diff --git a/.gitignore b/.gitignore index e43721a088c..1bb752fda18 100644 --- a/.gitignore +++ b/.gitignore @@ -76,6 +76,7 @@ tool-data/shared/igv/igv_build_sites.txt tool-data/shared/rviewer/rviewer_build_sites.txt tool-data/shared/ncbi/builds.txt tool-data/shared/ucsc/builds.txt +tool-data/shared/ucsc/manual_builds.txt tool-data/shared/ensembl/builds.txt tool-data/shared/ucsc/publicbuilds.txt tool-data/shared/ucsc/ucsc_build_sites.txt diff --git a/client/galaxy/scripts/mvc/collection/collection-model.js b/client/galaxy/scripts/mvc/collection/collection-model.js index 844309f6e6e..49da237372c 100644 --- a/client/galaxy/scripts/mvc/collection/collection-model.js +++ b/client/galaxy/scripts/mvc/collection/collection-model.js @@ -241,10 +241,12 @@ var DatasetCollection = Backbone.Model return json; }, - /** is the collection done with updates and ready to be used? (finished running, etc.) */ + /** Is this collection in a 'ready' state no processing (for the collection) is left + * to do on the server. + */ inReadyState : function(){ -//TODO: state currenly unimplemented for collections - return true; + var populated = this.get( 'populated' ); + return ( this.isDeletedOrPurged() || populated ); }, //TODO:?? the following are the same interface as DatasetAssociation - can we combine? diff --git a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js index 23a8181f3db..74d8c465913 100644 --- a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js +++ b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js @@ -159,20 +159,22 @@ var DatasetListItemEdit = _super.extend( /** Render icon-button to re-run the job that created this dataset. */ _renderRerunButton : function(){ var creating_job = this.model.get('creating_job'); - return faIconButton({ - title : _l( 'Run this job again' ), - href : this.model.urls.rerun, - classes : 'rerun-btn', - target : this.linkTarget, - faIcon : 'fa-refresh', - onclick : function(ev) { - ev.preventDefault(); - var form = new ToolsForm.View({'job_id' : creating_job}); - form.deferred.execute(function(){ - Galaxy.app.display(form.$el); - }); - } - }); + if (this.model.get('rerunnable')){ + return faIconButton({ + title : _l( 'Run this job again' ), + href : this.model.urls.rerun, + classes : 'rerun-btn', + target : this.linkTarget, + faIcon : 'fa-refresh', + onclick : function(ev) { + ev.preventDefault(); + var form = new ToolsForm.View({'job_id' : creating_job}); + form.deferred.execute(function(){ + Galaxy.app.display(form.$el); + }); + } + }); + } }, /** Render an icon-button or popupmenu of links based on the applicable visualizations */ diff --git a/client/galaxy/scripts/mvc/dataset/dataset-li.js b/client/galaxy/scripts/mvc/dataset/dataset-li.js index c8c80aaf774..09c390fe220 100644 --- a/client/galaxy/scripts/mvc/dataset/dataset-li.js +++ b/client/galaxy/scripts/mvc/dataset/dataset-li.js @@ -37,8 +37,6 @@ var DatasetListItemView = _super.extend( /** where should pages from links be displayed? (default to new tab/window) */ this.linkTarget = attributes.linkTarget || '_blank'; - - this._setUpListeners(); }, /** event listeners */ @@ -60,13 +58,21 @@ var DatasetListItemView = _super.extend( }, // ......................................................................... expandable - /** In this override, only get details if in the ready state. + /** In this override, only get details if in the ready state, get rerunnable if in other states. * Note: fetch with no 'change' event triggering to prevent automatic rendering. */ _fetchModelDetails : function(){ var view = this; if( view.model.inReadyState() && !view.model.hasDetails() ){ return view.model.fetch({ silent: true }); + + // special case the need for the rerunnable and creating_job attributes + // needed for rendering re-run button on queued, running datasets + } else if( !view.model.has( 'rerunnable' ) ){ + return view.model.fetch({ silent: true, data: { + // only fetch rerunnable and creating_job to keep overhead down + keys: [ 'rerunnable', 'creating_job' ].join(',') + }}); } return jQuery.when(); }, diff --git a/client/galaxy/scripts/mvc/history/hdca-li.js b/client/galaxy/scripts/mvc/history/hdca-li.js index ee633d82e87..b2b9977ef4e 100644 --- a/client/galaxy/scripts/mvc/history/hdca-li.js +++ b/client/galaxy/scripts/mvc/history/hdca-li.js @@ -21,11 +21,9 @@ var HDCAListItemView = _super.extend( /** event listeners */ _setUpListeners : function(){ _super.prototype._setUpListeners.call( this ); - // re-rendering on deletion + this.model.on( 'change', function( model, options ){ - if( _.isEqual( _.keys( model.changed ), [ 'visible' ] ) ){ - this.render(); - } + this.render(); }, this ); }, @@ -46,7 +44,7 @@ var HDCAListItemView = _super.extend( _swapNewRender : function( $newRender ){ _super.prototype._swapNewRender.call( this, $newRender ); //TODO: model currently has no state - var state = this.model.get( 'state' ) || STATES.OK; + var state = !this.model.get( 'populated' ) ? STATES.RUNNING : STATES.OK; //if( this.model.has( 'state' ) ){ this.$el.addClass( 'state-' + state ); //} diff --git a/client/galaxy/scripts/mvc/tools/tools-form-base.js b/client/galaxy/scripts/mvc/tools/tools-form-base.js index 890276934bd..5f4406d5bc2 100644 --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -120,12 +120,12 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', if (self.form == undefined){ self.form = new Form(); } - self.form.modal.show({ + Galaxy.modal.show({ title : 'Tool cannot be executed', body : error_message, buttons : { 'Close' : function() { - self.form.modal.hide(); + Galaxy.modal.hide(); } } }); diff --git a/client/galaxy/scripts/mvc/tools/tools-jobs.js b/client/galaxy/scripts/mvc/tools/tools-jobs.js index ccd746630bb..24e4bab3d76 100644 --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -35,6 +35,7 @@ return { success : function(response) { callback && callback(); form.reciept(ToolTemplate.success(response)); + // begin checking the history for updates self._refreshHdas(); }, error : function(response, response_full) { @@ -135,11 +136,11 @@ return { /** Refreshes the history panel */ - _refreshHdas: function() { + _refreshHdas: function(detailIds, options) { if (parent.Galaxy && parent.Galaxy.currHistoryPanel) { - parent.Galaxy.currHistoryPanel.refreshContents(); + parent.Galaxy.currHistoryPanel.refreshContents(detailIds, options); } } }; -}); \ No newline at end of file +}); diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index 5dadaaa29b4..f8eec9d56eb 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -574,6 +574,12 @@ nglims_config_file = tool-data/nglims.yaml # nodejs to wrap connections in SSL). #dynamic_proxy_external_proxy=False +# Additionally, when the dynamic proxy is proxied by an upstream server, you'll +# want to specify a prefixed URL so both Galaxy and the proxy reside under the +# same path that your cookies are under. This will result in a url like +# https://FQDN/galaxy-prefix/gie_proxy for proxying +#dynamic_proxy_prefix=gie_proxy + # -- Logging and Debugging # If True, Galaxy will attempt to configure a simple root logger if a @@ -648,6 +654,14 @@ use_interactive = True # lot of CPU. #use_heartbeat = False + +# Log to Sentry +# Sentry is an open source logging and error aggregation platform. Setting +# sentry_dsn will enable the Sentry middleware and errors will be sent to the +# indicated sentry instance. This connection string is available in your +# sentry instance under -> Settings -> API Keys. +#sentry_dsn = None + # -- Data Libraries # These library upload options are described in much more detail in the wiki: diff --git a/config/job_conf.xml.sample_advanced b/config/job_conf.xml.sample_advanced index 08df8099af7..ea093ce8af5 100644 --- a/config/job_conf.xml.sample_advanced +++ b/config/job_conf.xml.sample_advanced @@ -263,7 +263,7 @@ options should be reserved for defining cluster specific options. --> - -Xmx=6GB + -Xmx6G '5' diff --git a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample index c8624ca72ec..f2a73402e81 100644 --- a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample +++ b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample @@ -1,5 +1,4 @@ [main] - # Following options are ignored if using the Galaxy dynamic proxy but # are useful if mapping a range of ports for environment consumption. #apache_urls = False @@ -7,32 +6,39 @@ #ssl = False [docker] - -# Command to execute docker. For example `sudo docker` or `docker-lxc`. -command = docker +# Command to launch docker container. For example `sudo docker` or `docker-lxc`. +# If you need to use a command like `sg` you can do that here, just be sure to +# wrap all of the docker portion in single quotes. E.g. `sg 'docker' 'docker {docker_args}'` +# +# It is recommended that you use command_inject if you need to inject +# additional parameters. This command string is re-used for a `docker inspect` +# command and will likely cause errors if it is extensively modified, past the +# usual group/sudo changes. +#command = docker {docker_args} # The docker image name that should be started. image = bgruening/docker-ipython-notebook:dev # Additional arguments that are passed to the `docker run` command. -command_inject = --sig-proxy=true -e DEBUG=false - -# Command to wrap around the full docker command. -# For example, `sg 'docker' '{cmd}'` where {cmd} will be replaced by the full -# docker command. Make sure to surround the {cmd} with single quotes('). -# Default: