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Rename tool_shed_get to url_get.

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This commit is contained in:
Dave Bouvier
2016-03-15 09:04:06 -04:00
parent ff0bcd3920
commit edb51d876b
14 changed files with 52 additions and 50 deletions
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lib/galaxy/util/__init__.py
+20
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@@ -1342,6 +1342,26 @@ def parse_int(value, min_val=None, max_val=None, default=None, allow_none=False)
raise
def url_get( app, base_url, toolshed=True, pathspec=None, params=None ):
"""Make contact with the uri provided and return any contents."""
# urllib2 auto-detects system proxies, when passed a Proxyhandler.
# Refer: https://docs.python.org/2/howto/urllib2.html#proxies
proxy = urllib2.ProxyHandler()
urlopener = urllib2.build_opener( proxy )
urllib2.install_opener( urlopener )
if toolshed:
registry = app.tool_shed_registry
password_mgr = registry.password_manager_for_url( base_url )
if password_mgr is not None:
auth_handler = urllib2.HTTPBasicAuthHandler( password_mgr )
urlopener.add_handler( auth_handler )
full_url = url_join( base_url, pathspec=pathspec, params=params )
response = urlopener.open( full_url )
content = response.read()
response.close()
return content
def safe_relpath(path):
"""
Given what we expect to be a relative path, determine whether the path
lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+1 -1
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@@ -100,7 +100,7 @@ class ToolShedRepositoriesController( BaseAPIController ):
params = dict(name=name, owner=owner)
pathspec = ['api', 'repositories', 'get_ordered_installable_revisions']
try:
raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec, params )
raw_text = util.url_get( trans.app, tool_shed_url, pathspec, params )
except Exception, e:
message = "Error attempting to retrieve the latest installable revision from tool shed %s for repository %s owned by %s: %s" % \
( str( tool_shed_url ), str( name ), str( owner ), str( e ) )
lib/galaxy/webapps/galaxy/controllers/admin.py
+1 -1
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@@ -781,7 +781,7 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuotaMixin, QuotaP
changeset_revision = elem.get( 'changeset_revision' )
params = dict( name=repository_name, owner='devteam', changeset_revision=changeset_revision )
pathspec = [ 'repository', 'get_tool_dependencies' ]
text = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
text = url_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
if text:
tool_dependencies_dict = encoding_util.tool_shed_decode( text )
for dependency_key, requirements_dict in tool_dependencies_dict.items():
lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+7 -7
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@@ -413,7 +413,7 @@ class AdminToolshed( AdminGalaxy ):
raise Exception( message )
params = dict( name=repository_name, owner=repository_owner, changeset_revision=changeset_revision )
pathspec = [ 'repository', 'get_tool_dependencies' ]
raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
raw_text = util.url_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
if len( raw_text ) > 2:
encoded_text = json.loads( raw_text )
text = encoding_util.tool_shed_decode( encoded_text )
@@ -439,7 +439,7 @@ class AdminToolshed( AdminGalaxy ):
owner=str( repository_owner ),
changeset_revision=changeset_revision )
pathspec = [ 'repository', 'get_updated_repository_information' ]
raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
raw_text = util.url_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
repo_information_dict = json.loads( raw_text )
return repo_information_dict
@@ -529,7 +529,7 @@ class AdminToolshed( AdminGalaxy ):
name=name,
owner=owner )
pathspec = [ 'repository', 'get_latest_downloadable_changeset_revision' ]
raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
raw_text = util.url_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
url = common_util.url_join( tool_shed_url, pathspec=pathspec, params=params )
latest_downloadable_revision = json.loads( raw_text )
if latest_downloadable_revision == hg_util.INITIAL_CHANGELOG_HASH:
@@ -985,7 +985,7 @@ class AdminToolshed( AdminGalaxy ):
try:
params = dict( name=str( repository.name ), owner=str( repository.owner ) )
pathspec = [ 'repository', 'get_repository_id' ]
repository_ids = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
repository_ids = util.url_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
except Exception, e:
# The Tool Shed cannot handle the get_repository_id request, so the code must be older than the
# 04/2014 Galaxy release when it was introduced. It will be safest to error out and let the
@@ -1005,7 +1005,7 @@ class AdminToolshed( AdminGalaxy ):
