metadata.repository_metadata_manager module +----------------------------------------------------- .. automodule:: tool_shed.metadata.repository_metadata_manager :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.repository_types.rst b/doc/source/lib/tool_shed.repository_types.rst index b64e85a7a18..5e5cff1b7de 100644 --- a/doc/source/lib/tool_shed.repository_types.rst +++ b/doc/source/lib/tool_shed.repository_types.rst @@ -1,51 +1,60 @@ -repository_types Package -======================== +tool_shed.repository_types package +================================== -:mod:`metadata` Module ----------------------- +.. automodule:: tool_shed.repository_types + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.repository_types.metadata module +------------------------------------------ .. automodule:: tool_shed.repository_types.metadata :members: :undoc-members: :show-inheritance: -:mod:`registry` Module ----------------------- +tool_shed.repository_types.registry module +------------------------------------------ .. automodule:: tool_shed.repository_types.registry :members: :undoc-members: :show-inheritance: -:mod:`repository_suite_definition` Module ------------------------------------------ +tool_shed.repository_types.repository_suite_definition module +------------------------------------------------------------- .. automodule:: tool_shed.repository_types.repository_suite_definition :members: :undoc-members: :show-inheritance: -:mod:`tool_dependency_definition` Module ----------------------------------------- +tool_shed.repository_types.tool_dependency_definition module +------------------------------------------------------------ .. automodule:: tool_shed.repository_types.tool_dependency_definition :members: :undoc-members: :show-inheritance: -:mod:`unrestricted` Module --------------------------- +tool_shed.repository_types.unrestricted module +---------------------------------------------- .. automodule:: tool_shed.repository_types.unrestricted :members: :undoc-members: :show-inheritance: -:mod:`util` Module ------------------- +tool_shed.repository_types.util module +-------------------------------------- .. automodule:: tool_shed.repository_types.util :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.rst b/doc/source/lib/tool_shed.rst index 4bf54d75b21..9ea2997d843 100644 --- a/doc/source/lib/tool_shed.rst +++ b/doc/source/lib/tool_shed.rst @@ -1,18 +1,7 @@ -tool_shed Package +tool_shed package ================= -:mod:`repository_registry` Module ---------------------------------- - -.. automodule:: tool_shed.repository_registry - :members: - :undoc-members: - :show-inheritance: - -:mod:`tool_shed_registry` Module --------------------------------- - -.. automodule:: tool_shed.tool_shed_registry +.. automodule:: tool_shed :members: :undoc-members: :show-inheritance: @@ -33,3 +22,23 @@ Subpackages tool_shed.util tool_shed.utility_containers +Submodules +---------- + +tool_shed.repository_registry module +------------------------------------ + +.. automodule:: tool_shed.repository_registry + :members: + :undoc-members: + :show-inheritance: + +tool_shed.tool_shed_registry module +----------------------------------- + +.. automodule:: tool_shed.tool_shed_registry + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/tool_shed.tools.rst b/doc/source/lib/tool_shed.tools.rst index a734ba26f96..bfc71f2f4eb 100644 --- a/doc/source/lib/tool_shed.tools.rst +++ b/doc/source/lib/tool_shed.tools.rst @@ -1,27 +1,36 @@ -tools Package -============= +tool_shed.tools package +======================= -:mod:`data_table_manager` Module --------------------------------- +.. automodule:: tool_shed.tools + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.tools.data_table_manager module +----------------------------------------- .. automodule:: tool_shed.tools.data_table_manager :members: :undoc-members: :show-inheritance: -:mod:`tool_validator` Module ----------------------------- +tool_shed.tools.tool_validator module +------------------------------------- .. automodule:: tool_shed.tools.tool_validator :members: :undoc-members: :show-inheritance: -:mod:`tool_version_manager` Module ----------------------------------- +tool_shed.tools.tool_version_manager module +------------------------------------------- .. automodule:: tool_shed.tools.tool_version_manager :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.util.rst b/doc/source/lib/tool_shed.util.rst index