empty -#command_wrapper = +#command_inject = --sig-proxy=true -e DEBUG=false # URL to access the Galaxy API with from the spawn Docker containter, if empty # this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the # Docker host of the spawned container if that is also not set. -#galaxy_url = +#galaxy_url = # The Docker hostname. It can be useful to run the Docker daemon on a different # host than Galaxy. #docker_hostname = localhost # Try to set the tempdirectory to world execute - this can fix the issue -# where 'sudo docker' is not able to mount the folder otherwise. +# where 'sudo docker' is not able to mount the folder otherwise. # "finalize namespace chdir to /import permission denied" -wx_tempdir = False \ No newline at end of file +#wx_tempdir = False + +# Overwride the IE tempdirectory. This can be useful if you regular tempdir is +# located on an NFS share, which does not work well as Docker volume. In this case +# you can have a shared sshfs share which you can use as temporary directory to +# share data between the IE and Galaxy. +#docker_galaxy_temp_dir = None + diff --git a/config/plugins/interactive_environments/ipython/templates/ipython.mako b/config/plugins/interactive_environments/ipython/templates/ipython.mako index 118d72baf2f..2e87c5ae221 100644 --- a/config/plugins/interactive_environments/ipython/templates/ipython.mako +++ b/config/plugins/interactive_environments/ipython/templates/ipython.mako @@ -33,18 +33,16 @@ if hda.datatype.__class__.__name__ != "Ipynb": else: shutil.copy( hda.file_name, empty_nb_path ) - -## General IE specific -# Access URLs for the notebook from within galaxy. -notebook_access_url = ie_request.url_template('${PROXY_URL}/ipython/${PORT}/notebooks/ipython_galaxy_notebook.ipynb') -notebook_login_url = ie_request.url_template('${PROXY_URL}/ipython/${PORT}/login?next=%2Fipython%2F${PORT}%2Ftree') - - # Add all environment variables collected from Galaxy's IE infrastructure ie_request.launch(env_override={ 'notebook_password': PASSWORD, }) +## General IE specific +# Access URLs for the notebook from within galaxy. +notebook_access_url = ie_request.url_template('${PROXY_URL}/ipython/notebooks/ipython_galaxy_notebook.ipynb') +notebook_login_url = ie_request.url_template('${PROXY_URL}/ipython/login?next=${PROXY_PREFIX}%2Fipython%2Ftree') + %> diff --git a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample index ed0b64ff7ce..d678c8752dc 100644 --- a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample +++ b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample @@ -1,19 +1,44 @@ [main] -# This cannot be changed +# This CANNOT be changed. Eventually will be deprecated password_auth = True -# Other -apache_urls = False -ssl = False +# Following options are ignored if using the Galaxy dynamic proxy but +# are useful if mapping a range of ports for environment consumption. +#apache_urls = False +#ssl = False [docker] -command = docker +# Command to launch docker container. For example `sudo docker` or `docker-lxc`. +# If you need to use a command like `sg` you can do that here, just be sure to +# wrap all of the docker portion in single quotes. E.g. `sg 'docker' 'docker {docker_args}'` +# +# It is recommended that you use command_inject if you need to inject +# additional parameters. This command string is re-used for a `docker inspect` +# command and will likely cause errors if it is extensively modified, past the +# usual group/sudo changes. +#command = docker {docker_args} + +# The docker image name that should be started. image = erasche/docker-rstudio-notebook:dev -# Additional arguments that are passed to the `docker run` command. `-u` -# settings are completely ignored. -command_inject = --sig-proxy=true -e DEBUG=false +# Additional arguments that are passed to the `docker run` command. +#command_inject = --sig-proxy=true -e DEBUG=false -# URL to access the Galaxy API with from the spawned Docker container, if empty +# URL to access the Galaxy API with from the spawn Docker containter, if empty # this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the -# Docker host of the spawned container, if that is also not set. -#galaxy_url= +# Docker host of the spawned container if that is also not set. +#galaxy_url = + +# The Docker hostname. It can be useful to run the Docker daemon on a different +# host than Galaxy. +#docker_hostname = localhost + +# Try to set the tempdirectory to world execute - this can fix the issue +# where 'sudo docker' is not able to mount the folder otherwise. +# "finalize namespace chdir to /import permission denied" +#wx_tempdir = False + +# Overwride the IE tempdirectory. This can be useful if you regular tempdir is +# located on an NFS share, which does not work well as Docker volume. In this case +# you can have a shared sshfs share which you can use as temporary directory to +# share data between the IE and Galaxy. +#docker_galaxy_temp_dir = None diff --git a/config/plugins/interactive_environments/rstudio/templates/rstudio.mako b/config/plugins/interactive_environments/rstudio/templates/rstudio.mako index 0fc4d2a4ba2..9d35421ba5a 100644 --- a/config/plugins/interactive_environments/rstudio/templates/rstudio.mako +++ b/config/plugins/interactive_environments/rstudio/templates/rstudio.mako @@ -12,14 +12,6 @@ temp_dir = ie_request.temp_dir PASSWORD = ie_request.notebook_pw USERNAME = "galaxy" -## General IE specific -# Access URLs for the notebook from within galaxy. -# TODO: Make this work without pointing directly to IE. Currently does not work -# through proxy. -notebook_pubkey_url = ie_request.url_template('${PROXY_URL}/rstudio/${PORT}/auth-public-key') -notebook_access_url = ie_request.url_template('${PROXY_URL}/rstudio/${PORT}/') -notebook_login_url = ie_request.url_template('${PROXY_URL}/rstudio/${PORT}/auth-do-sign-in') - # Did the user give us an RData file? if hda.datatype.__class__.__name__ == "RData": shutil.copy( hda.file_name, os.path.join(temp_dir, '.RData') ) @@ -27,8 +19,16 @@ if hda.datatype.__class__.__name__ == "RData": ie_request.launch(env_override={ 'notebook_username': USERNAME, 'notebook_password': PASSWORD, - 'cors_origin': ie_request.attr.proxy_url, }) + +## General IE specific +# Access URLs for the notebook from within galaxy. +# TODO: Make this work without pointing directly to IE. Currently does not work +# through proxy. +notebook_pubkey_url = ie_request.url_template('${PROXY_URL}/rstudio/auth-public-key') +notebook_access_url = ie_request.url_template('${PROXY_URL}/rstudio/') +notebook_login_url = ie_request.url_template('${PROXY_URL}/rstudio/auth-do-sign-in') + %> diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index 28acdc42262..286ca8b38ef 100644 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -443,6 +443,7 @@ class Configuration( object ): self.dynamic_proxy_bind_port = int( kwargs.get( "dynamic_proxy_bind_port", "8800" ) ) self.dynamic_proxy_bind_ip = kwargs.get( "dynamic_proxy_bind_ip", "0.0.0.0" ) self.dynamic_proxy_external_proxy = string_as_bool( kwargs.get( "dynamic_proxy_external_proxy", "False" ) ) + self.dynamic_proxy_prefix = kwargs.get( "dynamic_proxy_prefix", "gie_proxy" ) # Default chunk size for chunkable datatypes -- 64k self.display_chunk_size = int( kwargs.get( 'display_chunk_size', 65536) ) diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py index 0951284a8d1..4496a72c6e4 100644 --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -39,11 +39,11 @@ class Binary( data.Data ): @staticmethod def register_sniffable_binary_format(data_type, ext, type_class): - Binary.sniffable_binary_formats.append({"type": data_type, "ext": ext, "class": type_class}) + Binary.sniffable_binary_formats.append({"type": data_type, "ext": ext.lower(), "class": type_class}) @staticmethod def register_unsniffable_binary_ext(ext): - Binary.unsniffable_binary_formats.append(ext) + Binary.unsniffable_binary_formats.append(ext.lower()) @staticmethod def is_sniffable_binary( filename ): diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py index 17100fec4e3..2ed8ee820e3 100644 --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1402,7 +1402,7 @@ class JobWrapper( object ): job = has_metrics.get_job() per_plugin_properties = self.app.job_metrics.collect_properties( job.destination_id, self.job_id, self.working_directory ) if per_plugin_properties: - log.info( "Collecting job metrics for %s: %s" % ( has_metrics, getattr( has_metrics, 'id', None ) ) ) + log.info( "Collecting metrics for %s %s" % ( type(has_metrics).