# Get the information necessary to install each repository.
params = dict( repository_ids=str( repository_ids ), changeset_revisions=str( changeset_revisions ) )
pathspec = [ 'repository', 'get_repository_information' ]
raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
raw_text = util.url_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
repo_information_dict = json.loads( raw_text )
for encoded_repo_info_dict in repo_information_dict.get( 'repo_info_dicts', [] ):
decoded_repo_info_dict = encoding_util.tool_shed_decode( encoded_repo_info_dict )
@@ -1539,7 +1539,7 @@ class AdminToolshed( AdminGalaxy ):
owner=tool_shed_repository.owner,
changeset_revision=tool_shed_repository.installed_changeset_revision )
pathspec = [ 'repository', 'get_readme_files' ]
raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
raw_text = util.url_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
readme_files_dict = json.loads( raw_text )
tool_dependencies = metadata.get( 'tool_dependencies', None )
rdim = repository_dependency_manager.RepositoryDependencyInstallManager( trans.app )
@@ -1739,7 +1739,7 @@ class AdminToolshed( AdminGalaxy ):
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) )
params = dict( name=repository.name, owner=repository.owner, changeset_revision=repository.changeset_revision )
pathspec = [ 'repository', 'get_tool_versions' ]
text = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
text = util.url_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
if text:
tool_version_dicts = json.loads( text )
tvm = tool_version_manager.ToolVersionManager( trans.app )
lib/galaxy/webapps/galaxy/controllers/workflow.py
+1 -1
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@@ -862,7 +862,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
workflow_name=encoding_util.tool_shed_encode( workflow_name ),
open_for_url=True )
pathspec = [ 'workflow', 'import_workflow' ]
workflow_text = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
workflow_text = util.url_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
import_button = True
if import_button:
workflow_data = None
lib/tool_shed/galaxy_install/dependency_display.py
+1 -1
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@@ -455,7 +455,7 @@ class DependencyDisplayer( object ):
owner=str( repository.owner ),
changeset_revision=str( repository.installed_changeset_revision ) )
pathspec = [ 'repository', 'get_readme_files' ]
raw_text = common_util.tool_shed_get( self.app, tool_shed_url, pathspec=pathspec, params=params )
raw_text = util.url_get( self.app, tool_shed_url, pathspec=pathspec, params=params )
readme_files_dict = json.loads( raw_text )
else:
readme_files_dict = readme_util.build_readme_files_dict( self.app,
lib/tool_shed/galaxy_install/install_manager.py
+2 -2
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@@ -460,7 +460,7 @@ class InstallRepositoryManager( object ):
changeset_revision=str( changeset_revision ) )
pathspec = [ 'api', 'repositories', 'get_repository_revision_install_info' ]
try:
raw_text = common_util.tool_shed_get( self.app, tool_shed_url, pathspec=pathspec, params=params )
raw_text = util.url_get( self.app, tool_shed_url, pathspec=pathspec, params=params )
except Exception, e:
message = "Error attempting to retrieve installation information from tool shed "
message += "%s for revision %s of repository %s owned by %s: %s" % \
@@ -1006,7 +1006,7 @@ def fetch_tool_versions( app, tool_shed_repository ):
changeset_revision=str( tool_shed_repository.changeset_revision ) )
pathspec = [ 'repository', 'get_tool_versions' ]
url = common_util.url_join( tool_shed_url, pathspec=pathspec, params=params )
text = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
text = util.url_get( app, tool_shed_url, pathspec=pathspec, params=params )
if text:
return json.loads( text )
else:
lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
+2 -2
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@@ -8,7 +8,7 @@ import os
import urllib
import urllib2
from galaxy.util import asbool
from galaxy.util import asbool, url_get
from tool_shed.galaxy_install.tools import tool_panel_manager
@@ -291,7 +291,7 @@ class RepositoryDependencyInstallManager( object ):
changeset_revision=str( repository.changeset_revision ) )
pathspec = [ 'repository', 'get_repository_dependencies' ]
try:
raw_text = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
raw_text = url_get( app, tool_shed_url, pathspec=pathspec, params=params )
except Exception, e:
log.error("The URL\n%s\nraised the exception:\n%s\n", common_util.url_join( tool_shed_url, pathspec=pathspec, params=params ), str( e ) )
return ''
lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
+2 -2
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@@ -3,7 +3,7 @@ import os
import tempfile
from galaxy.tools.deps.resolvers import INDETERMINATE_DEPENDENCY
from galaxy.util import listify
from galaxy.util import listify, url_get
from tool_shed.util import basic_util
from tool_shed.util import common_util
from tool_shed.util import shed_util_common as suc
@@ -249,7 +249,7 @@ class Repository( RecipeTag, SyncDatabase ):
owner=owner,
changeset_revision=changeset_revision )
pathspec = [ 'repository', 'get_tool_dependencies_config_contents' ]
text = common_util.tool_shed_get( self.app, tool_shed_url, pathspec=pathspec, params=params )
text = url_get( self.app, tool_shed_url, pathspec=pathspec, params=params )
if text:
# Write the contents to a temporary file on disk so it can be reloaded and parsed.
fh = tempfile.NamedTemporaryFile( 'wb', prefix="tmp-toolshed-cttdc" )
lib/tool_shed/galaxy_install/tool_migration_manager.py
+1 -1
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@@ -581,7 +581,7 @@ class ToolMigrationManager( object ):
owner=self.repository_owner,
changeset_revision=tool_shed_repository.installed_changeset_revision )
pathspec = [ 'repository', 'get_tool_versions' ]
text = common_util.tool_shed_get( self.app, self.tool_shed_url, pathspec=pathspec, params=params )
text = util.url_get( self.app, self.tool_shed_url, pathspec=pathspec, params=params )
if text:
tool_version_dicts = json.loads( text )
tvm.handle_tool_versions( tool_version_dicts, tool_shed_repository )
lib/tool_shed/galaxy_install/update_repository_manager.py
+2 -1
View File
@@ -9,6 +9,7 @@ from sqlalchemy import false
import tool_shed.util.shed_util_common as suc
from tool_shed.util import common_util
from tool_shed.util import encoding_util
from galaxy import util
log = logging.getLogger( __name__ )
@@ -36,7 +37,7 @@ class UpdateRepositoryManager( object ):
changeset_revision=str( repository.installed_changeset_revision ) )
pathspec = [ 'repository', 'get_changeset_revision_and_ctx_rev' ]
try:
encoded_update_dict = common_util.tool_shed_get( self.app, tool_shed_url, pathspec=pathspec, params=params )
encoded_update_dict = util.url_get( self.app, tool_shed_url, pathspec=pathspec, params=params )
if encoded_update_dict:
update_dict = encoding_util.tool_shed_decode( encoded_update_dict )
includes_data_managers = update_dict.get( 'includes_data_managers', False )
lib/tool_shed/util/common_util.py
+2 -21
View File
@@ -160,7 +160,7 @@ def get_repository_dependencies( app, tool_shed_url, repository_name, repository
params = dict( name=repository_name, owner=repository_owner, changeset_revision=changeset_revision )
pathspec = [ 'repository', 'get_repository_dependencies' ]
try:
raw_text = tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
raw_text = util.url_get( app, tool_shed_url, pathspec=pathspec, params=params )
tool_shed_accessible = True
except Exception, e:
tool_shed_accessible = False
@@ -192,7 +192,7 @@ def get_tool_dependencies( app, tool_shed_url, repository_name, repository_owner
params = dict( name=repository_name, owner=repository_owner, changeset_revision=changeset_revision )
pathspec = [ 'repository', 'get_tool_dependencies' ]
try:
text = tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
text = util.url_get( app, tool_shed_url, pathspec=pathspec, params=params )
tool_shed_accessible = True
except Exception, e:
tool_shed_accessible = False
@@ -341,25 +341,6 @@ def remove_protocol_from_tool_shed_url( tool_shed_url ):
return util.remove_protocol_from_url( tool_shed_url )
def tool_shed_get( app, base_url, pathspec=None, params=None ):
"""Make contact with the tool shed via the uri provided."""
registry = app.tool_shed_registry
# urllib2 auto-detects system proxies, when passed a Proxyhandler.
# Refer: https://docs.python.org/2/howto/urllib2.html#proxies
proxy = urllib2.ProxyHandler()
urlopener = urllib2.build_opener( proxy )
urllib2.install_opener( urlopener )
password_mgr = registry.password_manager_for_url( base_url )
if password_mgr is not None:
auth_handler = urllib2.HTTPBasicAuthHandler( password_mgr )
urlopener.add_handler( auth_handler )
full_url = url_join( base_url, pathspec=pathspec, params=params )
response = urlopener.open( full_url )
content = response.read()
response.close()
return content
def url_join( base_url, pathspec=None, params=None ):
"""Return a valid URL produced by appending a base URL and a set of request parameters."""