add05826aee..47b221ed9b5 100644 --- a/doc/source/lib/tool_shed.util.rst +++ b/doc/source/lib/tool_shed.util.rst @@ -1,147 +1,156 @@ -util Package -============ +tool_shed.util package +====================== -:mod:`basic_util` Module ------------------------- +.. automodule:: tool_shed.util + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.util.basic_util module +-------------------------------- .. automodule:: tool_shed.util.basic_util :members: :undoc-members: :show-inheritance: -:mod:`commit_util` Module -------------------------- +tool_shed.util.commit_util module +--------------------------------- .. automodule:: tool_shed.util.commit_util :members: :undoc-members: :show-inheritance: -:mod:`common_util` Module -------------------------- +tool_shed.util.common_util module +--------------------------------- .. automodule:: tool_shed.util.common_util :members: :undoc-members: :show-inheritance: -:mod:`container_util` Module ----------------------------- +tool_shed.util.container_util module +------------------------------------ .. automodule:: tool_shed.util.container_util :members: :undoc-members: :show-inheritance: -:mod:`encoding_util` Module ---------------------------- +tool_shed.util.encoding_util module +----------------------------------- .. automodule:: tool_shed.util.encoding_util :members: :undoc-members: :show-inheritance: -:mod:`hg_util` Module ---------------------- +tool_shed.util.hg_util module +----------------------------- .. automodule:: tool_shed.util.hg_util :members: :undoc-members: :show-inheritance: -:mod:`metadata_util` Module ---------------------------- +tool_shed.util.metadata_util module +----------------------------------- .. automodule:: tool_shed.util.metadata_util :members: :undoc-members: :show-inheritance: -:mod:`readme_util` Module -------------------------- +tool_shed.util.readme_util module +--------------------------------- .. automodule:: tool_shed.util.readme_util :members: :undoc-members: :show-inheritance: -:mod:`repository_content_util` Module -------------------------------------- +tool_shed.util.repository_content_util module +--------------------------------------------- .. automodule:: tool_shed.util.repository_content_util :members: :undoc-members: :show-inheritance: -:mod:`repository_util` Module ------------------------------ +tool_shed.util.repository_util module +------------------------------------- .. automodule:: tool_shed.util.repository_util :members: :undoc-members: :show-inheritance: -:mod:`review_util` Module -------------------------- +tool_shed.util.review_util module +--------------------------------- .. automodule:: tool_shed.util.review_util :members: :undoc-members: :show-inheritance: -:mod:`search_util` Module -------------------------- +tool_shed.util.search_util module +--------------------------------- .. automodule:: tool_shed.util.search_util :members: :undoc-members: :show-inheritance: -:mod:`shed_util_common` Module ------------------------------- +tool_shed.util.shed_util_common module +-------------------------------------- .. automodule:: tool_shed.util.shed_util_common :members: :undoc-members: :show-inheritance: -:mod:`tool_dependency_util` Module ----------------------------------- +tool_shed.util.tool_dependency_util module +------------------------------------------ .. automodule:: tool_shed.util.tool_dependency_util :members: :undoc-members: :show-inheritance: -:mod:`tool_util` Module ------------------------ +tool_shed.util.tool_util module +------------------------------- .. automodule:: tool_shed.util.tool_util :members: :undoc-members: :show-inheritance: -:mod:`web_util` Module ----------------------- +tool_shed.util.web_util module +------------------------------ .. automodule:: tool_shed.util.web_util :members: :undoc-members: :show-inheritance: -:mod:`workflow_util` Module ---------------------------- +tool_shed.util.workflow_util module +----------------------------------- .. automodule:: tool_shed.util.workflow_util :members: :undoc-members: :show-inheritance: -:mod:`xml_util` Module ----------------------- +tool_shed.util.xml_util module +------------------------------ .. automodule:: tool_shed.util.xml_util :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.utility_containers.rst b/doc/source/lib/tool_shed.utility_containers.rst index d5b2f756591..bfa484d7795 100644 --- a/doc/source/lib/tool_shed.utility_containers.rst +++ b/doc/source/lib/tool_shed.utility_containers.rst @@ -1,19 +1,20 @@ -utility_containers Package -========================== - -:mod:`utility_containers` Package ---------------------------------- +tool_shed.utility_containers package +==================================== .. automodule:: tool_shed.utility_containers :members: :undoc-members: :show-inheritance: -:mod:`utility_container_manager` Module ---------------------------------------- +Submodules +---------- + +tool_shed.utility_containers.utility_container_manager module +------------------------------------------------------------- .. automodule:: tool_shed.utility_containers.utility_container_manager :members: :undoc-members: :show-inheritance: + From 9567073475f28e94a1901000eae5e7c2fcd94af4 Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Mon, 29 Jun 2015 10:40:14 -0400 Subject: [PATCH 016/165] Fix for setting environment variable paths for installed tool dependencies in cases where $ENV[SOMEVAR] is used. This approach takes the value of SOMEVAR from the env_var_dict where the original approach called subprocess.Popen() to echo the value. This echoing occurred in the InstallEnvironment.handle_complex_command() function, which produces stdout in such a way that the value of the environment variable being echo'ed will likely be truncated or munged due to the way stdout logging works. --- .../tool_dependencies/recipe/step_handler.py | 34 +++++++++---------- 1 file changed, 16 insertions(+), 18 deletions(-) diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py index 4899327b865..dc81364ee3e 100755 --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -973,29 +973,27 @@ class SetEnvironment( RecipeStep ): ---- """ env_var_value = env_var_dict[ 'value' ] - # env_var_value is the text of an environment variable tag like this: + # env_var_value is the text of an environment variable tag like this: + # # Here is an example of what env_var_value could look like: $ENV[GRAPHICSMAGICK_ROOT_DIR]/lib/ if '$ENV[' in env_var_value and ']' in env_var_value: # Pull out the name of the environment variable to populate. inherited_env_var_name = env_var_value.split( '[' )[1].split( ']' )[0] to_replace = '$ENV[%s]' % inherited_env_var_name - # Build a command line that outputs VARIABLE_NAME: . - set_prior_environment_commands.append( 'echo %s: $%s' % ( inherited_env_var_name, inherited_env_var_name ) ) - command = ' ; '.join( set_prior_environment_commands ) - # Run the command and capture the output. - command_return = install_environment.handle_command( tool_dependency=tool_dependency, - cmd=command, - return_output=True ) - # And extract anything labeled with the name of the environment variable we're populating here. - if '%s: ' % inherited_env_var_name in command_return: - environment_variable_value = command_return.split( '\n' ) - for line in environment_variable_value: - if line.startswith( inherited_env_var_name ): - inherited_env_var_value = line.replace( '%s: ' % inherited_env_var_name, '' ) - log.info( 'Replacing %s with %s in env.sh for this repository.', to_replace, inherited_env_var_value ) - env_var_value = env_var_value.replace( to_replace, inherited_env_var_value ) - else: - # If the return is empty, replace the original $ENV[] with nothing, to avoid any shell misparsings later on. + found = False + for env_cmd in set_prior_environment_commands: + # LD_LIBRARY_PATH=//; export LD_LIBRARY_PATH + if env_cmd.startswith( inherited_env_var_name ): + env_val = env_cmd.split( '=' )[1] + # //; export LD_LIBRARY_PATH + env_val = env_val.split( ';' )[0] + # // + log.info( 'Replacing %s with %s in env.sh for this repository.', to_replace, env_val ) + env_var_value = env_var_value.replace( to_replace, env_val ) + found = True + break + if not found: + # Replace the original $ENV[] with nothing, to avoid any shell misparsings later on. log.debug( 'Environment variable %s not found, removing from set_environment.', inherited_env_var_name ) env_var_value = env_var_value.replace( to_replace, '$%s' % inherited_env_var_name ) env_var_dict[ 'value' ] = env_var_value From c53170f215e10fe14420e4f85a845c4fc1326410 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Sat, 27 Jun 2015 10:28:28 -0400 Subject: [PATCH 017/165] Fix managers to pass context necessary down the chain when purging. This should fix at least one quota calc error. Fix another bug in hda manager regarding quota reduction -- quota usage must be calculated prior to actually purging, otherwise the disk usage is 0 and this does nothing. Slight refactoring in manager purge -- we don't need to pass the user via context since we can just grab it where applicable from the history. Fix purge when handling an anonymous user --- lib/galaxy/managers/hdas.py | 10 +++++++--- lib/galaxy/managers/histories.py | 1 - 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py index e724d660a59..18e9955e906 100644 --- a/lib/galaxy/managers/hdas.py +++ b/lib/galaxy/managers/hdas.py @@ -143,14 +143,18 @@ class HDAManager( datasets.DatasetAssociationManager, return ldda.to_history_dataset_association( history, add_to_history=True ) # .... deletion and purging - def purge( self, hda, current_user=None, flush=True ): + def purge( self, hda, flush=True): """ Purge this HDA and the dataset underlying it. """ + user = hda.history.user or None + quota_amount_reduction = 0 + if user: + quota_amount_reduction = hda.quota_amount( user ) super( HDAManager, self ).purge( hda, flush=flush ) # decrease the user's space used - if current_user: - current_user.total_disk_usage -= hda.quota_amount( current_user ) + if quota_amount_reduction: + user.total_disk_usage -= quota_amount_reduction return hda # .... states diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py index 14e53aa230d..1ebe9269bdb 100644 --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -82,7 +82,6 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi Purge this history and all HDAs, Collections, and Datasets inside this history. """ self.hda_manager.dataset_manager.error_unless_dataset_purge_allowed() - # First purge all the datasets for hda in history.datasets: if not hda.purged: From c2917a78f87527bee5f3d0a531a2660d20eb24e5 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Mon, 29 Jun 2015 17:36:24 +0100 Subject: [PATCH 018/165] Change html_theme to sphinx_rtd_theme to fix left sidebar. --- doc/source/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/conf.py b/doc/source/conf.py index 9e8ae5b0f70..9444c4cb321 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -101,7 +101,7 @@ pygments_style = 'sphinx' # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. -html_theme = 'classic' +html_theme = 'sphinx_rtd_theme' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the From 2b1ce19e45ec66b6d16fcad31405d25ad536e002 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Mon, 29 Jun 2015 15:33:41 -0400 Subject: [PATCH 019/165] Change allow_tool_upgrades to allow_tool_state_corrections. --- lib/galaxy/webapps/galaxy/api/workflows.py | 4 ++-- lib/galaxy/workflow/modules.py | 4 ++-- lib/galaxy/workflow/run.py | 4 ++-- lib/galaxy/workflow/run_request.py | 8 ++++---- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py index 256fed9372e..3228d31a477 100644 --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -127,8 +127,8 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn :param workflow_name: If from_history_id is set - name of the workflow to create when extracting a workflow from history :type workflow_name: str - :param allow_tool_upgrades: If set to True, any Tool parameter upgrades will not prevent running workflow, defaults to False - :type allow_tool_upgrades: bool + :param allow_tool_state_corrections: If set to True, any Tool parameter changes will not prevent running workflow, defaults to False + :type allow_tool_state_corrections: bool """ ways_to_create = set( [ 'workflow_id', diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py index f07f2ab4a3c..3ff962d06dd 100644 --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -1075,7 +1075,7 @@ class WorkflowModuleInjector(object): return step_errors -def populate_module_and_state( trans, workflow, param_map, allow_tool_upgrades=False ): +def populate_module_and_state( trans, workflow, param_map, allow_tool_state_corrections=False ): """ Used by API but not web controller, walks through a workflow's steps and populates transient module and state attributes on each. """ @@ -1088,7 +1088,7 @@ def populate_module_and_state( trans, workflow, param_map, allow_tool_upgrades=F message = "Workflow cannot be run because of validation errors in some steps: %s" % step_errors raise exceptions.MessageException( message ) if step.upgrade_messages: - if allow_tool_upgrades: + if allow_tool_state_corrections: log.debug( 'Workflow step "%i" had upgrade messages: %s', step.id, step.upgrade_messages ) else: message = "Workflow cannot be run because of step upgrade messages: %s" % step.upgrade_messages diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py index da6f961cff4..1cc4fbac6fe 100644 --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -58,7 +58,7 @@ def __invoke( trans, workflow, workflow_run_config, workflow_invocation=None, po """ Run the supplied workflow in the supplied target_history. """ if populate_state: - modules.populate_module_and_state( trans, workflow, workflow_run_config.param_map, allow_tool_upgrades=workflow_run_config.allow_tool_upgrades ) + modules.populate_module_and_state( trans, workflow, workflow_run_config.param_map, allow_tool_state_corrections=workflow_run_config.allow_tool_state_corrections ) invoker = WorkflowInvoker( trans, @@ -95,7 +95,7 @@ def __invoke( trans, workflow, workflow_run_config, workflow_invocation=None, po def queue_invoke( trans, workflow, workflow_run_config, request_params={}, populate_state=True ): if populate_state: - modules.populate_module_and_state( trans, workflow, workflow_run_config.param_map, allow_tool_upgrades=workflow_run_config.allow_tool_upgrades ) + modules.populate_module_and_state( trans, workflow, workflow_run_config.param_map, allow_tool_state_corrections=workflow_run_config.allow_tool_state_corrections ) workflow_invocation = workflow_run_config_to_request( trans, workflow_run_config, workflow ) workflow_invocation.workflow = workflow return trans.app.workflow_scheduling_manager.queue( diff --git a/lib/galaxy/workflow/run_request.py b/lib/galaxy/workflow/run_request.py index 420784eed7d..a27d3833157 100644 --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -39,13 +39,13 @@ class WorkflowRunConfig( object ): :type param_map: dict """ - def __init__( self, target_history, replacement_dict, copy_inputs_to_history=False, inputs={}, param_map={}, allow_tool_upgrades=False ): + def __init__( self, target_history, replacement_dict, copy_inputs_to_history=False, inputs={}, param_map={}, allow_tool_state_corrections=False ): self.target_history = target_history self.replacement_dict = replacement_dict self.copy_inputs_to_history = copy_inputs_to_history self.inputs = inputs self.param_map = param_map - self.allow_tool_upgrades = allow_tool_upgrades + self.allow_tool_state_corrections = allow_tool_state_corrections def normalize_inputs(steps, inputs, inputs_by): @@ -182,7 +182,7 @@ def build_workflow_run_config( trans, workflow, payload ): add_to_history = 'no_add_to_history' not in payload history_param = payload.get('history', '') - allow_tool_upgrades = payload.get( 'allow_tool_upgrades', False ) + allow_tool_state_corrections = payload.get( 'allow_tool_state_corrections', False ) # Sanity checks. if len( workflow.steps ) == 0: @@ -273,7 +273,7 @@ def build_workflow_run_config( trans, workflow, payload ): replacement_dict=replacement_dict, inputs=normalized_inputs, param_map=param_map, - allow_tool_upgrades=allow_tool_upgrades + allow_tool_state_corrections=allow_tool_state_corrections ) return run_config From 1020d46c52b1fc0fa2effa2882f1fd64216d2c75 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 29 Jun 2015 16:51:00 -0400 Subject: [PATCH 020/165] fix paging issue with whoosh due to missing str to int conversion --- lib/galaxy/webapps/tool_shed/api/repositories.py | 4 ++++ lib/galaxy/webapps/tool_shed/api/tools.py | 4 ++++ lib/galaxy/webapps/tool_shed/search/repo_search.py | 7 ++++++- lib/galaxy/webapps/tool_shed/search/tool_search.py | 7 ++++++- 4 files changed, 20 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/webapps/tool_shed/api/repositories.py b/lib/galaxy/webapps/tool_shed/api/repositories.py index 3424cd2ac4f..55f04a4cf48 100644 --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -357,6 +357,10 @@ class RepositoriesController( BaseAPIController ): q = kwd.get( 'q', '' ) if q: page = kwd.get( 'page', 1 ) + try: + page = int( page ) + except ValueError: + raise RequestParameterInvalidException( 'The "page" requested has to be an integer.' ) return_jsonp = util.asbool( kwd.get( 'jsonp', False ) ) callback = kwd.get( 'callback', 'callback' ) search_results = self._search( trans, q, page ) diff --git a/lib/galaxy/webapps/tool_shed/api/tools.py b/lib/galaxy/webapps/tool_shed/api/tools.py index d2109221f27..19b48ae68c9 100644 --- a/lib/galaxy/webapps/tool_shed/api/tools.py +++ b/lib/galaxy/webapps/tool_shed/api/tools.py @@ -46,6 +46,10 @@ class ToolsController( BaseAPIController ): raise NotImplemented( 'Listing of all the tools is not implemented. Provide parameter "q" to search instead.' ) else: page = kwd.get( 'page', 1 ) + try: + page = int( page ) + except ValueError: + raise RequestParameterInvalidException( 'The "page" requested has to be an integer.' ) return_jsonp = util.asbool( kwd.get( 'jsonp', False ) ) callback = kwd.get( 'callback', 'callback' ) search_results = self._search( trans, q, page ) diff --git a/lib/galaxy/webapps/tool_shed/search/repo_search.py b/lib/galaxy/webapps/tool_shed/search/repo_search.py index a6a295e5dc6..bf59bcf69b3 100644 --- a/lib/galaxy/webapps/tool_shed/search/repo_search.py +++ b/lib/galaxy/webapps/tool_shed/search/repo_search.py @@ -3,6 +3,7 @@ import datetime from galaxy import exceptions from galaxy import eggs from galaxy.webapps.tool_shed import model +from galaxy.exceptions import ObjectNotFound import logging log = logging.getLogger( __name__ ) @@ -100,7 +101,11 @@ class RepoSearch( object ): 'repo_owner_username' ], schema = schema ) user_query = parser.parse( '*' + search_term + '*' ) - hits = searcher.search_page( user_query, page, pagelen = 10, terms = True ) + + try: + hits = searcher.search_page( user_query, page, pagelen = 10, terms = True ) + except ValueError: + raise ObjectNotFound( 'The requested page does not exist.' ) log.debug( 'searching for: #' + str( search_term ) ) log.debug( 'total hits: ' + str( len( hits ) ) ) diff --git a/lib/galaxy/webapps/tool_shed/search/tool_search.py b/lib/galaxy/webapps/tool_shed/search/tool_search.py index c829932b6ae..e49820ca1d9 100644 --- a/lib/galaxy/webapps/tool_shed/search/tool_search.py +++ b/lib/galaxy/webapps/tool_shed/search/tool_search.py @@ -6,6 +6,7 @@ from galaxy import exceptions from galaxy import eggs from galaxy import web from galaxy.webapps.tool_shed import model +from galaxy.exceptions import ObjectNotFound eggs.require( "Whoosh" ) import whoosh.index from whoosh import scoring @@ -60,7 +61,11 @@ class ToolSearch( object ): 'repo_owner_username' ], schema = tool_schema ) user_query = parser.parse( '*' + search_term + '*' ) - hits = searcher.search_page( user_query, page, pagelen = 10, terms = True ) + + try: + hits = searcher.search_page( user_query, page, pagelen = 10, terms = True ) + except ValueError: + raise ObjectNotFound( 'The requested page does not exist.' ) log.debug( 'searching tools for: #' + str( search_term ) ) log.debug( 'total hits: ' + str( len( hits ) ) ) From ebdd5e5d468deea70fc5bda89177caae65f11a10 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Sat, 27 Jun 2015 10:28:28 -0400 Subject: [PATCH 021/165] Fix managers to pass context necessary down the chain when purging. This should fix at least one quota calc error. Fix another bug in hda manager regarding quota reduction -- quota usage must be calculated prior to actually purging, otherwise the disk usage is 0 and this does nothing. Slight refactoring in manager purge -- we don't need to pass the user via context since we can just grab it where applicable from the history. Fix purge when handling an anonymous user --- lib/galaxy/managers/hdas.py | 10 +++++++--- lib/galaxy/managers/histories.py | 1 - 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py index e724d660a59..18e9955e906 100644 --- a/lib/galaxy/managers/hdas.py +++ b/lib/galaxy/managers/hdas.py @@ -143,14 +143,18 @@ class HDAManager( datasets.DatasetAssociationManager, return ldda.to_history_dataset_association( history, add_to_history=True ) # .... deletion and purging - def purge( self, hda, current_user=None, flush=True ): + def purge( self, hda, flush=True): """ Purge this HDA and the dataset underlying it. """ + user = hda.history.user or None + quota_amount_reduction = 0 + if user: + quota_amount_reduction = hda.quota_amount( user ) super( HDAManager, self ).purge( hda, flush=flush ) # decrease the user's space used - if current_user: - current_user.total_disk_usage -= hda.quota_amount( current_user ) + if quota_amount_reduction: + user.total_disk_usage -= quota_amount_reduction return hda # .... states diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py index 14e53aa230d..1ebe9269bdb 100644 --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -82,7 +82,6 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi Purge this history and all HDAs, Collections, and Datasets inside this history. """ self.hda_manager.dataset_manager.error_unless_dataset_purge_allowed() - # First purge all the datasets for hda in history.datasets: if not hda.purged: From daae1876c39f361bbfd1ea3cd0a5c394196df294 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Sat, 27 Jun 2015 10:28:28 -0400 Subject: [PATCH 022/165] Fix managers to pass context necessary down the chain when purging. This should fix at least one quota calc error. Fix another bug in hda manager regarding quota reduction -- quota usage must be calculated prior to actually purging, otherwise the disk usage is 0 and this does nothing. Slight refactoring in manager purge -- we don't need to pass the user via context since we can just grab it where applicable from the history. Fix purge when handling an anonymous user --- lib/galaxy/managers/hdas.py | 10 +++++++--- lib/galaxy/managers/histories.py | 1 - 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py index e724d660a59..18e9955e906 100644 --- a/lib/galaxy/managers/hdas.py +++ b/lib/galaxy/managers/hdas.py @@ -143,14 +143,18 @@ class HDAManager( datasets.DatasetAssociationManager, return ldda.to_history_dataset_association( history, add_to_history=True ) # .... deletion and purging - def purge( self, hda, current_user=None, flush=True ): + def purge( self, hda, flush=True): """ Purge this HDA and the dataset underlying it. """ + user = hda.history.user or None + quota_amount_reduction = 0 + if user: + quota_amount_reduction = hda.quota_amount( user ) super( HDAManager, self ).purge( hda, flush=flush ) # decrease the user's space used - if current_user: - current_user.total_disk_usage -= hda.quota_amount( current_user ) + if quota_amount_reduction: + user.total_disk_usage -= quota_amount_reduction return hda # .... states diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py index 14e53aa230d..1ebe9269bdb 100644 --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -82,7 +82,6 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi Purge this history and all HDAs, Collections, and Datasets inside this history. """ self.hda_manager.dataset_manager.error_unless_dataset_purge_allowed() - # First purge all the datasets for hda in history.datasets: if not hda.purged: From 4d20a61a345252e636befde68170291a506bfe9e Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Tue, 30 Jun 2015 17:20:11 +0200 Subject: [PATCH 023/165] Use web.url_for( '/', qualified=True ) instead of '/' to generate URL for toolshed repository downloads. Fixes repository downloads from toolsheds that are on a subfolder (e.g. http://example.com/toolshed). --- lib/galaxy/webapps/tool_shed/controllers/repository.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py index b7f7bf71056..188e35329b6 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1226,7 +1226,8 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ): repository.times_downloaded += 1 trans.sa_session.add( repository ) trans.sa_session.flush() - download_url = common_util.url_join( '/', + tool_shed_url = web.url_for( '/', qualified=True ) + download_url = common_util.url_join( tool_shed_url, 'repos', str( repository.user.username ), str( repository.name ), From 0357a43f55d6f5cb66baa27e6c72456fd6b8cbad Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 30 Jun 2015 11:29:44 -0400 Subject: [PATCH 024/165] Fix workflow run for certain kinds of explicit output collections. Workflows with steps that produce an unknown number of datasets must explicitly be sent to the new workflow engine - since the workflow needs be re-evaluated after such steps have completed. This change updates the force_queue to check workflow steps for such collections and return True if any are found - this is what causes certain GUI driven workflows to use the new workflow engine. --- lib/galaxy/tools/__init__.py | 10 ++++++++++ lib/galaxy/workflow/run.py | 2 ++ 2 files changed, 12 insertions(+) diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index 88af8170c98..1f2d5dd3ba3 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -500,6 +500,16 @@ class Tool( object, Dictifiable ): def produces_collections( self ): return any( o.collection for o in self.outputs.values() ) + @property + def produces_collections_with_unknown_structure( self ): + + def output_is_dynamic(output): + if not output.collection: + return False + return output.dynamic_structure + + return any( map( output_is_dynamic, self.outputs.values() ) ) + def __get_job_tool_configuration(self, job_params=None): """Generalized method for getting this tool's job configuration. diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py index 6a07fe4869b..1eb7ed0c40c 100644 --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -50,6 +50,8 @@ def force_queue( trans, workflow ): if step.type == "data_collection_input" and force_for_collection: log.info("Found collection input step - backgrounding execution") return True + if step.type == "tool" and step.module.tool.produces_collections_with_unknown_structure: + return True return False From af62976cc87a968be1ee4fb920c0fcc6316c41b6 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 30 Jun 2015 11:41:00 -0400 Subject: [PATCH 025/165] Add log statement in previous fix for consistency. Thanks for the tip @dannon. --- lib/galaxy/workflow/run.py | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py index 1eb7ed0c40c..7d587ca1aca 100644 --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -51,6 +51,7 @@ def force_queue( trans, workflow ): log.info("Found collection input step - backgrounding execution") return True if step.type == "tool" and step.module.tool.produces_collections_with_unknown_structure: + log.info("Found dynamically structured output collection - backgrounding execution") return True return False From fcc706e8d0c888a2a6b6b91e1b9312feb8021a7c Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Tue, 30 Jun 2015 11:50:27 -0500 Subject: [PATCH 026/165] Whitespace/other small fixes --- .../interactive_environments/ipython/templates/ipython.mako | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/config/plugins/interactive_environments/ipython/templates/ipython.mako b/config/plugins/interactive_environments/ipython/templates/ipython.mako index a0a3b1e7059..118d72baf2f 100644 --- a/config/plugins/interactive_environments/ipython/templates/ipython.mako +++ b/config/plugins/interactive_environments/ipython/templates/ipython.mako @@ -1,4 +1,4 @@ - <%namespace name="ie" file="ie.mako" /> +<%namespace name="ie" file="ie.mako" /> <% import os @@ -16,7 +16,7 @@ if ie_request.attr.PASSWORD_AUTH: m.update( ie_request.notebook_pw + ie_request.notebook_pw_salt ) PASSWORD = 'sha1:%s:%s' % (ie_request.notebook_pw_salt, m.hexdigest()) else: - PASSWORD = "none" + PASSWORD = "none" ## IPython Specific # Prepare an empty notebook @@ -26,6 +26,7 @@ with open( os.path.join( ie_request.attr.our_template_dir, 'notebook.ipynb' ), ' empty_nb = empty_nb % notebook_id # Copy over default notebook, unless the dataset this viz is running on is a notebook empty_nb_path = os.path.join(temp_dir, 'ipython_galaxy_notebook.ipynb') + if hda.datatype.__class__.__name__ != "Ipynb": with open( empty_nb_path, 'w+' ) as handle: handle.write( empty_nb ) From 5409bf3be304adc0bf376613ecf7003c0431826f Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Tue, 30 Jun 2015 11:54:19 -0500 Subject: [PATCH 027/165] Switch to full template It looks a *lot* nicer --- lib/galaxy/datatypes/text.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py index 2fc438181fd..7bebd6b329e 100644 --- a/lib/galaxy/datatypes/text.py +++ b/lib/galaxy/datatypes/text.py @@ -107,7 +107,7 @@ class Ipynb( Json ): ofilename = ofile_handle.name ofile_handle.close() try: - cmd = 'ipython nbconvert --to html --template basic %s --output %s' % (dataset.file_name, ofilename) + cmd = 'ipython nbconvert --to html --template full %s --output %s' % (dataset.file_name, ofilename) log.info("Calling command %s" % cmd) subprocess.call(cmd, shell=True) ofilename = '%s.html' % ofilename From 8b7a455b01f8394925fb0398fa57a7ffad241139 Mon Sep 17 00:00:00 2001 From: guerler Date: Tue, 30 Jun 2015 13:46:12 -0400 Subject: [PATCH 028/165] Disable custome tooltips for histograms --- config/plugins/visualizations/charts/static/build-app.js | 7 +------ .../charts/static/charts/nvd3/histogram/config.js | 7 ++++--- .../charts/static/charts/nvd3/histogram_discrete/config.js | 7 ++++--- .../plugins/visualizations/charts/static/views/editor.js | 4 ++-- .../plugins/visualizations/charts/static/views/viewport.js | 2 +- 5 files changed, 12 insertions(+), 15 deletions(-) diff --git a/config/plugins/visualizations/charts/static/build-app.js b/config/plugins/visualizations/charts/static/build-app.js index ccd7acfa3b3..f3d997cf9e7 100644 --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -1,6 +1 @@ -// Underscore.js 1.7.0 -// http://underscorejs.org -// (c) 2009-2014 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors -// Underscore may be freely distributed under the MIT license. - 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