__name__, getattr( has_metrics, 'id', None ) ) ) for plugin, properties in per_plugin_properties.iteritems(): for metric_name, metric_value in properties.iteritems(): if metric_value is not None: diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py index db6e767d442..5165098bbfe 100644 --- a/lib/galaxy/managers/hdas.py +++ b/lib/galaxy/managers/hdas.py @@ -280,6 +280,7 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerialize 'peek', 'creating_job', + 'rerunnable', 'uuid', 'permissions', @@ -328,6 +329,7 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerialize 'resubmitted' : lambda i, k, **c: self.hda_manager.has_been_resubmitted( i ), 'creating_job' : self.serialize_creating_job, + 'rerunnable' : self.rerunnable, 'display_apps' : self.serialize_display_apps, 'display_types' : self.serialize_old_display_applications, @@ -439,6 +441,13 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerialize else: return None + def rerunnable( self, hda, key, **context ): + if hda.creating_job: + tool = self.app.toolbox.get_tool(hda.creating_job.tool_id, hda.creating_job.tool_version) + if tool and tool.is_workflow_compatible: + return True + return False + class HDADeserializer( datasets.DatasetAssociationDeserializer, taggable.TaggableDeserializerMixin, diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 4811890336f..37a292ea510 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3047,6 +3047,9 @@ class DatasetCollectionInstance( object, HasName ): id=self.id, name=self.name, collection_type=self.collection.collection_type, + populated=self.collection.populated, + populated_state=self.collection.populated_state, + populated_state_message=self.collection.populated_state_message, type="collection", # contents type (distinguished from file or folder (in case of library)) ) diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index 8c9ab61ffd5..1c7c56c20fa 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1538,6 +1538,8 @@ class Tool( object, Dictifiable ): group_errors[-1] = { '__index__': 'Cannot add repeat (max size=%i).' % input.max } any_group_errors = True rep_index += 1 + if any_group_errors: + errors[ input.name ] = group_errors elif isinstance( input, Conditional ): group_state = state[input.name] group_prefix = "%s|" % ( key ) diff --git a/lib/galaxy/tools/parser/yaml.py b/lib/galaxy/tools/parser/yaml.py index f4f05a15c9e..76211d6ff85 100644 --- a/lib/galaxy/tools/parser/yaml.py +++ b/lib/galaxy/tools/parser/yaml.py @@ -75,7 +75,7 @@ class YamlToolSource(ToolSource): for output in output_defs: outputs[output.name] = output # TODO: parse outputs collections - return output_defs, odict() + return outputs, odict() def _parse_output(self, tool, name, output_dict): # TODO: handle filters, actions, change_format diff --git a/lib/galaxy/web/base/interactive_environments.py b/lib/galaxy/web/base/interactive_environments.py index 297ffef099b..52c5886f569 100644 --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -1,6 +1,7 @@ import ConfigParser import os +import json import stat import random import tempfile @@ -40,18 +41,15 @@ class InteractiveEnviornmentRequest(object): self.load_deploy_config() self.attr.docker_hostname = self.attr.viz_config.get("docker", "docker_hostname") - self.attr.proxy_request = trans.app.proxy_manager.setup_proxy( - trans, host=self.attr.docker_hostname - ) - self.attr.proxy_url = self.attr.proxy_request[ 'proxy_url' ] - self.attr.PORT = self.attr.proxy_request[ 'proxied_port' ] # Generate per-request passwords the IE plugin can use to configure # the destination container. self.notebook_pw_salt = self.generate_password(length=12) self.notebook_pw = self.generate_password(length=24) - self.temp_dir = os.path.abspath( tempfile.mkdtemp() ) + ie_parent_temp_dir = self.attr.viz_config.get("docker", "docker_galaxy_temp_dir") or None + self.temp_dir = os.path.abspath( tempfile.mkdtemp( dir=ie_parent_temp_dir ) ) + if self.attr.viz_config.getboolean("docker", "wx_tempdir"): # Ensure permissions are set try: @@ -60,15 +58,26 @@ class InteractiveEnviornmentRequest(object): log.error( "Could not change permissions of tmpdir %s" % self.temp_dir ) # continue anyway + # This duplicates the logic in the proxy manager + if self.attr.galaxy_config.dynamic_proxy_external_proxy: + self.attr.proxy_prefix = '%s/%s' % ( + self.attr.galaxy_config.cookie_path, + self.attr.galaxy_config.dynamic_proxy_prefix) + else: + self.attr.proxy_prefix = '' + def load_deploy_config(self, default_dict={}): # For backwards compat, any new variables added to the base .ini file # will need to be recorded here. The ConfigParser doesn't provide a # .get() that will ignore missing sections, so we must make use of # their defaults dictionary instead. - default_dict['command_inject'] = '--sig-proxy=true' - default_dict['docker_hostname'] = 'localhost' - default_dict['wx_tempdir'] = 'False' - default_dict['command_wrapper'] = '' + default_dict = { + 'command': 'docker {docker_args}', + 'command_inject': '--sig-proxy=true -e DEBUG=false', + 'docker_hostname': 'localhost', + 'wx_tempdir': 'False', + 'docker_galaxy_temp_dir': None + } viz_config = ConfigParser.SafeConfigParser(default_dict) conf_path = os.path.join( self.attr.our_config_dir, self.attr.viz_id + ".ini" ) if not os.path.exists( conf_path ): @@ -102,8 +111,10 @@ class InteractiveEnviornmentRequest(object): 'history_id': self.attr.history_id, 'api_key': api_key, 'remote_host': request.remote_addr, - 'docker_port': self.attr.PORT, + # DOCKER_PORT is NO LONGER AVAILABLE. All IEs must update. 'cors_origin': request.host_url, + 'user_email': self.trans.user.email, + 'proxy_prefix': self.attr.proxy_prefix, } if self.attr.viz_config.has_option("docker", "galaxy_url"): @@ -138,36 +149,27 @@ class InteractiveEnviornmentRequest(object): return "false" def url_template(self, url_template): + """Process a URL template + + There are several variables accessible to the user: + + - ${PROXY_URL} will be replaced with the dynamically create proxy's url + - ${PROXY_PREFIX} will be replaced with the prefix that may occur """ - Process a URL template - - There are several variables accessible to the user: - - - ${PROXY_URL} will be replaced with dynamically create proxy - - ${PORT} will be replaced with the port the docker image is attached to - """ - # Figure out our substitutions - # Next several lines for older style replacements (not used with Galaxy dynamic # proxy) - if self.attr.SSL_URLS: protocol = 'https' else: protocol = 'http' - if not self.attr.APACHE_URLS: - # If they are not using apache URLs, that implies there's a port attached to the host - # string, thus we replace just the first instance of host that we see. - url_template = url_template.replace('${HOST}', '${HOST}:${PORT}', 1) - url_template = url_template.replace('${PROTO}', protocol) \ .replace('${HOST}', self.attr.HOST) # Only the following replacements are used with Galaxy dynamic proxy # URLs url = url_template.replace('${PROXY_URL}', str(self.attr.proxy_url)) \ - .replace('${PORT}', str(self.attr.PORT)) + .replace('${PROXY_PREFIX}', str(self.attr.proxy_prefix.replace('/', '%2F'))) return url def volume(self, host_path, container_path, **kwds): @@ -182,18 +184,22 @@ class InteractiveEnviornmentRequest(object): conf.update(env_override) env_str = ' '.join(['-e "%s=%s"' % (key.upper(), item) for key, item in conf.items()]) volume_str = ' '.join(['-v "%s"' % volume for volume in volumes]) - cmd = '%s run %s -d %s -p %s:%s -v "%s:/import/" %s %s' % \ - (self.attr.viz_config.get("docker", "command"), - env_str, - self.attr.viz_config.get("docker", "command_inject"), - self.attr.PORT, self.attr.docker_port, - temp_dir, - volume_str, - self.attr.viz_config.get("docker", "image")) - cmd_wrapper = self.attr.viz_config.get("docker", "command_wrapper") - if cmd_wrapper != '' and '{cmd}' in cmd_wrapper: - cmd = cmd_wrapper.format( cmd=cmd ) - return cmd + # This is the basic docker command such as "sudo -u docker docker {docker_args}" + # or just "docker {docker_args}" + command = self.attr.viz_config.get("docker", "command") + # Then we format in the entire docker command in place of + # {docker_args}, so as to let the admin not worry about which args are + # getting passed + command = command.format(docker_args='run {command_inject} {environment} -d -P -v "{temp_dir}:/import/" {volume_str} {image}') + # Once that's available, we format again with all of our arguments + command = command.format( + command_inject=self.attr.viz_config.get("docker", "command_inject"), + environment=env_str, + temp_dir=temp_dir, + volume_str=volume_str, + image=self.attr.viz_config.get("docker", "image") + ) + return command def launch(self, raw_cmd=None, env_override={}, volumes=[]): if raw_cmd is None: @@ -206,5 +212,81 @@ class InteractiveEnviornmentRequest(object): stdout, stderr = p.communicate() if p.returncode != 0 or len(stderr): log.error( "%s\n%s" % (stdout, stderr) ) + return None else: log.debug( "Container id: %s" % stdout) + port_mappings = self.get_proxied_ports(stdout) + if len(port_mappings) > 1: + log.warning("Don't know how to handle proxies to containers with multiple exposed ports. Arbitrarily choosing first") + elif len(port_mappings) == 0: + log.warning("No exposed ports to map! Images MUST EXPOSE") + return None + # Fetch the first port_mapping + (service, host_ip, host_port) = port_mappings[0] + + # Now we configure our proxy_requst object and we manually specify + # the port to map to and ensure the proxy is available. + self.attr.proxy_request = self.trans.app.proxy_manager.setup_proxy( + self.trans, + host=self.attr.docker_hostname, + port=host_port, + proxy_prefix=self.attr.proxy_prefix, + ) + # These variables then become available for use in templating URLs + self.attr.proxy_url = self.attr.proxy_request[ 'proxy_url' ] + # Commented out because it needs to be documented and visible that + # this variable was moved here. Usually would remove commented + # code, but again, needs to be clear where this went. Remove at a + # later time. + # + # PORT is no longer exposed internally. All requests are forced to + # go through the proxy we ship. + # self.attr.PORT = self.attr.proxy_request[ 'proxied_port' ] + + def get_proxied_ports(self, container_id): + """Run docker inspect on a container to figure out which ports were + mapped where. + + :type container_id: str + :param container_id: a docker container ID + + :returns: a list of triples containing (internal_port, external_ip, + external_port), of which the ports are probably the only + useful information. + + Someday code that calls this should be refactored whenever we get + containers with multiple ports working. + """ + command = self.attr.viz_config.get("docker", "command") + command = command.format(docker_args="inspect %s" % container_id) + log.info("Inspecting docker container {0} with command [{1}]".format( + container_id, + command + )) + + p = Popen(command, stdout=PIPE, stderr=PIPE, close_fds=True, shell=True) + stdout, stderr = p.communicate() + if p.returncode != 0 or len(stderr): + log.error( "%s\n%s" % (stdout, stderr) ) + return None + + inspect_data = json.loads(stdout) + # [{ + # "NetworkSettings" : { + # "Ports" : { + # "3306/tcp" : [ + # { + # "HostIp" : "127.0.0.1", + # "HostPort" : "3306" + # } + # ] + mappings = [] + port_mappings = inspect_data[0]['NetworkSettings']['Ports'] + for port_name in port_mappings: + for binding in port_mappings[port_name]: + mappings.append(( + port_name.replace('/tcp', '').replace('/udp', ''), + binding['HostIp'], + binding['HostPort'] + )) + return mappings diff --git a/lib/galaxy/web/proxy/__init__.py b/lib/galaxy/web/proxy/__init__.py index 30738ad6c11..a23b42a285c 100644 --- a/lib/galaxy/web/proxy/__init__.py +++ b/lib/galaxy/web/proxy/__init__.py @@ -17,7 +17,9 @@ SECURE_COOKIE = "galaxysession" class ProxyManager(object): def __init__( self, config ): - for option in [ "manage_dynamic_proxy", "dynamic_proxy_bind_port", "dynamic_proxy_bind_ip", "dynamic_proxy_debug", "dynamic_proxy_external_proxy" ]: + for option in ["manage_dynamic_proxy", "dynamic_proxy_bind_port", + "dynamic_proxy_bind_ip", "dynamic_proxy_debug", + "dynamic_proxy_external_proxy", "dynamic_proxy_prefix"]: setattr( self, option, getattr( config, option ) ) self.launch_by = "node" # TODO: Support docker if self.manage_dynamic_proxy: @@ -29,7 +31,7 @@ class ProxyManager(object): def shutdown( self ): self.lazy_process.shutdown() - def setup_proxy( self, trans, host=DEFAULT_PROXY_TO_HOST, port=None ): + def setup_proxy( self, trans, host=DEFAULT_PROXY_TO_HOST, port=None, proxy_prefix="" ): if self.manage_dynamic_proxy: log.info("Attempting to start dynamic proxy process") self.lazy_process.start_process() @@ -46,7 +48,7 @@ class ProxyManager(object): if not self.dynamic_proxy_external_proxy: proxy_url = '%s://%s:%d' % (scheme, host, self.dynamic_proxy_bind_port) else: - proxy_url = '%s://%s' % (scheme, host) + proxy_url = '%s://%s%s' % (scheme, host, proxy_prefix) return { 'proxy_url': proxy_url, 'proxied_port': proxy_requests.port, diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py index d6f53557b69..8025c10873b 100644 --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -285,7 +285,10 @@ class WorkflowProgress( object ): raise modules.DelayedWorkflowEvaluation() return replacement - def set_outputs_for_input( self, step, outputs={} ): + def set_outputs_for_input( self, step, outputs=None ): + if outputs is None: + outputs = {} + if self.inputs_by_step_id: outputs[ 'output' ] = self.inputs_by_step_id[ step.id ] diff --git a/scripts/common_startup.sh b/scripts/common_startup.sh index 34c7e261500..a0ed759db95 100755 --- a/scripts/common_startup.sh +++ b/scripts/common_startup.sh @@ -16,6 +16,7 @@ SAMPLES=" config/shed_data_manager_conf.xml.sample lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample tool-data/shared/ucsc/builds.txt.sample + tool-data/shared/ucsc/manual_builds.txt.sample tool-data/shared/ucsc/ucsc_build_sites.txt.sample tool-data/shared/igv/igv_build_sites.txt.sample tool-data/shared/rviewer/rviewer_build_sites.txt.sample diff --git a/static/maps/mvc/collection/collection-model.js.map b/static/maps/mvc/collection/collection-model.js.map index 512f3e27839..534ce4c9de0 100644 --- a/static/maps/mvc/collection/collection-model.js.map +++ b/static/maps/mvc/collection/collection-model.js.map @@ -1 +1 @@ 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a=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",a,")"].join("")}})),l=e.extend({model:k,initialize:function(a,b){this.debug(this+"(NestedDCDCECollection).initialize:",a,b),e.prototype.initialize.call(this,a,b)},toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),m=j.extend(b.mixin(c,{constructor:function(a,b){this.debug(" NestedPairDCDCE.constructor:",a,b),c.constructor.call(this,a,b)},toString:function(){var a=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",a,")"].join("")}})),n=l.extend({model:m,initialize:function(a,b){this.debug(this+"(NestedPairDCDCECollection).initialize:",a,b),l.prototype.initialize.call(this,a,b)},toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),o=h.extend({collectionClass:n,initialize:function(a,b){this.debug(this+"(ListPairedDatasetCollection).initialize:",a,b),h.prototype.initialize.call(this,a,b)},toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:i,PairDatasetCollection:j,ListPairedDatasetCollection:o}}); +define(["mvc/dataset/dataset-model","mvc/base-mvc","utils/localization"],function(a,b){var c={defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(a){return _.extend(a,a.object,{element_id:a.id}),delete a.object,a},constructor:function(a){a=this._mergeObject(a),this.idAttribute="element_id",Backbone.Model.apply(this,arguments)},parse:function(a){var b=a;return b=this._mergeObject(b)}},d=Backbone.Model.extend(b.LoggableMixin).extend(c),e=Backbone.Collection.extend(b.LoggableMixin).extend({model:d,initialize:function(a,b){this.debug(this+"(DCECollection).initialize:",a,b),b=b||{}},toString:function(){return["DatasetCollectionElementCollection(",this.length,")"].join("")}}),f=a.DatasetAssociation.extend(b.mixin(c,{defaults:_.extend({},a.DatasetAssociation.prototype.defaults,c.defaults),constructor:function(a,b){this.debug(" DatasetDCE.constructor:",a,b),c.constructor.call(this,a,b)},initialize:function(b,c){this.debug(this+"(DatasetDCE).initialize:",b,c),a.DatasetAssociation.prototype.initialize.call(this,b,c)},toString:function(){var a=this.get("element_identifier");return["DatasetDCE(",a,")"].join("")}})),g=e.extend({model:f,initialize:function(a,b){this.debug(this+"(DatasetDCECollection).initialize:",a,b),e.prototype.initialize.call(this,a,b)},toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),h=Backbone.Model.extend(b.LoggableMixin).extend(b.SearchableModelMixin).extend({defaults:{collection_type:null,deleted:!1},collectionClass:e,initialize:function(a,b){this.debug(this+"(DatasetCollection).initialize:",a,b,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){this.debug(this+"._createElementsModel",this.collectionClass,this.get("elements"),this.elements);var a=this.get("elements")||[];return this.unset("elements",{silent:!0}),this.elements=new this.collectionClass(a),this.elements},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);return this.elements&&(a.elements=this.elements.toJSON()),a},inReadyState:function(){var a=this.get("populated");return this.isDeletedOrPurged()||a},hasDetails:function(){return this.debug("hasDetails:",this.elements.length),0!==this.elements.length},getVisibleContents:function(){return this.elements},"delete":function(a){return this.get("deleted")?jQuery.when():this.save({deleted:!0},a)},undelete:function(a){return!this.get("deleted")||this.get("purged")?jQuery.when():this.save({deleted:!1},a)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name"],toString:function(){var a=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+a.join(",")+")"}}),i=h.extend({collectionClass:g,initialize:function(a,b){this.debug(this+"(ListDatasetCollection).initialize:",a,b),h.prototype.initialize.call(this,a,b)},toString:function(){return["ListDatasetCollection(",this.get("name"),")"].join("")}}),j=i.extend({initialize:function(a,b){this.debug(this+"(PairDatasetCollection).initialize:",a,b),i.prototype.initialize.call(this,a,b)},toString:function(){return["PairDatasetCollection(",this.get("name"),")"].join("")}}),k=h.extend(b.mixin(c,{constructor:function(a,b){this.debug(" NestedDCDCE.constructor:",a,b),c.constructor.call(this,a,b)},toString:function(){var a=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",a,")"].join("")}})),l=e.extend({model:k,initialize:function(a,b){this.debug(this+"(NestedDCDCECollection).initialize:",a,b),e.prototype.initialize.call(this,a,b)},toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),m=j.extend(b.mixin(c,{constructor:function(a,b){this.debug(" NestedPairDCDCE.constructor:",a,b),c.constructor.call(this,a,b)},toString:function(){var a=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",a,")"].join("")}})),n=l.extend({model:m,initialize:function(a,b){this.debug(this+"(NestedPairDCDCECollection).initialize:",a,b),l.prototype.initialize.call(this,a,b)},toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),o=h.extend({collectionClass:n,initialize:function(a,b){this.debug(this+"(ListPairedDatasetCollection).initialize:",a,b),h.prototype.initialize.call(this,a,b)},toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:i,PairDatasetCollection:j,ListPairedDatasetCollection:o}}); //# sourceMappingURL=../../../maps/mvc/collection/collection-model.js.map \ No newline at end of file diff --git a/static/scripts/mvc/dataset/dataset-li-edit.js b/static/scripts/mvc/dataset/dataset-li-edit.js index f44b3f96cb1..031e28ce9fe 100644 --- a/static/scripts/mvc/dataset/dataset-li-edit.js +++ b/static/scripts/mvc/dataset/dataset-li-edit.js @@ -1,2 +1,2 @@ -define(["mvc/dataset/states","mvc/dataset/dataset-li","mvc/tags","mvc/annotations","ui/fa-icon-button","mvc/base-mvc","mvc/tools/tools-form","utils/localization"],function(a,b,c,d,e,f,g,h){var i=b.DatasetListItemView,j=i.extend({initialize:function(a){i.prototype.initialize.call(this,a),this.hasUser=a.hasUser,this.purgeAllowed=a.purgeAllowed||!1,this.tagsEditorShown=a.tagsEditorShown||!1,this.annotationEditorShown=a.annotationEditorShown||!1},_renderPrimaryActions:function(){var b=i.prototype._renderPrimaryActions.call(this);return this.model.get("state")===a.NOT_VIEWABLE?b:i.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===a.DISCARDED||!this.model.get("accessible"))return null;var b=this.model.get("purged"),c=this.model.get("deleted"),d={title:h("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return c||b?(d.disabled=!0,b?d.title=h("Cannot edit attributes of datasets removed from disk"):c&&(d.title=h("Undelete dataset to edit attributes"))):_.contains([a.UPLOAD,a.NEW],this.model.get("state"))&&(d.disabled=!0,d.title=h("This dataset is not yet editable")),e(d)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var a=this,b=this.model.isDeletedOrPurged();return e({title:h(b?"Dataset is already deleted":"Delete"),disabled:b,faIcon:"fa-times",classes:"delete-btn",onclick:function(){a.$el.find(".icon-btn.delete-btn").trigger("mouseout"),a.model.delete()}})},_renderDetails:function(){var b=i.prototype._renderDetails.call(this),c=this.model.get("state");return!this.model.isDeletedOrPurged()&&_.contains([a.OK,a.FAILED_METADATA],c)&&(this._renderTags(b),this._renderAnnotation(b),this._makeDbkeyEditLink(b)),this._setUpBehaviors(b),b},_renderSecondaryActions:function(){var b=i.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case a.UPLOAD:case a.NEW:case a.NOT_VIEWABLE:return b;case a.ERROR:return b.unshift(this._renderErrButton()),b.concat([this._renderRerunButton()]);case a.OK:case a.FAILED_METADATA:return b.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return b.concat([this._renderRerunButton()])},_renderErrButton:function(){return e({title:h("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){var a=this.model.get("creating_job");return e({title:h("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(b){b.preventDefault();var c=new g.View({job_id:a});c.deferred.execute(function(){Galaxy.app.display(c.$el)})}})},_renderVisualizationsButton:function(){var a=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||_.isEmpty(a))return null;if(!_.isObject(a[0]))return this.warn("Visualizations have been switched off"),null;var b=$(this.templates.visualizations(a,this));return b.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(b.find(".visualization-link").addBack(".visualization-link")),b},_addScratchBookFn:function(a){a.click(function(a){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",type:"url",content:$(this).attr("href")}),a.preventDefault(),a.stopPropagation())})},_renderTags:function(a){if(this.hasUser){var b=this;this.tagsEditor=new c.TagsEditor({model:this.model,el:a.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.tagsEditorShown=!0},onhide:function(){b.tagsEditorShown=!1},$activator:e({title:h("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(a.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(a){if(this.hasUser){var b=this;this.annotationEditor=new d.AnnotationEditor({model:this.model,el:a.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.annotationEditorShown=!0},onhide:function(){b.annotationEditorShown=!1},$activator:e({title:h("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(a.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(a){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var b=$('?').attr("href",this.model.urls.edit).attr("target",this.linkTarget);a.find(".dbkey .value").replaceWith(b)}},events:_.extend(_.clone(i.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(a){this.trigger("edit",this,a)},"click .delete-btn":function(a){this.trigger("delete",this,a)},"click .rerun-btn":function(a){this.trigger("rerun",this,a)},"click .report-err-btn":function(a){this.trigger("report-err",this,a)},"click .visualization-btn":function(a){this.trigger("visualize",this,a)},"click .dbkey a":function(a){this.trigger("edit",this,a)}}),_clickUndeleteLink:function(){return this.model.undelete(),!1},_clickPurgeLink:function(){return this.model.purge(),!1},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDAEditView("+a+")"}});return j.prototype.templates=function(){var a=_.extend({},i.prototype.templates.warnings,{failed_metadata:f.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
',h("An error occurred setting the metadata for this dataset"),'
',h("Set it manually or retry auto-detection"),"","
","<% } %>"],"dataset"),deleted:f.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
',h("This dataset has been deleted"),'
',h("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
',h("Permanently remove it from disk"),"","<% } %>","
","<% } %>"],"dataset")}),b=f.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'
','','',"",'","
","<% } %>"],"visualizations");return _.extend({},i.prototype.templates,{warnings:a,visualizations:b})}(),{DatasetListItemEdit:j}}); +define(["mvc/dataset/states","mvc/dataset/dataset-li","mvc/tags","mvc/annotations","ui/fa-icon-button","mvc/base-mvc","mvc/tools/tools-form","utils/localization"],function(a,b,c,d,e,f,g,h){var i=b.DatasetListItemView,j=i.extend({initialize:function(a){i.prototype.initialize.call(this,a),this.hasUser=a.hasUser,this.purgeAllowed=a.purgeAllowed||!1,this.tagsEditorShown=a.tagsEditorShown||!1,this.annotationEditorShown=a.annotationEditorShown||!1},_renderPrimaryActions:function(){var b=i.prototype._renderPrimaryActions.call(this);return this.model.get("state")===a.NOT_VIEWABLE?b:i.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===a.DISCARDED||!this.model.get("accessible"))return null;var b=this.model.get("purged"),c=this.model.get("deleted"),d={title:h("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return c||b?(d.disabled=!0,b?d.title=h("Cannot edit attributes of datasets removed from disk"):c&&(d.title=h("Undelete dataset to edit attributes"))):_.contains([a.UPLOAD,a.NEW],this.model.get("state"))&&(d.disabled=!0,d.title=h("This dataset is not yet editable")),e(d)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var a=this,b=this.model.isDeletedOrPurged();return e({title:h(b?"Dataset is already deleted":"Delete"),disabled:b,faIcon:"fa-times",classes:"delete-btn",onclick:function(){a.$el.find(".icon-btn.delete-btn").trigger("mouseout"),a.model.delete()}})},_renderDetails:function(){var b=i.prototype._renderDetails.call(this),c=this.model.get("state");return!this.model.isDeletedOrPurged()&&_.contains([a.OK,a.FAILED_METADATA],c)&&(this._renderTags(b),this._renderAnnotation(b),this._makeDbkeyEditLink(b)),this._setUpBehaviors(b),b},_renderSecondaryActions:function(){var b=i.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case a.UPLOAD:case a.NEW:case a.NOT_VIEWABLE:return b;case a.ERROR:return b.unshift(this._renderErrButton()),b.concat([this._renderRerunButton()]);case a.OK:case a.FAILED_METADATA:return b.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return b.concat([this._renderRerunButton()])},_renderErrButton:function(){return e({title:h("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){var a=this.model.get("creating_job");return this.model.get("rerunnable")?e({title:h("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(b){b.preventDefault();var c=new g.View({job_id:a});c.deferred.execute(function(){Galaxy.app.display(c.$el)})}}):void 0},_renderVisualizationsButton:function(){var a=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||_.isEmpty(a))return null;if(!_.isObject(a[0]))return this.warn("Visualizations have been switched off"),null;var b=$(this.templates.visualizations(a,this));return b.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(b.find(".visualization-link").addBack(".visualization-link")),b},_addScratchBookFn:function(a){a.click(function(a){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",type:"url",content:$(this).attr("href")}),a.preventDefault(),a.stopPropagation())})},_renderTags:function(a){if(this.hasUser){var b=this;this.tagsEditor=new c.TagsEditor({model:this.model,el:a.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.tagsEditorShown=!0},onhide:function(){b.tagsEditorShown=!1},$activator:e({title:h("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(a.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(a){if(this.hasUser){var b=this;this.annotationEditor=new d.AnnotationEditor({model:this.model,el:a.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.annotationEditorShown=!0},onhide:function(){b.annotationEditorShown=!1},$activator:e({title:h("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(a.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(a){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var b=$('?').attr("href",this.model.urls.edit).attr("target",this.linkTarget);a.find(".dbkey .value").replaceWith(b)}},events:_.extend(_.clone(i.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(a){this.trigger("edit",this,a)},"click .delete-btn":function(a){this.trigger("delete",this,a)},"click .rerun-btn":function(a){this.trigger("rerun",this,a)},"click .report-err-btn":function(a){this.trigger("report-err",this,a)},"click .visualization-btn":function(a){this.trigger("visualize",this,a)},"click .dbkey a":function(a){this.trigger("edit",this,a)}}),_clickUndeleteLink:function(){return this.model.undelete(),!1},_clickPurgeLink:function(){return this.model.purge(),!1},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDAEditView("+a+")"}});return j.prototype.templates=function(){var a=_.extend({},i.prototype.templates.warnings,{failed_metadata:f.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
',h("An error occurred setting the metadata for this dataset"),'
',h("Set it manually or retry auto-detection"),"","
","<% } %>"],"dataset"),deleted:f.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
',h("This dataset has been deleted"),'
',h("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
',h("Permanently remove it from disk"),"","<% } %>","
","<% } %>"],"dataset")}),b=f.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'
','','',"",'","
","<% } %>"],"visualizations");return _.extend({},i.prototype.templates,{warnings:a,visualizations:b})}(),{DatasetListItemEdit:j}}); //# sourceMappingURL=../../../maps/mvc/dataset/dataset-li-edit.js.map \ No newline at end of file diff --git a/static/scripts/mvc/dataset/dataset-li.js b/static/scripts/mvc/dataset/dataset-li.js index 65584155f28..8ad909e596e 100644 --- a/static/scripts/mvc/dataset/dataset-li.js +++ b/static/scripts/mvc/dataset/dataset-li.js @@ -1,2 +1,2 @@ -define(["mvc/list/list-item","mvc/dataset/states","ui/fa-icon-button","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){var f=a.ListItemView,g=f.extend({className:f.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(a){a.logger&&(this.logger=this.model.logger=a.logger),this.log(this+".initialize:",a),f.prototype.initialize.call(this,a),this.linkTarget=a.linkTarget||"_blank",this._setUpListeners()},_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.model.on("change",function(){this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()?this.model.fetch():this.render()},this)},_fetchModelDetails:function(){var a=this;return a.model.inReadyState()&&!a.model.hasDetails()?a.model.fetch({silent:!0}):jQuery.when()},remove:function(a,b){var c=this;a=a||this.fxSpeed,this.$el.fadeOut(a,function(){Backbone.View.prototype.remove.call(c),b&&b.call(c)})},render:function(a){return f.prototype.render.call(this,a)},_swapNewRender:function(a){return f.prototype._swapNewRender.call(this,a),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var a=this.model.get("state");if(a===b.NOT_VIEWABLE||a===b.DISCARDED||!this.model.get("accessible"))return null;var d={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))d.disabled=!0,d.title=e("Cannot display datasets removed from disk");else if(a===b.UPLOAD)d.disabled=!0,d.title=e("This dataset must finish uploading before it can be viewed");else if(a===b.NEW)d.disabled=!0,d.title=e("This dataset is not yet viewable");else{d.title=e("View data"),d.href=this.model.urls.display;var f=this;d.onclick=function(a){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add_dataset(f.model.get("id")),a.preventDefault())}}return d.faIcon="fa-eye",c(d)},_renderDetails:function(){if(this.model.get("state")===b.NOT_VIEWABLE)return $(this.templates.noAccess(this.model.toJSON(),this));var a=f.prototype._renderDetails.call(this);return a.find(".actions .left").empty().append(this._renderSecondaryActions()),a.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),a.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(a),a},_renderSummary:function(){var a=this.model.toJSON(),b=this.templates.summaries[a.state];return(b=b||this.templates.summaries.unknown)(a,this)},_renderDetailMessages:function(){var a=this,b=$('
'),c=a.model.toJSON();return _.each(a.templates.detailMessages,function(d){b.append($(d(c,a)))}),b},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case b.NOT_VIEWABLE:return[];case b.OK:case b.FAILED_METADATA:case b.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return c({title:e("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:_.isEmpty(this.model.get("meta_files"))?$(['','',""].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var a=this.model.urls;return $(['
','','',"",'","
"].join("\n"))},events:_.extend(_.clone(f.prototype.events),{"click .display-btn":function(a){this.trigger("display",this,a)},"click .params-btn":function(a){this.trigger("params",this,a)},"click .download-btn":function(a){this.trigger("download",this,a)}}),toString:function(){var a=this.model?this.model+"":"(no model)";return"DatasetListItemView("+a+")"}});return g.prototype.templates=function(){var a=_.extend({},f.prototype.templates.warnings,{failed_metadata:d.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','
',e("An error occurred setting the metadata for this dataset"),"
","<% } %>"]),error:d.wrapTemplate(["<% if( model.error ){ %>",'
',e("There was an error getting the data for this dataset"),": <%- model.error %>","
","<% } %>"]),purged:d.wrapTemplate(["<% if( model.purged ){ %>",'
',e("This dataset has been deleted and removed from disk"),"
","<% } %>"]),deleted:d.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
',e("This dataset has been deleted"),"
","<% } %>"])}),c=d.wrapTemplate(['
','
','
','
','
',"
","<% if( !dataset.deleted && !dataset.purged ){ %>",'
','
','
',"<% if( dataset.peek ){ %>",'
<%= dataset.peek %>
',"<% } %>","<% } %>","
"],"dataset"),g=d.wrapTemplate(['
','
',e("You do not have permission to view this dataset"),"
","
"],"dataset"),h={};h[b.OK]=h[b.FAILED_METADATA]=d.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'
','<%- dataset.misc_blurb %>',"
","<% } %>","<% if( dataset.file_ext ){ %>",'
','",'<%- dataset.file_ext %>',"
","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'
','",'',"<%- dataset.metadata_dbkey %>","","
","<% } %>","<% if( dataset.misc_info ){ %>",'
','<%- dataset.misc_info %>',"
","<% } %>"],"dataset"),h[b.NEW]=d.wrapTemplate(["
",e("This is a new dataset and not all of its data are available yet"),"
"],"dataset"),h[b.NOT_VIEWABLE]=d.wrapTemplate(["
",e("You do not have permission to view this dataset"),"
"],"dataset"),h[b.DISCARDED]=d.wrapTemplate(["
",e("The job creating this dataset was cancelled before completion"),"
"],"dataset"),h[b.QUEUED]=d.wrapTemplate(["
",e("This job is waiting to run"),"
"],"dataset"),h[b.RUNNING]=d.wrapTemplate(["
",e("This job is currently running"),"
"],"dataset"),h[b.UPLOAD]=d.wrapTemplate(["
",e("This dataset is currently uploading"),"
"],"dataset"),h[b.SETTING_METADATA]=d.wrapTemplate(["
",e("Metadata is being auto-detected"),"
"],"dataset"),h[b.PAUSED]=d.wrapTemplate(["
",e('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"
"],"dataset"),h[b.ERROR]=d.wrapTemplate(["<% if( !dataset.purged ){ %>","
<%- dataset.misc_blurb %>
","<% } %>",'',e("An error occurred with this dataset"),":",'
<%- dataset.misc_info %>
'],"dataset"),h[b.EMPTY]=d.wrapTemplate(["
",e("No data"),": <%- dataset.misc_blurb %>
"],"dataset"),h.unknown=d.wrapTemplate(['
Error: unknown dataset state: "<%- dataset.state %>"
'],"dataset");var i={resubmitted:d.wrapTemplate(["<% if( model.resubmitted ){ %>",'
',e("The job creating this dataset has been resubmitted"),"
","<% } %>"])},j=d.wrapTemplate(["<% _.each( apps, function( app ){ %>",'
','<%- app.label %> ','',"<% _.each( app.links, function( link ){ %>",'',"<% print( _l( link.text ) ); %>"," ","<% }); %>","","
","<% }); %>"],"apps");return _.extend({},f.prototype.templates,{warnings:a,details:c,noAccess:g,summaries:h,detailMessages:i,displayApplications:j})}(),{DatasetListItemView:g}}); +define(["mvc/list/list-item","mvc/dataset/states","ui/fa-icon-button","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){var f=a.ListItemView,g=f.extend({className:f.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(a){a.logger&&(this.logger=this.model.logger=a.logger),this.log(this+".initialize:",a),f.prototype.initialize.call(this,a),this.linkTarget=a.linkTarget||"_blank"},_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.model.on("change",function(){this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()?this.model.fetch():this.render()},this)},_fetchModelDetails:function(){var a=this;return a.model.inReadyState()&&!a.model.hasDetails()?a.model.fetch({silent:!0}):a.model.has("rerunnable")?jQuery.when():a.model.fetch({silent:!0,data:{keys:["rerunnable","creating_job"].join(",")}})},remove:function(a,b){var c=this;a=a||this.fxSpeed,this.$el.fadeOut(a,function(){Backbone.View.prototype.remove.call(c),b&&b.call(c)})},render:function(a){return f.prototype.render.call(this,a)},_swapNewRender:function(a){return f.prototype._swapNewRender.call(this,a),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var a=this.model.get("state");if(a===b.NOT_VIEWABLE||a===b.DISCARDED||!this.model.get("accessible"))return null;var d={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))d.disabled=!0,d.title=e("Cannot display datasets removed from disk");else if(a===b.UPLOAD)d.disabled=!0,d.title=e("This dataset must finish uploading before it can be viewed");else if(a===b.NEW)d.disabled=!0,d.title=e("This dataset is not yet viewable");else{d.title=e("View data"),d.href=this.model.urls.display;var f=this;d.onclick=function(a){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add_dataset(f.model.get("id")),a.preventDefault())}}return d.faIcon="fa-eye",c(d)},_renderDetails:function(){if(this.model.get("state")===b.NOT_VIEWABLE)return $(this.templates.noAccess(this.model.toJSON(),this));var a=f.prototype._renderDetails.call(this);return a.find(".actions .left").empty().append(this._renderSecondaryActions()),a.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),a.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(a),a},_renderSummary:function(){var a=this.model.toJSON(),b=this.templates.summaries[a.state];return(b=b||this.templates.summaries.unknown)(a,this)},_renderDetailMessages:function(){var a=this,b=$('
'),c=a.model.toJSON();return _.each(a.templates.detailMessages,function(d){b.append($(d(c,a)))}),b},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case b.NOT_VIEWABLE:return[];case b.OK:case b.FAILED_METADATA:case b.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return c({title:e("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:_.isEmpty(this.model.get("meta_files"))?$(['','',""].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var a=this.model.urls;return $(['
','','',"",'","
"].join("\n"))},events:_.extend(_.clone(f.prototype.events),{"click .display-btn":function(a){this.trigger("display",this,a)},"click .params-btn":function(a){this.trigger("params",this,a)},"click .download-btn":function(a){this.trigger("download",this,a)}}),toString:function(){var a=this.model?this.model+"":"(no model)";return"DatasetListItemView("+a+")"}});return g.prototype.templates=function(){var a=_.extend({},f.prototype.templates.warnings,{failed_metadata:d.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','
',e("An error occurred setting the metadata for this dataset"),"
","<% } %>"]),error:d.wrapTemplate(["<% if( model.error ){ %>",'
',e("There was an error getting the data for this dataset"),": <%- model.error %>","
","<% } %>"]),purged:d.wrapTemplate(["<% if( model.purged ){ %>",'
',e("This dataset has been deleted and removed from disk"),"
","<% } %>"]),deleted:d.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
',e("This dataset has been deleted"),"
","<% } %>"])}),c=d.wrapTemplate(['
','
','
','
','
',"
","<% if( !dataset.deleted && !dataset.purged ){ %>",'
','
','
',"<% if( dataset.peek ){ %>",'
<%= dataset.peek %>
',"<% } %>","<% } %>","
"],"dataset"),g=d.wrapTemplate(['
','
',e("You do not have permission to view this dataset"),"
","
"],"dataset"),h={};h[b.OK]=h[b.FAILED_METADATA]=d.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'
','<%- dataset.misc_blurb %>',"
","<% } %>","<% if( dataset.file_ext ){ %>",'
','",'<%- dataset.file_ext %>',"
","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'
','",'',"<%- dataset.metadata_dbkey %>","","
","<% } %>","<% if( dataset.misc_info ){ %>",'
','<%- dataset.misc_info %>',"
","<% } %>"],"dataset"),h[b.NEW]=d.wrapTemplate(["
",e("This is a new dataset and not all of its data are available yet"),"
"],"dataset"),h[b.NOT_VIEWABLE]=d.wrapTemplate(["
",e("You do not have permission to view this dataset"),"
"],"dataset"),h[b.DISCARDED]=d.wrapTemplate(["
",e("The job creating this dataset was cancelled before completion"),"
"],"dataset"),h[b.QUEUED]=d.wrapTemplate(["
",e("This job is waiting to run"),"
"],"dataset"),h[b.RUNNING]=d.wrapTemplate(["
",e("This job is currently running"),"
"],"dataset"),h[b.UPLOAD]=d.wrapTemplate(["
",e("This dataset is currently uploading"),"
"],"dataset"),h[b.SETTING_METADATA]=d.wrapTemplate(["
",e("Metadata is being auto-detected"),"
"],"dataset"),h[b.PAUSED]=d.wrapTemplate(["
",e('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"
"],"dataset"),h[b.ERROR]=d.wrapTemplate(["<% if( !dataset.purged ){ %>","
<%- dataset.misc_blurb %>
","<% } %>",'',e("An error occurred with this dataset"),":",'
<%- dataset.misc_info %>
'],"dataset"),h[b.EMPTY]=d.wrapTemplate(["
",e("No data"),": <%- dataset.misc_blurb %>
"],"dataset"),h.unknown=d.wrapTemplate(['
Error: unknown dataset state: "<%- dataset.state %>"
'],"dataset");var i={resubmitted:d.wrapTemplate(["<% if( model.resubmitted ){ %>",'
',e("The job creating this dataset has been resubmitted"),"
","<% } %>"])},j=d.wrapTemplate(["<% _.each( apps, function( app ){ %>",'
','<%- app.label %> ','',"<% _.each( app.links, function( link ){ %>",'',"<% print( _l( link.text ) ); %>"," ","<% }); %>","","
","<% }); %>"],"apps");return _.extend({},f.prototype.templates,{warnings:a,details:c,noAccess:g,summaries:h,detailMessages:i,displayApplications:j})}(),{DatasetListItemView:g}}); //# sourceMappingURL=../../../maps/mvc/dataset/dataset-li.js.map \ No newline at end of file diff --git a/static/scripts/mvc/history/hdca-li.js b/static/scripts/mvc/history/hdca-li.js index aa10e9096d2..05eb43b6674 100644 --- a/static/scripts/mvc/history/hdca-li.js +++ b/static/scripts/mvc/history/hdca-li.js @@ -1,2 +1,2 @@ -define(["mvc/dataset/states","mvc/collection/collection-li","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){var f=b.DCListItemView,g=f.extend({className:f.prototype.className+" history-content",_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.model.on("change",function(a){_.isEqual(_.keys(a.changed),["visible"])&&this.render()},this)},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return c.ListCollectionPanel;case"paired":return c.PairCollectionPanel;case"list:paired":return c.ListOfPairsCollectionPanel}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(b){f.prototype._swapNewRender.call(this,b);var c=this.model.get("state")||a.OK;return this.$el.addClass("state-"+c),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDCAListItemView("+a+")"}});return g.prototype.templates=function(){var a=_.extend({},f.prototype.templates.warnings,{hidden:d.wrapTemplate(["<% if( !collection.visible ){ %>",'
',e("This collection has been hidden"),"
","<% } %>"],"collection")}),b=d.wrapTemplate(['
','','
','<%- collection.hid %> ','<%- collection.name %>',"
",'
',"
"],"collection");return _.extend({},f.prototype.templates,{warnings:a,titleBar:b})}(),{HDCAListItemView:g}}); +define(["mvc/dataset/states","mvc/collection/collection-li","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){var f=b.DCListItemView,g=f.extend({className:f.prototype.className+" history-content",_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.model.on("change",function(){this.render()},this)},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return c.ListCollectionPanel;case"paired":return c.PairCollectionPanel;case"list:paired":return c.ListOfPairsCollectionPanel}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(b){f.prototype._swapNewRender.call(this,b);var c=this.model.get("populated")?a.OK:a.RUNNING;return this.$el.addClass("state-"+c),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDCAListItemView("+a+")"}});return g.prototype.templates=function(){var a=_.extend({},f.prototype.templates.warnings,{hidden:d.wrapTemplate(["<% if( !collection.visible ){ %>",'
',e("This collection has been hidden"),"
","<% } %>"],"collection")}),b=d.wrapTemplate(['
','','
','<%- collection.hid %> ','<%- collection.name %>',"
",'
',"
"],"collection");return _.extend({},f.prototype.templates,{warnings:a,titleBar:b})}(),{HDCAListItemView:g}}); //# sourceMappingURL=../../../maps/mvc/history/hdca-li.js.map \ No newline at end of file diff --git a/static/scripts/mvc/tools/tools-form-base.js b/static/scripts/mvc/tools/tools-form-base.js index 6fc8d75a707..da10226a9aa 100644 --- a/static/scripts/mvc/tools/tools-form-base.js +++ b/static/scripts/mvc/tools/tools-form-base.js @@ -1,2 +1,2 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(c){this.options=a.merge(c,{}),this.setElement("
"),this.deferred=new b,c.inputs?this._buildForm(c):this._buildModel(c,!0)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:""+b.name+" "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,c){var e=this;if(this.options.id=b.id,this.options.version=b.version,b.job_id)f=Galaxy.root+"api/jobs/"+b.job_id+"/build_for_rerun";else{var f=Galaxy.root+"api/tools/"+b.id+"/build?";if(b.dataset_id)f+="dataset_id="+b.dataset_id;else{f+="tool_version="+b.version+"&";var g=top.location.href,h=g.indexOf("?");-1!=g.indexOf("tool_id=")&&-1!==h&&(f+=g.slice(h+1))}}var i=this.deferred.register();a.request({type:"GET",url:f,success:function(a){e._buildForm(a.tool_model||a),!c&&e.form.message.update({status:"success",message:"Now you are using '"+e.options.name+"' version "+e.options.version+".",persistent:!1}),e.deferred.done(i),console.debug("tools-form::initialize() - Initial tool model ready."),console.debug(a)},error:function(a){e.deferred.done(i),console.debug("tools-form::initialize() - Initial tool model request failed."),console.debug(a);var b=a.error||a.err_msg||"Uncaught error.";void 0==e.form&&(e.form=new d),e.form.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){e.form.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();console.debug("tools-form-base::_updateModel() - Sending current state (see below)."),console.debug(e),a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),console.debug("tools-form-base::_updateModel() - Received new model (see below)."),console.debug(a),c.deferred.done(f)},error:function(a){c.deferred.done(f),console.debug("tools-form-base::_updateModel() - Refresh request failed."),console.debug(a)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("
"),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})}); +define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(c){this.options=a.merge(c,{}),this.setElement("
"),this.deferred=new b,c.inputs?this._buildForm(c):this._buildModel(c,!0)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:""+b.name+" "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,c){var e=this;if(this.options.id=b.id,this.options.version=b.version,b.job_id)f=Galaxy.root+"api/jobs/"+b.job_id+"/build_for_rerun";else{var f=Galaxy.root+"api/tools/"+b.id+"/build?";if(b.dataset_id)f+="dataset_id="+b.dataset_id;else{f+="tool_version="+b.version+"&";var g=top.location.href,h=g.indexOf("?");-1!=g.indexOf("tool_id=")&&-1!==h&&(f+=g.slice(h+1))}}var i=this.deferred.register();a.request({type:"GET",url:f,success:function(a){e._buildForm(a.tool_model||a),!c&&e.form.message.update({status:"success",message:"Now you are using '"+e.options.name+"' version "+e.options.version+".",persistent:!1}),e.deferred.done(i),console.debug("tools-form::initialize() - Initial tool model ready."),console.debug(a)},error:function(a){e.deferred.done(i),console.debug("tools-form::initialize() - Initial tool model request failed."),console.debug(a);var b=a.error||a.err_msg||"Uncaught error.";void 0==e.form&&(e.form=new d),Galaxy.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){Galaxy.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();console.debug("tools-form-base::_updateModel() - Sending current state (see below)."),console.debug(e),a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),console.debug("tools-form-base::_updateModel() - Received new model (see below)."),console.debug(a),c.deferred.done(f)},error:function(a){c.deferred.done(f),console.debug("tools-form-base::_updateModel() - Refresh request failed."),console.debug(a)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("
"),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})}); //# sourceMappingURL=../../../maps/mvc/tools/tools-form-base.js.map \ No newline at end of file diff --git a/static/scripts/mvc/tools/tools-jobs.js b/static/scripts/mvc/tools/tools-jobs.js index d4b1708c3a3..8dc40d3c962 100644 --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/tools/tools-template"],function(a,b){return{submit:function(c,d,e){var f=this,g={tool_id:d.id,tool_version:d.version,inputs:c.data.create()};return c.trigger("reset"),this._validation(c,g)?(console.debug(g),void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:g,success:function(a){e&&e(),c.reciept(b.success(a)),f._refreshHdas()},error:function(a){if(e&&e(),a&&a.message&&a.message.data){var d=c.data.matchResponse(a.message.data);for(var f in d){c.highlight(f,d[f]);break}}else console.debug(a),a&&c.modal.show({title:"Job submission failed",body:b.error(g),buttons:{Close:function(){c.modal.hide()}}})}})):(console.debug("tools-jobs::submit - Submission canceled. Validation failed."),void(e&&e()))},_validation:function(a,b){var c=b.inputs,d=-1,e=null;for(var f in c){var g=c[f],h=a.data.match(f),i=a.field_list[h],j=a.input_list[h];if(h&&j&&i){if(!j.optional&&null==g)return a.highlight(h),!1;if(g&&g.batch){var k=g.values.length,l=null;if(k>0&&(l=g.values[0]&&g.values[0].src),l)if(null===e)e=l;else if(e!==l)return a.highlight(h,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===d)d=k;else if(d!==k)return a.highlight(h,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+k+" selection(s) while a previous field contains "+d+"."),!1}}else console.debug("tools-jobs::_validation - Retrieving input objects failed.")}return!0},_refreshHdas:function(){parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()}}}); +define(["utils/utils","mvc/tools/tools-template"],function(a,b){return{submit:function(c,d,e){var f=this,g={tool_id:d.id,tool_version:d.version,inputs:c.data.create()};return c.trigger("reset"),this._validation(c,g)?(console.debug(g),void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:g,success:function(a){e&&e(),c.reciept(b.success(a)),f._refreshHdas()},error:function(a){if(e&&e(),a&&a.message&&a.message.data){var d=c.data.matchResponse(a.message.data);for(var f in d){c.highlight(f,d[f]);break}}else console.debug(a),a&&c.modal.show({title:"Job submission failed",body:b.error(g),buttons:{Close:function(){c.modal.hide()}}})}})):(console.debug("tools-jobs::submit - Submission canceled. Validation failed."),void(e&&e()))},_validation:function(a,b){var c=b.inputs,d=-1,e=null;for(var f in c){var g=c[f],h=a.data.match(f),i=a.field_list[h],j=a.input_list[h];if(h&&j&&i){if(!j.optional&&null==g)return a.highlight(h),!1;if(g&&g.batch){var k=g.values.length,l=null;if(k>0&&(l=g.values[0]&&g.values[0].src),l)if(null===e)e=l;else if(e!==l)return a.highlight(h,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===d)d=k;else if(d!==k)return a.highlight(h,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+k+" selection(s) while a previous field contains "+d+"."),!1}}else console.debug("tools-jobs::_validation - Retrieving input objects failed.")}return!0},_refreshHdas:function(a,b){parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents(a,b)}}}); //# sourceMappingURL=../../../maps/mvc/tools/tools-jobs.js.map \ No newline at end of file diff --git a/static/scripts/mvc/upload/upload-row.js b/static/scripts/mvc/upload/upload-row.js new file mode 100644 index 00000000000..823daa9ad71 --- /dev/null +++ b/static/scripts/mvc/upload/upload-row.js @@ -0,0 +1,2 @@ +define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-settings","mvc/ui/ui-popover","mvc/ui/ui-select"],function(a,b,c,d,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(a,c){this.app=a;var f=this;this.model=new b.Model(c),this.setElement(this._template(c));var g=this.$el;this.settings=new d.View({title:"Upload configuration",container:g.find("#settings"),placement:"bottom"});var h=this.app.select_genome.value();this.select_genome=new e.View({css:"genome",onchange:function(a){f.model.set("genome",a),f.app.updateGenome(a,!0)},data:f.app.list_genomes,container:g.find("#genome"),value:h}),this.model.set("genome",h);var i=this.app.select_extension.value();this.select_extension=new e.View({css:"extension",onchange:function(a){f.model.set("extension",a),f.app.updateExtension(a,!0)},data:f.app.list_extensions,container:g.find("#extension"),value:i}),this.model.set("extension",i),g.find("#symbol").on("click",function(){f._removeRow()}),g.find("#extension-info").on("click",function(a){f.app.showExtensionInfo({$el:$(a.target),title:f.select_extension.text(),extension:f.select_extension.value()})}).on("mousedown",function(a){a.preventDefault()}),g.find("#settings").on("click",function(){f._showSettings()}).on("mousedown",function(a){a.preventDefault()}),g.find("#text-content").on("change input",function(a){f.model.set("url_paste",$(a.target).val()),f.model.set("file_size",$(a.target).val().length)}),g.find("#space_to_tabs").on("change",function(a){f.model.set("space_to_tabs",$(a.target).prop("checked"))}),this.model.on("change:percentage",function(){f._refreshPercentage()}),this.model.on("change:status",function(){f._refreshStatus()}),this.model.on("change:info",function(){f._refreshInfo()}),this.model.on("change:genome",function(){f._refreshGenome()}),this.model.on("change:extension",function(){f._refreshExtension()}),this.model.on("change:file_size",function(){f._refreshFileSize()}),this.model.on("remove",function(){f.remove()}),this.app.collection.on("reset",function(){f.remove()})},render:function(){var b=this.model.get("file_name"),c=this.model.get("file_size"),d=this.model.get("file_mode"),e=this.$el;if(e.find("#title").html(b),e.find("#size").html(a.bytesToString(c)),e.find("#mode").removeClass().addClass("mode"),"new"==d){var f=e.find("#text"),g=this.options.padding,h=e.width()-2*g,i=e.height()-g;f.css("width",h+"px"),f.css("top",i+"px"),e.height(i+f.height()+2*g),f.show(),e.find("#mode").addClass("fa fa-pencil")}"local"==d&&e.find("#mode").addClass("fa fa-laptop"),"ftp"==d&&e.find("#mode").addClass("fa fa-code-fork")},remove:function(){this.select_genome.remove(),this.select_extension.remove(),Backbone.View.prototype.remove.apply(this)},_refreshExtension:function(){this.select_extension.value(this.model.get("extension"))},_refreshGenome:function(){this.select_genome.value(this.model.get("genome"))},_refreshInfo:function(){var a=this.model.get("info");a?this.$el.find("#info").html("Failed: "+a).show():this.$el.find("#info").hide()},_refreshPercentage:function(){var a=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:a+"%"}),this.$el.find("#percentage").html(100!=a?a+"%":"Adding to history...")},_refreshStatus:function(){var a=this.$el,b=this.model.get("status"),c=this.status_classes[b],d=this.$el.find("#symbol");d.removeClass(),d.addClass(c),"init"==b?(this.select_genome.enable(),this.select_extension.enable(),a.find("#text-content").attr("disabled",!1),a.find("#space_to_tabs").attr("disabled",!1)):(this.select_genome.disable(),this.select_extension.disable(),a.find("#text-content").attr("disabled",!0),a.find("#space_to_tabs").attr("disabled",!0)),"success"==b&&(a.addClass("success"),a.find("#percentage").html("100%")),"error"==b&&(a.addClass("danger"),a.find(".progress").remove())},_refreshFileSize:function(){var b=this.model.get("file_size");this.$el.find("#size").html(a.bytesToString(b))},_removeRow:function(){var a=this.model.get("status");("init"==a||"success"==a||"error"==a)&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new c(this).$el),this.settings.show())},_template:function(a){return'
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.