url = base_url.rstrip( '/' )
lib/tool_shed/util/readme_util.py
+2 -2
View File
@@ -7,7 +7,7 @@ from mako.template import Template
import tool_shed.util.shed_util_common as suc
from galaxy import web
from galaxy.util import rst_to_html, unicodify
from galaxy.util import rst_to_html, unicodify, url_get
from tool_shed.util import basic_util, common_util, hg_util
log = logging.getLogger( __name__ )
@@ -97,7 +97,7 @@ def get_readme_files_dict_for_display( app, tool_shed_url, repo_info_dict ):
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
params = dict( name=name, owner=repository_owner, changeset_revision=changeset_revision )
pathspec = [ 'repository', 'get_readme_files' ]
raw_text = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
raw_text = url_get( app, tool_shed_url, pathspec=pathspec, params=params )
readme_files_dict = json.loads( raw_text )
return readme_files_dict
lib/tool_shed/util/shed_util_common.py
+8 -8
View File
@@ -301,7 +301,7 @@ def get_ctx_rev( app, tool_shed_url, name, owner, changeset_revision ):
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
params = dict( name=name, owner=owner, changeset_revision=changeset_revision )
pathspec = [ 'repository', 'get_ctx_rev' ]
ctx_rev = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
ctx_rev = util.url_get( app, tool_shed_url, pathspec=pathspec, params=params )
return ctx_rev
@@ -369,7 +369,7 @@ def get_tool_dependency_definition_metadata_from_tool_shed( app, tool_shed_url,
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
params = dict( name=name, owner=owner )
pathspec = [ 'repository', 'get_tool_dependency_definition_metadata' ]
metadata = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
metadata = util.url_get( app, tool_shed_url, pathspec=pathspec, params=params )
return metadata
@@ -626,7 +626,7 @@ def get_repository_for_dependency_relationship( app, tool_shed, name, owner, cha
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed )
params = dict( name=name, owner=owner, changeset_revision=changeset_revision )
pathspec = [ 'repository', 'next_installable_changeset_revision' ]
text = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
text = util.url_get( app, tool_shed_url, pathspec=pathspec, params=params )
if text:
repository = get_installed_repository( app=app,
tool_shed=tool_shed,
@@ -828,7 +828,7 @@ def get_repository_type_from_tool_shed( app, tool_shed_url, name, owner ):
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
params = dict( name=name, owner=owner )
pathspec = [ 'repository', 'get_repository_type' ]
repository_type = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
repository_type = util.url_get( app, tool_shed_url, pathspec=pathspec, params=params )
return repository_type
@@ -914,7 +914,7 @@ def get_tool_shed_status_for_installed_repository( app, repository ):
params = dict( name=repository.name, owner=repository.owner, changeset_revision=repository.changeset_revision )
pathspec = [ 'repository', 'status_for_installed_repository' ]
try:
encoded_tool_shed_status_dict = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
encoded_tool_shed_status_dict = util.url_get( app, tool_shed_url, pathspec=pathspec, params=params )
tool_shed_status_dict = encoding_util.tool_shed_decode( encoded_tool_shed_status_dict )
return tool_shed_status_dict
except HTTPError, e:
@@ -926,7 +926,7 @@ def get_tool_shed_status_for_installed_repository( app, repository ):
params[ 'from_update_manager' ] = True
try:
# The value of text will be 'true' or 'false', depending upon whether there is an update available for the installed revision.
text = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
text = util.url_get( app, tool_shed_url, pathspec=pathspec, params=params )
return dict( revision_update=text )
except Exception, e:
# The required tool shed may be unavailable, so default the revision_update value to 'false'.
@@ -1021,7 +1021,7 @@ def get_updated_changeset_revisions_from_tool_shed( app, tool_shed_url, name, ow
raise Exception( message )
params = dict( name=name, owner=owner, changeset_revision=changeset_revision )
pathspec = [ 'repository', 'updated_changeset_revisions' ]
text = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
text = util.url_get( app, tool_shed_url, pathspec=pathspec, params=params )
return text
@@ -1227,7 +1227,7 @@ def repository_was_previously_installed( app, tool_shed_url, repository_name, re
changeset_revision=changeset_revision,
from_tip=str( from_tip ) )
pathspec = [ 'repository', 'previous_changeset_revisions' ]
text = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
text = util.url_get( app, tool_shed_url, pathspec=pathspec, params=params )
if text:
changeset_revisions = util.listify( text )
for previous_changeset_revision in changeset_revisions: