- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 2 new changesets
by Bitbucket 18 Jan '13

18 Jan '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9a440d0b2a1c/ changeset: 9a440d0b2a1c user: james_taylor date: 2013-01-18 16:44:18 summary: modals: make wider by default and scroll like trello affected #: 3 files diff -r a4113cc1cb5eaa68091c9a73375f00555b66dd11 -r 9a440d0b2a1ca00e71564f9258211a9eb9830fee static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -311,9 +311,10 @@ } #overlay { - position: fixed; + position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: 20000; + overflow-y: auto; } #overlay.is_modal #overlay-background, .overlay-background { diff -r a4113cc1cb5eaa68091c9a73375f00555b66dd11 -r 9a440d0b2a1ca00e71564f9258211a9eb9830fee static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -537,6 +537,9 @@ .btn.active,.btn:active{color:inherit;} .dropdown-menu{max-width:auto;} input[type="checkbox"],input[type="radio"]{margin-left:0.5ex;margin-right:0.5ex;} +.modal{position:absolute;top:50px;width:660px;margin-left:-330px;} +.modal:after{content:"";height:0px;position:relative;top:50px;display:block;border:solid transparent 1px;} +.modal-body{height:auto;max-height:none;} .nav-tabs{border-bottom:1px solid #999999;} .nav-tabs>li>a:hover{border-color:#eeeeee #eeeeee #999999;} .nav-tabs>.active>a,.nav-tabs>.active>a:hover{border:1px solid #999999;border-bottom-color:transparent;} @@ -865,7 +868,7 @@ .panel-header-button{color:#333;text-decoration:none;display:inline-block;cursor:pointer;margin:-1px;padding:1px;margin-top:-0.2em;padding-right:0.5em;padding-left:0.5em;}.panel-header-button:hover{color:maroon;-webkit-transition:color 0.25s linear;-moz-transition:color 0.25s linear;-o-transition:color 0.25s linear;transition:color 0.25s linear;} .panel-header-button .caret{margin-top:7px;} .panel-header-button.popup{padding-right:1.75em;background:url(../images/dropdownarrow.png) no-repeat right 7px;} -#overlay{position:fixed;top:0;left:0;width:100%;height:100%;z-index:20000;} +#overlay{position:absolute;top:0;left:0;width:100%;height:100%;z-index:20000;overflow-y:auto;} #overlay.is_modal #overlay-background,.overlay-background{background:rgba(0, 0, 0, 0.5);} .panel-error-message,.panel-warning-message,.panel-done-message,.panel-info-message{height:24px;line-height:24px;color:#303030;padding:0px;padding-left:26px;background-color:#ffcccc;background-image:url(error_small.png);background-repeat:no-repeat;background-position:6px 50%;} .panel-warning-message{background-image:url(warn_small.png);background-color:#ffffcc;} diff -r a4113cc1cb5eaa68091c9a73375f00555b66dd11 -r 9a440d0b2a1ca00e71564f9258211a9eb9830fee static/june_2007_style/galaxy_bootstrap.less --- a/static/june_2007_style/galaxy_bootstrap.less +++ b/static/june_2007_style/galaxy_bootstrap.less @@ -98,6 +98,31 @@ margin-right: 0.5ex; } +// Modal -- wider by default, scroll like Trello + +.modal { + position: absolute; + top: 50px; + width: 660px; + margin-left: -330px; +} + + +.modal:after { + content: ""; + height: 0px; + position: relative; + top: 50px; + display: block; + border: solid transparent 1px; +}; + + +.modal-body { + height: auto; + max-height: none; +} + // Tabs -- border color is hardcoded in navs.less, change to @btnBorder here .nav-tabs { https://bitbucket.org/galaxy/galaxy-central/commits/add133ca7596/ changeset: add133ca7596 user: james_taylor date: 2013-01-18 17:31:21 summary: merge affected #: 3 files diff -r b9d44cf4b68e2c4a76bc2b7f7eb54950e2c077be -r add133ca7596281900e31933e6b0748812323517 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -311,9 +311,10 @@ } #overlay { - position: fixed; + position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: 20000; + overflow-y: auto; } #overlay.is_modal #overlay-background, .overlay-background { diff -r b9d44cf4b68e2c4a76bc2b7f7eb54950e2c077be -r add133ca7596281900e31933e6b0748812323517 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -537,6 +537,9 @@ .btn.active,.btn:active{color:inherit;} .dropdown-menu{max-width:auto;} input[type="checkbox"],input[type="radio"]{margin-left:0.5ex;margin-right:0.5ex;} +.modal{position:absolute;top:50px;width:660px;margin-left:-330px;} +.modal:after{content:"";height:0px;position:relative;top:50px;display:block;border:solid transparent 1px;} +.modal-body{height:auto;max-height:none;} .nav-tabs{border-bottom:1px solid #999999;} .nav-tabs>li>a:hover{border-color:#eeeeee #eeeeee #999999;} .nav-tabs>.active>a,.nav-tabs>.active>a:hover{border:1px solid #999999;border-bottom-color:transparent;} @@ -865,7 +868,7 @@ .panel-header-button{color:#333;text-decoration:none;display:inline-block;cursor:pointer;margin:-1px;padding:1px;margin-top:-0.2em;padding-right:0.5em;padding-left:0.5em;}.panel-header-button:hover{color:maroon;-webkit-transition:color 0.25s linear;-moz-transition:color 0.25s linear;-o-transition:color 0.25s linear;transition:color 0.25s linear;} .panel-header-button .caret{margin-top:7px;} .panel-header-button.popup{padding-right:1.75em;background:url(../images/dropdownarrow.png) no-repeat right 7px;} -#overlay{position:fixed;top:0;left:0;width:100%;height:100%;z-index:20000;} +#overlay{position:absolute;top:0;left:0;width:100%;height:100%;z-index:20000;overflow-y:auto;} #overlay.is_modal #overlay-background,.overlay-background{background:rgba(0, 0, 0, 0.5);} .panel-error-message,.panel-warning-message,.panel-done-message,.panel-info-message{height:24px;line-height:24px;color:#303030;padding:0px;padding-left:26px;background-color:#ffcccc;background-image:url(error_small.png);background-repeat:no-repeat;background-position:6px 50%;} .panel-warning-message{background-image:url(warn_small.png);background-color:#ffffcc;} diff -r b9d44cf4b68e2c4a76bc2b7f7eb54950e2c077be -r add133ca7596281900e31933e6b0748812323517 static/june_2007_style/galaxy_bootstrap.less --- a/static/june_2007_style/galaxy_bootstrap.less +++ b/static/june_2007_style/galaxy_bootstrap.less @@ -98,6 +98,31 @@ margin-right: 0.5ex; } +// Modal -- wider by default, scroll like Trello + +.modal { + position: absolute; + top: 50px; + width: 660px; + margin-left: -330px; +} + + +.modal:after { + content: ""; + height: 0px; + position: relative; + top: 50px; + display: block; + border: solid transparent 1px; +}; + + +.modal-body { + height: auto; + max-height: none; +} + // Tabs -- border color is hardcoded in navs.less, change to @btnBorder here .nav-tabs { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: history panel: Show/enable display icon-button for non-ready-state hdas
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b9d44cf4b68e/ changeset: b9d44cf4b68e user: carlfeberhard date: 2013-01-18 16:45:20 summary: history panel: Show/enable display icon-button for non-ready-state hdas affected #: 1 file diff -r c8cb184472b913c635fb34f31e4122c3c1f77e87 -r b9d44cf4b68e2c4a76bc2b7f7eb54950e2c077be static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -198,15 +198,14 @@ * @returns {jQuery} rendered DOM */ _render_displayButton : function(){ - // don't show display if not in ready state or not accessible - // DO show if in error (ala previous history panel) - if( ( !this.model.inReadyState() ) - //|| ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) - || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + // don't show display if not viewable or not accessible + // (do show if in error, running) + if( ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) || ( !this.model.get( 'accessible' ) ) ){ this.displayButton = null; return null; } + //NOTE: line 88 in history_common.mako should be handled by the url template generation var displayBtnData = { icon_class : 'display', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Sphinx Doc: Remove enable_api step from the api quickstart as it is no longer necessary.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c8cb184472b9/ changeset: c8cb184472b9 user: dannon date: 2013-01-18 16:26:57 summary: Sphinx Doc: Remove enable_api step from the api quickstart as it is no longer necessary. affected #: 1 file diff -r d36e35dd83bf18a47f26dc6eb779549c15782fbd -r c8cb184472b913c635fb34f31e4122c3c1f77e87 doc/source/lib/galaxy.webapps.galaxy.api.rst --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -23,10 +23,6 @@ Quickstart ========== -Set the following option in universe_wsgi.ini and start the server:: - - enable_api = True - Log in as your user, navigate to the API Keys page in the User menu, and generate a new API key. Make a note of the API key, and then pull up a terminal. Now we'll use the display.py script in your galaxy/scripts/api Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix circular repository dependency issue that so far uccurs only on the test tool shed.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d36e35dd83bf/ changeset: d36e35dd83bf user: greg date: 2013-01-18 16:16:20 summary: Fix circular repository dependency issue that so far uccurs only on the test tool shed. affected #: 1 file diff -r c86a704ba3f60bc51c9f998e0061d9b9f9507242 -r d36e35dd83bf18a47f26dc6eb779549c15782fbd lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -2779,6 +2779,7 @@ def populate_repository_dependency_objects_for_processing( trans, current_repository_key, repository_dependencies_dict, key_rd_dicts_to_be_processed, handled_key_rd_dicts, circular_repository_dependencies, all_repository_dependencies ): current_repository_key_rd_dicts = [] + filtered_current_repository_key_rd_dicts = [] for rd in repository_dependencies_dict[ 'repository_dependencies' ]: new_key_rd_dict = {} new_key_rd_dict[ current_repository_key ] = rd @@ -2790,6 +2791,7 @@ for key_rd_dict in current_repository_key_rd_dicts: is_circular = False if not in_key_rd_dicts( key_rd_dict, handled_key_rd_dicts ) and not in_key_rd_dicts( key_rd_dict, key_rd_dicts_to_be_processed ): + filtered_current_repository_key_rd_dicts.append( key_rd_dict ) repository_dependency = key_rd_dict[ current_repository_key ] if current_repository_key in all_repository_dependencies: # Add all repository dependencies for the current repository into it's entry in all_repository_dependencies. @@ -2813,7 +2815,7 @@ new_key_rd_dict = {} new_key_rd_dict[ current_repository_key ] = repository_dependency key_rd_dicts_to_be_processed.append( new_key_rd_dict ) - return current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, all_repository_dependencies + return filtered_current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, all_repository_dependencies def remove_dir( dir ): if os.path.exists( dir ): try: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Add missing imports to shed_util_common.
by Bitbucket 17 Jan '13

17 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c86a704ba3f6/ changeset: c86a704ba3f6 user: greg date: 2013-01-17 22:42:11 summary: Add missing imports to shed_util_common. affected #: 1 file diff -r dd395d9b8a01255412b3e56219d11639ccce2e50 -r c86a704ba3f60bc51c9f998e0061d9b9f9507242 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1,4 +1,6 @@ import os, shutil, tempfile, logging, string, threading, urllib2, filecmp +from datetime import datetime +from time import gmtime, strftime from galaxy import web, util from galaxy.tools import parameters from galaxy.util import inflector, json Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Refactor the tool shed's common controller for planned elimination.
by Bitbucket 17 Jan '13

17 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dd395d9b8a01/ changeset: dd395d9b8a01 user: greg date: 2013-01-17 22:34:26 summary: Refactor the tool shed's common controller for planned elimination. affected #: 7 files diff -r 6538175fb3e6483895aaadfdeddd09aac558fdf5 -r dd395d9b8a01255412b3e56219d11639ccce2e50 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1,12 +1,14 @@ import os, shutil, tempfile, logging, string, threading, urllib2, filecmp -from galaxy import util +from galaxy import web, util from galaxy.tools import parameters from galaxy.util import inflector, json +from galaxy.util.odict import odict from galaxy.web import url_for from galaxy.web.form_builder import SelectField from galaxy.webapps.community.util import container_util from galaxy.datatypes import checkers from galaxy.model.orm import and_ +import sqlalchemy.orm.exc from galaxy.tools.parameters import dynamic_options from galaxy.tool_shed import encoding_util @@ -38,6 +40,60 @@ TOOL_SHED_ADMIN_CONTROLLER = 'TOOL_SHED_ADMIN_CONTROLLER' VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" ) +new_repo_email_alert_template = """ +Repository name: ${repository_name} +Revision: ${revision} +Change description: +${description} + +Uploaded by: ${username} +Date content uploaded: ${display_date} + +${content_alert_str} + +----------------------------------------------------------------------------- +This change alert was sent from the Galaxy tool shed hosted on the server +"${host}" +----------------------------------------------------------------------------- +You received this alert because you registered to receive email when +new repositories were created in the Galaxy tool shed named "${host}". +----------------------------------------------------------------------------- +""" + +email_alert_template = """ +Repository name: ${repository_name} +Revision: ${revision} +Change description: +${description} + +Changed by: ${username} +Date of change: ${display_date} + +${content_alert_str} + +----------------------------------------------------------------------------- +This change alert was sent from the Galaxy tool shed hosted on the server +"${host}" +----------------------------------------------------------------------------- +You received this alert because you registered to receive email whenever +changes were made to the repository named "${repository_name}". +----------------------------------------------------------------------------- +""" + +contact_owner_template = """ +GALAXY TOOL SHED REPOSITORY MESSAGE +------------------------ + +The user '${username}' sent you the following message regarding your tool shed +repository named '${repository_name}'. You can respond by sending a reply to +the user's email address: ${email}. +----------------------------------------------------------------------------- +${message} +----------------------------------------------------------------------------- +This message was sent from the Galaxy Tool Shed instance hosted on the server +'${host}' +""" + def add_installation_directories_to_tool_dependencies( trans, tool_dependencies ): """ Determine the path to the installation directory for each of the received tool dependencies. This path will be displayed within the tool dependencies @@ -65,6 +121,18 @@ requirements_dict[ 'install_dir' ] = install_dir tool_dependencies[ dependency_key ] = requirements_dict return tool_dependencies +def add_tool_versions( trans, id, repository_metadata, changeset_revisions ): + # Build a dictionary of { 'tool id' : 'parent tool id' } pairs for each tool in repository_metadata. + metadata = repository_metadata.metadata + tool_versions_dict = {} + for tool_dict in metadata.get( 'tools', [] ): + # We have at least 2 changeset revisions to compare tool guids and tool ids. + parent_id = get_parent_id( trans, id, tool_dict[ 'id' ], tool_dict[ 'version' ], tool_dict[ 'guid' ], changeset_revisions ) + tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id + if tool_versions_dict: + repository_metadata.tool_versions = tool_versions_dict + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() def build_readme_files_dict( metadata, tool_path=None ): """Return a dictionary of valid readme file name <-> readme file content pairs for all readme files contained in the received metadata.""" readme_files_dict = {} @@ -439,6 +507,30 @@ except: pass return can_use_disk_file +def changeset_is_malicious( trans, id, changeset_revision, **kwd ): + """Check the malicious flag in repository metadata for a specified change set""" + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + if repository_metadata: + return repository_metadata.malicious + return False +def changeset_revision_reviewed_by_user( trans, user, repository, changeset_revision ): + """Determine if the current changeset revision has been reviewed by the current user.""" + for review in repository.reviews: + if review.changeset_revision == changeset_revision and review.user == user: + return True + return False +def check_file_contents( trans ): + """See if any admin users have chosen to receive email alerts when a repository is updated. If so, the file contents of the update must be + checked for inappropriate content. + """ + admin_users = trans.app.config.get( "admin_users", "" ).split( "," ) + for repository in trans.sa_session.query( trans.model.Repository ) \ + .filter( trans.model.Repository.table.c.email_alerts != None ): + email_alerts = json.from_json_string( repository.email_alerts ) + for user_email in email_alerts: + if user_email in admin_users: + return True + return False def check_tool_input_params( app, repo_dir, tool_config_name, tool, sample_files ): """ Check all of the tool's input parameters, looking for any that are dynamically generated using external data files to make @@ -1411,13 +1503,49 @@ if name == stripped_file_name: return os.path.abspath( os.path.join( root, name ) ) return file_path +def get_categories( trans ): + """Get all categories from the database.""" + return trans.sa_session.query( trans.model.Category ) \ + .filter( trans.model.Category.table.c.deleted==False ) \ + .order_by( trans.model.Category.table.c.name ) \ + .all() +def get_category( trans, id ): + """Get a category from the database.""" + return trans.sa_session.query( trans.model.Category ).get( trans.security.decode_id( id ) ) +def get_category_by_name( trans, name ): + """Get a category from the database via name.""" + try: + return trans.sa_session.query( trans.model.Category ).filter_by( name=name ).one() + except sqlalchemy.orm.exc.NoResultFound: + return None def get_changectx_for_changeset( repo, changeset_revision, **kwd ): - """Retrieve a specified changectx from a repository""" + """Retrieve a specified changectx from a repository.""" for changeset in repo.changelog: ctx = repo.changectx( changeset ) if str( ctx ) == changeset_revision: return ctx return None +def get_component( trans, id ): + """Get a component from the database.""" + return trans.sa_session.query( trans.model.Component ).get( trans.security.decode_id( id ) ) +def get_component_by_name( trans, name ): + """Get a component from the database via a name.""" + return trans.sa_session.query( trans.app.model.Component ) \ + .filter( trans.app.model.Component.table.c.name==name ) \ + .first() +def get_component_review( trans, id ): + """Get a component_review from the database""" + return trans.sa_session.query( trans.model.ComponentReview ).get( trans.security.decode_id( id ) ) +def get_component_review_by_repository_review_id_component_id( trans, repository_review_id, component_id ): + """Get a component_review from the database via repository_review_id and component_id.""" + return trans.sa_session.query( trans.model.ComponentReview ) \ + .filter( and_( trans.model.ComponentReview.table.c.repository_review_id == trans.security.decode_id( repository_review_id ), + trans.model.ComponentReview.table.c.component_id == trans.security.decode_id( component_id ) ) ) \ + .first() +def get_components( trans ): + return trans.sa_session.query( trans.app.model.Component ) \ + .order_by( trans.app.model.Component.name ) \ + .all() def get_config_from_disk( config_file, relative_install_dir ): for root, dirs, files in os.walk( relative_install_dir ): if root.find( '.hg' ) < 0: @@ -1426,7 +1554,7 @@ return os.path.abspath( os.path.join( root, name ) ) return None def get_configured_ui(): - # Configure any desired ui settings. + """Configure any desired ui settings.""" _ui = ui.ui() # The following will suppress all messages. This is # the same as adding the following setting to the repo @@ -1479,6 +1607,12 @@ def get_installed_tool_shed_repository( trans, id ): """Get a repository on the Galaxy side from the database via id""" return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) +def get_latest_repository_metadata( trans, decoded_repository_id ): + """Get last metadata defined for a specified repository from the database.""" + return trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( trans.model.RepositoryMetadata.table.c.repository_id == decoded_repository_id ) \ + .order_by( trans.model.RepositoryMetadata.table.c.id.desc() ) \ + .first() def get_latest_tool_config_revision_from_repository_manifest( repo, filename, changeset_revision ): """ Get the latest revision of a tool config file named filename from the repository manifest up to the value of changeset_revision. @@ -1649,6 +1783,21 @@ return INITIAL_CHANGELOG_HASH else: previous_changeset_revision = changeset_revision +def get_previous_repository_reviews( trans, repository, changeset_revision ): + """Return an ordered dictionary of repository reviews up to and including the received changeset revision.""" + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) + reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] + previous_reviews_dict = odict() + for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ): + previous_changeset_revision = str( repo.changectx( changeset ) ) + if previous_changeset_revision in reviewed_revision_hashes: + previous_rev, previous_changeset_revision_label = get_rev_label_from_changeset_revision( repo, previous_changeset_revision ) + revision_reviews = get_reviews_by_repository_id_changeset_revision( trans, + trans.security.encode_id( repository.id ), + previous_changeset_revision ) + previous_reviews_dict[ previous_changeset_revision ] = dict( changeset_revision_label=previous_changeset_revision_label, + reviews=revision_reviews ) + return previous_reviews_dict def get_readme_file_names( repository_name ): readme_files = [ 'readme', 'read_me', 'install' ] valid_filenames = [ r for r in readme_files ] @@ -1664,6 +1813,9 @@ elif len( repo_info_tuple ) == 7: description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple return description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies +def get_repository_by_name( trans, name ): + """Get a repository from the database via name.""" + return trans.sa_session.query( trans.model.Repository ).filter_by( name=name ).one() def get_repository_by_name_and_owner( trans, name, owner ): """Get a repository from the database via name and owner""" if trans.webapp.name == 'galaxy': @@ -1819,6 +1971,25 @@ .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ), trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \ .first() +def get_repository_metadata_revisions_for_review( repository, reviewed=True ): + repository_metadata_revisions = [] + metadata_changeset_revision_hashes = [] + if reviewed: + for metadata_revision in repository.metadata_revisions: + metadata_changeset_revision_hashes.append( metadata_revision.changeset_revision ) + for review in repository.reviews: + if review.changeset_revision in metadata_changeset_revision_hashes: + rmcr_hashes = [ rmr.changeset_revision for rmr in repository_metadata_revisions ] + if review.changeset_revision not in rmcr_hashes: + repository_metadata_revisions.append( review.repository_metadata ) + else: + for review in repository.reviews: + if review.changeset_revision not in metadata_changeset_revision_hashes: + metadata_changeset_revision_hashes.append( review.changeset_revision ) + for metadata_revision in repository.metadata_revisions: + if metadata_revision.changeset_revision not in metadata_changeset_revision_hashes: + repository_metadata_revisions.append( metadata_revision ) + return repository_metadata_revisions def get_repository_tools_tups( app, metadata_dict ): repository_tools_tups = [] index, shed_conf_dict = get_shed_tool_conf_dict( app, metadata_dict.get( 'shed_config_filename' ) ) @@ -1849,6 +2020,48 @@ relative_path_to_file.startswith( os.path.join( shed_config_dict.get( 'tool_path' ), relative_install_dir ) ): relative_path_to_file = relative_path_to_file[ len( shed_config_dict.get( 'tool_path' ) ) + 1: ] return relative_path_to_file +def get_reversed_changelog_changesets( repo ): + reversed_changelog = [] + for changeset in repo.changelog: + reversed_changelog.insert( 0, changeset ) + return reversed_changelog +def get_review( trans, id ): + """Get a repository_review from the database via id.""" + return trans.sa_session.query( trans.model.RepositoryReview ).get( trans.security.decode_id( id ) ) +def get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ): + """Get all repository_reviews from the database via repository id and changeset_revision.""" + return trans.sa_session.query( trans.model.RepositoryReview ) \ + .filter( and_( trans.model.RepositoryReview.repository_id == trans.security.decode_id( repository_id ), + trans.model.RepositoryReview.changeset_revision == changeset_revision ) ) \ + .all() +def get_review_by_repository_id_changeset_revision_user_id( trans, repository_id, changeset_revision, user_id ): + """Get a repository_review from the database via repository id, changeset_revision and user_id.""" + return trans.sa_session.query( trans.model.RepositoryReview ) \ + .filter( and_( trans.model.RepositoryReview.repository_id == trans.security.decode_id( repository_id ), + trans.model.RepositoryReview.changeset_revision == changeset_revision, + trans.model.RepositoryReview.user_id == trans.security.decode_id( user_id ) ) ) \ + .first() +def get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=None ): + if repository is None: + repository = repository_metadata.repository + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) + changeset_revision = repository_metadata.changeset_revision + ctx = get_changectx_for_changeset( repo, changeset_revision ) + if ctx: + rev = '%04d' % ctx.rev() + label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + else: + rev = '-1' + label = "-1:%s" % changeset_revision + return rev, label, changeset_revision +def get_revision_label( trans, repository, changeset_revision ): + """Return a string consisting of the human read-able changeset rev and the changeset revision string.""" + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) + if ctx: + return "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + else: + return "-1:%s" % changeset_revision def get_sample_files_from_disk( repository_files_dir, tool_path=None, relative_install_dir=None, resetting_all_metadata_on_repository=False ): if resetting_all_metadata_on_repository: # Keep track of the location where the repository is temporarily cloned so that we can strip it when setting metadata. @@ -1877,6 +2090,15 @@ relative_path_to_sample_file = relative_path_to_sample_file[ len( tool_path ) + 1 :] sample_file_metadata_paths.append( relative_path_to_sample_file ) return sample_file_metadata_paths, sample_file_copy_paths +def get_rev_label_from_changeset_revision( repo, changeset_revision ): + ctx = get_changectx_for_changeset( repo, changeset_revision ) + if ctx: + rev = '%04d' % ctx.rev() + label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + else: + rev = '-1' + label = "-1:%s" % changeset_revision + return rev, label def get_shed_tool_conf_dict( app, shed_tool_conf ): """ Return the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry @@ -2004,8 +2226,11 @@ return shed_url # The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml. return None +def get_user( trans, id ): + """Get a user from the database by id.""" + return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) def get_user_by_username( trans, username ): - """Get a user from the database by username""" + """Get a user from the database by username.""" return trans.sa_session.query( trans.model.User ) \ .filter( trans.model.User.table.c.username == username ) \ .one() @@ -2044,6 +2269,94 @@ all_repository_dependencies=all_repository_dependencies, handled_key_rd_dicts=handled_key_rd_dicts, circular_repository_dependencies=circular_repository_dependencies ) +def handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=False, admin_only=False ): + # There are 2 complementary features that enable a tool shed user to receive email notification: + # 1. Within User Preferences, they can elect to receive email when the first (or first valid) + # change set is produced for a new repository. + # 2. When viewing or managing a repository, they can check the box labeled "Receive email alerts" + # which caused them to receive email alerts when updates to the repository occur. This same feature + # is available on a per-repository basis on the repository grid within the tool shed. + # + # There are currently 4 scenarios for sending email notification when a change is made to a repository: + # 1. An admin user elects to receive email when the first change set is produced for a new repository + # from User Preferences. The change set does not have to include any valid content. This allows for + # the capture of inappropriate content being uploaded to new repositories. + # 2. A regular user elects to receive email when the first valid change set is produced for a new repository + # from User Preferences. This differs from 1 above in that the user will not receive email until a + # change set tha tincludes valid content is produced. + # 3. An admin user checks the "Receive email alerts" check box on the manage repository page. Since the + # user is an admin user, the email will include information about both HTML and image content that was + # included in the change set. + # 4. A regular user checks the "Receive email alerts" check box on the manage repository page. Since the + # user is not an admin user, the email will not include any information about both HTML and image content + # that was included in the change set. + repo_dir = repository.repo_path( trans.app ) + repo = hg.repository( get_configured_ui(), repo_dir ) + smtp_server = trans.app.config.smtp_server + if smtp_server and ( new_repo_alert or repository.email_alerts ): + # Send email alert to users that want them. + if trans.app.config.email_from is not None: + email_from = trans.app.config.email_from + elif trans.request.host.split( ':' )[0] == 'localhost': + email_from = 'galaxy-no-reply@' + socket.getfqdn() + else: + email_from = 'galaxy-no-reply@' + trans.request.host.split( ':' )[0] + tip_changeset = repo.changelog.tip() + ctx = repo.changectx( tip_changeset ) + t, tz = ctx.date() + date = datetime( *gmtime( float( t ) - tz )[:6] ) + display_date = date.strftime( "%Y-%m-%d" ) + try: + username = ctx.user().split()[0] + except: + username = ctx.user() + # We'll use 2 template bodies because we only want to send content + # alerts to tool shed admin users. + if new_repo_alert: + template = new_repo_email_alert_template + else: + template = email_alert_template + admin_body = string.Template( template ).safe_substitute( host=trans.request.host, + repository_name=repository.name, + revision='%s:%s' %( str( ctx.rev() ), ctx ), + display_date=display_date, + description=ctx.description(), + username=username, + content_alert_str=content_alert_str ) + body = string.Template( template ).safe_substitute( host=trans.request.host, + repository_name=repository.name, + revision='%s:%s' %( str( ctx.rev() ), ctx ), + display_date=display_date, + description=ctx.description(), + username=username, + content_alert_str='' ) + admin_users = trans.app.config.get( "admin_users", "" ).split( "," ) + frm = email_from + if new_repo_alert: + subject = "Galaxy tool shed alert for new repository named %s" % str( repository.name ) + subject = subject[ :80 ] + email_alerts = [] + for user in trans.sa_session.query( trans.model.User ) \ + .filter( and_( trans.model.User.table.c.deleted == False, + trans.model.User.table.c.new_repo_alert == True ) ): + if admin_only: + if user.email in admin_users: + email_alerts.append( user.email ) + else: + email_alerts.append( user.email ) + else: + subject = "Galaxy tool shed update alert for repository named %s" % str( repository.name ) + email_alerts = json.from_json_string( repository.email_alerts ) + for email in email_alerts: + to = email.strip() + # Send it + try: + if to in admin_users: + util.send_mail( frm, to, subject, admin_body, trans.app.config ) + else: + util.send_mail( frm, to, subject, body, trans.app.config ) + except Exception, e: + log.exception( "An error occurred sending a tool shed repository update alert by email." ) def handle_existing_tool_dependencies_that_changed_in_update( app, repository, original_dependency_dict, new_dependency_dict ): """ This method is called when a Galaxy admin is getting updates for an installed tool shed repository in order to cover the case where an @@ -2160,6 +2473,15 @@ message = str( e ) error = True return error, message +def has_previous_repository_reviews( trans, repository, changeset_revision ): + """Determine if a repository has a changeset revision review prior to the received changeset revision.""" + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) + reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] + for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ): + previous_changeset_revision = str( repo.changectx( changeset ) ) + if previous_changeset_revision in reviewed_revision_hashes: + return True + return False def in_all_repository_dependencies( repository_key, repository_dependency, all_repository_dependencies ): """Return True if { repository_key :repository_dependency } is in all_repository_dependencies.""" for key, val in all_repository_dependencies.items(): @@ -2348,6 +2670,89 @@ containers_dict[ 'tool_dependencies' ] = root_container containers_dict[ 'missing_tool_dependencies' ] = None return containers_dict +def new_repository_dependency_metadata_required( trans, repository, metadata_dict ): + """ + Compare the last saved metadata for each repository dependency in the repository with the new metadata in metadata_dict to determine if a new + repository_metadata table record is required or if the last saved metadata record can be updated instead. + """ + if 'repository_dependencies' in metadata_dict: + repository_metadata = get_latest_repository_metadata( trans, repository.id ) + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + if 'repository_dependencies' in metadata: + saved_repository_dependencies = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] + new_repository_dependencies = metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ] + # The saved metadata must be a subset of the new metadata. + for new_repository_dependency_metadata in new_repository_dependencies: + if new_repository_dependency_metadata not in saved_repository_dependencies: + return True + for saved_repository_dependency_metadata in saved_repository_dependencies: + if saved_repository_dependency_metadata not in new_repository_dependencies: + return True + else: + # We have repository metadata that does not include metadata for any repository dependencies in the + # repository, so we can update the existing repository metadata. + return False + else: + # There is no saved repository metadata, so we need to create a new repository_metadata table record. + return True + # The received metadata_dict includes no metadata for repository dependencies, so a new repository_metadata table record is not needed. + return False +def new_tool_metadata_required( trans, repository, metadata_dict ): + """ + Compare the last saved metadata for each tool in the repository with the new metadata in metadata_dict to determine if a new repository_metadata + table record is required, or if the last saved metadata record can be updated instead. + """ + if 'tools' in metadata_dict: + repository_metadata = get_latest_repository_metadata( trans, repository.id ) + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + if 'tools' in metadata: + saved_tool_ids = [] + # The metadata for one or more tools was successfully generated in the past + # for this repository, so we first compare the version string for each tool id + # in metadata_dict with what was previously saved to see if we need to create + # a new table record or if we can simply update the existing record. + for new_tool_metadata_dict in metadata_dict[ 'tools' ]: + for saved_tool_metadata_dict in metadata[ 'tools' ]: + if saved_tool_metadata_dict[ 'id' ] not in saved_tool_ids: + saved_tool_ids.append( saved_tool_metadata_dict[ 'id' ] ) + if new_tool_metadata_dict[ 'id' ] == saved_tool_metadata_dict[ 'id' ]: + if new_tool_metadata_dict[ 'version' ] != saved_tool_metadata_dict[ 'version' ]: + return True + # So far, a new metadata record is not required, but we still have to check to see if + # any new tool ids exist in metadata_dict that are not in the saved metadata. We do + # this because if a new tarball was uploaded to a repository that included tools, it + # may have removed existing tool files if they were not included in the uploaded tarball. + for new_tool_metadata_dict in metadata_dict[ 'tools' ]: + if new_tool_metadata_dict[ 'id' ] not in saved_tool_ids: + return True + else: + # We have repository metadata that does not include metadata for any tools in the + # repository, so we can update the existing repository metadata. + return False + else: + # There is no saved repository metadata, so we need to create a new repository_metadata table record. + return True + # The received metadata_dict includes no metadata for tools, so a new repository_metadata table record is not needed. + return False +def new_workflow_metadata_required( trans, repository, metadata_dict ): + """ + Currently everything about an exported workflow except the name is hard-coded, so there's no real way to differentiate versions of + exported workflows. If this changes at some future time, this method should be enhanced accordingly. + """ + if 'workflows' in metadata_dict: + repository_metadata = get_latest_repository_metadata( trans, repository.id ) + if repository_metadata: + # The repository has metadata, so update the workflows value - no new record is needed. + return False + else: + # There is no saved repository metadata, so we need to create a new repository_metadata table record. + return True + # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table record is not needed. + return False def open_repository_files_folder( trans, folder_path ): try: files_list = get_repository_files( trans, folder_path ) @@ -2701,6 +3106,77 @@ return reversed_changelog def reversed_upper_bounded_changelog( repo, included_upper_bounds_changeset_revision ): return reversed_lower_upper_bounded_changelog( repo, INITIAL_CHANGELOG_HASH, included_upper_bounds_changeset_revision ) +def set_repository_metadata( trans, repository, content_alert_str='', **kwd ): + """ + Set metadata using the repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset + has problems. + """ + message = '' + status = 'done' + encoded_id = trans.security.encode_id( repository.id ) + repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans, repository ) + repo_dir = repository.repo_path( trans.app ) + repo = hg.repository( get_configured_ui(), repo_dir ) + metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, + repository=repository, + repository_clone_url=repository_clone_url, + relative_install_dir=repo_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=False ) + if metadata_dict: + downloadable = is_downloadable( metadata_dict ) + repository_metadata = None + if new_repository_dependency_metadata_required( trans, repository, metadata_dict ) or \ + new_tool_metadata_required( trans, repository, metadata_dict ) or \ + new_workflow_metadata_required( trans, repository, metadata_dict ): + # Create a new repository_metadata table row. + repository_metadata = create_or_update_repository_metadata( trans, encoded_id, repository, repository.tip( trans.app ), metadata_dict ) + # If this is the first record stored for this repository, see if we need to send any email alerts. + if len( repository.downloadable_revisions ) == 1: + handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False ) + else: + repository_metadata = get_latest_repository_metadata( trans, repository.id ) + if repository_metadata: + downloadable = is_downloadable( metadata_dict ) + # Update the last saved repository_metadata table row. + repository_metadata.changeset_revision = repository.tip( trans.app ) + repository_metadata.metadata = metadata_dict + repository_metadata.downloadable = downloadable + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() + else: + # There are no tools in the repository, and we're setting metadata on the repository tip. + repository_metadata = create_or_update_repository_metadata( trans, encoded_id, repository, repository.tip( trans.app ), metadata_dict ) + if 'tools' in metadata_dict and repository_metadata and status != 'error': + # Set tool versions on the new downloadable change set. The order of the list of changesets is critical, so we use the repo's changelog. + changeset_revisions = [] + for changeset in repo.changelog: + changeset_revision = str( repo.changectx( changeset ) ) + if get_repository_metadata_by_changeset_revision( trans, encoded_id, changeset_revision ): + changeset_revisions.append( changeset_revision ) + add_tool_versions( trans, encoded_id, repository_metadata, changeset_revisions ) + elif len( repo ) == 1 and not invalid_file_tups: + message = "Revision '%s' includes no tools, datatypes or exported workflows for which metadata can " % str( repository.tip( trans.app ) ) + message += "be defined so this revision cannot be automatically installed into a local Galaxy instance." + status = "error" + if invalid_file_tups: + message = generate_message_for_invalid_tools( trans, invalid_file_tups, repository, metadata_dict ) + status = 'error' + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) + return message, status +def set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=None, **kwd ): + # Set metadata on the repository tip. + error_message, status = set_repository_metadata( trans, repository, content_alert_str=content_alert_str, **kwd ) + if error_message: + # If there is an error, display it. + return trans.response.send_redirect( web.url_for( controller='repository', + action='manage_repository', + id=trans.security.encode_id( repository.id ), + message=error_message, + status='error' ) ) def strip_path( fpath ): if not fpath: return fpath @@ -2862,10 +3338,8 @@ # ? = not tracked # I = ignored # It would be nice if we could use mercurial's purge extension to remove untracked files. The problem is that - # purging is not supported by the mercurial API. See the deprecated update_for_browsing() method in common.py. - commands.update( get_configured_ui(), - repo, - rev=ctx_rev ) + # purging is not supported by the mercurial API. + commands.update( get_configured_ui(), repo, rev=ctx_rev ) def url_join( *args ): parts = [] for arg in args: diff -r 6538175fb3e6483895aaadfdeddd09aac558fdf5 -r dd395d9b8a01255412b3e56219d11639ccce2e50 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -6,7 +6,6 @@ from galaxy.web.form_builder import SelectField from galaxy.util import inflector import galaxy.util.shed_util_common as suc -import common from repository import RepositoryGrid, CategoryGrid from galaxy import eggs @@ -474,7 +473,7 @@ if k.startswith( 'f-' ): del kwd[ k ] if 'user_id' in kwd: - user = common.get_user( trans, kwd[ 'user_id' ] ) + user = suc.get_user( trans, kwd[ 'user_id' ] ) kwd[ 'f-email' ] = user.email del kwd[ 'user_id' ] else: @@ -489,7 +488,7 @@ if k.startswith( 'f-' ): del kwd[ k ] category_id = kwd.get( 'id', None ) - category = common.get_category( trans, category_id ) + category = suc.get_category( trans, category_id ) kwd[ 'f-Category.name' ] = category.name elif operation == "receive email alerts": if kwd[ 'id' ]: @@ -554,7 +553,7 @@ if not name or not description: message = 'Enter a valid name and a description' status = 'error' - elif common.get_category_by_name( trans, name ): + elif suc.get_category_by_name( trans, name ): message = 'A category with that name already exists' status = 'error' else: @@ -641,7 +640,7 @@ action='manage_categories', message=message, status='error' ) ) - category = common.get_category( trans, id ) + category = suc.get_category( trans, id ) if params.get( 'edit_category_button', False ): new_name = util.restore_text( params.get( 'name', '' ) ).strip() new_description = util.restore_text( params.get( 'description', '' ) ).strip() @@ -649,7 +648,7 @@ if not new_name: message = 'Enter a valid name' status = 'error' - elif category.name != new_name and common.get_category_by_name( trans, name ): + elif category.name != new_name and suc.get_category_by_name( trans, name ): message = 'A category with that name already exists' status = 'error' else: @@ -772,7 +771,7 @@ ids = util.listify( id ) message = "Deleted %d categories: " % len( ids ) for category_id in ids: - category = common.get_category( trans, category_id ) + category = suc.get_category( trans, category_id ) category.deleted = True trans.sa_session.add( category ) trans.sa_session.flush() @@ -800,7 +799,7 @@ purged_categories = "" message = "Purged %d categories: " % len( ids ) for category_id in ids: - category = common.get_category( trans, category_id ) + category = suc.get_category( trans, category_id ) if category.deleted: # Delete RepositoryCategoryAssociations for rca in category.repositories: @@ -827,7 +826,7 @@ count = 0 undeleted_categories = "" for category_id in ids: - category = common.get_category( trans, category_id ) + category = suc.get_category( trans, category_id ) if category.deleted: category.deleted = False trans.sa_session.add( category ) diff -r 6538175fb3e6483895aaadfdeddd09aac558fdf5 -r dd395d9b8a01255412b3e56219d11639ccce2e50 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -1,13 +1,4 @@ -import os, string, socket, logging, simplejson, binascii, tempfile -from time import gmtime, strftime -from datetime import * -from galaxy.tools import * -from galaxy.util.odict import odict -from galaxy.util.json import from_json_string, to_json_string -import galaxy.util.shed_util_common as suc -from galaxy.web.base.controllers.admin import * -from galaxy.webapps.community import model -from galaxy.model.orm import and_ +import logging from galaxy.model.item_attrs import UsesItemRatings from galaxy import eggs @@ -16,63 +7,6 @@ log = logging.getLogger( __name__ ) -new_repo_email_alert_template = """ -Repository name: ${repository_name} -Revision: ${revision} -Change description: -${description} - -Uploaded by: ${username} -Date content uploaded: ${display_date} - -${content_alert_str} - ------------------------------------------------------------------------------ -This change alert was sent from the Galaxy tool shed hosted on the server -"${host}" ------------------------------------------------------------------------------ -You received this alert because you registered to receive email when -new repositories were created in the Galaxy tool shed named "${host}". ------------------------------------------------------------------------------ -""" - -email_alert_template = """ -Repository name: ${repository_name} -Revision: ${revision} -Change description: -${description} - -Changed by: ${username} -Date of change: ${display_date} - -${content_alert_str} - ------------------------------------------------------------------------------ -This change alert was sent from the Galaxy tool shed hosted on the server -"${host}" ------------------------------------------------------------------------------ -You received this alert because you registered to receive email whenever -changes were made to the repository named "${repository_name}". ------------------------------------------------------------------------------ -""" - -contact_owner_template = """ -GALAXY TOOL SHED REPOSITORY MESSAGE ------------------------- - -The user '${username}' sent you the following message regarding your tool shed -repository named '${repository_name}'. You can respond by sending a reply to -the user's email address: ${email}. ------------------------------------------------------------------------------ -${message} ------------------------------------------------------------------------------ -This message was sent from the Galaxy Tool Shed instance hosted on the server -'${host}' -""" - -malicious_error = " This changeset cannot be downloaded because it potentially produces malicious behavior or contains inappropriate content." -malicious_error_can_push = " Correct this changeset as soon as possible, it potentially produces malicious behavior or contains inappropriate content." - class ItemRatings( UsesItemRatings ): """Overrides rate_item method since we also allow for comments""" def rate_item( self, trans, user, item, rating, comment='' ): @@ -95,503 +29,3 @@ trans.sa_session.add( item_rating ) trans.sa_session.flush() return item_rating - -def add_tool_versions( trans, id, repository_metadata, changeset_revisions ): - # Build a dictionary of { 'tool id' : 'parent tool id' } pairs for each tool in repository_metadata. - metadata = repository_metadata.metadata - tool_versions_dict = {} - for tool_dict in metadata.get( 'tools', [] ): - # We have at least 2 changeset revisions to compare tool guids and tool ids. - parent_id = suc.get_parent_id( trans, - id, - tool_dict[ 'id' ], - tool_dict[ 'version' ], - tool_dict[ 'guid' ], - changeset_revisions ) - tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id - if tool_versions_dict: - repository_metadata.tool_versions = tool_versions_dict - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() -def changeset_is_malicious( trans, id, changeset_revision, **kwd ): - """Check the malicious flag in repository metadata for a specified change set""" - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) - if repository_metadata: - return repository_metadata.malicious - return False -def changeset_revision_reviewed_by_user( trans, user, repository, changeset_revision ): - """Determine if the current changeset revision has been reviewed by the current user.""" - for review in repository.reviews: - if review.changeset_revision == changeset_revision and review.user == user: - return True - return False -def check_file_contents( trans ): - # See if any admin users have chosen to receive email alerts when a repository is updated. - # If so, the file contents of the update must be checked for inappropriate content. - admin_users = trans.app.config.get( "admin_users", "" ).split( "," ) - for repository in trans.sa_session.query( trans.model.Repository ) \ - .filter( trans.model.Repository.table.c.email_alerts != None ): - email_alerts = from_json_string( repository.email_alerts ) - for user_email in email_alerts: - if user_email in admin_users: - return True - return False -def get_category( trans, id ): - """Get a category from the database""" - return trans.sa_session.query( trans.model.Category ).get( trans.security.decode_id( id ) ) -def get_category_by_name( trans, name ): - """Get a category from the database via name""" - try: - return trans.sa_session.query( trans.model.Category ).filter_by( name=name ).one() - except sqlalchemy.orm.exc.NoResultFound: - return None -def get_categories( trans ): - """Get all categories from the database""" - return trans.sa_session.query( trans.model.Category ) \ - .filter( trans.model.Category.table.c.deleted==False ) \ - .order_by( trans.model.Category.table.c.name ) \ - .all() -def get_component( trans, id ): - """Get a component from the database""" - return trans.sa_session.query( trans.model.Component ).get( trans.security.decode_id( id ) ) -def get_component_by_name( trans, name ): - return trans.sa_session.query( trans.app.model.Component ) \ - .filter( trans.app.model.Component.table.c.name==name ) \ - .first() -def get_component_review( trans, id ): - """Get a component_review from the database""" - return trans.sa_session.query( trans.model.ComponentReview ).get( trans.security.decode_id( id ) ) -def get_component_review_by_repository_review_id_component_id( trans, repository_review_id, component_id ): - """Get a component_review from the database via repository_review_id and component_id""" - return trans.sa_session.query( trans.model.ComponentReview ) \ - .filter( and_( trans.model.ComponentReview.table.c.repository_review_id == trans.security.decode_id( repository_review_id ), - trans.model.ComponentReview.table.c.component_id == trans.security.decode_id( component_id ) ) ) \ - .first() -def get_components( trans ): - return trans.sa_session.query( trans.app.model.Component ) \ - .order_by( trans.app.model.Component.name ) \ - .all() -def get_latest_repository_metadata( trans, decoded_repository_id ): - """Get last metadata defined for a specified repository from the database""" - return trans.sa_session.query( trans.model.RepositoryMetadata ) \ - .filter( trans.model.RepositoryMetadata.table.c.repository_id == decoded_repository_id ) \ - .order_by( trans.model.RepositoryMetadata.table.c.id.desc() ) \ - .first() -def get_previous_repository_reviews( trans, repository, changeset_revision ): - """Return an ordered dictionary of repository reviews up to and including the received changeset revision.""" - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] - previous_reviews_dict = odict() - for changeset in suc.reversed_upper_bounded_changelog( repo, changeset_revision ): - previous_changeset_revision = str( repo.changectx( changeset ) ) - if previous_changeset_revision in reviewed_revision_hashes: - previous_rev, previous_changeset_revision_label = get_rev_label_from_changeset_revision( repo, previous_changeset_revision ) - revision_reviews = get_reviews_by_repository_id_changeset_revision( trans, - trans.security.encode_id( repository.id ), - previous_changeset_revision ) - previous_reviews_dict[ previous_changeset_revision ] = dict( changeset_revision_label=previous_changeset_revision_label, - reviews=revision_reviews ) - return previous_reviews_dict -def get_repository_by_name( trans, name ): - """Get a repository from the database via name""" - return trans.sa_session.query( trans.model.Repository ).filter_by( name=name ).one() -def get_repository_metadata_revisions_for_review( repository, reviewed=True ): - repository_metadata_revisions = [] - metadata_changeset_revision_hashes = [] - if reviewed: - for metadata_revision in repository.metadata_revisions: - metadata_changeset_revision_hashes.append( metadata_revision.changeset_revision ) - for review in repository.reviews: - if review.changeset_revision in metadata_changeset_revision_hashes: - rmcr_hashes = [ rmr.changeset_revision for rmr in repository_metadata_revisions ] - if review.changeset_revision not in rmcr_hashes: - repository_metadata_revisions.append( review.repository_metadata ) - else: - for review in repository.reviews: - if review.changeset_revision not in metadata_changeset_revision_hashes: - metadata_changeset_revision_hashes.append( review.changeset_revision ) - for metadata_revision in repository.metadata_revisions: - if metadata_revision.changeset_revision not in metadata_changeset_revision_hashes: - repository_metadata_revisions.append( metadata_revision ) - return repository_metadata_revisions -def get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=None ): - if repository is None: - repository = repository_metadata.repository - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - changeset_revision = repository_metadata.changeset_revision - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) - if ctx: - rev = '%04d' % ctx.rev() - label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) - else: - rev = '-1' - label = "-1:%s" % changeset_revision - return rev, label, changeset_revision -def get_rev_label_from_changeset_revision( repo, changeset_revision ): - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) - if ctx: - rev = '%04d' % ctx.rev() - label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) - else: - rev = '-1' - label = "-1:%s" % changeset_revision - return rev, label -def get_reversed_changelog_changesets( repo ): - reversed_changelog = [] - for changeset in repo.changelog: - reversed_changelog.insert( 0, changeset ) - return reversed_changelog -def get_review( trans, id ): - """Get a repository_review from the database via id""" - return trans.sa_session.query( trans.model.RepositoryReview ).get( trans.security.decode_id( id ) ) -def get_review_by_repository_id_changeset_revision_user_id( trans, repository_id, changeset_revision, user_id ): - """Get a repository_review from the database via repository id, changeset_revision and user_id""" - return trans.sa_session.query( trans.model.RepositoryReview ) \ - .filter( and_( trans.model.RepositoryReview.repository_id == trans.security.decode_id( repository_id ), - trans.model.RepositoryReview.changeset_revision == changeset_revision, - trans.model.RepositoryReview.user_id == trans.security.decode_id( user_id ) ) ) \ - .first() -def get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ): - """Get all repository_reviews from the database via repository id and changeset_revision""" - return trans.sa_session.query( trans.model.RepositoryReview ) \ - .filter( and_( trans.model.RepositoryReview.repository_id == trans.security.decode_id( repository_id ), - trans.model.RepositoryReview.changeset_revision == changeset_revision ) ) \ - .all() -def get_revision_label( trans, repository, changeset_revision ): - """ - Return a string consisting of the human read-able - changeset rev and the changeset revision string. - """ - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) - if ctx: - return "%s:%s" % ( str( ctx.rev() ), changeset_revision ) - else: - return "-1:%s" % changeset_revision -def get_user( trans, id ): - """Get a user from the database by id""" - return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) -def handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=False, admin_only=False ): - # There are 2 complementary features that enable a tool shed user to receive email notification: - # 1. Within User Preferences, they can elect to receive email when the first (or first valid) - # change set is produced for a new repository. - # 2. When viewing or managing a repository, they can check the box labeled "Receive email alerts" - # which caused them to receive email alerts when updates to the repository occur. This same feature - # is available on a per-repository basis on the repository grid within the tool shed. - # - # There are currently 4 scenarios for sending email notification when a change is made to a repository: - # 1. An admin user elects to receive email when the first change set is produced for a new repository - # from User Preferences. The change set does not have to include any valid content. This allows for - # the capture of inappropriate content being uploaded to new repositories. - # 2. A regular user elects to receive email when the first valid change set is produced for a new repository - # from User Preferences. This differs from 1 above in that the user will not receive email until a - # change set tha tincludes valid content is produced. - # 3. An admin user checks the "Receive email alerts" check box on the manage repository page. Since the - # user is an admin user, the email will include information about both HTML and image content that was - # included in the change set. - # 4. A regular user checks the "Receive email alerts" check box on the manage repository page. Since the - # user is not an admin user, the email will not include any information about both HTML and image content - # that was included in the change set. - repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) - smtp_server = trans.app.config.smtp_server - if smtp_server and ( new_repo_alert or repository.email_alerts ): - # Send email alert to users that want them. - if trans.app.config.email_from is not None: - email_from = trans.app.config.email_from - elif trans.request.host.split( ':' )[0] == 'localhost': - email_from = 'galaxy-no-reply@' + socket.getfqdn() - else: - email_from = 'galaxy-no-reply@' + trans.request.host.split( ':' )[0] - tip_changeset = repo.changelog.tip() - ctx = repo.changectx( tip_changeset ) - t, tz = ctx.date() - date = datetime( *gmtime( float( t ) - tz )[:6] ) - display_date = date.strftime( "%Y-%m-%d" ) - try: - username = ctx.user().split()[0] - except: - username = ctx.user() - # We'll use 2 template bodies because we only want to send content - # alerts to tool shed admin users. - if new_repo_alert: - template = new_repo_email_alert_template - else: - template = email_alert_template - admin_body = string.Template( template ).safe_substitute( host=trans.request.host, - repository_name=repository.name, - revision='%s:%s' %( str( ctx.rev() ), ctx ), - display_date=display_date, - description=ctx.description(), - username=username, - content_alert_str=content_alert_str ) - body = string.Template( template ).safe_substitute( host=trans.request.host, - repository_name=repository.name, - revision='%s:%s' %( str( ctx.rev() ), ctx ), - display_date=display_date, - description=ctx.description(), - username=username, - content_alert_str='' ) - admin_users = trans.app.config.get( "admin_users", "" ).split( "," ) - frm = email_from - if new_repo_alert: - subject = "Galaxy tool shed alert for new repository named %s" % str( repository.name ) - subject = subject[ :80 ] - email_alerts = [] - for user in trans.sa_session.query( trans.model.User ) \ - .filter( and_( trans.model.User.table.c.deleted == False, - trans.model.User.table.c.new_repo_alert == True ) ): - if admin_only: - if user.email in admin_users: - email_alerts.append( user.email ) - else: - email_alerts.append( user.email ) - else: - subject = "Galaxy tool shed update alert for repository named %s" % str( repository.name ) - email_alerts = from_json_string( repository.email_alerts ) - for email in email_alerts: - to = email.strip() - # Send it - try: - if to in admin_users: - util.send_mail( frm, to, subject, admin_body, trans.app.config ) - else: - util.send_mail( frm, to, subject, body, trans.app.config ) - except Exception, e: - log.exception( "An error occurred sending a tool shed repository update alert by email." ) -def has_previous_repository_reviews( trans, repository, changeset_revision ): - """Determine if a repository has a changeset revision review prior to the received changeset revision.""" - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] - for changeset in suc.reversed_upper_bounded_changelog( repo, changeset_revision ): - previous_changeset_revision = str( repo.changectx( changeset ) ) - if previous_changeset_revision in reviewed_revision_hashes: - return True - return False -def new_repository_dependency_metadata_required( trans, repository, metadata_dict ): - """ - Compare the last saved metadata for each repository dependency in the repository with the new - metadata in metadata_dict to determine if a new repository_metadata table record is required, - or if the last saved metadata record can be updated instead. - """ - if 'repository_dependencies' in metadata_dict: - repository_metadata = get_latest_repository_metadata( trans, repository.id ) - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - if 'repository_dependencies' in metadata: - saved_repository_dependencies = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] - new_repository_dependencies = metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ] - # The saved metadata must be a subset of the new metadata. - for new_repository_dependency_metadata in new_repository_dependencies: - if new_repository_dependency_metadata not in saved_repository_dependencies: - return True - for saved_repository_dependency_metadata in saved_repository_dependencies: - if saved_repository_dependency_metadata not in new_repository_dependencies: - return True - else: - # We have repository metadata that does not include metadata for any repository dependencies in the - # repository, so we can update the existing repository metadata. - return False - else: - # There is no saved repository metadata, so we need to create a new repository_metadata table record. - return True - # The received metadata_dict includes no metadata for repository dependencies, so a new repository_metadata table record is not needed. - return False -def new_tool_metadata_required( trans, repository, metadata_dict ): - """ - Compare the last saved metadata for each tool in the repository with the new metadata in metadata_dict to determine if a new repository_metadata - table record is required, or if the last saved metadata record can be updated instead. - """ - if 'tools' in metadata_dict: - repository_metadata = get_latest_repository_metadata( trans, repository.id ) - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - if 'tools' in metadata: - saved_tool_ids = [] - # The metadata for one or more tools was successfully generated in the past - # for this repository, so we first compare the version string for each tool id - # in metadata_dict with what was previously saved to see if we need to create - # a new table record or if we can simply update the existing record. - for new_tool_metadata_dict in metadata_dict[ 'tools' ]: - for saved_tool_metadata_dict in metadata[ 'tools' ]: - if saved_tool_metadata_dict[ 'id' ] not in saved_tool_ids: - saved_tool_ids.append( saved_tool_metadata_dict[ 'id' ] ) - if new_tool_metadata_dict[ 'id' ] == saved_tool_metadata_dict[ 'id' ]: - if new_tool_metadata_dict[ 'version' ] != saved_tool_metadata_dict[ 'version' ]: - return True - # So far, a new metadata record is not required, but we still have to check to see if - # any new tool ids exist in metadata_dict that are not in the saved metadata. We do - # this because if a new tarball was uploaded to a repository that included tools, it - # may have removed existing tool files if they were not included in the uploaded tarball. - for new_tool_metadata_dict in metadata_dict[ 'tools' ]: - if new_tool_metadata_dict[ 'id' ] not in saved_tool_ids: - return True - else: - # We have repository metadata that does not include metadata for any tools in the - # repository, so we can update the existing repository metadata. - return False - else: - # There is no saved repository metadata, so we need to create a new repository_metadata table record. - return True - # The received metadata_dict includes no metadata for tools, so a new repository_metadata table record is not needed. - return False -def new_workflow_metadata_required( trans, repository, metadata_dict ): - """ - Currently everything about an exported workflow except the name is hard-coded, so there's no real way to differentiate versions of - exported workflows. If this changes at some future time, this method should be enhanced accordingly. - """ - if 'workflows' in metadata_dict: - repository_metadata = get_latest_repository_metadata( trans, repository.id ) - if repository_metadata: - # The repository has metadata, so update the workflows value - no new record is needed. - return False - else: - # There is no saved repository metadata, so we need to create a new repository_metadata table record. - return True - # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table record is not needed. - return False -def set_repository_metadata( trans, repository, content_alert_str='', **kwd ): - """ - Set metadata using the repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset - has problems. - """ - message = '' - status = 'done' - encoded_id = trans.security.encode_id( repository.id ) - repository_clone_url = suc.generate_clone_url_for_repository_in_tool_shed( trans, repository ) - repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) - metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, - repository=repository, - repository_clone_url=repository_clone_url, - relative_install_dir=repo_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) - if metadata_dict: - downloadable = suc.is_downloadable( metadata_dict ) - repository_metadata = None - if new_repository_dependency_metadata_required( trans, repository, metadata_dict ) or \ - new_tool_metadata_required( trans, repository, metadata_dict ) or \ - new_workflow_metadata_required( trans, repository, metadata_dict ): - # Create a new repository_metadata table row. - repository_metadata = suc.create_or_update_repository_metadata( trans, - encoded_id, - repository, - repository.tip( trans.app ), - metadata_dict ) - # If this is the first record stored for this repository, see if we need to send any email alerts. - if len( repository.downloadable_revisions ) == 1: - handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False ) - else: - repository_metadata = get_latest_repository_metadata( trans, repository.id ) - if repository_metadata: - downloadable = suc.is_downloadable( metadata_dict ) - # Update the last saved repository_metadata table row. - repository_metadata.changeset_revision = repository.tip( trans.app ) - repository_metadata.metadata = metadata_dict - repository_metadata.downloadable = downloadable - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() - else: - # There are no tools in the repository, and we're setting metadata on the repository tip. - repository_metadata = suc.create_or_update_repository_metadata( trans, - encoded_id, - repository, - repository.tip( trans.app ), - metadata_dict ) - if 'tools' in metadata_dict and repository_metadata and status != 'error': - # Set tool versions on the new downloadable change set. The order of the list of changesets is critical, so we use the repo's changelog. - changeset_revisions = [] - for changeset in repo.changelog: - changeset_revision = str( repo.changectx( changeset ) ) - if suc.get_repository_metadata_by_changeset_revision( trans, encoded_id, changeset_revision ): - changeset_revisions.append( changeset_revision ) - add_tool_versions( trans, encoded_id, repository_metadata, changeset_revisions ) - elif len( repo ) == 1 and not invalid_file_tups: - message = "Revision '%s' includes no tools, datatypes or exported workflows for which metadata can " % str( repository.tip( trans.app ) ) - message += "be defined so this revision cannot be automatically installed into a local Galaxy instance." - status = "error" - if invalid_file_tups: - message = suc.generate_message_for_invalid_tools( trans, invalid_file_tups, repository, metadata_dict ) - status = 'error' - # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. - suc.reset_tool_data_tables( trans.app ) - return message, status -def set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=None, **kwd ): - # Set metadata on the repository tip. - error_message, status = set_repository_metadata( trans, repository, content_alert_str=content_alert_str, **kwd ) - if error_message: - # If there is an error, display it. - return trans.response.send_redirect( web.url_for( controller='repository', - action='manage_repository', - id=trans.security.encode_id( repository.id ), - message=error_message, - status='error' ) ) -def update_for_browsing( trans, repository, current_working_dir, commit_message='' ): - # This method id deprecated, but we'll keep it around for a while in case we need it. The problem is that hg purge - # is not supported by the mercurial API. - # Make a copy of a repository's files for browsing, remove from disk all files that are not tracked, and commit all - # added, modified or removed files that have not yet been committed. - repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) - # The following will delete the disk copy of only the files in the repository. - #os.system( 'hg update -r null > /dev/null 2>&1' ) - files_to_remove_from_disk = [] - files_to_commit = [] - # We may have files on disk in the repo directory that aren't being tracked, so they must be removed. - # The codes used to show the status of files are as follows. - # M = modified - # A = added - # R = removed - # C = clean - # ! = deleted, but still tracked - # ? = not tracked - # I = ignored - # We'll use mercurial's purge extension to remove untracked file. Using this extension requires the - # following entry in the repository's hgrc file which was not required for some time, so we'll add it - # if it's missing. - # [extensions] - # hgext.purge= - lines = repo.opener( 'hgrc', 'rb' ).readlines() - if not '[extensions]\n' in lines: - # No extensions have been added at all, so just append to the file. - fp = repo.opener( 'hgrc', 'a' ) - fp.write( '[extensions]\n' ) - fp.write( 'hgext.purge=\n' ) - fp.close() - elif not 'hgext.purge=\n' in lines: - # The file includes and [extensions] section, but we need to add the - # purge extension. - fp = repo.opener( 'hgrc', 'wb' ) - for line in lines: - if line.startswith( '[extensions]' ): - fp.write( line ) - fp.write( 'hgext.purge=\n' ) - else: - fp.write( line ) - fp.close() - cmd = 'hg purge' - os.chdir( repo_dir ) - proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT ) - return_code = proc.wait() - os.chdir( current_working_dir ) - if return_code != 0: - output = proc.stdout.read( 32768 ) - log.debug( 'hg purge failed in repository directory %s, reason: %s' % ( repo_dir, output ) ) - if files_to_commit: - if not commit_message: - commit_message = 'Committed changes to: %s' % ', '.join( files_to_commit ) - repo.dirstate.write() - repo.commit( user=trans.user.username, text=commit_message ) - cmd = 'hg update > /dev/null 2>&1' - os.chdir( repo_dir ) - proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT ) - return_code = proc.wait() - os.chdir( current_working_dir ) - if return_code != 0: - output = proc.stdout.read( 32768 ) - log.debug( 'hg update > /dev/null 2>&1 failed in repository directory %s, reason: %s' % ( repo_dir, output ) ) diff -r 6538175fb3e6483895aaadfdeddd09aac558fdf5 -r dd395d9b8a01255412b3e56219d11639ccce2e50 lib/galaxy/webapps/community/controllers/hg.py --- a/lib/galaxy/webapps/community/controllers/hg.py +++ b/lib/galaxy/webapps/community/controllers/hg.py @@ -1,7 +1,6 @@ import os, logging from galaxy.web.base.controller import * -from galaxy.util.shed_util_common import get_repository_by_name_and_owner -from galaxy.webapps.community.controllers.common import set_repository_metadata +from galaxy.util.shed_util_common import get_repository_by_name_and_owner, set_repository_metadata from galaxy import eggs eggs.require('mercurial') diff -r 6538175fb3e6483895aaadfdeddd09aac558fdf5 -r dd395d9b8a01255412b3e56219d11639ccce2e50 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -25,6 +25,8 @@ log = logging.getLogger( __name__ ) VALID_REPOSITORYNAME_RE = re.compile( "^[a-z0-9\_]+$" ) +malicious_error = " This changeset cannot be downloaded because it potentially produces malicious behavior or contains inappropriate content." +malicious_error_can_push = " Correct this changeset as soon as possible, it potentially produces malicious behavior or contains inappropriate content." class CategoryGrid( grids.Grid ): class NameColumn( grids.TextColumn ): @@ -540,7 +542,7 @@ # The value of 'id' has been set to the search string, which is a repository name. We'll try to get the desired encoded repository # id to pass on. try: - repository = common.get_repository_by_name( trans, kwd[ 'id' ] ) + repository = suc.get_repository_by_name( trans, kwd[ 'id' ] ) kwd[ 'id' ] = trans.security.encode_id( repository.id ) except: pass @@ -615,7 +617,7 @@ if k.startswith( 'f-' ): del kwd[ k ] if 'user_id' in kwd: - user = common.get_user( trans, kwd[ 'user_id' ] ) + user = suc.get_user( trans, kwd[ 'user_id' ] ) kwd[ 'f-email' ] = user.email del kwd[ 'user_id' ] else: @@ -655,7 +657,7 @@ if k.startswith( 'f-' ): del kwd[ k ] category_id = kwd.get( 'id', None ) - category = common.get_category( trans, category_id ) + category = suc.get_category( trans, category_id ) kwd[ 'f-Category.name' ] = category.name elif operation == "receive email alerts": if trans.user: @@ -696,7 +698,7 @@ repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) # Update repository files for browsing. suc.update_repository( repo ) - is_malicious = common.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) + is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) return trans.fill_template( '/webapps/community/repository/browse_repository.mako', repository=repository, @@ -722,7 +724,7 @@ # We'll try to get the desired encoded repository id to pass on. try: name = kwd[ 'id' ] - repository = common.get_repository_by_name( trans, name ) + repository = suc.get_repository_by_name( trans, name ) kwd[ 'id' ] = trans.security.encode_id( repository.id ) except: pass @@ -745,7 +747,7 @@ if 'f-Category.name' in kwd: # The user browsed to a category and then entered a search string, so get the category associated with it's value. category_name = kwd[ 'f-Category.name' ] - category = common.get_category_by_name( trans, category_name ) + category = suc.get_category_by_name( trans, category_name ) # Set the id value in kwd since it is required by the ValidRepositoryGrid.build_initial_query method. kwd[ 'id' ] = trans.security.encode_id( category.id ) if galaxy_url: @@ -755,7 +757,7 @@ if operation == "preview_tools_in_changeset": repository_id = kwd.get( 'id', None ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) - repository_metadata = common.get_latest_repository_metadata( trans, repository.id ) + repository_metadata = suc.get_latest_repository_metadata( trans, repository.id ) latest_installable_changeset_revision = repository_metadata.changeset_revision return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', @@ -767,7 +769,7 @@ if k.startswith( 'f-' ): del kwd[ k ] category_id = kwd.get( 'id', None ) - category = common.get_category( trans, category_id ) + category = suc.get_category( trans, category_id ) kwd[ 'f-Category.name' ] = category.name # The changeset_revision_select_field in the ValidRepositoryGrid performs a refresh_on_change which sends in request parameters like # changeset_revison_1, changeset_revision_2, etc. One of the many select fields on the grid performed the refresh_on_change, so we loop @@ -927,7 +929,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - categories = common.get_categories( trans ) + categories = suc.get_categories( trans ) if not categories: message = 'No categories have been configured in this instance of the Galaxy Tool Shed. ' + \ 'An administrator needs to create some via the Administrator control panel before creating repositories.', @@ -1028,7 +1030,7 @@ if message: status = 'error' tool_state = self.__new_state( trans ) - is_malicious = common.changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) + is_malicious = suc.changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, repository_id, changeset_revision ) try: return trans.fill_template( "/webapps/community/repository/tool_form.mako", @@ -1685,7 +1687,7 @@ status = params.get( 'status', 'error' ) repository, tool, error_message = suc.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) tool_state = self.__new_state( trans ) - is_malicious = common.changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) + is_malicious = suc.changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) invalid_file_tups = [] if tool: invalid_file_tups = suc.check_tool_input_params( trans.app, @@ -1883,7 +1885,7 @@ selected_value=changeset_revision, add_id_to_name=False, downloadable=False ) - revision_label = common.get_revision_label( trans, repository, repository.tip( trans.app ) ) + revision_label = suc.get_revision_label( trans, repository, repository.tip( trans.app ) ) repository_metadata = None repository_metadata_id = None metadata = None @@ -1892,7 +1894,7 @@ if changeset_revision != suc.INITIAL_CHANGELOG_HASH: repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: - revision_label = common.get_revision_label( trans, repository, changeset_revision ) + revision_label = suc.get_revision_label( trans, repository, changeset_revision ) repository_metadata_id = trans.security.encode_id( repository_metadata.id ) metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious @@ -1902,7 +1904,7 @@ if previous_changeset_revision != suc.INITIAL_CHANGELOG_HASH: repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, previous_changeset_revision ) if repository_metadata: - revision_label = common.get_revision_label( trans, repository, previous_changeset_revision ) + revision_label = suc.get_revision_label( trans, repository, previous_changeset_revision ) repository_metadata_id = trans.security.encode_id( repository_metadata.id ) metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious @@ -1917,20 +1919,20 @@ handled_key_rd_dicts=None ) if is_malicious: if trans.app.security_agent.can_push( trans.app, trans.user, repository ): - message += common.malicious_error_can_push + message += malicious_error_can_push else: - message += common.malicious_error + message += malicious_error status = 'error' malicious_check_box = CheckboxField( 'malicious', checked=is_malicious ) - categories = common.get_categories( trans ) + categories = suc.get_categories( trans ) selected_categories = [ rca.category_id for rca in repository.categories ] # Determine if the current changeset revision has been reviewed by the current user. - reviewed_by_user = common.changeset_revision_reviewed_by_user( trans, trans.user, repository, changeset_revision ) + reviewed_by_user = suc.changeset_revision_reviewed_by_user( trans, trans.user, repository, changeset_revision ) if reviewed_by_user: - review = common.get_review_by_repository_id_changeset_revision_user_id( trans=trans, - repository_id=id, - changeset_revision=changeset_revision, - user_id=trans.security.encode_id( trans.user.id ) ) + review = suc.get_review_by_repository_id_changeset_revision_user_id( trans=trans, + repository_id=id, + changeset_revision=changeset_revision, + user_id=trans.security.encode_id( trans.user.id ) ) review_id = trans.security.encode_id( review.id ) else: review_id = None @@ -2031,7 +2033,7 @@ repository_metadata_id = None metadata = None repository_dependencies = None - revision_label = common.get_revision_label( trans, repository, changeset_revision ) + revision_label = suc.get_revision_label( trans, repository, changeset_revision ) changeset_revision_select_field = build_changeset_revision_select_field( trans, repository, selected_value=changeset_revision, @@ -2103,7 +2105,7 @@ avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model ) - is_malicious = common.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) + is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) return trans.fill_template( '/webapps/community/repository/rate_repository.mako', repository=repository, @@ -2263,7 +2265,7 @@ if not commit_message: commit_message = 'Deleted selected files' commands.commit( repo.ui, repo, repo_dir, user=trans.user.username, message=commit_message ) - common.handle_email_alerts( trans, repository ) + suc.handle_email_alerts( trans, repository ) # Update the repository files for browsing. suc.update_repository( repo ) # Get the new repository tip. @@ -2275,11 +2277,11 @@ else: message += 'The selected files were deleted from the repository. ' kwd[ 'message' ] = message - common.set_repository_metadata_due_to_new_tip( trans, repository, **kwd ) + suc.set_repository_metadata_due_to_new_tip( trans, repository, **kwd ) else: message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>." status = "error" - is_malicious = common.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) + is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) return trans.fill_template( '/webapps/community/repository/browse_repository.mako', repo=repo, repository=repository, @@ -2302,7 +2304,7 @@ # Get the name of the server hosting the tool shed instance. host = trans.request.host # Build the email message - body = string.Template( common.contact_owner_template ) \ + body = string.Template( suc.contact_owner_template ) \ .safe_substitute( username=trans.user.username, repository_name=repository.name, email=trans.user.email, @@ -2434,7 +2436,7 @@ 'has_metadata' : has_metadata } # Make sure we'll view latest changeset first. changesets.insert( 0, change_dict ) - is_malicious = common.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) + is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) return trans.fill_template( '/webapps/community/repository/view_changelog.mako', repository=repository, @@ -2465,7 +2467,7 @@ diffs = [] for diff in patch.diff( repo, node1=ctx_parent.node(), node2=ctx.node() ): diffs.append( suc.to_safe_string( diff, to_html=True ) ) - is_malicious = common.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) + is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, id, ctx_str ) return trans.fill_template( '/webapps/community/repository/view_changeset.mako', repository=repository, @@ -2535,7 +2537,7 @@ selected_value=changeset_revision, add_id_to_name=False, downloadable=False ) - revision_label = common.get_revision_label( trans, repository, changeset_revision ) + revision_label = suc.get_revision_label( trans, repository, changeset_revision ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: repository_metadata_id = trans.security.encode_id( repository_metadata.id ) @@ -2551,20 +2553,20 @@ else: repository_metadata_id = None metadata = None - is_malicious = common.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) + is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) if is_malicious: if trans.app.security_agent.can_push( trans.app, trans.user, repository ): - message += common.malicious_error_can_push + message += malicious_error_can_push else: - message += common.malicious_error + message += malicious_error status = 'error' # Determine if the current changeset revision has been reviewed by the current user. - reviewed_by_user = common.changeset_revision_reviewed_by_user( trans, trans.user, repository, changeset_revision ) + reviewed_by_user = suc.changeset_revision_reviewed_by_user( trans, trans.user, repository, changeset_revision ) if reviewed_by_user: - review = common.get_review_by_repository_id_changeset_revision_user_id( trans=trans, - repository_id=id, - changeset_revision=changeset_revision, - user_id=trans.security.encode_id( trans.user.id ) ) + review = suc.get_review_by_repository_id_changeset_revision_user_id( trans=trans, + repository_id=id, + changeset_revision=changeset_revision, + user_id=trans.security.encode_id( trans.user.id ) ) review_id = trans.security.encode_id( review.id ) else: review_id = None @@ -2601,7 +2603,7 @@ tool = None guid = None original_tool_data_path = trans.app.config.tool_data_path - revision_label = common.get_revision_label( trans, repository, changeset_revision ) + revision_label = suc.get_revision_label( trans, repository, changeset_revision ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: metadata = repository_metadata.metadata @@ -2636,19 +2638,19 @@ tool_lineage = self.get_versions_of_tool( trans, repository, repository_metadata, guid ) else: metadata = None - is_malicious = common.changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) + is_malicious = suc.changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) changeset_revision_select_field = build_changeset_revision_select_field( trans, repository, selected_value=changeset_revision, add_id_to_name=False, downloadable=False ) trans.app.config.tool_data_path = original_tool_data_path - reviewed_by_user = common.changeset_revision_reviewed_by_user( trans, trans.user, repository, changeset_revision ) + reviewed_by_user = suc.changeset_revision_reviewed_by_user( trans, trans.user, repository, changeset_revision ) if reviewed_by_user: - review = common.get_review_by_repository_id_changeset_revision_user_id( trans=trans, - repository_id=repository_id, - changeset_revision=changeset_revision, - user_id=trans.security.encode_id( trans.user.id ) ) + review = suc.get_review_by_repository_id_changeset_revision_user_id( trans=trans, + repository_id=repository_id, + changeset_revision=changeset_revision, + user_id=trans.security.encode_id( trans.user.id ) ) review_id = trans.security.encode_id( review.id ) else: review_id = None @@ -2719,7 +2721,7 @@ # Restrict the options to all revisions that have associated metadata. repository_metadata_revisions = repository.metadata_revisions for repository_metadata in repository_metadata_revisions: - rev, label, changeset_revision = common.get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=repository ) + rev, label, changeset_revision = suc.get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=repository ) changeset_tups.append( ( rev, label, changeset_revision ) ) refresh_on_change_values.append( changeset_revision ) # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, diff -r 6538175fb3e6483895aaadfdeddd09aac558fdf5 -r dd395d9b8a01255412b3e56219d11639ccce2e50 lib/galaxy/webapps/community/controllers/repository_review.py --- a/lib/galaxy/webapps/community/controllers/repository_review.py +++ b/lib/galaxy/webapps/community/controllers/repository_review.py @@ -59,7 +59,7 @@ repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) for review in repository.reviews: changeset_revision = review.changeset_revision - rev, label = common.get_rev_label_from_changeset_revision( repo, changeset_revision ) + rev, label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) rval += '<a href="manage_repository_reviews_of_revision' rval += '?id=%s&changeset_revision=%s">%s</a><br/>' % ( trans.security.encode_id( repository.id ), changeset_revision, label ) return rval @@ -67,13 +67,13 @@ class WithoutReviewsRevisionColumn( grids.GridColumn ): def get_value( self, trans, grid, repository ): # Restrict the options to revisions that have not yet been reviewed. - repository_metadata_revisions = common.get_repository_metadata_revisions_for_review( repository, reviewed=False ) + repository_metadata_revisions = suc.get_repository_metadata_revisions_for_review( repository, reviewed=False ) if repository_metadata_revisions: rval = '' for repository_metadata in repository_metadata_revisions: - rev, label, changeset_revision = common.get_rev_label_changeset_revision_from_repository_metadata( trans, - repository_metadata, - repository=repository ) + rev, label, changeset_revision = suc.get_rev_label_changeset_revision_from_repository_metadata( trans, + repository_metadata, + repository=repository ) rval += '<a href="manage_repository_reviews_of_revision' rval += '?id=%s&changeset_revision=%s">%s</a><br/>' % ( trans.security.encode_id( repository.id ), changeset_revision, label ) return rval @@ -177,7 +177,7 @@ rval += 'edit_review' else: rval +='browse_review' - rval += '?id=%s">%s</a>' % ( encoded_review_id, common.get_revision_label( trans, review.repository, review.changeset_revision ) ) + rval += '?id=%s">%s</a>' % ( encoded_review_id, suc.get_revision_label( trans, review.repository, review.changeset_revision ) ) return rval class RatingColumn( grids.TextColumn ): def get_value( self, trans, grid, review ): @@ -277,7 +277,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) encoded_review_id = kwd[ 'id' ] - review = common.get_review( trans, encoded_review_id ) + review = suc.get_review( trans, encoded_review_id ) if kwd.get( 'approve_repository_review_button', False ): approved_select_field_name = '%s%sapproved' % ( encoded_review_id, STRSEP ) approved_select_field_value = str( kwd[ approved_select_field_name ] ) @@ -309,10 +309,10 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - review = common.get_review( trans, kwd[ 'id' ] ) + review = suc.get_review( trans, kwd[ 'id' ] ) repository = review.repository repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - rev, changeset_revision_label = common.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) + rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) return trans.fill_template( '/webapps/community/repository_review/browse_review.mako', repository=repository, changeset_revision_label=changeset_revision_label, @@ -345,7 +345,7 @@ if not name or not description: message = 'Enter a valid name and a description' status = 'error' - elif common.get_component_by_name( trans, name ): + elif suc.get_component_by_name( trans, name ): message = 'A component with that name already exists' status = 'error' else: @@ -378,15 +378,15 @@ if changeset_revision: # Make sure there is not already a review of the revision by the user. repository = suc.get_repository_in_tool_shed( trans, repository_id ) - if common.get_review_by_repository_id_changeset_revision_user_id( trans=trans, - repository_id=repository_id, - changeset_revision=changeset_revision, - user_id=trans.security.encode_id( trans.user.id ) ): + if suc.get_review_by_repository_id_changeset_revision_user_id( trans=trans, + repository_id=repository_id, + changeset_revision=changeset_revision, + user_id=trans.security.encode_id( trans.user.id ) ): message = "You have already created a review for revision <b>%s</b> of repository <b>%s</b>." % ( changeset_revision, repository.name ) status = "error" else: # See if there are any reviews for previous changeset revisions that the user can copy. - if not create_without_copying and not previous_review_id and common.has_previous_repository_reviews( trans, repository, changeset_revision ): + if not create_without_copying and not previous_review_id and suc.has_previous_repository_reviews( trans, repository, changeset_revision ): return trans.response.send_redirect( web.url_for( controller='repository_review', action='select_previous_review', **kwd ) ) @@ -404,7 +404,7 @@ trans.sa_session.add( review ) trans.sa_session.flush() if previous_review_id: - review_to_copy = common.get_review( trans, previous_review_id ) + review_to_copy = suc.get_review( trans, previous_review_id ) self.copy_review( trans, review_to_copy, review ) review_id = trans.security.encode_id( review.id ) message = "Begin your review of revision <b>%s</b> of repository <b>%s</b>." \ @@ -440,7 +440,7 @@ action='manage_categories', message=message, status='error' ) ) - component = common.get_component( trans, id ) + component = suc.get_component( trans, id ) if params.get( 'edit_component_button', False ): new_description = util.restore_text( params.get( 'description', '' ) ).strip() if component.description != new_description: @@ -465,9 +465,9 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) review_id = kwd.get( 'id', None ) - review = common.get_review( trans, review_id ) + review = suc.get_review( trans, review_id ) components_dict = odict() - for component in common.get_components( trans ): + for component in suc.get_components( trans ): components_dict[ component.name ] = dict( component=component, component_review=None ) repository = review.repository repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) @@ -517,8 +517,8 @@ approved = str( v ) elif component_review_attr == 'rating': rating = int( str( v ) ) - component = common.get_component( trans, component_id ) - component_review = common.get_component_review_by_repository_review_id_component_id( trans, review_id, component_id ) + component = suc.get_component( trans, component_id ) + component_review = suc.get_component_review_by_repository_review_id_component_id( trans, review_id, component_id ) if component_review: # See if the existing component review should be updated. if component_review.comment != comment or \ @@ -572,7 +572,7 @@ name='revision_approved', selected_value=selected_value, for_component=False ) - rev, changeset_revision_label = common.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) + rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) return trans.fill_template( '/webapps/community/repository_review/edit_review.mako', repository=repository, review=review, @@ -659,14 +659,14 @@ metadata_revision_hashes = [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] reviews_dict = odict() - for changeset in common.get_reversed_changelog_changesets( repo ): + for changeset in suc.get_reversed_changelog_changesets( repo ): ctx = repo.changectx( changeset ) changeset_revision = str( ctx ) if changeset_revision in metadata_revision_hashes or changeset_revision in reviewed_revision_hashes: - rev, changeset_revision_label = common.get_rev_label_from_changeset_revision( repo, changeset_revision ) + rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) if changeset_revision in reviewed_revision_hashes: # Find the review for this changeset_revision - repository_reviews = common.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) + repository_reviews = suc.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) # Determine if the current user can add a review to this revision. can_add_review = trans.user not in [ repository_review.user for repository_review in repository_reviews ] repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) @@ -704,8 +704,8 @@ repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) installable = changeset_revision in [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] - rev, changeset_revision_label = common.get_rev_label_from_changeset_revision( repo, changeset_revision ) - reviews = common.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) + rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) + reviews = suc.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) return trans.fill_template( '/webapps/community/repository_review/reviews_of_changeset_revision.mako', repository=repository, changeset_revision=changeset_revision, @@ -724,7 +724,7 @@ if 'operation' in kwd: operation = kwd['operation'].lower() # The value of the received id is the encoded review id. - review = common.get_review( trans, kwd[ 'id' ] ) + review = suc.get_review( trans, kwd[ 'id' ] ) repository = review.repository kwd[ 'id' ] = trans.security.encode_id( repository.id ) if operation == "inspect repository revisions": @@ -737,7 +737,7 @@ action='view_or_manage_repository', **kwd ) ) # The user may not be the current user. The value of the received id is the encoded user id. - user = common.get_user( trans, kwd[ 'id' ] ) + user = suc.get_user( trans, kwd[ 'id' ] ) self.repository_reviews_by_user_grid.title = "All repository revision reviews for user '%s'" % user.username return self.repository_reviews_by_user_grid( trans, **kwd ) @web.expose @@ -768,8 +768,8 @@ repository = suc.get_repository_in_tool_shed( trans, kwd[ 'id' ] ) changeset_revision = kwd.get( 'changeset_revision', None ) repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - previous_reviews_dict = common.get_previous_repository_reviews( trans, repository, changeset_revision ) - rev, changeset_revision_label = common.get_rev_label_from_changeset_revision( repo, changeset_revision ) + previous_reviews_dict = suc.get_previous_repository_reviews( trans, repository, changeset_revision ) + rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) return trans.fill_template( '/webapps/community/repository_review/select_previous_review.mako', repository=repository, changeset_revision=changeset_revision, diff -r 6538175fb3e6483895aaadfdeddd09aac558fdf5 -r dd395d9b8a01255412b3e56219d11639ccce2e50 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -1,7 +1,6 @@ import sys, os, shutil, logging, tarfile, tempfile, urllib from galaxy.web.base.controller import * from galaxy.datatypes import checkers -import common import galaxy.util.shed_util_common as suc from galaxy import eggs @@ -23,7 +22,7 @@ status = params.get( 'status', 'done' ) commit_message = util.restore_text( params.get( 'commit_message', 'Uploaded' ) ) category_ids = util.listify( params.get( 'category_id', '' ) ) - categories = common.get_categories( trans ) + categories = suc.get_categories( trans ) repository_id = params.get( 'repository_id', '' ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) @@ -37,7 +36,7 @@ url = params.get( 'url', '' ) # Part of the upload process is sending email notification to those that have registered to # receive them. One scenario occurs when the first change set is produced for the repository. - # See the common.handle_email_alerts() method for the definition of the scenarios. + # See the suc.handle_email_alerts() method for the definition of the scenarios. new_repo_alert = repository.is_new( trans.app ) uploaded_directory = None if params.get( 'upload_button', False ): @@ -104,22 +103,11 @@ # Uploaded directory istar = False if istar: - ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = self.upload_tar( trans, - repository, - tar, - uploaded_file, - upload_point, - remove_repo_files_not_in_tar, - commit_message, - new_repo_alert ) + ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ + self.upload_tar( trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ) elif uploaded_directory: - ok,message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = self.upload_directory( trans, - repository, - uploaded_directory, - upload_point, - remove_repo_files_not_in_tar, - commit_message, - new_repo_alert ) + ok,message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ + self.upload_directory( trans, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ) else: if ( isgzip or isbz2 ) and uncompress_file: uploaded_file_filename = self.uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ) @@ -131,7 +119,7 @@ shutil.move( uploaded_file_name, full_path ) # See if any admin users have chosen to receive email alerts when a repository is # updated. If so, check every uploaded file to ensure content is appropriate. - check_contents = common.check_file_contents( trans ) + check_contents = suc.check_file_contents( trans ) if check_contents and os.path.isfile( full_path ): content_alert_str = self.__check_file_content( full_path ) else: @@ -148,7 +136,7 @@ message = '%s<br/>%s' % ( message, error_message ) # See if the content of the change set was valid. admin_only = len( repository.downloadable_revisions ) != 1 - common.handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only ) + suc.handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only ) if ok: # Update the repository files for browsing. suc.update_repository( repo ) @@ -177,17 +165,20 @@ else: message += " %d files were removed from the repository root. " % len( files_to_remove ) kwd[ 'message' ] = message - common.set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=content_alert_str, **kwd ) - # Provide a warning message if a tool_dependencies.xml file is provided, but tool dependencies weren't loaded due to e.g. a requirement tag mismatch + suc.set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=content_alert_str, **kwd ) + # Provide a warning message if a tool_dependencies.xml file is provided, but tool dependencies weren't loaded due to a requirement tag mismatch + # or some other problem. if suc.get_config_from_disk( 'tool_dependencies.xml', repo_dir ): if repository.metadata_revisions: + # A repository's metadata revisions are order descending by update_time, so the zeroth revision will be the tip just after an upload. metadata_dict = repository.metadata_revisions[0].metadata else: metadata_dict = {} if 'tool_dependencies' not in metadata_dict: - message += 'Name, version and type from a tool requirement tag does not match the information in the "tool_dependencies.xml file". ' + message += 'Name, version and type from a tool requirement tag does not match the information in the "tool_dependencies.xml file", ' + message += 'so the tool dependency definitions will be ignored.' status = 'warning' - log.debug( 'Error in tool dependencies for repository %s: %s.' % ( repository.id, repository.name ) ) + log.debug( 'Error in tool dependencies for repository with id %s and name %s: %s' % ( str( repository.id ), str( repository.name ), message ) ) # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. suc.reset_tool_data_tables( trans.app ) trans.response.send_redirect( web.url_for( controller='repository', @@ -327,7 +318,7 @@ pass # See if any admin users have chosen to receive email alerts when a repository is # updated. If so, check every uploaded file to ensure content is appropriate. - check_contents = common.check_file_contents( trans ) + check_contents = suc.check_file_contents( trans ) for filename_in_archive in filenames_in_archive: # Check file content to ensure it is appropriate. if check_contents and os.path.isfile( filename_in_archive ): @@ -341,7 +332,7 @@ return False, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) admin_only = len( repository.downloadable_revisions ) != 1 - common.handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only ) + suc.handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only ) return True, '', files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed def uncompress( self, repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ): if isgzip: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Remove incorrect test parameter.
by Bitbucket 17 Jan '13

17 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6538175fb3e6/ changeset: 6538175fb3e6 user: jgoecks date: 2013-01-17 21:57:21 summary: Remove incorrect test parameter. affected #: 1 file diff -r d4a61389668164e833eef418ab03c1467ba64d13 -r 6538175fb3e6483895aaadfdeddd09aac558fdf5 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -462,7 +462,6 @@ <param name="use_annotations" value="No" /><param name="use_juncs" value="No" /><param name="no_novel_juncs" value="No" /> - <param name="report_discordant_pairs" value="No" /><param name="use_search" value="Yes" /><param name="min_coverage_intron" value="50" /><param name="max_coverage_intron" value="20000" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 4 new changesets
by Bitbucket 17 Jan '13

17 Jan '13

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/44d9d215b9c3/ changeset: 44d9d215b9c3 user: epaniagu date: 2011-11-22 21:42:18 summary: fix add/remove buttons in Repeat elements affected #: 1 file diff -r 9d6a9963b0da21fe3139fcefbd11c1ec6290a529 -r 44d9d215b9c337cf9b988976bf93f429dbd84ccb templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -139,13 +139,17 @@ %><div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div> ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} - <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + %if input.min < len( repeat_state ): + <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + %endif </div> %if rep_errors.has_key( '__index__' ): <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div> %endif %endfor - <div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> + %if input.max > len( repeat_state ): + <div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> + %endif </div> %elif input.type == "conditional": <% https://bitbucket.org/galaxy/galaxy-central/commits/b6ff1a695e07/ changeset: b6ff1a695e07 user: epaniagu date: 2011-11-22 21:53:56 summary: replace len( repeat_state ) with a variable so there's only one call affected #: 1 file diff -r 44d9d215b9c337cf9b988976bf93f429dbd84ccb -r b6ff1a695e07e6a2443a3d6d0aa9a9066a155dbc templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -127,8 +127,11 @@ </div> %endif </div> - <% repeat_state = tool_state[input.name] %> - %for i in range( len( repeat_state ) ): + <% + repeat_state = tool_state[input.name] + num_repeats = len( repeat_state ) + %> + %for i in range( num_repeats ): <div class="repeat-group-item"><% if input.name in errors: @@ -139,7 +142,7 @@ %><div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div> ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} - %if input.min < len( repeat_state ): + %if input.min < num_repeats: <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> %endif </div> @@ -147,7 +150,7 @@ <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div> %endif %endfor - %if input.max > len( repeat_state ): + %if input.max > num_repeats: <div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> %endif </div> https://bitbucket.org/galaxy/galaxy-central/commits/8d068273cf5b/ changeset: 8d068273cf5b user: jgoecks date: 2013-01-17 21:32:34 summary: Merged in epaniagu/galaxy-central (pull request #24: Fix Add/Remove buttons for Repeat groups) affected #: 1 file diff -r 7848d6fd1b7a3ef8330ad1b31f5a3521094ad706 -r 8d068273cf5b1160a27977727a7ab6f2237d4bb7 templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -135,8 +135,11 @@ </div> %endif </div> - <% repeat_state = tool_state[input.name] %> - %for i in range( len( repeat_state ) ): + <% + repeat_state = tool_state[input.name] + num_repeats = len( repeat_state ) + %> + %for i in range( num_repeats ): <div class="repeat-group-item"><% if input.name in errors: @@ -147,13 +150,25 @@ %><div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div> ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} +<<<<<<< local <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> +======= + %if input.min < num_repeats: + <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + %endif +>>>>>>> other </div> %if rep_errors.has_key( '__index__' ): <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div> %endif %endfor +<<<<<<< local <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> +======= + %if input.max > num_repeats: + <div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> + %endif +>>>>>>> other </div> %elif input.type == "conditional": <% https://bitbucket.org/galaxy/galaxy-central/commits/d4a613896681/ changeset: d4a613896681 user: jgoecks date: 2013-01-17 21:34:04 summary: Automated merge. affected #: 1 file diff -r 8d068273cf5b1160a27977727a7ab6f2237d4bb7 -r d4a61389668164e833eef418ab03c1467ba64d13 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -50,6 +50,41 @@ migrated_tool_panel_config = 'migrated_tools_conf.xml' installed_tool_panel_configs = [ 'shed_tool_conf.xml' ] +# should this serve static resources (scripts, images, styles, etc.) +STATIC_ENABLED = True + +def get_static_settings(): + """Returns dictionary of the settings necessary for a galaxy App + to be wrapped in the static middleware. + + This mainly consists of the filesystem locations of url-mapped + static resources. + """ + cwd = os.getcwd() + static_dir = os.path.join( cwd, 'static' ) + #TODO: these should be copied from universe_wsgi.ini + return dict( + #TODO: static_enabled needed here? + static_enabled = True, + static_cache_time = 360, + static_dir = static_dir, + static_images_dir = os.path.join( static_dir, 'images', '' ), + static_favicon_dir = os.path.join( static_dir, 'favicon.ico' ), + static_scripts_dir = os.path.join( static_dir, 'scripts', '' ), + static_style_dir = os.path.join( static_dir, 'june_2007_style', 'blue' ), + static_robots_txt = os.path.join( static_dir, 'robots.txt' ), + ) + +def get_webapp_global_conf(): + """Get the global_conf dictionary sent as the first argument to app_factory. + """ + # (was originally sent 'dict()') - nothing here for now except static settings + global_conf = dict() + if STATIC_ENABLED: + global_conf.update( get_static_settings() ) + return global_conf + + def parse_tool_panel_config( config, shed_tools_dict ): """ Parse a shed-related tool panel config to generate the shed_tools_dict. This only happens when testing tools installed from the tool shed. @@ -289,7 +324,8 @@ server = None if start_server: - webapp = buildapp.app_factory( dict(), use_translogger=False, static_enabled=False, app=app ) + webapp = buildapp.app_factory( get_webapp_global_conf(), app=app, + use_translogger=False, static_enabled=STATIC_ENABLED ) if galaxy_test_port is not None: server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: Enable serving static files when running functional tests
by Bitbucket 17 Jan '13

17 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/da89c3556c27/ changeset: da89c3556c27 user: carlfeberhard date: 2013-01-17 20:58:43 summary: Enable serving static files when running functional tests affected #: 1 file diff -r 7848d6fd1b7a3ef8330ad1b31f5a3521094ad706 -r da89c3556c27c8f1e5acf943c6983be5437efac6 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -50,6 +50,41 @@ migrated_tool_panel_config = 'migrated_tools_conf.xml' installed_tool_panel_configs = [ 'shed_tool_conf.xml' ] +# should this serve static resources (scripts, images, styles, etc.) +STATIC_ENABLED = True + +def get_static_settings(): + """Returns dictionary of the settings necessary for a galaxy App + to be wrapped in the static middleware. + + This mainly consists of the filesystem locations of url-mapped + static resources. + """ + cwd = os.getcwd() + static_dir = os.path.join( cwd, 'static' ) + #TODO: these should be copied from universe_wsgi.ini + return dict( + #TODO: static_enabled needed here? + static_enabled = True, + static_cache_time = 360, + static_dir = static_dir, + static_images_dir = os.path.join( static_dir, 'images', '' ), + static_favicon_dir = os.path.join( static_dir, 'favicon.ico' ), + static_scripts_dir = os.path.join( static_dir, 'scripts', '' ), + static_style_dir = os.path.join( static_dir, 'june_2007_style', 'blue' ), + static_robots_txt = os.path.join( static_dir, 'robots.txt' ), + ) + +def get_webapp_global_conf(): + """Get the global_conf dictionary sent as the first argument to app_factory. + """ + # (was originally sent 'dict()') - nothing here for now except static settings + global_conf = dict() + if STATIC_ENABLED: + global_conf.update( get_static_settings() ) + return global_conf + + def parse_tool_panel_config( config, shed_tools_dict ): """ Parse a shed-related tool panel config to generate the shed_tools_dict. This only happens when testing tools installed from the tool shed. @@ -289,7 +324,8 @@ server = None if start_server: - webapp = buildapp.app_factory( dict(), use_translogger=False, static_enabled=False, app=app ) + webapp = buildapp.app_factory( get_webapp_global_conf(), app=app, + use_translogger=False, static_enabled=STATIC_ENABLED ) if galaxy_test_port is not None: server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 4 new changesets
by Bitbucket 17 Jan '13

17 Jan '13

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2eb6dddb3866/ changeset: 2eb6dddb3866 user: fangly date: 2011-10-05 10:04:58 summary: Paired-end code that properly ignores description part of FASTQ headers affected #: 1 file diff -r 087a766b3eca312d49caffa6b821d304658825ae -r 2eb6dddb3866adef30b72e92e747d9ece4e11da9 lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py +++ b/lib/galaxy_utils/sequence/fastq.py @@ -514,9 +514,13 @@ self.apply_galaxy_conventions = apply_galaxy_conventions def close( self ): return self.file.close() - def get( self, sequence_id ): - if not isinstance( sequence_id, basestring ): - sequence_id = sequence_id.identifier + def get( self, sequence_identifier ): + # Input is either a sequence ID or a sequence object + if not isinstance( sequence_identifier, basestring ): + # Input was a sequence object (not a sequence ID). Get the sequence ID + sequence_identifier = sequence_identifier.identifier + # Get only the ID part of the sequence header + sequence_id, sequence_sep, sequence_desc = sequence_identifier.partition(' ') rval = None if sequence_id in self.offset_dict: initial_offset = self.file.tell() @@ -525,7 +529,7 @@ del self.offset_dict[ sequence_id ] self.file.seek( seq_offset ) rval = self.reader.next() - #assert rval.identifier == sequence_id, 'seq id mismatch' #should be able to remove this + #assert rval.id == sequence_id, 'seq id mismatch' #should be able to remove this self.file.seek( initial_offset ) else: while True: @@ -535,13 +539,14 @@ except StopIteration: self.eof = True break #eof, id not found, will return None - if fastq_read.identifier == sequence_id: + fastq_read_id, fastq_read_sep, fastq_read_desc = fastq_read.identifier.partition(' ') + if fastq_read_id == sequence_id: rval = fastq_read break else: - if fastq_read.identifier not in self.offset_dict: - self.offset_dict[ fastq_read.identifier ] = [] - self.offset_dict[ fastq_read.identifier ].append( offset ) + if fastq_read_id not in self.offset_dict: + self.offset_dict[ fastq_read_id ] = [] + self.offset_dict[ fastq_read_id ].append( offset ) if rval is not None and self.apply_galaxy_conventions: rval.apply_galaxy_conventions() return rval @@ -582,16 +587,18 @@ self.format = format self.force_quality_encoding = force_quality_encoding def join( self, read1, read2 ): - if read1.identifier.endswith( '/2' ) and read2.identifier.endswith( '/1' ): + read1_id, read1_sep, read1_desc = read1.identifier.partition(' ') + read2_id, read2_sep, read2_desc = read2.identifier.partition(' ') + if read1_id.endswith( '/2' ) and read2_id.endswith( '/1' ): #swap 1 and 2 tmp = read1 read1 = read2 read2 = tmp del tmp - if read1.identifier.endswith( '/1' ) and read2.identifier.endswith( '/2' ): - identifier = read1.identifier[:-2] - else: - identifier = read1.identifier + if read1_id.endswith( '/1' ) and read2_id.endswith( '/2' ): + read1_id = read1_id[:-2] + + identifier = read1_id + ' ' + read1_desc #use force quality encoding, if not present force to encoding of first read force_quality_encoding = self.force_quality_encoding @@ -621,17 +628,18 @@ rval.quality = "%s %s" % ( new_read1.quality.strip(), new_read2.quality.strip() ) return rval def get_paired_identifier( self, fastq_read ): - identifier = fastq_read.identifier - if identifier[-2] == '/': - if identifier[-1] == "1": - identifier = "%s2" % identifier[:-1] - elif identifier[-1] == "2": - identifier = "%s1" % identifier[:-1] - return identifier + read_id, read_sep, read_desc = fastq_read.identifier.partition(' ') + if read_id[-2] == '/': + if read_id[-1] == "1": + read_id = "%s2" % read_id[:-1] + elif read_id[-1] == "2": + read_id = "%s1" % read_id[:-1] + return read_id def is_first_mate( self, sequence_id ): is_first = None if not isinstance( sequence_id, basestring ): sequence_id = sequence_id.identifier + sequence_id, sequence_sep, sequence_desc = sequence_id.partition(' ') if sequence_id[-2] == '/': if sequence_id[-1] == "1": is_first = True https://bitbucket.org/galaxy/galaxy-central/commits/34e7cf3bcef0/ changeset: 34e7cf3bcef0 user: fangly date: 2011-11-30 02:38:52 summary: Avoid trailing whitespace affected #: 1 file diff -r 2eb6dddb3866adef30b72e92e747d9ece4e11da9 -r 34e7cf3bcef0eb7bf7d0684e8ac5d91e03750d8c lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py +++ b/lib/galaxy_utils/sequence/fastq.py @@ -597,8 +597,10 @@ del tmp if read1_id.endswith( '/1' ) and read2_id.endswith( '/2' ): read1_id = read1_id[:-2] - - identifier = read1_id + ' ' + read1_desc + + identifier = read1_id + if read1_desc: + identifier = identifier + ' ' + read1_desc #use force quality encoding, if not present force to encoding of first read force_quality_encoding = self.force_quality_encoding https://bitbucket.org/galaxy/galaxy-central/commits/7d4a431f7188/ changeset: 7d4a431f7188 user: fangly date: 2011-11-30 03:01:07 summary: Updated tests for FASTQ interlacer/deinterlacer tool affected #: 2 files diff -r 34e7cf3bcef0eb7bf7d0684e8ac5d91e03750d8c -r 7d4a431f7188d71d5e0ba2655a10145ecbdb4468 test-data/paired_end_2.fastqsanger --- a/test-data/paired_end_2.fastqsanger +++ b/test-data/paired_end_2.fastqsanger @@ -1,6 +1,6 @@ -@1539:931/2 +@1539:931/2 this read has a description GCGCGTAACGTTTCACCTCGAGATCGTTGTCGGCCGCAATCTCCTGGGGGCGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT -+1539:931/2 ++1539:931/2 this read has a description aee_dcadeeWcaaadJbdaff[fffc]dcfe[dRc^\[^QVOZXXZSPFWNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB @2971:937/2 CTCGCACGGCCGCCTCGACCACTTGGTCTGGCGTCATGCGCAATTTTTTCTCCATGTGGAACGGGCTGGTGGCGATGAACGTATGAATATGCCCCCGCGCT diff -r 34e7cf3bcef0eb7bf7d0684e8ac5d91e03750d8c -r 7d4a431f7188d71d5e0ba2655a10145ecbdb4468 test-data/paired_end_merged.fastqsanger --- a/test-data/paired_end_merged.fastqsanger +++ b/test-data/paired_end_merged.fastqsanger @@ -2,9 +2,9 @@ NACATCAACACTCAGTAACGGCTGGCGCAAAATGGCATTGATTAACGAAGACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG +1539:931/1 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB -@1539:931/2 +@1539:931/2 this read has a description GCGCGTAACGTTTCACCTCGAGATCGTTGTCGGCCGCAATCTCCTGGGGGCGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT -+1539:931/2 ++1539:931/2 this read has a description aee_dcadeeWcaaadJbdaff[fffc]dcfe[dRc^\[^QVOZXXZSPFWNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB @2971:937/1 NCGGAGACTTCGAGGCCATCCAGTCGATTGCCAAAGTCATCAAGGGGTCGACGATCTGCTCCCTTGCCCGTTCCAACGAGAATGAAATCCGCCGCGCGTGG https://bitbucket.org/galaxy/galaxy-central/commits/7848d6fd1b7a/ changeset: 7848d6fd1b7a user: jgoecks date: 2013-01-17 20:12:57 summary: Merged in fangly/galaxy-central (pull request #8: Paired-end code mishandles description of FASTQ headers) affected #: 3 files diff -r 1b95e5b076fee018402e5c94534a2e65ea6c5315 -r 7848d6fd1b7a3ef8330ad1b31f5a3521094ad706 lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py +++ b/lib/galaxy_utils/sequence/fastq.py @@ -514,9 +514,13 @@ self.apply_galaxy_conventions = apply_galaxy_conventions def close( self ): return self.file.close() - def get( self, sequence_id ): - if not isinstance( sequence_id, basestring ): - sequence_id = sequence_id.identifier + def get( self, sequence_identifier ): + # Input is either a sequence ID or a sequence object + if not isinstance( sequence_identifier, basestring ): + # Input was a sequence object (not a sequence ID). Get the sequence ID + sequence_identifier = sequence_identifier.identifier + # Get only the ID part of the sequence header + sequence_id, sequence_sep, sequence_desc = sequence_identifier.partition(' ') rval = None if sequence_id in self.offset_dict: initial_offset = self.file.tell() @@ -525,7 +529,7 @@ del self.offset_dict[ sequence_id ] self.file.seek( seq_offset ) rval = self.reader.next() - #assert rval.identifier == sequence_id, 'seq id mismatch' #should be able to remove this + #assert rval.id == sequence_id, 'seq id mismatch' #should be able to remove this self.file.seek( initial_offset ) else: while True: @@ -535,13 +539,14 @@ except StopIteration: self.eof = True break #eof, id not found, will return None - if fastq_read.identifier == sequence_id: + fastq_read_id, fastq_read_sep, fastq_read_desc = fastq_read.identifier.partition(' ') + if fastq_read_id == sequence_id: rval = fastq_read break else: - if fastq_read.identifier not in self.offset_dict: - self.offset_dict[ fastq_read.identifier ] = [] - self.offset_dict[ fastq_read.identifier ].append( offset ) + if fastq_read_id not in self.offset_dict: + self.offset_dict[ fastq_read_id ] = [] + self.offset_dict[ fastq_read_id ].append( offset ) if rval is not None and self.apply_galaxy_conventions: rval.apply_galaxy_conventions() return rval @@ -582,16 +587,20 @@ self.format = format self.force_quality_encoding = force_quality_encoding def join( self, read1, read2 ): - if read1.identifier.endswith( '/2' ) and read2.identifier.endswith( '/1' ): + read1_id, read1_sep, read1_desc = read1.identifier.partition(' ') + read2_id, read2_sep, read2_desc = read2.identifier.partition(' ') + if read1_id.endswith( '/2' ) and read2_id.endswith( '/1' ): #swap 1 and 2 tmp = read1 read1 = read2 read2 = tmp del tmp - if read1.identifier.endswith( '/1' ) and read2.identifier.endswith( '/2' ): - identifier = read1.identifier[:-2] - else: - identifier = read1.identifier + if read1_id.endswith( '/1' ) and read2_id.endswith( '/2' ): + read1_id = read1_id[:-2] + + identifier = read1_id + if read1_desc: + identifier = identifier + ' ' + read1_desc #use force quality encoding, if not present force to encoding of first read force_quality_encoding = self.force_quality_encoding @@ -621,17 +630,18 @@ rval.quality = "%s %s" % ( new_read1.quality.strip(), new_read2.quality.strip() ) return rval def get_paired_identifier( self, fastq_read ): - identifier = fastq_read.identifier - if identifier[-2] == '/': - if identifier[-1] == "1": - identifier = "%s2" % identifier[:-1] - elif identifier[-1] == "2": - identifier = "%s1" % identifier[:-1] - return identifier + read_id, read_sep, read_desc = fastq_read.identifier.partition(' ') + if read_id[-2] == '/': + if read_id[-1] == "1": + read_id = "%s2" % read_id[:-1] + elif read_id[-1] == "2": + read_id = "%s1" % read_id[:-1] + return read_id def is_first_mate( self, sequence_id ): is_first = None if not isinstance( sequence_id, basestring ): sequence_id = sequence_id.identifier + sequence_id, sequence_sep, sequence_desc = sequence_id.partition(' ') if sequence_id[-2] == '/': if sequence_id[-1] == "1": is_first = True diff -r 1b95e5b076fee018402e5c94534a2e65ea6c5315 -r 7848d6fd1b7a3ef8330ad1b31f5a3521094ad706 test-data/paired_end_2.fastqsanger --- a/test-data/paired_end_2.fastqsanger +++ b/test-data/paired_end_2.fastqsanger @@ -1,6 +1,6 @@ -@1539:931/2 +@1539:931/2 this read has a description GCGCGTAACGTTTCACCTCGAGATCGTTGTCGGCCGCAATCTCCTGGGGGCGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT -+1539:931/2 ++1539:931/2 this read has a description aee_dcadeeWcaaadJbdaff[fffc]dcfe[dRc^\[^QVOZXXZSPFWNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB @2971:937/2 CTCGCACGGCCGCCTCGACCACTTGGTCTGGCGTCATGCGCAATTTTTTCTCCATGTGGAACGGGCTGGTGGCGATGAACGTATGAATATGCCCCCGCGCT diff -r 1b95e5b076fee018402e5c94534a2e65ea6c5315 -r 7848d6fd1b7a3ef8330ad1b31f5a3521094ad706 test-data/paired_end_merged.fastqsanger --- a/test-data/paired_end_merged.fastqsanger +++ b/test-data/paired_end_merged.fastqsanger @@ -2,9 +2,9 @@ NACATCAACACTCAGTAACGGCTGGCGCAAAATGGCATTGATTAACGAAGACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG +1539:931/1 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB -@1539:931/2 +@1539:931/2 this read has a description GCGCGTAACGTTTCACCTCGAGATCGTTGTCGGCCGCAATCTCCTGGGGGCGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT -+1539:931/2 ++1539:931/2 this read has a description aee_dcadeeWcaaadJbdaff[fffc]dcfe[dRc^\[^QVOZXXZSPFWNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB @2971:937/1 NCGGAGACTTCGAGGCCATCCAGTCGATTGCCAAAGTCATCAAGGGGTCGACGATCTGCTCCCTTGCCCGTTCCAACGAGAATGAAATCCGCCGCGCGTGG Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Comment and naming fix for migration script 108.
by Bitbucket 17 Jan '13

17 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1b95e5b076fe/ changeset: 1b95e5b076fe user: jgoecks date: 2013-01-17 19:56:26 summary: Comment and naming fix for migration script 108. affected #: 1 file diff -r 1314572f86e121aa734ea27a52601fbcdb450278 -r 1b95e5b076fee018402e5c94534a2e65ea6c5315 lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py --- a/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py +++ b/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py @@ -71,10 +71,10 @@ except Exception, e: log.debug( "Dropping 'extended_metadata' table failed: %s" % ( str( e ) ) ) - # Drop the Job table's exit_code column. + # Drop the LDDA table's extended metadata ID column. try: - job_table = Table( "library_dataset_dataset_association", metadata, autoload=True ) - extended_metadata_id = job_table.c.extended_metadata_id + ldda_table = Table( "library_dataset_dataset_association", metadata, autoload=True ) + extended_metadata_id = ldda_table.c.extended_metadata_id extended_metadata_id.drop() except Exception, e: log.debug( "Dropping 'extended_metadata_id' column from library_dataset_dataset_association table failed: %s" % ( str( e ) ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 17 Jan '13

17 Jan '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ccc640f65971/ changeset: ccc640f65971 user: kellrott date: 2013-01-15 22:57:14 summary: Adding exception catches to database 108 downgrade step to fix failure issue with downgrading postgres database (foreign key rules violated...) affected #: 1 file diff -r 4bd419751ed3e8cc54913fa37389111a0e7faaa9 -r ccc640f65971632ea6de7a94bc01d24954102487 lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py --- a/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py +++ b/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py @@ -61,8 +61,15 @@ def downgrade(): metadata.reflect() - ExtendedMetadata_table.drop() - ExtendedMetadataIndex_table.drop() + try: + ExtendedMetadataIndex_table.drop() + except Exception, e: + log.debug( "Dropping 'extended_metadata_index' table failed: %s" % ( str( e ) ) ) + + try: + ExtendedMetadata_table.drop() + except Exception, e: + log.debug( "Dropping 'extended_metadata' table failed: %s" % ( str( e ) ) ) # Drop the Job table's exit_code column. try: https://bitbucket.org/galaxy/galaxy-central/commits/1314572f86e1/ changeset: 1314572f86e1 user: jgoecks date: 2013-01-17 19:52:01 summary: Merged in kellrott/galaxy-central (pull request #109: Fixing database v108 downgrade failure) affected #: 1 file diff -r b14f68fb3e853313d944f934cf279b3517d4a7e6 -r 1314572f86e121aa734ea27a52601fbcdb450278 lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py --- a/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py +++ b/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py @@ -61,8 +61,15 @@ def downgrade(): metadata.reflect() - ExtendedMetadata_table.drop() - ExtendedMetadataIndex_table.drop() + try: + ExtendedMetadataIndex_table.drop() + except Exception, e: + log.debug( "Dropping 'extended_metadata_index' table failed: %s" % ( str( e ) ) ) + + try: + ExtendedMetadata_table.drop() + except Exception, e: + log.debug( "Dropping 'extended_metadata' table failed: %s" % ( str( e ) ) ) # Drop the Job table's exit_code column. try: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Use correct index tables for setting dbkey of Tophat2 outputs.
by Bitbucket 17 Jan '13

17 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b14f68fb3e85/ changeset: b14f68fb3e85 user: jgoecks date: 2013-01-17 18:56:03 summary: Use correct index tables for setting dbkey of Tophat2 outputs. affected #: 1 file diff -r f11abc888753d0b8efeb4cae653a21ca64a2ae5b -r b14f68fb3e853313d944f934cf279b3517d4a7e6 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -323,7 +323,7 @@ <conditional name="refGenomeSource.genomeSource"><when value="indexed"><action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat_indexes" column="1" offset="0"> + <option type="from_data_table" name="tophat2_indexes" column="1" offset="0"><filter type="param_value" column="0" value="#" compare="startswith" keep="False"/><filter type="param_value" ref="refGenomeSource.index" column="0"/></option> @@ -342,7 +342,7 @@ <conditional name="refGenomeSource.genomeSource"><when value="indexed"><action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat_indexes" column="1" offset="0"> + <option type="from_data_table" name="tophat2_indexes" column="1" offset="0"><filter type="param_value" column="0" value="#" compare="startswith" keep="False"/><filter type="param_value" ref="refGenomeSource.index" column="0"/></option> @@ -361,7 +361,7 @@ <conditional name="refGenomeSource.genomeSource"><when value="indexed"><action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat_indexes" column="1" offset="0"> + <option type="from_data_table" name="tophat2_indexes" column="1" offset="0"><filter type="param_value" column="0" value="#" compare="startswith" keep="False"/><filter type="param_value" ref="refGenomeSource.index" column="0"/></option> @@ -380,7 +380,7 @@ <conditional name="refGenomeSource.genomeSource"><when value="indexed"><action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat_indexes" column="1" offset="0"> + <option type="from_data_table" name="tophat2_indexes" column="1" offset="0"><filter type="param_value" column="0" value="#" compare="startswith" keep="False"/><filter type="param_value" ref="refGenomeSource.index" column="0"/></option> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Readd a request param that is no longer needed to a request between Galaxy and the tool shed to ensure backward compatibility.
by Bitbucket 17 Jan '13

17 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f11abc888753/ changeset: f11abc888753 user: greg date: 2013-01-17 16:40:01 summary: Readd a request param that is no longer needed to a request between Galaxy and the tool shed to ensure backward compatibility. affected #: 1 file diff -r 6e1e7bee1e6f1b10eed3ba023e6ed0badf16ed38 -r f11abc888753d0b8efeb4cae653a21ca64a2ae5b lib/galaxy/webapps/galaxy/controllers/admin.py --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -711,7 +711,8 @@ tool_dependencies_dict = {} repository_name = elem.get( 'name' ) changeset_revision = elem.get( 'changeset_revision' ) - url = '%s/repository/get_tool_dependencies?name=%s&owner=devteam&changeset_revision=%s' % ( tool_shed_url, repository_name, changeset_revision ) + url = '%s/repository/get_tool_dependencies?name=%s&owner=devteam&changeset_revision=%s&from_install_manager=True' % \ + ( tool_shed_url, repository_name, changeset_revision ) response = urllib2.urlopen( url ) text = response.read() response.close() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: inithello: Test for reinstalling an uninstalled repository that now has a new changeset adding repository dependencies.
by Bitbucket 17 Jan '13

17 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6e1e7bee1e6f/ changeset: 6e1e7bee1e6f user: inithello date: 2013-01-17 16:18:36 summary: Test for reinstalling an uninstalled repository that now has a new changeset adding repository dependencies. affected #: 2 files diff -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 -r 6e1e7bee1e6f1b10eed3ba023e6ed0badf16ed38 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -711,6 +711,8 @@ url = '/admin_toolshed/reselect_tool_panel_section?id=%s' % self.security.encode_id( installed_repository.id ) self.visit_galaxy_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed=[] ) + # Build the url that will simulate a filled-out form being submitted. Due to a limitation in twill, the reselect_tool_panel_section + # form doesn't get parsed correctly. repo_dependencies = self.create_checkbox_query_string( field_name='install_repository_dependencies', value=install_repository_dependencies ) tool_dependencies = self.create_checkbox_query_string( field_name='install_tool_dependencies', value=install_tool_dependencies ) encoded_repository_id = self.security.encode_id( installed_repository.id ) diff -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 -r 6e1e7bee1e6f1b10eed3ba023e6ed0badf16ed38 test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py --- /dev/null +++ b/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py @@ -0,0 +1,105 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os, logging +import tool_shed.base.test_db_util as test_db_util + +column_repository_name = 'column_maker_1087' +column_repository_description = "Add column" +column_repository_long_description = "Compute an expression on every row" + +convert_repository_name = 'convert_chars_1087' +convert_repository_description = "Convert delimiters" +convert_repository_long_description = "Convert delimiters to tab" + +category_name = 'Test 1087 Advanced Circular Dependencies' +category_description = 'Test circular dependency features' + +log = logging.getLogger( __name__ ) + +class TestRepositoryDependencies( ShedTwillTestCase ): + '''Test installing a repository, then updating it to include repository dependencies.''' + def test_0000_create_or_login_admin_user( self ): + """Create necessary user accounts and login as an admin user.""" + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + galaxy_admin_user = test_db_util.get_galaxy_user( common.admin_email ) + assert galaxy_admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + galaxy_admin_user_private_role = test_db_util.get_galaxy_private_role( galaxy_admin_user ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_and_populate_column_repository( self ): + """Create a category for this test suite and add repositories to it.""" + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=column_repository_name, + description=column_repository_description, + long_description=column_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + self.upload_file( repository, + 'column_maker/column_maker.tar', + strings_displayed=[], + commit_message='Uploaded column_maker.tar.' ) + def test_0010_create_and_populate_convert_repository( self ): + '''Create and populate the convert_chars repository.''' + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=convert_repository_name, + description=convert_repository_description, + long_description=convert_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + self.upload_file( repository, + 'convert_chars/convert_chars.tar', + strings_displayed=[], + commit_message='Uploaded convert_chars.tar.' ) + def test_0015_install_and_uninstall_column_repository( self ): + '''Install and uninstall the column_maker repository.''' + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + self.install_repository( column_repository_name, + common.test_user_1_name, + category_name, + install_tool_dependencies=False, + install_repository_dependencies=True, + new_tool_panel_section='column_maker', + strings_not_displayed=[ 'install_repository_dependencies' ] ) + installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) + self.uninstall_repository( installed_column_repository, remove_from_disk=True ) + def test_0020_upload_dependency_xml( self ): + '''Upload a repository_dependencies.xml file to column_maker that specifies convert_chars.''' + convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) + repository_dependencies_path = self.generate_temp_path( 'test_1085', additional_paths=[ 'column' ] ) + self.create_repository_dependency( column_repository, depends_on=[ convert_repository ], filepath=repository_dependencies_path ) + def test_0025_verify_repository_dependency( self ): + '''Verify that the new revision of column_maker now depends on convert_chars.''' + convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) + self.check_repository_dependency( column_repository, convert_repository ) + log.debug( [ repository.id for repository in test_db_util.get_all_installed_repositories() ] ) + def test_0030_reinstall_column_repository( self ): + '''Reinstall column_maker and verify that it now shows repository dependencies.''' + installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) + convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + strings_displayed=[ 'Handle repository dependencies', convert_repository.name, self.get_repository_tip( convert_repository ) ] + # Due to twill's limitations, only check for strings on the (redirected) reselect tool panel section page, don't actually reinstall. + url = '/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=%s' % self.security.encode_id( installed_column_repository.id ) + self.visit_galaxy_url( url ) + self.check_for_strings( strings_displayed ) + uninstalled_repositories = [ ( column_repository_name, common.test_user_1_name ) ] + self.verify_installed_uninstalled_repositories( uninstalled_repositories=uninstalled_repositories, installed_repositories=[] ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Properly handle updates which have become available for tool shed repositories while they were ninstalled when reinstalling them.
by Bitbucket 16 Jan '13

16 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e6302ee56ed0/ changeset: e6302ee56ed0 user: greg date: 2013-01-16 21:39:22 summary: Properly handle updates which have become available for tool shed repositories while they were ninstalled when reinstalling them. affected #: 8 files diff -r f199b236ceb08e9588351223b6277861e9f87325 -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -596,8 +596,7 @@ # In this case, a record for the repository will exist in the database with the status of 'New'. repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed_url, name, repository_owner, changeset_revision ) if repository and repository.metadata: - installed_rd, missing_rd = \ - get_installed_and_missing_repository_dependencies( trans, repository ) + installed_rd, missing_rd = get_installed_and_missing_repository_dependencies( trans, repository ) else: installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple ) # Discover all repository dependencies and retrieve information for installing them. diff -r f199b236ceb08e9588351223b6277861e9f87325 -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -66,7 +66,7 @@ tool_dependencies[ dependency_key ] = requirements_dict return tool_dependencies def build_readme_files_dict( metadata, tool_path=None ): - """Return a dictionary of valid readme file name <-> readme file content pairs for all readme files contained in the received repository_metadata.""" + """Return a dictionary of valid readme file name <-> readme file content pairs for all readme files contained in the received metadata.""" readme_files_dict = {} if metadata: if 'readme_files' in metadata: @@ -128,10 +128,14 @@ containers_dict[ 'readme_files' ] = readme_files_root_folder # Installed repository dependencies container. if repository_dependencies: + if new_install: + label = 'Repository dependencies' + else: + label = 'Installed repository dependencies' folder_id, repository_dependencies_root_folder = container_util.build_repository_dependencies_folder( trans=trans, folder_id=folder_id, repository_dependencies=repository_dependencies, - label='Installed repository dependencies', + label=label, installed=True ) containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder # Missing repository dependencies container. @@ -777,17 +781,20 @@ sa_session.flush() return tool_shed_repository def create_repo_info_dict( trans, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_name=None, repository=None, - repository_metadata=None, metadata=None, repository_dependencies=None ): + repository_metadata=None, tool_dependencies=None, repository_dependencies=None ): """ Return a dictionary that includes all of the information needed to install a repository into a local Galaxy instance. The dictionary will also contain the recursive list of repository dependencies defined for the repository, as well as the defined tool dependencies. - This method is called from Galaxy in two places: - 1. During the tool shed repository installation process (via the tool shed's get_repository_information() method)- in this case both the received - repository and repository_metadata will be objects. - 2. When a tool shed repository that was uninstalled from a Galaxy instance is being re-installed - in this case, both repository and - repository_metadata will be None, but metadata will be the tool_shed_repository metadata on the Galaxy side, and the repository_dependencies will - be an object previously retrieved from the tool shed. + This method is called from Galaxy unser three scenarios: + 1. During the tool shed repository installation process via the tool shed's get_repository_information() method. In this case both the received + repository and repository_metadata will be objects., but tool_dependencies and repository_dependencies will be None + 2. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no updates available. In this case, both + repository and repository_metadata will be None, but tool_dependencies and repository_dependencies will be objects previously retrieved from the + tool shed if the repository includes definitions for them. + 3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates available. In this case, this + method is reached via the tool shed's get_updated_repository_information() method, and both repository and repository_metadata will be objects + but tool_dependencies and repository_dependencies will be None. """ repo_info_dict = {} repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner ) @@ -806,27 +813,24 @@ all_repository_dependencies=None, handled_key_rd_dicts=None, circular_repository_dependencies=None ) - if metadata: - tool_dependencies = metadata.get( 'tool_dependencies', None ) - if tool_dependencies: - new_tool_dependencies = {} - for dependency_key, requirements_dict in tool_dependencies.items(): - if dependency_key in [ 'set_environment' ]: - new_set_environment_dict_list = [] - for set_environment_dict in requirements_dict: - set_environment_dict[ 'repository_name' ] = repository_name - set_environment_dict[ 'repository_owner' ] = repository_owner - set_environment_dict[ 'changeset_revision' ] = changeset_revision - new_set_environment_dict_list.append( set_environment_dict ) - new_tool_dependencies[ dependency_key ] = new_set_environment_dict_list - else: - requirements_dict[ 'repository_name' ] = repository_name - requirements_dict[ 'repository_owner' ] = repository_owner - requirements_dict[ 'changeset_revision' ] = changeset_revision - new_tool_dependencies[ dependency_key ] = requirements_dict - tool_dependencies = new_tool_dependencies - else: - tool_dependencies = None + tool_dependencies = metadata.get( 'tool_dependencies', None ) + if tool_dependencies: + new_tool_dependencies = {} + for dependency_key, requirements_dict in tool_dependencies.items(): + if dependency_key in [ 'set_environment' ]: + new_set_environment_dict_list = [] + for set_environment_dict in requirements_dict: + set_environment_dict[ 'repository_name' ] = repository_name + set_environment_dict[ 'repository_owner' ] = repository_owner + set_environment_dict[ 'changeset_revision' ] = changeset_revision + new_set_environment_dict_list.append( set_environment_dict ) + new_tool_dependencies[ dependency_key ] = new_set_environment_dict_list + else: + requirements_dict[ 'repository_name' ] = repository_name + requirements_dict[ 'repository_owner' ] = repository_owner + requirements_dict[ 'changeset_revision' ] = changeset_revision + new_tool_dependencies[ dependency_key ] = requirements_dict + tool_dependencies = new_tool_dependencies # Cast unicode to string. repo_info_dict[ str( repository.name ) ] = ( str( repository.description ), str( repository_clone_url ), diff -r f199b236ceb08e9588351223b6277861e9f87325 -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1406,7 +1406,7 @@ a local Galaxy instance. """ includes_tools = False - includes_repository_dependencies = False + has_repository_dependencies = False includes_tool_dependencies = False repo_info_dicts = [] for tup in zip( util.listify( repository_ids ), util.listify( changeset_revisions ) ): @@ -1417,8 +1417,8 @@ metadata = repository_metadata.metadata if not includes_tools and 'tools' in metadata: includes_tools = True - if not includes_repository_dependencies and 'repository_dependencies' in metadata: - includes_repository_dependencies = True + if not has_repository_dependencies and 'repository_dependencies' in metadata: + has_repository_dependencies = True if not includes_tool_dependencies and 'tool_dependencies' in metadata: includes_tool_dependencies = True repo_dir = repository.repo_path( trans.app ) @@ -1431,11 +1431,12 @@ repository_owner=repository.user.username, repository_name=repository.name, repository=repository, - metadata=None, - repository_metadata=repository_metadata ) + repository_metadata=repository_metadata, + tool_dependencies=None, + repository_dependencies=None ) repo_info_dicts.append( encoding_util.tool_shed_encode( repo_info_dict ) ) return dict( includes_tools=includes_tools, - includes_repository_dependencies=includes_repository_dependencies, + has_repository_dependencies=has_repository_dependencies, includes_tool_dependencies=includes_tool_dependencies, repo_info_dicts=repo_info_dicts ) @web.json @@ -1465,10 +1466,6 @@ def get_tool_dependencies( self, trans, **kwd ): """Handle a request from a Galaxy instance.""" params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - # If the request originated with the UpdateManager, it will not include a galaxy_url. - galaxy_url = kwd.get( 'galaxy_url', '' ) name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) @@ -1478,10 +1475,8 @@ break metadata = downloadable_revision.metadata tool_dependencies = metadata.get( 'tool_dependencies', '' ) - from_install_manager = kwd.get( 'from_install_manager', False ) - if from_install_manager: - if tool_dependencies: - return encoding_util.tool_shed_encode( tool_dependencies ) + if tool_dependencies: + return encoding_util.tool_shed_encode( tool_dependencies ) return '' @web.expose def get_tool_versions( self, trans, **kwd ): @@ -1506,6 +1501,53 @@ if tool_version_dicts: return json.to_json_string( tool_version_dicts ) return '' + @web.json + def get_updated_repository_information( self, trans, name, owner, changeset_revision, **kwd ): + """Generate a disctionary that contains the information about a repository that is necessary for installing it into a local Galaxy instance.""" + repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + repository_id = trans.security.encode_id( repository.id ) + repository_clone_url = suc.generate_clone_url_for_repository_in_tool_shed( trans, repository ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) + repo_dir = repository.repo_path( trans.app ) + repo = hg.repository( suc.get_configured_ui(), repo_dir ) + ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + repo_info_dict = suc.create_repo_info_dict( trans=trans, + repository_clone_url=repository_clone_url, + changeset_revision=changeset_revision, + ctx_rev=str( ctx.rev() ), + repository_owner=repository.user.username, + repository_name=repository.name, + repository=repository, + repository_metadata=repository_metadata, + tool_dependencies=None, + repository_dependencies=None ) + metadata = repository_metadata.metadata + if metadata: + readme_files_dict = suc.build_readme_files_dict( metadata ) + if 'tools' in metadata: + includes_tools = True + else: + includes_tools = False + else: + readme_files_dict = None + includes_tools = False + # See if the repo_info_dict was populated with repository_dependencies or tool_dependencies. + for name, repo_info_tuple in repo_info_dict.items(): + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tuple ) + if repository_dependencies: + has_repository_dependencies = True + else: + has_repository_dependencies = False + if tool_dependencies: + includes_tool_dependencies = True + else: + includes_tool_dependencies = False + return dict( includes_tools=includes_tools, + has_repository_dependencies=has_repository_dependencies, + includes_tool_dependencies=includes_tool_dependencies, + readme_files_dict=readme_files_dict, + repo_info_dict=repo_info_dict ) def get_versions_of_tool( self, trans, repository, repository_metadata, guid ): """Return the tool lineage in descendant order for the received guid contained in the received repsitory_metadata.tool_versions.""" encoded_id = trans.security.encode_id( repository.id ) diff -r f199b236ceb08e9588351223b6277861e9f87325 -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 lib/galaxy/webapps/community/util/container_util.py --- a/lib/galaxy/webapps/community/util/container_util.py +++ b/lib/galaxy/webapps/community/util/container_util.py @@ -485,10 +485,14 @@ sub_folder.repository_dependencies.append( repository_dependency ) for repository_dependency in rd_value: if trans.webapp.name == 'galaxy': - # We have two extra items in the tuple, repository.id and repository.status. - tool_shed_repository_id = repository_dependency[ 4 ] - installation_status = repository_dependency[ 5 ] - repository_dependency = repository_dependency[ 0:4 ] + if len( repository_dependency ) == 6: + # We have two extra items in the tuple, repository.id and repository.status. + tool_shed_repository_id = repository_dependency[ 4 ] + installation_status = repository_dependency[ 5 ] + repository_dependency = repository_dependency[ 0:4 ] + else: + tool_shed_repository_id = None + installation_status = 'unknown' else: tool_shed_repository_id = None installation_status = None diff -r f199b236ceb08e9588351223b6277861e9f87325 -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 lib/galaxy/webapps/galaxy/controllers/admin.py --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -711,8 +711,7 @@ tool_dependencies_dict = {} repository_name = elem.get( 'name' ) changeset_revision = elem.get( 'changeset_revision' ) - url = '%s/repository/get_tool_dependencies?name=%s&owner=devteam&changeset_revision=%s&from_install_manager=True' % \ - ( tool_shed_url, repository_name, changeset_revision ) + url = '%s/repository/get_tool_dependencies?name=%s&owner=devteam&changeset_revision=%s' % ( tool_shed_url, repository_name, changeset_revision ) response = urllib2.urlopen( url ) text = response.read() response.close() diff -r f199b236ceb08e9588351223b6277861e9f87325 -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -374,21 +374,41 @@ if repository.uninstalled: # Since we're reinstalling the repository we need to find the latest changeset revision to which it can be updated so that we # can reset the metadata if necessary. This will ensure that information about repository dependencies and tool dependencies - # will be current. + # will be current. Only allow selecting a different section in the tool panel if the repository was uninstalled. current_changeset_revision, current_ctx_rev, includes_tools, has_repository_dependencies = \ shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, repository ) if current_ctx_rev == repository.ctx_rev: - includes_tools = repository.includes_tools - has_repository_dependencies = repository.has_repository_dependencies - if includes_tools or has_repository_dependencies: - # Only allow selecting a different section in the tool panel if the repository was uninstalled. - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='reselect_tool_panel_section', - **kwd ) ) + # The uninstalled repository is current. + if repository.includes_tools or repository.has_repository_dependencies: + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='reselect_tool_panel_section', + **kwd ) ) + else: + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='reinstall_repository', + **kwd ) ) else: - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='reinstall_repository', - **kwd ) ) + # The uninstalled repository has updates available in the tool shed. + updated_repo_info_dict = self.get_updated_repository_information( trans=trans, + repository_id=trans.security.encode_id( repository.id ), + repository_name=repository.name, + repository_owner=repository.owner, + changeset_revision=current_changeset_revision ) + has_repository_dependencies = updated_repo_info_dict.get( 'has_repository_dependencies', False ) + includes_tool_dependencies = updated_repo_info_dict.get( 'includes_tool_dependencies', False ) + if has_repository_dependencies or includes_tool_dependencies: + json_repo_info_dict = json.to_json_string( updated_repo_info_dict ) + encoded_repo_info_dict = encoding_util.tool_shed_encode( json_repo_info_dict ) + kwd[ 'latest_changeset_revision' ] = current_changeset_revision + kwd[ 'latest_ctx_rev' ] = current_ctx_rev + kwd[ 'updated_repo_info_dict' ] = encoded_repo_info_dict + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='reselect_tool_panel_section', + **kwd ) ) + else: + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='reinstall_repository', + **kwd ) ) else: return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='activate_repository', @@ -581,6 +601,45 @@ else: text = '' return text + @web.expose + @web.require_admin + def get_tool_dependencies( self, trans, repository_id, repository_name, repository_owner, changeset_revision ): + """ + Send a request to the appropriate tool shed to retrieve the dictionary of tool dependencies defined for the received repository name, + owner and changeset revision. The received repository_id is the encoded id of the installed tool shed repository in Galaxy. We need + it so that we can derive the tool shed from which it was installed. + """ + repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + url = suc.url_join( tool_shed_url, + 'repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s' % \ + ( repository_name, repository_owner, changeset_revision ) ) + response = urllib2.urlopen( url ) + raw_text = response.read() + response.close() + if len( raw_text ) > 2: + encoded_text = json.from_json_string( raw_text ) + text = encoding_util.tool_shed_decode( encoded_text ) + else: + text = '' + return text + @web.expose + @web.require_admin + def get_updated_repository_information( self, trans, repository_id, repository_name, repository_owner, changeset_revision ): + """ + Send a request to the appropriate tool shed to retrieve the dictionary of information required to reinstall an updated revision of an + uninstalled tool shed repository. + """ + repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + url = suc.url_join( tool_shed_url, + 'repository/get_updated_repository_information?name=%s&owner=%s&changeset_revision=%s' % \ + ( repository_name, repository_owner, changeset_revision ) ) + response = urllib2.urlopen( url ) + raw_text = response.read() + response.close() + repo_information_dict = json.from_json_string( raw_text ) + return repo_information_dict def get_versions_of_tool( self, app, guid ): tool_version = shed_util.get_tool_version( app, guid ) return tool_version.get_version_ids( app, reverse=True ) @@ -1149,7 +1208,7 @@ status = kwd.get( 'status', 'done' ) tool_shed_url = kwd[ 'tool_shed_url' ] # Handle repository dependencies. - includes_repository_dependencies = util.string_as_bool( kwd.get( 'includes_repository_dependencies', False ) ) + has_repository_dependencies = util.string_as_bool( kwd.get( 'has_repository_dependencies', False ) ) install_repository_dependencies = kwd.get( 'install_repository_dependencies', '' ) # Every repository will be installed into the same tool panel section or all will be installed outside of any sections. new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) @@ -1173,12 +1232,12 @@ response.close() repo_information_dict = json.from_json_string( raw_text ) includes_tools = util.string_as_bool( repo_information_dict.get( 'includes_tools', False ) ) - includes_repository_dependencies = util.string_as_bool( repo_information_dict.get( 'includes_repository_dependencies', False ) ) + has_repository_dependencies = util.string_as_bool( repo_information_dict.get( 'has_repository_dependencies', False ) ) includes_tool_dependencies = util.string_as_bool( repo_information_dict.get( 'includes_tool_dependencies', False ) ) encoded_repo_info_dicts = util.listify( repo_information_dict.get( 'repo_info_dicts', [] ) ) repo_info_dicts = [ encoding_util.tool_shed_decode( encoded_repo_info_dict ) for encoded_repo_info_dict in encoded_repo_info_dicts ] - if ( not includes_tools and not includes_repository_dependencies ) or \ - ( ( includes_tools or includes_repository_dependencies ) and kwd.get( 'select_tool_panel_section_button', False ) ): + if ( not includes_tools and not has_repository_dependencies ) or \ + ( ( includes_tools or has_repository_dependencies ) and kwd.get( 'select_tool_panel_section_button', False ) ): install_repository_dependencies = CheckboxField.is_checked( install_repository_dependencies ) if includes_tools: shed_tool_conf = kwd[ 'shed_tool_conf' ] @@ -1241,7 +1300,7 @@ for tsr in created_or_updated_tool_shed_repositories: tool_panel_section_keys.append( tool_panel_section_key ) new_kwd = dict( includes_tools=includes_tools, - includes_repository_dependencies=includes_repository_dependencies, + has_repository_dependencies=has_repository_dependencies, install_repository_dependencies=install_repository_dependencies, includes_tool_dependencies=includes_tool_dependencies, install_tool_dependencies=install_tool_dependencies, @@ -1331,7 +1390,7 @@ includes_tools=includes_tools, includes_tool_dependencies=includes_tool_dependencies, install_tool_dependencies_check_box=install_tool_dependencies_check_box, - includes_repository_dependencies=includes_repository_dependencies, + has_repository_dependencies=has_repository_dependencies, install_repository_dependencies_check_box=install_repository_dependencies_check_box, new_tool_panel_section=new_tool_panel_section, containers_dict=containers_dict, @@ -1364,7 +1423,7 @@ tool_panel_section_key = None tool_panel_section_keys = [] metadata = tool_shed_repository.metadata - # Keep track of tool dependencies define dfor the current repository or those defined for any of it's repository dependencies. + # Keep track of tool dependencies defined for the current repository or those defined for any of it's repository dependencies. includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies if tool_shed_repository.includes_tools: # Handle the selected tool panel location for loading tools included in the tool shed repository. @@ -1381,7 +1440,7 @@ tool_shed_repository.installed_changeset_revision, tool_shed_repository.ctx_rev, repository_clone_url, - tool_shed_repository.metadata, + metadata, trans.model.ToolShedRepository.installation_status.NEW, tool_shed_repository.installed_changeset_revision, tool_shed_repository.owner, @@ -1402,6 +1461,10 @@ changeset_revision=tool_shed_repository.changeset_revision ) else: repository_dependencies = None + if metadata: + tool_dependencies = metadata.get( 'tool_dependencies', None ) + else: + tool_dependencies = None repo_info_dict = suc.create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, changeset_revision=tool_shed_repository.changeset_revision, @@ -1410,15 +1473,15 @@ repository_name=tool_shed_repository.name, repository=None, repository_metadata=None, - metadata=metadata, + tool_dependencies=tool_dependencies, repository_dependencies=repository_dependencies ) repo_info_dicts.append( repo_info_dict ) # Make sure all tool_shed_repository records exist. created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \ - shed_util.create_repository_dependency_objects( trans, - tool_path, - tool_shed_url, - repo_info_dicts, + shed_util.create_repository_dependency_objects( trans=trans, + tool_path=tool_path, + tool_shed_url=tool_shed_url, + repo_info_dicts=repo_info_dicts, reinstalling=True, install_repository_dependencies=install_repository_dependencies, no_changes_checked=no_changes_checked, @@ -1472,40 +1535,62 @@ @web.expose @web.require_admin def reselect_tool_panel_section( self, trans, **kwd ): - """Select or change the tool panel section to contain the tools included in the tool shed repositories being reinstalled.""" + """ + Select or change the tool panel section to contain the tools included in the tool shed repository being reinstalled. If there are updates + available for the repository in the tool shed, the tool_dependencies and repository_dependencies associated with the updated changeset revision + will have been retrieved from the tool shed and passed in the received kwd. In this case, the stored tool shed repository metqdata from the + Galaxy database will not be used since it is outdated. + """ message = '' - repository_id = kwd[ 'id' ] + repository_id = kwd.get( 'id', None ) + latest_changeset_revision = kwd.get( 'latest_changeset_revision', None ) + latest_ctx_rev = kwd.get( 'latest_ctx_rev', None ) tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository ) metadata = tool_shed_repository.metadata tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) - ctx_rev = suc.get_ctx_rev( tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) - repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository ) tool_path, relative_install_dir = tool_shed_repository.get_tool_relative_path( trans.app ) - repository_dependencies = self.get_repository_dependencies( trans=trans, - repository_id=repository_id, - repository_name=tool_shed_repository.name, - repository_owner=tool_shed_repository.owner, - changeset_revision=tool_shed_repository.changeset_revision ) - if repository_dependencies: - includes_repository_dependencies = True + if latest_changeset_revision and latest_ctx_rev: + # There are updates available in the tool shed for the repository, so use the receieved dependency information which was retrieved from + # the tool shed. + encoded_updated_repo_info_dict = kwd.get( 'updated_repo_info_dict', None ) + updated_repo_info_dict = encoding_util.tool_shed_decode( encoded_updated_repo_info_dict ) + readme_files_dict = updated_repo_info_dict.get( 'readme_files_dict', None ) + includes_tools = updated_repo_info_dict.get( 'includes_tools', False ) + has_repository_dependencies = updated_repo_info_dict.get( 'has_repository_dependencies', False ) + includes_tool_dependencies = updated_repo_info_dict.get( 'includes_tool_dependencies', False ) + repo_info_dict = updated_repo_info_dict[ 'repo_info_dict' ] else: - includes_repository_dependencies = False - includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies - repo_info_dict = suc.create_repo_info_dict( trans=trans, - repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.changeset_revision, - ctx_rev=ctx_rev, - repository_owner=tool_shed_repository.owner, - repository_name=tool_shed_repository.name, - repository=None, - repository_metadata=None, - metadata=metadata, - repository_dependencies=repository_dependencies ) - if includes_repository_dependencies: - # Discover all repository dependencies and retrieve information for installing them. - required_repo_info_dicts = shed_util.get_required_repo_info_dicts( tool_shed_url, util.listify( repo_info_dict ) ) + # There are no updates available from the tool shed for the repository, so use it's locally stored metadata. + if metadata: + readme_files_dict = suc.build_readme_files_dict( metadata ) + tool_dependencies = metadata.get( 'tool_dependencies', None ) + else: + readme_files_dict = None + tool_dependencies = None + includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies + repository_dependencies = self.get_repository_dependencies( trans=trans, + repository_id=repository_id, + repository_name=tool_shed_repository.name, + repository_owner=tool_shed_repository.owner, + changeset_revision=tool_shed_repository.changeset_revision ) + repo_info_dict = suc.create_repo_info_dict( trans=trans, + repository_clone_url=repository_clone_url, + changeset_revision=tool_shed_repository.changeset_revision, + ctx_rev=tool_shed_repository.ctx_rev, + repository_owner=tool_shed_repository.owner, + repository_name=tool_shed_repository.name, + repository=None, + repository_metadata=None, + tool_dependencies=tool_dependencies, + repository_dependencies=repository_dependencies ) + repository_name, repository_owner, changeset_revision, includes_tool_dependencies, installed_repository_dependencies, \ + missing_repository_dependencies, installed_tool_dependencies, missing_tool_dependencies = \ + shed_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) + if installed_repository_dependencies or missing_repository_dependencies: + has_repository_dependencies = True else: - required_repo_info_dicts = None + has_repository_dependencies = False # Get the location in the tool panel in which the tool was originally loaded. if 'tool_panel_section' in metadata: tool_panel_dict = metadata[ 'tool_panel_section' ] @@ -1533,14 +1618,14 @@ message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % tool_shed_repository.name message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section. " status = 'warning' - # Populate the containers_dict from the metadata for the tool shed repository we're reinstalling, but make sure to include tool dependencies defined for - # all of the repository's repository dependencies. - containers_dict = shed_util.populate_containers_dict_from_repository_metadata( trans=trans, - tool_shed_url=tool_shed_url, - tool_path=tool_path, - repository=tool_shed_repository, - reinstalling=True, - required_repo_info_dicts=required_repo_info_dicts ) + containers_dict = shed_util.populate_containers_dict_for_new_install( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + readme_files_dict=readme_files_dict, + installed_repository_dependencies=installed_repository_dependencies, + missing_repository_dependencies=missing_repository_dependencies, + installed_tool_dependencies=installed_tool_dependencies, + missing_tool_dependencies=missing_tool_dependencies ) # Since we're reinstalling we'll merge the list of missing repository dependencies into the list of installed repository dependencies since each displayed # repository dependency will display a status, whether installed or missing. containers_dict = suc.merge_missing_repository_dependencies_to_installed_container( containers_dict ) @@ -1561,7 +1646,7 @@ no_changes_check_box=no_changes_check_box, original_section_name=original_section_name, includes_tool_dependencies=includes_tool_dependencies, - includes_repository_dependencies=includes_repository_dependencies, + has_repository_dependencies=has_repository_dependencies, install_repository_dependencies_check_box=install_repository_dependencies_check_box, install_tool_dependencies_check_box=install_tool_dependencies_check_box, containers_dict=containers_dict, diff -r f199b236ceb08e9588351223b6277861e9f87325 -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 templates/admin/tool_shed_repository/reselect_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako @@ -33,7 +33,7 @@ ${render_readme_section( containers_dict )} <div style="clear: both"></div> %endif - %if includes_repository_dependencies or includes_tool_dependencies: + %if has_repository_dependencies or includes_tool_dependencies: <div class="form-row"><table class="colored" width="100%"><th bgcolor="#EBD9B2">Confirm dependency installation</th> diff -r f199b236ceb08e9588351223b6277861e9f87325 -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -17,10 +17,10 @@ <% # Handle the case where an uninstalled repository encountered errors during the process of being reinstalled. In - # this case, the repository metadata is an empty dictionary, but one or both of includes_repository_dependencies + # this case, the repository metadata is an empty dictionary, but one or both of has_repository_dependencies # and includes_tool_dependencies may be True. If either of these are True but we have no metadata, we cannot install # repository dependencies on this pass. - if includes_repository_dependencies: + if has_repository_dependencies: repository_dependencies = containers_dict[ 'repository_dependencies' ] missing_repository_dependencies = containers_dict[ 'missing_repository_dependencies' ] if repository_dependencies or missing_repository_dependencies: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: inithello: Fix missing import that was breaking unit tests.
by Bitbucket 16 Jan '13

16 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f199b236ceb0/ changeset: f199b236ceb0 user: inithello date: 2013-01-16 21:14:36 summary: Fix missing import that was breaking unit tests. affected #: 1 file diff -r 3a2211dc42f15e0bd357de6abb7dca73221854c7 -r f199b236ceb08e9588351223b6277861e9f87325 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -13,7 +13,7 @@ from galaxy.datatypes import metadata from galaxy.datatypes.checkers import is_gzip from galaxy.datatypes.metadata import MetadataElement -from galaxy.datatypes.sniff import get_headers +from galaxy.datatypes.sniff import get_headers, get_test_fname from galaxy.util.json import to_json_string log = logging.getLogger(__name__) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: inithello: Tool shed functional test enhancements. Tests for installing repositories via the tool search. Tests for reviewing repository components.
by Bitbucket 16 Jan '13

16 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3a2211dc42f1/ changeset: 3a2211dc42f1 user: inithello date: 2013-01-16 19:19:45 summary: Tool shed functional test enhancements. Tests for installing repositories via the tool search. Tests for reviewing repository components. affected #: 16 files diff -r 974d7c41b8dfb7e77c6dfa24da05b31d684fd2e6 -r 3a2211dc42f15e0bd357de6abb7dca73221854c7 test/tool_shed/base/common.py --- a/test/tool_shed/base/common.py +++ b/test/tool_shed/base/common.py @@ -8,6 +8,16 @@ test_user_1_email = 'test-1(a)bx.psu.edu' test_user_1_name = 'user1' +test_user_2 = None +test_user_2_private_role = None +test_user_2_email = 'test-2(a)bx.psu.edu' +test_user_2_name = 'user2' + +test_user_3 = None +test_user_3_private_role = None +test_user_3_email = 'test-3(a)bx.psu.edu' +test_user_3_name = 'user3' + new_repository_dependencies_xml = '''<?xml version="1.0"?><repositories${description}> ${dependency_lines} diff -r 974d7c41b8dfb7e77c6dfa24da05b31d684fd2e6 -r 3a2211dc42f15e0bd357de6abb7dca73221854c7 test/tool_shed/base/test_db_util.py --- a/test/tool_shed/base/test_db_util.py +++ b/test/tool_shed/base/test_db_util.py @@ -61,6 +61,17 @@ return sa_session.query( model.Repository ) \ .filter( model.Repository.table.c.id == repository_id ) \ .first() +def get_repository_review_by_user_id_changeset_revision( user_id, repository_id, changeset_revision ): + review = sa_session.query( model.RepositoryReview ) \ + .filter( and_( model.RepositoryReview.table.c.user_id == user_id, + model.RepositoryReview.table.c.repository_id == repository_id, + model.RepositoryReview.table.c.changeset_revision == changeset_revision ) ) \ + .first() + return review +def get_role_by_name( role_name ): + return sa_session.query( model.Role ) \ + .filter( model.Role.table.c.name == role_name ) \ + .first() def get_user( email ): return sa_session.query( model.User ) \ .filter( model.User.table.c.email==email ) \ diff -r 974d7c41b8dfb7e77c6dfa24da05b31d684fd2e6 -r 3a2211dc42f15e0bd357de6abb7dca73221854c7 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -35,11 +35,19 @@ self.galaxy_tool_dependency_dir = None # os.environ.get( 'GALAXY_TEST_TOOL_DEPENDENCY_DIR' ) self.shed_tools_dict = {} self.home() + def add_repository_review_component( self, **kwd ): + url = '/repository_review/create_component?operation=create' + self.visit_url( url ) + self.submit_form( 1, 'create_component_button', **kwd ) def browse_category( self, category, strings_displayed=[], strings_not_displayed=[] ): url = '/repository/browse_valid_categories?sort=name&operation=valid_repositories_by_category&id=%s' % \ self.security.encode_id( category.id ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def browse_component_review( self, review, strings_displayed=[], strings_not_displayed=[] ): + url = '/repository_review/browse_review?id=%s' % self.security.encode_id( review.id ) + self.visit_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) def browse_repository( self, repository, strings_displayed=[], strings_not_displayed=[] ): url = '/repository/browse_repository?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) @@ -173,6 +181,23 @@ self.submit_form( form_no=1, button="create_category_button", **kwd ) return test_db_util.get_category_by_name( kwd[ 'name' ] ) def create_checkbox_query_string( self, field_name, value ): + ''' + From galaxy.web.form_builder.CheckboxField: + The hidden field is necessary because if the check box is not checked on the form, it will + not be included in the request params. The hidden field ensure that this will happen. When + parsing the request, the value 'true' in the hidden field actually means it is NOT checked. + See the is_checked() method below. The prefix is necessary in each case to ensure functional + correctness when the param is inside a conditional. + + This may look strange upon initial inspection, but see the comments in the get_html() method + above for clarification. Basically, if value is not True, then it will always be a list with + 2 input fields ( a checkbox and a hidden field ) if the checkbox is checked. If it is not + checked, then value will be only the hidden field. + + The create_checkbox_query_string method emulates the described behavior with URL query parameters. + This is currently necessary because twill does not correctly parse certain forms, so the test + method has to visit the intended form target "manually". + ''' field_value = str( value ).lower() if value: return '%s=%s&%s=%s' % ( field_name, field_value, field_name, field_value ) @@ -187,6 +212,27 @@ 'repository_dependencies.xml', filepath=filepath, commit_message='Uploaded dependency on %s.' % ', '.join( repo.name for repo in depends_on ) ) + def create_repository_review( self, repository, review_contents_dict, changeset_revision=None, copy_from=None): + strings_displayed = [] + if not copy_from: + strings_displayed.append( 'Begin your review' ) + strings_not_displayed = [] + kwd = dict() + if not changeset_revision: + changeset_revision = self.get_repository_tip( repository ) + url = '/repository_review/create_review?changeset_revision=%s&id=%s' % ( changeset_revision, self.security.encode_id( repository.id ) ) + self.visit_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + strings_displayed = [] + if copy_from: + old_changeset_revision, review_id = copy_from + strings_displayed = [ 'You have elected to create a new review', 'Select previous revision', changeset_revision ] + self.check_for_strings( strings_displayed ) + strings_displayed = [] + url = '/repository_review/create_review?changeset_revision=%s&id=%s&previous_review_id=%s' % \ + ( self.get_repository_tip( repository ), self.security.encode_id( repository.id ), self.security.encode_id( review_id ) ) + self.visit_url( url ) + self.fill_review_form( review_contents_dict, strings_displayed, strings_not_displayed ) def create_user_in_galaxy( self, cntrller='user', email='test(a)bx.psu.edu', password='testuser', username='admin-user', redirect='' ): self.visit_galaxy_url( "/user/create?cntrller=%s&use_panels=False" % cntrller ) tc.fv( '1', 'email', email ) @@ -293,6 +339,10 @@ url = '/repository/get_file_contents?file_path=%s' % os.path.join( relative_path, filename ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def display_reviewed_repositories_owned_by_user( self, strings_displayed=[], strings_not_displayed=[] ): + url = '/repository_review/reviewed_repositories_i_own' + self.visit_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) def edit_repository_categories( self, repository, categories_to_add=[], categories_to_remove=[], restore_original=True ): url = '/repository/manage_repository?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) @@ -317,6 +367,10 @@ strings_not_displayed.append( "selected>%s" % category ) tc.submit( "manage_categories_button" ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def display_repository_reviews_by_user( self, user, strings_displayed=[], strings_not_displayed=[] ): + url = '/repository_review/repository_reviews_by_user?id=%s' % self.security.encode_id( user.id ) + self.visit_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) def edit_repository_information( self, repository, **kwd ): url = '/repository/manage_repository?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) @@ -343,6 +397,21 @@ else: string = string.replace( character, replacement ) return string + def fill_review_form( self, review_contents_dict, strings_displayed=[], strings_not_displayed=[] ): + kwd = dict() + for label, contents in review_contents_dict.items(): + strings_displayed.append( label ) + if contents: + kwd[ '%s__ESEP__comment' % label ] = contents[ 'comment' ] + kwd[ '%s__ESEP__rating' % label ] = contents[ 'rating' ] + if 'private' in contents: + kwd[ '%s__ESEP__private' % label ] = contents[ 'private' ] + kwd[ '%s__ESEP__approved' % label ] = contents[ 'approved' ] + else: + kwd[ '%s__ESEP__approved' % label ] = 'not_applicable' + self.submit_form( 1, 'Workflows__ESEP__review_button', **kwd ) + strings_displayed.append( 'Reviews were saved' ) + self.check_for_strings( strings_displayed, strings_not_displayed ) def galaxy_login( self, email='test(a)bx.psu.edu', password='testuser', username='admin-user', redirect='' ): previously_created, username_taken, invalid_username = \ self.create_user_in_galaxy( email=email, password=password, username=username, redirect=redirect ) @@ -409,7 +478,7 @@ raise Exception( "Entry for repository %s missing in hgweb config file %s." % ( lhs, self.hgweb_config_manager.hgweb_config ) ) def get_repository_changelog( self, repository ): repo = hg.repository( ui.ui(), self.get_repo_path( repository ) ) - return [repo.changectx( changeset ) for changeset in repo.changelog ] + return [ ( repo.changectx( changeset ), changeset ) for changeset in repo.changelog ] def get_repository_datatypes_count( self, repository ): metadata = self.get_repository_metadata( repository )[0].metadata if 'datatypes' not in metadata: @@ -469,6 +538,22 @@ if include_invalid and 'invalid_tools' in repository_metadata.metadata: invalid_tools.append( dict( tools=repository_metadata.metadata[ 'invalid_tools' ], changeset_revision=repository_metadata.changeset_revision ) ) return valid_tools, invalid_tools + def grant_role_to_user( self, user, role ): + strings_displayed = [ self.security.encode_id( role.id ), role.name ] + strings_not_displayed = [] + self.visit_url( '/admin/roles' ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + url = '/admin/roles?operation=manage+users+and+groups&id=%s' % self.security.encode_id( role.id ) + self.visit_url( url ) + strings_displayed = [ common.test_user_1_email, common.test_user_2_email ] + self.check_for_strings( strings_displayed, strings_not_displayed ) + # As elsewhere, twill limits the possibility of submitting the form, this time due to not executing the javascript + # attached to the role selection form. Visit the action url directly with the necessary parameters. + url = '/admin/manage_users_and_groups_for_role?id=%s&in_users=%d&operation=manage+users+and+groups&role_members_edit_button=Save' % \ + ( self.security.encode_id( role.id ), user.id ) + self.visit_url( url ) + strings_displayed = [ "Role '%s' has been updated" % role.name ] + self.check_for_strings( strings_displayed, strings_not_displayed ) def grant_write_access( self, repository, usernames=[], strings_displayed=[], strings_not_displayed=[] ): self.display_manage_repository_page( repository ) tc.fv( "3", "allow_push", '-Select one' ) @@ -508,10 +593,38 @@ ( ','.join( util.listify( repository_ids ) ), encoded_kwd, reinstalling ) self.visit_galaxy_url( url ) return util.listify( repository_ids ) + def install_repositories_from_search_results( self, repositories, strings_displayed=[], strings_not_displayed=[], **kwd ): + ''' + Normally, it would be possible to check the appropriate boxes in the search results, and click the install button. This works + in a browser, but Twill manages to lose the 'toolshedgalaxyurl' cookie between one page and the next, so it's necessary to work + around this by explicitly visiting the prepare_for_install method on the Galaxy side. + ''' + url = '/admin_toolshed/prepare_for_install?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \ + ( self.url, ','.join( self.security.encode_id( repository.id ) for repository in repositories ), \ + ','.join( self.get_repository_tip( repository ) for repository in repositories ) ) + self.visit_galaxy_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + if 'install_tool_dependencies' in self.last_page(): + form = tc.browser.get_form( 'select_tool_panel_section' ) + checkbox = form.find_control( id="install_tool_dependencies" ) + checkbox.disabled = False + if 'install_tool_dependencies' in kwd: + install_tool_dependencies = kwd[ 'install_tool_dependencies' ] + del kwd[ 'install_tool_dependencies' ] + else: + install_tool_dependencies = False + if install_tool_dependencies: + checkbox.selected = True + else: + checkbox.selected = False + self.submit_form( 1, 'select_tool_panel_section_button', **kwd ) + repository_ids = self.initiate_installation_process() + self.wait_for_repository_installation( repository_ids ) def install_repository( self, name, owner, category_name, install_tool_dependencies=False, install_repository_dependencies=True, changeset_revision=None, strings_displayed=[], strings_not_displayed=[], preview_strings_displayed=[], - post_submit_strings_displayed=[], new_tool_panel_section=None, **kwd ): + post_submit_strings_displayed=[], new_tool_panel_section=None, includes_tools=True, + **kwd ): self.browse_tool_shed( url=self.url ) self.browse_category( test_db_util.get_category_by_name( category_name ) ) self.preview_repository_in_tool_shed( name, owner, strings_displayed=preview_strings_displayed ) @@ -539,8 +652,9 @@ kwd[ 'shed_tool_conf' ] = self.shed_tool_conf if new_tool_panel_section: kwd[ 'new_tool_panel_section' ] = new_tool_panel_section - self.submit_form( 1, 'select_tool_panel_section_button', **kwd ) - self.check_for_strings( post_submit_strings_displayed, strings_not_displayed ) + if includes_tools: + self.submit_form( 1, 'select_tool_panel_section_button', **kwd ) + self.check_for_strings( post_submit_strings_displayed, strings_not_displayed ) repository_ids = self.initiate_installation_process( new_tool_panel_section=new_tool_panel_section ) self.wait_for_repository_installation( repository_ids ) def load_invalid_tool_page( self, repository, tool_xml, changeset_revision, strings_displayed=[], strings_not_displayed=[] ): @@ -563,6 +677,10 @@ ( self.security.encode_id( metadata.id ), tool_shed_encode( workflow_name ) ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def manage_review_components( self, strings_displayed=[], strings_not_displayed=[] ): + url = '/repository_review/manage_components' + self.visit_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) def preview_repository_in_tool_shed( self, name, owner, changeset_revision=None, strings_displayed=[], strings_not_displayed=[] ): repository = test_db_util.get_repository_by_name_and_owner( name, owner ) if not changeset_revision: @@ -587,31 +705,19 @@ install_repository_dependencies=True, install_tool_dependencies=False, no_changes=True, - new_tool_panel_section='' ): + new_tool_panel_section='', + strings_displayed=[], + strings_not_displayed=[] ): url = '/admin_toolshed/reselect_tool_panel_section?id=%s' % self.security.encode_id( installed_repository.id ) self.visit_galaxy_url( url ) - # From galaxy.web.form_builder.CheckboxField: - # The hidden field is necessary because if the check box is not checked on the form, it will - # not be included in the request params. The hidden field ensure that this will happen. When - # parsing the request, the value 'true' in the hidden field actually means it is NOT checked. - # See the is_checked() method below. The prefix is necessary in each case to ensure functional - # correctness when the param is inside a conditional. - # - # This may look strange upon initial inspection, but see the comments in the get_html() method - # above for clarification. Basically, if value is not True, then it will always be a list with - # 2 input fields ( a checkbox and a hidden field ) if the checkbox is checked. If it is not - # checked, then value will be only the hidden field. - # - # The create_checkbox_query_string method emulates the described behavior with URL query parameters. - # This is currently necessary because twill does not correctly parse the reselect tool panel section - # form, so the test method has to visit the intended form target "manually". + self.check_for_strings( strings_displayed, strings_not_displayed=[] ) repo_dependencies = self.create_checkbox_query_string( field_name='install_repository_dependencies', value=install_repository_dependencies ) tool_dependencies = self.create_checkbox_query_string( field_name='install_tool_dependencies', value=install_tool_dependencies ) encoded_repository_id = self.security.encode_id( installed_repository.id ) url = '/admin_toolshed/reinstall_repository?id=%s&%s&%s&no_changes=%s&new_tool_panel_section=%s' % \ ( encoded_repository_id, repo_dependencies, tool_dependencies, str( no_changes ), new_tool_panel_section ) self.visit_galaxy_url( url ) - # Then manually initiate the install process, as with installing a repository. See comments in the + # Manually initiate the install process, as with installing a repository. See comments in the # initiate_installation_process method for details. repository_ids = self.initiate_installation_process( install_tool_dependencies, install_repository_dependencies, @@ -639,13 +745,28 @@ url = '/repository/reset_all_metadata?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) self.check_for_strings( [ 'All repository metadata has been reset.' ] ) + def review_repository( self, repository, review_contents_dict, user=None, changeset_revision=None ): + strings_displayed = [] + strings_not_displayed = [] + kwd = dict() + if not changeset_revision: + changeset_revision = self.get_repository_tip( repository ) + if user: + review = test_db_util.get_repository_review_by_user_id_changeset_revision( user.id, repository.id, changeset_revision ) + url = '/repository_review/edit_review?id=%s' % self.security.encode_id( review.id ) + self.visit_url( url ) + self.fill_review_form( review_contents_dict, strings_displayed, strings_not_displayed ) def revoke_write_access( self, repository, username ): url = '/repository/manage_repository?user_access_button=Remove&id=%s&remove_auth=%s' % \ ( self.security.encode_id( repository.id ), username ) self.visit_url( url ) - def search_for_valid_tools( self, search_fields={}, exact_matches=False, strings_displayed=[], strings_not_displayed=[] ): + def search_for_valid_tools( self, search_fields={}, exact_matches=False, strings_displayed=[], strings_not_displayed=[], from_galaxy=False ): + if from_galaxy: + galaxy_url = '?galaxy_url=%s' % self.galaxy_url + else: + galaxy_url = '' for field_name, search_string in search_fields.items(): - url = '/repository/find_tools' + url = '/repository/find_tools%s' % galaxy_url self.visit_url( url ) tc.fv( "1", "exact_matches", exact_matches ) tc.fv( "1", field_name, search_string ) @@ -746,6 +867,17 @@ found = True break assert found, 'No entry for %s in %s.' % ( data_table, self.shed_tool_data_table_conf ) + def verify_repository_reviews( self, repository, reviewer=None, strings_displayed=[], strings_not_displayed=[] ): + changeset_revision = self.get_repository_tip( repository ) + # Verify that the currently logged in user has a repository review for the specified repository, reviewer, and changeset revision. + strings_displayed=[ repository.name, reviewer.username, changeset_revision ] + self.display_reviewed_repositories_owned_by_user( strings_displayed=strings_displayed ) + # Verify that the reviewer has reviewed the specified repository's changeset revision. + strings_displayed=[ repository.name, repository.description, changeset_revision ] + self.display_repository_reviews_by_user( reviewer, strings_displayed=strings_displayed ) + # Load the review and check for the components passed in strings_displayed. + review = test_db_util.get_repository_review_by_user_id_changeset_revision( reviewer.id, repository.id, changeset_revision ) + self.browse_component_review( review, strings_displayed=strings_displayed ) def verify_tool_metadata_for_installed_repository( self, installed_repository, strings_displayed=[], strings_not_displayed=[] ): repository_id = self.security.encode_id( installed_repository.id ) for tool in installed_repository.metadata[ 'tools' ]: diff -r 974d7c41b8dfb7e77c6dfa24da05b31d684fd2e6 -r 3a2211dc42f15e0bd357de6abb7dca73221854c7 test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -6,7 +6,7 @@ repository_long_description = "Long description of Galaxy's filtering tool for test 0000" class TestBasicRepositoryFeatures( ShedTwillTestCase ): - + '''Test core repository features.''' def test_0000_initiate_users( self ): """Create necessary user accounts and login as an admin user.""" self.login( email=common.test_user_1_email, username=common.test_user_1_name ) diff -r 974d7c41b8dfb7e77c6dfa24da05b31d684fd2e6 -r 3a2211dc42f15e0bd357de6abb7dca73221854c7 test/tool_shed/functional/test_0040_repository_circular_dependencies.py --- a/test/tool_shed/functional/test_0040_repository_circular_dependencies.py +++ b/test/tool_shed/functional/test_0040_repository_circular_dependencies.py @@ -10,7 +10,7 @@ filtering_repository_long_description = "Long description of Galaxy's filtering tool" class TestRepositoryCircularDependencies( ShedTwillTestCase ): - '''Verify that the code correctly handles circular dependencies.''' + '''Verify that the code correctly displays repositories with circular repository dependencies.''' def test_0000_initiate_users( self ): """Create necessary user accounts.""" self.logout() diff -r 974d7c41b8dfb7e77c6dfa24da05b31d684fd2e6 -r 3a2211dc42f15e0bd357de6abb7dca73221854c7 test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py --- a/test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py +++ b/test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py @@ -169,6 +169,12 @@ freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) bismark_repository = test_db_util.get_repository_by_name_and_owner( bismark_repository_name, common.test_user_1_name ) dependency_xml_path = self.generate_temp_path( 'test_0050', additional_paths=[ 'freebayes' ] ) + # convert_chars depends on column_maker + # column_maker depends on convert_chars + # emboss depends on emboss_datatypes + # emboss_datatypes depends on bismark + # freebayes depends on freebayes, emboss, emboss_datatypes, and column_maker + # filtering depends on emboss self.create_repository_dependency( convert_repository, depends_on=[ column_repository ], filepath=dependency_xml_path ) self.create_repository_dependency( column_repository, depends_on=[ convert_repository ], filepath=dependency_xml_path ) self.create_repository_dependency( emboss_datatypes_repository, depends_on=[ bismark_repository ], filepath=dependency_xml_path ) diff -r 974d7c41b8dfb7e77c6dfa24da05b31d684fd2e6 -r 3a2211dc42f15e0bd357de6abb7dca73221854c7 test/tool_shed/functional/test_0060_workflows.py --- a/test/tool_shed/functional/test_0060_workflows.py +++ b/test/tool_shed/functional/test_0060_workflows.py @@ -8,6 +8,7 @@ workflow_name = 'Workflow for 0060_filter_workflow_repository' class TestToolShedWorkflowFeatures( ShedTwillTestCase ): + '''Test valid and invalid workflows.''' def test_0000_initiate_users( self ): """Create necessary user accounts and login as an admin user.""" self.logout() @@ -39,7 +40,8 @@ workflow = file( self.get_filename( 'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga' ), 'r' ).read() workflow = workflow.replace( '__TEST_TOOL_SHED_URL__', self.url.replace( 'http://', '' ) ) workflow_filepath = self.generate_temp_path( 'test_0060', additional_paths=[ 'filtering_workflow' ] ) - os.makedirs( workflow_filepath ) + if not os.path.exists( workflow_filepath ): + os.makedirs( workflow_filepath ) file( os.path.join( workflow_filepath, workflow_filename ), 'w+' ).write( workflow ) self.upload_file( repository, workflow_filename, diff -r 974d7c41b8dfb7e77c6dfa24da05b31d684fd2e6 -r 3a2211dc42f15e0bd357de6abb7dca73221854c7 test/tool_shed/functional/test_0090_tool_search.py --- /dev/null +++ b/test/tool_shed/functional/test_0090_tool_search.py @@ -0,0 +1,171 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +emboss_datatypes_repository_name = 'emboss_datatypes_0090' +emboss_datatypes_repository_description = "Datatypes for emboss" +emboss_datatypes_repository_long_description = "Long description of Emboss' datatypes" + +emboss_repository_name = 'emboss_0090' +emboss_repository_description = "Galaxy's emboss tool" +emboss_repository_long_description = "Long description of Galaxy's emboss tool" + +filtering_repository_name = 'filtering_0090' +filtering_repository_description = "Galaxy's filtering tool" +filtering_repository_long_description = "Long description of Galaxy's filtering tool" + +freebayes_repository_name = 'freebayes_0090' +freebayes_repository_description = "Galaxy's freebayes tool" +freebayes_repository_long_description = "Long description of Galaxy's freebayes tool" + +bwa_base_repository_name = 'bwa_base_0090' +bwa_base_repository_description = "BWA Base" +bwa_base_repository_long_description = "NT space mapping with BWA" + +bwa_color_repository_name = 'bwa_color_0090' +bwa_color_repository_description = "BWA Color" +bwa_color_repository_long_description = "Color space mapping with BWA" + +category_name = 'Test 0090 Tool Search And Installation' +category_description = 'Test 0090 Tool Search And Installation' + +class TestRepositoryCircularDependenciesAgain( ShedTwillTestCase ): + '''Test more features related to repository dependencies.''' + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_bwa_base_repository( self ): + '''Create and populate bwa_base_0090.''' + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=bwa_base_repository_name, + description=bwa_base_repository_description, + long_description=bwa_base_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + 'bwa/bwa_base.tar', + strings_displayed=[], + commit_message='Uploaded bwa_base.tar.' ) + def test_0010_create_bwa_color_repository( self ): + '''Create and populate bwa_color_0090.''' + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=bwa_color_repository_name, + description=bwa_color_repository_description, + long_description=bwa_color_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + 'bwa/bwa_color.tar', + strings_displayed=[], + commit_message='Uploaded bwa_color.tar.' ) + def test_0015_create_emboss_datatypes_repository( self ): + '''Create and populate emboss_datatypes_0090.''' + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=emboss_datatypes_repository_name, + description=emboss_datatypes_repository_description, + long_description=emboss_datatypes_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + 'emboss/datatypes/datatypes_conf.xml', + strings_displayed=[], + commit_message='Uploaded datatypes_conf.xml.' ) + def test_0020_create_emboss_repository( self ): + '''Create and populate emboss_0090.''' + category = self.create_category( name=category_name, description=category_description ) + repository = self.get_or_create_repository( name=emboss_repository_name, + description=emboss_repository_description, + long_description=emboss_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + 'emboss/emboss.tar', + strings_displayed=[], + commit_message='Uploaded tool tarball.' ) + datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) + repository_dependencies_path = self.generate_temp_path( 'test_0090', additional_paths=[ 'emboss' ] ) + self.generate_repository_dependency_xml( [ datatypes_repository ], + self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), + dependency_description='Emboss depends on the emboss_datatypes repository.' ) + self.upload_file( repository, + 'repository_dependencies.xml', + filepath=repository_dependencies_path, + commit_message='Uploaded dependency on emboss_datatypes.' ) + def test_0025_create_filtering_repository( self ): + '''Create and populate filtering_0090.''' + category = self.create_category( name=category_name, description=category_description ) + filtering_repository = self.get_or_create_repository( name=filtering_repository_name, + description=filtering_repository_description, + long_description=filtering_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( filtering_repository, + 'filtering/filtering_1.1.0.tar', + strings_displayed=[], + commit_message='Uploaded filtering.tar.' ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + repository_dependencies_path = self.generate_temp_path( 'test_0090', additional_paths=[ 'filtering' ] ) + self.generate_repository_dependency_xml( [ emboss_repository ], + self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), + dependency_description='Filtering depends on the emboss repository.' ) + self.upload_file( filtering_repository, + 'repository_dependencies.xml', + filepath=repository_dependencies_path, + commit_message='Uploaded dependency on emboss.' ) + def test_0030_create_freebayes_repository( self ): + '''Create and populate freebayes_0090.''' + category = self.create_category( name=category_name, description=category_description ) + repository = self.get_or_create_repository( name=freebayes_repository_name, + description=freebayes_repository_description, + long_description=freebayes_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + 'freebayes/freebayes.tar', + strings_displayed=[], + commit_message='Uploaded freebayes.tar.' ) + def test_0035_create_and_upload_dependency_definitions( self ): + '''Create and upload repository dependency definitions.''' + bwa_color_repository = test_db_util.get_repository_by_name_and_owner( bwa_color_repository_name, common.test_user_1_name ) + bwa_base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + dependency_xml_path = self.generate_temp_path( 'test_0090', additional_paths=[ 'freebayes' ] ) + self.create_repository_dependency( emboss_repository, depends_on=[ emboss_datatypes_repository ], filepath=dependency_xml_path ) + self.create_repository_dependency( filtering_repository, depends_on=[ freebayes_repository ], filepath=dependency_xml_path ) + self.create_repository_dependency( bwa_base_repository, depends_on=[ emboss_repository ], filepath=dependency_xml_path ) + self.create_repository_dependency( bwa_color_repository, depends_on=[ filtering_repository ], filepath=dependency_xml_path ) + def test_0040_verify_repository_dependencies( self ): + '''Verify the generated dependency structure.''' + bwa_color_repository = test_db_util.get_repository_by_name_and_owner( bwa_color_repository_name, common.test_user_1_name ) + bwa_base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + self.check_repository_dependency( emboss_repository, emboss_datatypes_repository ) + self.check_repository_dependency( filtering_repository, freebayes_repository ) + self.check_repository_dependency( bwa_base_repository, emboss_repository ) + self.check_repository_dependency( bwa_color_repository, filtering_repository ) diff -r 974d7c41b8dfb7e77c6dfa24da05b31d684fd2e6 -r 3a2211dc42f15e0bd357de6abb7dca73221854c7 test/tool_shed/functional/test_0400_repository_component_reviews.py --- /dev/null +++ b/test/tool_shed/functional/test_0400_repository_component_reviews.py @@ -0,0 +1,279 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +repository_name = 'filtering_0400' +repository_description = 'Galaxy filtering tool for test 0400' +repository_long_description = 'Long description of Galaxy filtering tool for test 0400' + +class TestRepositoryComponentReviews( ShedTwillTestCase ): + '''Test repository component review features.''' + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin user.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + test_user_2 = test_db_util.get_user( common.test_user_2_email ) + assert test_user_2 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_2_email + test_user_2_private_role = test_db_util.get_private_role( test_user_2 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_grant_reviewer_role( self ): + '''Grant the repository reviewer role to test_user_2.''' + reviewer_role = test_db_util.get_role_by_name( 'Repository Reviewer' ) + test_user_2 = test_db_util.get_user( common.test_user_2_email ) + self.grant_role_to_user( test_user_2, reviewer_role ) + def test_0010_verify_repository_review_components( self ): + '''Ensure that the required review components exist.''' + strings_not_displayed=[ 'Repository dependencies' ] + self.manage_review_components( strings_not_displayed=strings_not_displayed ) + self.add_repository_review_component( name='Repository dependencies', + description='Repository dependencies defined in a file named repository_dependencies.xml included in the repository' ) + strings_displayed=[ 'Data types', 'Functional tests', 'README', 'Repository dependencies', 'Tool dependencies', 'Tools', 'Workflows' ] + self.manage_review_components( strings_displayed=strings_displayed ) + def test_0015_create_repository( self ): + """Create and populate the filtering repository""" + category = self.create_category( name='Test 0400 Repository Component Reviews', description='Test 0400 Repository Component Reviews' ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + strings_displayed = [ 'Repository %s' % "'%s'" % repository_name, + 'Repository %s has been created' % "'%s'" % repository_name ] + repository = self.get_or_create_repository( name=repository_name, + description=repository_description, + long_description=repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=strings_displayed ) + self.upload_file( repository, 'filtering/filtering_1.1.0.tar', commit_message="Uploaded filtering 1.1.0" ) + def test_0020_review_initial_revision_data_types( self ): + '''Review the datatypes component for the current tip revision.''' + # Review this revision: + # Data types (N/A) + # Functional tests (One star, comment 'functional tests missing') + # README (N/A) + # Repository dependencies (N/A) + # Tool dependencies (N/A) + # Tools (5 stars, good review) + # Workflows (N/A) + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + review_contents_dict = { 'Data types': dict() } + self.create_repository_review( repository, review_contents_dict ) + def test_0025_verify_datatype_review( self ): + '''Verify that the datatypes component review displays correctly.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + strings_displayed = [ 'Data types', 'not_applicable' ] + strings_not_displayed = [ 'Functional tests', 'README', 'Repository dependencies', 'Tool dependencies', 'Tools', 'Workflows' ] + self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) + def test_0030_review_initial_revision_functional_tests( self ): + '''Review the datatypes component for the current tip revision.''' + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + review_contents_dict = { 'Functional tests': dict( rating=1, comment='Functional tests missing', approved='no', private='yes' ) } + self.review_repository( repository, review_contents_dict, user ) +# def test_0030_verify_review_display( self ): +# '''Verify that private reviews are restricted to owner and reviewer, and non-private views are viewable by others.''' +# # Currently not implemented because third parties cannot view reviews whether they are private or not. +# self.logout() +# self.login( email=common.test_user_3_email, username=common.test_user_3_name ) + def test_0035_verify_functional_test_review( self ): + '''Verify that the datatypes component review displays correctly.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + strings_displayed=[ 'Functional tests', 'Functional tests missing', 'no' ] + strings_not_displayed = [ 'README', 'Repository dependencies', 'Tool dependencies', 'Tools', 'Workflows' ] + self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) + def test_0040_review_readme( self ): + '''Review the readme component for the current tip revision.''' + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + review_contents_dict = { 'README': dict() } + self.review_repository( repository, review_contents_dict, user ) + def test_0045_verify_readme_review( self ): + '''Verify that the datatypes component review displays correctly.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + strings_displayed=[ 'README', 'not_applicable' ] + strings_not_displayed = [ 'Repository dependencies', 'Tool dependencies', 'Tools', 'Workflows' ] + self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) + def test_0050_review_repository_dependencies( self ): + '''Review the repository dependencies component for the current tip revision.''' + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + review_contents_dict = { 'Repository dependencies': dict() } + self.review_repository( repository, review_contents_dict, user ) + def test_0055_verify_repository_dependency_review( self ): + '''Verify that the datatypes component review displays correctly.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + strings_displayed=[ 'Repository dependencies', 'not_applicable' ] + strings_not_displayed = [ 'Tool dependencies', 'Tools', 'Workflows' ] + self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) + def test_0060_review_tool_dependencies( self ): + '''Review the tool dependencies component for the current tip revision.''' + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + review_contents_dict = { 'Tool dependencies': dict() } + self.review_repository( repository, review_contents_dict, user ) + def test_0065_verify_tool_dependency_review( self ): + '''Verify that the datatypes component review displays correctly.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + strings_displayed=[ 'Tool dependencies', 'not_applicable' ] + strings_not_displayed = [ 'Tools', 'Workflows' ] + self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) + def test_0070_review_tools( self ): + '''Review the tools component for the current tip revision.''' + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + review_contents_dict = { 'Tools': dict( rating=5, comment='Excellent tool, easy to use.', approved='yes', private='no' ) } + self.review_repository( repository, review_contents_dict, test_db_util.get_user( common.test_user_2_email ) ) + def test_0075_verify_tools_review( self ): + '''Verify that the datatypes component review displays correctly.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + strings_displayed=[ 'Tools', 'yes', 'Excellent tool, easy to use.' ] + strings_not_displayed = [ 'Workflows' ] + self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) + def test_0080_review_workflows( self ): + '''Review the workflows component for the current tip revision.''' + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + review_contents_dict = { 'Workflows': dict() } + self.review_repository( repository, review_contents_dict, user ) + def test_0085_verify_workflows_review( self ): + '''Verify that the datatypes component review displays correctly.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + strings_displayed=[ 'Workflows', 'not_applicable' ] + self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) + def test_0090_upload_readme_file( self ): + '''Upload a readme file to the filtering repository.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + self.upload_file( repository, 'readme.txt', commit_message="Uploaded readme.txt" ) + def test_0095_review_new_changeset_readme_component( self ): + '''Update the filtering repository's readme component review to reflect the presence of the readme file.''' + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + # Get the changeset immediately prior to the tip, and pass it to the create review method. + changelog = self.get_repository_changelog( repository ) + changeset_revision, ctx_revision = changelog[-2] + previous_review = test_db_util.get_repository_review_by_user_id_changeset_revision( user.id, repository.id, str( changeset_revision ) ) + review_contents_dict = { 'README': dict( rating=5, comment='Clear and concise readme file, a true pleasure to read.', approved='yes', private='no' ) } + self.create_repository_review( repository, + review_contents_dict, + changeset_revision=self.get_repository_tip( repository ), + copy_from=( str( changeset_revision ), previous_review.id ) ) + def test_0100_verify_readme_review( self ): + '''Verify that the readme component review displays correctly.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + strings_displayed = [ 'README', 'yes', 'Clear and concise readme file, a true pleasure to read.' ] + self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) + def test_0105_upload_test_data( self ): + '''Upload the missing test data to the filtering repository.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + self.upload_file( repository, 'filtering/filtering_test_data.tar', commit_message="Uploaded test data." ) + def test_0110_review_new_changeset_functional_tests( self ): + '''Update the filtering repository's readme component review to reflect the presence of the readme file.''' + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + # Get the changeset immediately prior to the tip, and pass it to the create review method. + changelog = self.get_repository_changelog( repository ) + changeset_revision, ctx_revision = changelog[-2] + previous_review = test_db_util.get_repository_review_by_user_id_changeset_revision( user.id, repository.id, str( changeset_revision ) ) + review_contents_dict = { 'Functional tests': dict( rating=5, comment='A good set of functional tests.', approved='yes', private='no' ) } + self.create_repository_review( repository, + review_contents_dict, + changeset_revision=self.get_repository_tip( repository ), + copy_from=( str( changeset_revision ), previous_review.id ) ) + def test_0115_verify_functional_tests_review( self ): + '''Verify that the functional tests component review displays correctly.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + strings_displayed=[ 'Functional tests', 'yes', 'A good set of functional tests.' ] + self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) + def test_0120_upload_new_tool_version( self ): + '''Upload filtering 2.2.0 to the filtering repository.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + self.upload_file( repository, + 'filtering/filtering_2.2.0.tar', + commit_message="Uploaded filtering 2.2.0", + remove_repo_files_not_in_tar='No' ) + def test_0125_review_new_changeset_functional_tests( self ): + '''Update the filtering repository's review to apply to the new changeset with filtering 2.2.0.''' + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + # Get the changeset immediately prior to the tip, and pass it to the create review method. + changelog = self.get_repository_changelog( repository ) + changeset_revision, ctx_revision = changelog[-2] + previous_review = test_db_util.get_repository_review_by_user_id_changeset_revision( user.id, repository.id, str( changeset_revision ) ) + # Something needs to change so that the review will save. + review_contents_dict = { 'Tools': dict( rating=5, comment='Version 2.2.0 does the impossible and improves this tool.', approved='yes', private='yes' ) } + self.create_repository_review( repository, + review_contents_dict, + changeset_revision=self.get_repository_tip( repository ), + copy_from=( str( changeset_revision ), previous_review.id ) ) + def test_0135_verify_review_for_new_version( self ): + '''Verify that the reviews display correctly for this changeset revision.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + strings_displayed = [ 'Data types', 'Functional tests', 'yes', 'A good set of functional tests.', 'README', 'yes', 'Workflows', 'Tools' ] + strings_displayed.extend( [ 'Clear and concise readme file, a true pleasure to read.', 'Tool dependencies', 'not_applicable' ] ) + strings_displayed.extend( [ 'Repository dependencies', 'Version 2.2.0 does the impossible and improves this tool.' ] ) + self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) diff -r 974d7c41b8dfb7e77c6dfa24da05b31d684fd2e6 -r 3a2211dc42f15e0bd357de6abb7dca73221854c7 test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py --- a/test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py +++ b/test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py @@ -163,6 +163,12 @@ freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) bismark_repository = test_db_util.get_repository_by_name_and_owner( bismark_repository_name, common.test_user_1_name ) dependency_xml_path = self.generate_temp_path( 'test_1050', additional_paths=[ 'dependencies' ] ) + # convert_chars depends on column_maker + # column_maker depends on convert_chars + # emboss depends on emboss_datatypes + # emboss_datatypes depends on bismark + # freebayes depends on freebayes, emboss, emboss_datatypes, and column_maker + # filtering depends on emboss self.create_repository_dependency( convert_repository, depends_on=[ column_repository ], filepath=dependency_xml_path ) self.create_repository_dependency( column_repository, depends_on=[ convert_repository ], filepath=dependency_xml_path ) self.create_repository_dependency( emboss_datatypes_repository, depends_on=[ bismark_repository ], filepath=dependency_xml_path ) @@ -224,6 +230,7 @@ install_tool_dependencies=False, install_repository_dependencies=True, new_tool_panel_section='column_maker' ) + # This should result in column_maker and convert_chars being installed, and the rest never installed. installed_repositories = [ ( column_repository_name, common.test_user_1_name ), ( convert_repository_name, common.test_user_1_name ) ] uninstalled_repositories = [ ( emboss_datatypes_repository_name, common.test_user_1_name ), @@ -244,6 +251,7 @@ new_tool_panel_section='emboss_5_0050' ) if running_standalone: assert original_datatypes < self.get_datatypes_count(), 'Installing a repository that depends on emboss_datatypes did not add datatypes.' + # Now we have emboss_datatypes, emboss, bismark, column_maker, and convert_chars installed, filtering and freebayes never installed. installed_repositories = [ ( emboss_datatypes_repository_name, common.test_user_1_name ), ( column_repository_name, common.test_user_1_name ), ( emboss_repository_name, common.test_user_1_name ), @@ -258,6 +266,7 @@ repository = test_db_util.get_installed_repository_by_name_owner( emboss_datatypes_repository_name, common.test_user_1_name ) self.uninstall_repository( repository, remove_from_disk=False ) assert original_datatypes > self.get_datatypes_count(), 'Deactivating emboss_datatypes did not remove datatypes.' + # Now we have emboss, bismark, column_maker, and convert_chars installed, filtering and freebayes never installed, and emboss_datatypes deactivated. installed_repositories = [ ( column_repository_name, common.test_user_1_name ), ( emboss_repository_name, common.test_user_1_name ), ( convert_repository_name, common.test_user_1_name ), @@ -276,6 +285,8 @@ self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) test_db_util.ga_refresh( repository ) self.check_galaxy_repository_tool_panel_section( repository, 'emboss_5_0050' ) + # Now we have bismark, column_maker, and convert_chars installed, filtering and freebayes never installed, emboss_datatypes deactivated, + # and emboss uninstalled. installed_repositories = [ ( column_repository_name, common.test_user_1_name ), ( convert_repository_name, common.test_user_1_name ), ( bismark_repository_name, common.test_user_1_name ) ] @@ -303,6 +314,8 @@ datatypes_repository.name, datatypes_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) + # Installing freebayes should automatically reinstall emboss and reactivate emboss_datatypes. + # Now column_maker, convert_chars, emboss, emboss_datatypes, freebayes, and bismark should be installed. installed_repositories = [ ( column_repository_name, common.test_user_1_name ), ( emboss_datatypes_repository_name, common.test_user_1_name ), ( emboss_repository_name, common.test_user_1_name ), diff -r 974d7c41b8dfb7e77c6dfa24da05b31d684fd2e6 -r 3a2211dc42f15e0bd357de6abb7dca73221854c7 test/tool_shed/functional/test_1070_invalid_tool.py --- a/test/tool_shed/functional/test_1070_invalid_tool.py +++ b/test/tool_shed/functional/test_1070_invalid_tool.py @@ -7,7 +7,7 @@ category_name = 'Test 0070 Invalid Tool Revisions' class TestFreebayesRepository( ShedTwillTestCase ): - '''Testing freebayes with tool data table entries, .loc files, and tool dependencies.''' + '''Test repository with multiple revisions with invalid tools.''' def test_0000_create_or_login_admin_user( self ): """Create necessary user accounts and login as an admin user.""" self.galaxy_logout() diff -r 974d7c41b8dfb7e77c6dfa24da05b31d684fd2e6 -r 3a2211dc42f15e0bd357de6abb7dca73221854c7 test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py --- a/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py +++ b/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py @@ -17,7 +17,7 @@ running_standalone = False class TestRepositoryDependencies( ShedTwillTestCase ): - '''Testing freebayes with tool data table entries, .loc files, and tool dependencies.''' + '''Testing uninstalling and reinstalling repository dependencies, and setting tool panel sections.''' def test_0000_create_or_login_admin_user( self ): """Create necessary user accounts and login as an admin user.""" self.galaxy_logout() diff -r 974d7c41b8dfb7e77c6dfa24da05b31d684fd2e6 -r 3a2211dc42f15e0bd357de6abb7dca73221854c7 test/tool_shed/functional/test_1085_repository_dependency_handling.py --- a/test/tool_shed/functional/test_1085_repository_dependency_handling.py +++ b/test/tool_shed/functional/test_1085_repository_dependency_handling.py @@ -15,7 +15,7 @@ log = logging.getLogger( __name__ ) class TestRepositoryDependencies( ShedTwillTestCase ): - '''Testing freebayes with tool data table entries, .loc files, and tool dependencies.''' + '''Testing the behavior of repository dependencies with tool panel sections.''' def test_0000_create_or_login_admin_user( self ): """Create necessary user accounts and login as an admin user.""" self.galaxy_logout() diff -r 974d7c41b8dfb7e77c6dfa24da05b31d684fd2e6 -r 3a2211dc42f15e0bd357de6abb7dca73221854c7 test/tool_shed/functional/test_1090_install_tool_from_tool_search.py --- /dev/null +++ b/test/tool_shed/functional/test_1090_install_tool_from_tool_search.py @@ -0,0 +1,266 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +emboss_datatypes_repository_name = 'emboss_datatypes_0090' +emboss_datatypes_repository_description = "Datatypes for emboss" +emboss_datatypes_repository_long_description = "Long description of Emboss' datatypes" + +emboss_repository_name = 'emboss_0090' +emboss_repository_description = "Galaxy's emboss tool" +emboss_repository_long_description = "Long description of Galaxy's emboss tool" + +filtering_repository_name = 'filtering_0090' +filtering_repository_description = "Galaxy's filtering tool" +filtering_repository_long_description = "Long description of Galaxy's filtering tool" + +freebayes_repository_name = 'freebayes_0090' +freebayes_repository_description = "Galaxy's freebayes tool" +freebayes_repository_long_description = "Long description of Galaxy's freebayes tool" + +bwa_base_repository_name = 'bwa_base_0090' +bwa_base_repository_description = "BWA Base" +bwa_base_repository_long_description = "NT space mapping with BWA" + +bwa_color_repository_name = 'bwa_color_0090' +bwa_color_repository_description = "BWA Color" +bwa_color_repository_long_description = "Color space mapping with BWA" + +category_name = 'Test 0090 Tool Search And Installation' +category_description = 'Test 0090 Tool Search And Installation' + +running_standalone = False + +class TestToolSearchAndInstall( ShedTwillTestCase ): + '''Verify that the code correctly handles circular dependencies down to n levels.''' + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_bwa_base_repository( self ): + '''Create and populate bwa_base_0090.''' + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + global running_standalone + repository = self.get_or_create_repository( name=bwa_base_repository_name, + description=bwa_base_repository_description, + long_description=bwa_base_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + running_standalone = True + self.upload_file( repository, + 'bwa/bwa_base.tar', + strings_displayed=[], + commit_message='Uploaded bwa_base.tar.' ) + def test_0010_create_bwa_color_repository( self ): + '''Create and populate bwa_color_0090.''' + category = self.create_category( name=category_name, description=category_description ) + global running_standalone + repository = self.get_or_create_repository( name=bwa_color_repository_name, + description=bwa_color_repository_description, + long_description=bwa_color_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + running_standalone = True + self.upload_file( repository, + 'bwa/bwa_color.tar', + strings_displayed=[], + commit_message='Uploaded bwa_color.tar.' ) + def test_0015_create_emboss_datatypes_repository( self ): + '''Create and populate emboss_datatypes_0090.''' + category = self.create_category( name=category_name, description=category_description ) + global running_standalone + repository = self.get_or_create_repository( name=emboss_datatypes_repository_name, + description=emboss_datatypes_repository_description, + long_description=emboss_datatypes_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + running_standalone = True + self.upload_file( repository, + 'emboss/datatypes/datatypes_conf.xml', + strings_displayed=[], + commit_message='Uploaded datatypes_conf.xml.' ) + def test_0020_create_emboss_repository( self ): + '''Create and populate emboss_0090.''' + category = self.create_category( name=category_name, description=category_description ) + global running_standalone + repository = self.get_or_create_repository( name=emboss_repository_name, + description=emboss_repository_description, + long_description=emboss_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + running_standalone = True + self.upload_file( repository, + 'emboss/emboss.tar', + strings_displayed=[], + commit_message='Uploaded tool tarball.' ) + def test_0025_create_filtering_repository( self ): + '''Create and populate filtering_0090.''' + category = self.create_category( name=category_name, description=category_description ) + global running_standalone + repository = self.get_or_create_repository( name=filtering_repository_name, + description=filtering_repository_description, + long_description=filtering_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + running_standalone = True + self.upload_file( repository, + 'filtering/filtering_1.1.0.tar', + strings_displayed=[], + commit_message='Uploaded filtering.tar.' ) + def test_0030_create_freebayes_repository( self ): + '''Create and populate freebayes_0090.''' + category = self.create_category( name=category_name, description=category_description ) + global running_standalone + repository = self.get_or_create_repository( name=freebayes_repository_name, + description=freebayes_repository_description, + long_description=freebayes_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + running_standalone = True + self.upload_file( repository, + 'freebayes/freebayes.tar', + strings_displayed=[], + commit_message='Uploaded freebayes.tar.' ) + def test_0035_create_and_upload_dependency_definitions( self ): + '''Create and upload repository dependency definitions.''' + global running_standalone + if running_standalone: + bwa_color_repository = test_db_util.get_repository_by_name_and_owner( bwa_color_repository_name, common.test_user_1_name ) + bwa_base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + dependency_xml_path = self.generate_temp_path( 'test_0090', additional_paths=[ 'freebayes' ] ) + self.create_repository_dependency( emboss_repository, depends_on=[ emboss_datatypes_repository ], filepath=dependency_xml_path ) + self.create_repository_dependency( filtering_repository, depends_on=[ freebayes_repository ], filepath=dependency_xml_path ) + self.create_repository_dependency( bwa_base_repository, depends_on=[ emboss_repository ], filepath=dependency_xml_path ) + self.create_repository_dependency( bwa_color_repository, depends_on=[ filtering_repository ], filepath=dependency_xml_path ) + def test_0040_verify_repository_dependencies( self ): + '''Verify the generated dependency structure.''' + bwa_color_repository = test_db_util.get_repository_by_name_and_owner( bwa_color_repository_name, common.test_user_1_name ) + bwa_base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + self.check_repository_dependency( emboss_repository, emboss_datatypes_repository ) + self.check_repository_dependency( filtering_repository, freebayes_repository ) + self.check_repository_dependency( bwa_base_repository, emboss_repository ) + self.check_repository_dependency( bwa_color_repository, filtering_repository ) + def test_0045_install_freebayes_repository( self ): + '''Install freebayes without repository dependencies.''' + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + # After this test, the repositories should be in the following states: + # Installed: freebayes + # Never installed: filtering, emboss, emboss_datatypes, bwa_color, bwa_base + self.install_repository( freebayes_repository_name, + common.test_user_1_name, + category_name, + install_tool_dependencies=False, + install_repository_dependencies=False, + new_tool_panel_section='freebayes_1090' ) + installed_repositories = [ ( freebayes_repository_name, common.test_user_1_name ) ] + uninstalled_repositories = [ ( filtering_repository_name, common.test_user_1_name ), + ( emboss_repository_name, common.test_user_1_name ), + ( emboss_datatypes_repository_name, common.test_user_1_name ), + ( bwa_color_repository_name, common.test_user_1_name ), + ( bwa_base_repository_name, common.test_user_1_name ) ] + self.verify_installed_uninstalled_repositories( installed_repositories=installed_repositories, uninstalled_repositories=uninstalled_repositories ) + def test_0050_install_deactivate_filtering_repository( self ): + '''Install and deactivate filtering.''' + global running_standalone + original_datatypes = self.get_datatypes_count() + # After this test, the repositories should be in the following states: + # Installed: freebayes + # Deactivated: filtering + # Never installed: emboss, emboss_datatypes, bwa_color, bwa_base + self.install_repository( filtering_repository_name, + common.test_user_1_name, + category_name, + install_tool_dependencies=False, + install_repository_dependencies=False, + new_tool_panel_section='filtering_1090' ) + installed_repositories = [ ( filtering_repository_name, common.test_user_1_name ), + ( freebayes_repository_name, common.test_user_1_name ) ] + uninstalled_repositories = [ ( emboss_repository_name, common.test_user_1_name ), + ( emboss_datatypes_repository_name, common.test_user_1_name ), + ( bwa_color_repository_name, common.test_user_1_name ), + ( bwa_base_repository_name, common.test_user_1_name ) ] + self.verify_installed_uninstalled_repositories( installed_repositories=installed_repositories, uninstalled_repositories=uninstalled_repositories ) + filtering_repository = test_db_util.get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name ) + self.uninstall_repository( filtering_repository, remove_from_disk=False ) + def test_0055_install_uninstall_datatypes_repository( self ): + '''Install and uninstall emboss_datatypes.''' + # After this test, the repositories should be in the following states: + # Installed: freebayes + # Deactivated: filtering + # Uninstalled: emboss_datatypes + # Never installed: emboss, bwa_color, bwa_base + self.install_repository( emboss_datatypes_repository_name, + common.test_user_1_name, + category_name, + includes_tools=False ) + installed_repositories = [ ( emboss_datatypes_repository_name, common.test_user_1_name ), + ( freebayes_repository_name, common.test_user_1_name ) ] + uninstalled_repositories = [ ( emboss_repository_name, common.test_user_1_name ), + ( filtering_repository_name, common.test_user_1_name ), + ( bwa_color_repository_name, common.test_user_1_name ), + ( bwa_base_repository_name, common.test_user_1_name ) ] + self.verify_installed_uninstalled_repositories( installed_repositories=installed_repositories, uninstalled_repositories=uninstalled_repositories ) + datatypes_repository = test_db_util.get_installed_repository_by_name_owner( emboss_datatypes_repository_name, common.test_user_1_name ) + self.uninstall_repository( datatypes_repository, remove_from_disk=True ) + def test_0060_search_for_bwa_tools( self ): + '''Search for and install the repositories with BWA tools, and verify that this reinstalls emboss_datatypes and reactivates filtering.''' + bwa_color_repository = test_db_util.get_repository_by_name_and_owner( bwa_color_repository_name, common.test_user_1_name ) + bwa_base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + bwa_base_revision = self.get_repository_tip( bwa_base_repository ) + bwa_color_revision = self.get_repository_tip( bwa_color_repository ) + self.search_for_valid_tools( search_fields={ 'tool_id': 'bwa' }, + exact_matches=False, from_galaxy=True, + strings_displayed=[ bwa_color_repository_name, bwa_base_repository_name, bwa_base_revision, bwa_color_revision ] ) + strings_displayed=[ freebayes_repository_name, emboss_repository_name, filtering_repository_name ] + strings_displayed.extend( [ bwa_color_repository_name, bwa_base_repository_name, emboss_datatypes_repository_name ] ) + strings_displayed.extend( [ 'bwa', 'Handle', 'tool dependencies' ] ) + repositories_to_install = [ bwa_color_repository, bwa_base_repository ] + # BWA is a good candidate for testing the installation of tool dependencies, but it is a core requirement of functional + # tests that they be able to run independently of any network connection or remote data. + # + # After this test, the repositories should be in the following state: + # Installed: bwa_color, bwa_base, emboss_datatypes, emboss, filtering, freebayes + self.install_repositories_from_search_results( repositories_to_install, + install_repository_dependencies='True', + install_tool_dependencies=False, + new_tool_panel_section='bwa_1090', + strings_displayed=strings_displayed ) + + installed_repositories = [ ( emboss_repository_name, common.test_user_1_name ), + ( filtering_repository_name, common.test_user_1_name ), + ( bwa_color_repository_name, common.test_user_1_name ), + ( bwa_base_repository_name, common.test_user_1_name ), + ( emboss_datatypes_repository_name, common.test_user_1_name ), + ( freebayes_repository_name, common.test_user_1_name ) ] + uninstalled_repositories = [] + self.verify_installed_uninstalled_repositories( installed_repositories=installed_repositories, uninstalled_repositories=uninstalled_repositories ) diff -r 974d7c41b8dfb7e77c6dfa24da05b31d684fd2e6 -r 3a2211dc42f15e0bd357de6abb7dca73221854c7 test/tool_shed/test_data/bwa/bwa_base.tar Binary file test/tool_shed/test_data/bwa/bwa_base.tar has changed diff -r 974d7c41b8dfb7e77c6dfa24da05b31d684fd2e6 -r 3a2211dc42f15e0bd357de6abb7dca73221854c7 test/tool_shed/test_data/bwa/bwa_color.tar Binary file test/tool_shed/test_data/bwa/bwa_color.tar has changed Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 16 Jan '13

16 Jan '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5e710a6f1c99/ changeset: 5e710a6f1c99 user: inithello date: 2013-01-16 18:35:36 summary: Fix for removing roles from users in the tool shed. affected #: 1 file diff -r 4f01c6a8693e855da6abad43112afe7447da6e82 -r 5e710a6f1c99e56abb5eb7964cd1c673526866b2 lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -224,19 +224,20 @@ role = get_role( trans, id ) if params.get( 'role_members_edit_button', False ): in_users = [ trans.sa_session.query( trans.app.model.User ).get( x ) for x in util.listify( params.in_users ) ] - for ura in role.users: - user = trans.sa_session.query( trans.app.model.User ).get( ura.user_id ) - if user not in in_users: - # Delete DefaultUserPermissions for previously associated users that have been removed from the role - for dup in user.default_permissions: - if role == dup.role: - trans.sa_session.delete( dup ) - # Delete DefaultHistoryPermissions for previously associated users that have been removed from the role - for history in user.histories: - for dhp in history.default_permissions: - if role == dhp.role: - trans.sa_session.delete( dhp ) - trans.sa_session.flush() + if trans.webapp.name == 'galaxy': + for ura in role.users: + user = trans.sa_session.query( trans.app.model.User ).get( ura.user_id ) + if user not in in_users: + # Delete DefaultUserPermissions for previously associated users that have been removed from the role + for dup in user.default_permissions: + if role == dup.role: + trans.sa_session.delete( dup ) + # Delete DefaultHistoryPermissions for previously associated users that have been removed from the role + for history in user.histories: + for dhp in history.default_permissions: + if role == dhp.role: + trans.sa_session.delete( dhp ) + trans.sa_session.flush() in_groups = [ trans.sa_session.query( trans.app.model.Group ).get( x ) for x in util.listify( params.in_groups ) ] trans.app.security_agent.set_entity_role_associations( roles=[ role ], users=in_users, groups=in_groups ) trans.sa_session.refresh( role ) https://bitbucket.org/galaxy/galaxy-central/commits/974d7c41b8df/ changeset: 974d7c41b8df user: inithello date: 2013-01-16 18:36:19 summary: Fix server error when trying to create a component review for a repository when one already exists for that changeset revision. affected #: 1 file diff -r 5e710a6f1c99e56abb5eb7964cd1c673526866b2 -r 974d7c41b8dfb7e77c6dfa24da05b31d684fd2e6 lib/galaxy/webapps/community/controllers/repository_review.py --- a/lib/galaxy/webapps/community/controllers/repository_review.py +++ b/lib/galaxy/webapps/community/controllers/repository_review.py @@ -377,6 +377,7 @@ if repository_id: if changeset_revision: # Make sure there is not already a review of the revision by the user. + repository = suc.get_repository_in_tool_shed( trans, repository_id ) if common.get_review_by_repository_id_changeset_revision_user_id( trans=trans, repository_id=repository_id, changeset_revision=changeset_revision, @@ -384,7 +385,6 @@ message = "You have already created a review for revision <b>%s</b> of repository <b>%s</b>." % ( changeset_revision, repository.name ) status = "error" else: - repository = suc.get_repository_in_tool_shed( trans, repository_id ) # See if there are any reviews for previous changeset revisions that the user can copy. if not create_without_copying and not previous_review_id and common.has_previous_repository_reviews( trans, repository, changeset_revision ): return trans.response.send_redirect( web.url_for( controller='repository_review', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Remove spurious debugging statement.
by Bitbucket 16 Jan '13

16 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4f01c6a8693e/ changeset: 4f01c6a8693e user: natefoo date: 2013-01-16 18:30:24 summary: Remove spurious debugging statement. affected #: 1 file diff -r ee6ddbd3fcb35845239ea82c9062c4893e88c37e -r 4f01c6a8693e855da6abad43112afe7447da6e82 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -274,7 +274,6 @@ from galaxy.web.base.controller import ControllerUnavailable package = import_module( package_name ) controller_dir = package.__path__[0] - print ">>>", controller_dir, package.__path__ for fname in os.listdir( controller_dir ): if not( fname.startswith( "_" ) ) and fname.endswith( ".py" ): name = fname[:-3] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Update history functional tests for changes in f93113b
by Bitbucket 15 Jan '13

15 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ee6ddbd3fcb3/ changeset: ee6ddbd3fcb3 user: jgoecks date: 2013-01-15 23:17:32 summary: Update history functional tests for changes in f93113b affected #: 2 files diff -r 06cdf8b0b582c40fa89fc7e398fecacb3943dbfc -r ee6ddbd3fcb35845239ea82c9062c4893e88c37e test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -417,7 +417,7 @@ if active_datasets: self.check_page_for_string( 'Create</a> a new empty history' ) self.check_page_for_string( 'Construct workflow</a> from current history' ) - self.check_page_for_string( 'Clone</a> current history' ) + self.check_page_for_string( 'Copy</a> current history' ) self.check_page_for_string( 'Share</a> current history' ) self.check_page_for_string( 'Change default permissions</a> for current history' ) if histories_shared_by_others: @@ -534,13 +534,13 @@ for check_str in strings_displayed: self.check_page_for_string( check_str ) self.home() - def clone_history( self, history_id, clone_choice, strings_displayed=[], strings_displayed_after_submit=[] ): + def copy_history( self, history_id, copy_choice, strings_displayed=[], strings_displayed_after_submit=[] ): self.home() - self.visit_page( "history/clone?id=%s" % history_id ) + self.visit_page( "history/copy?id=%s" % history_id ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - tc.fv( '1', 'clone_choice', clone_choice ) - tc.submit( 'clone_choice_button' ) + tc.fv( '1', 'copy_choice', copy_choice ) + tc.submit( 'copy_choice_button' ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) self.home() diff -r 06cdf8b0b582c40fa89fc7e398fecacb3943dbfc -r ee6ddbd3fcb35845239ea82c9062c4893e88c37e test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py +++ b/test/functional/test_history_functions.py @@ -215,7 +215,7 @@ # Logged in as admin_user self.delete_current_history( strings_displayed=[ "History (%s) has been shared with others, unshare it before deleting it." % history3.name ] ) def test_030_clone_shared_history( self ): - """Testing cloning a shared history""" + """Testing copying a shared history""" # logged in as admin user self.logout() self.login( email=regular_user1.email ) @@ -223,9 +223,9 @@ self.history_options( user=True, histories_shared_by_others=True ) # Shared history3 should be in regular_user1's list of shared histories self.view_shared_histories( strings_displayed=[ history3.name, admin_user.email ] ) - self.clone_history( self.security.encode_id( history3.id ), + self.copy_history( self.security.encode_id( history3.id ), 'activatable', - strings_displayed_after_submit=[ 'is now included in your previously stored histories.' ] ) + strings_displayed_after_submit=[ 'has been created.' ] ) global history3_clone1 history3_clone1 = sa_session.query( galaxy.model.History ) \ .filter( and_( galaxy.model.History.table.c.deleted==False, @@ -234,11 +234,11 @@ .first() assert history3_clone1 is not None, "Problem retrieving history3_clone1 from database" # Check list of histories to make sure shared history3 was cloned - strings_displayed=[ "Clone of '%s' shared by '%s'" % ( history3.name, admin_user.email ) ] + strings_displayed=[ "Copy of '%s' shared by '%s'" % ( history3.name, admin_user.email ) ] self.view_stored_active_histories( strings_displayed=strings_displayed ) def test_035_clone_current_history( self ): - """Testing cloning the current history""" + """Testing copying the current history""" # logged in as regular_user1 self.logout() self.login( email=admin_user.email ) @@ -264,9 +264,9 @@ self.delete_history_item( str( hda_3_bed.id ) ) # Test cloning activatable datasets - self.clone_history( self.security.encode_id( history3.id ), + self.copy_history( self.security.encode_id( history3.id ), 'activatable', - strings_displayed_after_submit=['is now included in your previously stored histories.' ] ) + strings_displayed_after_submit=['has been created.' ] ) global history3_clone2 history3_clone2 = sa_session.query( galaxy.model.History ) \ .filter( and_( galaxy.model.History.table.c.deleted==False, @@ -276,7 +276,7 @@ assert history3_clone2 is not None, "Problem retrieving history3_clone2 from database" # Check list of histories to make sure shared history3 was cloned - self.view_stored_active_histories( strings_displayed=[ "Clone of '%s'" % history3.name ] ) + self.view_stored_active_histories( strings_displayed=[ "Copy of '%s'" % history3.name ] ) # Switch to the cloned history to make sure activatable datasets were cloned self.switch_history( id=self.security.encode_id( history3_clone2.id ), name=history3_clone2.name ) hda_2_bed = ( @@ -301,10 +301,10 @@ self.check_history_for_exact_string( self.security.encode_id( hda_3_bed.id ), show_deleted=True ) # Test cloning only active datasets - self.clone_history( + self.copy_history( self.security.encode_id( history3.id ), 'active', - strings_displayed_after_submit=[ 'is now included in your previously stored histories.' ] ) + strings_displayed_after_submit=[ 'has been created.' ] ) global history3_clone3 history3_clone3 = ( sa_session.query( galaxy.model.History ) @@ -316,7 +316,7 @@ assert history3_clone3 is not None, "Problem retrieving history3_clone3 from database" # Check list of histories to make sure shared history3 was cloned - self.view_stored_active_histories( strings_displayed = ["Clone of '%s'" % history3.name ] ) + self.view_stored_active_histories( strings_displayed = ["Copy of '%s'" % history3.name ] ) # Switch to the cloned history to make sure ONLY activatable datasets were cloned self.switch_history( id=self.security.encode_id( history3_clone3.id ) ) @@ -428,9 +428,9 @@ # Shared history5 should be in regular_user1's list of shared histories self.view_shared_histories( strings_displayed=[ history5.name, admin_user.email ] ) # Clone restricted history5 - self.clone_history( self.security.encode_id( history5.id ), + self.copy_history( self.security.encode_id( history5.id ), 'activatable', - strings_displayed_after_submit=[ 'is now included in your previously stored histories.' ] ) + strings_displayed_after_submit=[ 'has been created.' ] ) global history5_clone1 history5_clone1 = sa_session.query( galaxy.model.History ) \ .filter( and_( galaxy.model.History.table.c.deleted==False, @@ -439,7 +439,7 @@ .first() assert history5_clone1 is not None, "Problem retrieving history5_clone1 from database" # Check list of histories to make sure shared history5 was cloned - self.view_stored_active_histories( strings_displayed=[ "Clone of '%s'" % history5.name ] ) + self.view_stored_active_histories( strings_displayed=[ "Copy of '%s'" % history5.name ] ) # Make sure the dataset is accessible self.switch_history( id=self.security.encode_id( history5_clone1.id ), name=history5_clone1.name ) self.check_history_for_string( 'chr1' ) @@ -486,9 +486,9 @@ # Shared history5 should be in regular_user2's list of shared histories self.view_shared_histories( strings_displayed=[ history5.name, admin_user.email ] ) # Clone restricted history5 - self.clone_history( self.security.encode_id( history5.id ), + self.copy_history( self.security.encode_id( history5.id ), 'activatable', - strings_displayed_after_submit=[ 'is now included in your previously stored histories.' ] ) + strings_displayed_after_submit=[ 'has been created.' ] ) global history5_clone2 history5_clone2 = sa_session.query( galaxy.model.History ) \ .filter( and_( galaxy.model.History.table.c.deleted==False, @@ -497,7 +497,7 @@ .first() assert history5_clone2 is not None, "Problem retrieving history5_clone2 from database" # Check list of histories to make sure shared history3 was cloned - self.view_stored_active_histories( strings_displayed=[ "Clone of '%s'" % history5.name ] ) + self.view_stored_active_histories( strings_displayed=[ "Copy of '%s'" % history5.name ] ) # Make sure the dataset is accessible self.switch_history( id=self.security.encode_id( history5_clone2.id ), name=history5_clone2.name ) # Make sure both datasets are in the history @@ -557,15 +557,15 @@ self.share_current_history( email, strings_displayed_after_submit=strings_displayed_after_submit, action='share_anyway' ) - # Check security on clone of history5 for regular_user2 + # Check security on copy of history5 for regular_user2 self.logout() self.login( email=regular_user2.email ) # Shared history5 should be in regular_user2's list of shared histories self.view_shared_histories( strings_displayed=[ history5.name, admin_user.email ] ) # Clone restricted history5 - self.clone_history( self.security.encode_id( history5.id ), + self.copy_history( self.security.encode_id( history5.id ), 'activatable', - strings_displayed_after_submit=[ 'is now included in your previously stored histories.' ] ) + strings_displayed_after_submit=[ 'has been created.' ] ) global history5_clone3 history5_clone3 = ( sa_session.query( galaxy.model.History ) @@ -576,7 +576,7 @@ assert history5_clone3 is not None, "Problem retrieving history5_clone3 from database" # Check list of histories to make sure shared history3 was cloned - self.view_stored_active_histories( strings_displayed=[ "Clone of '%s'" % history5.name ] ) + self.view_stored_active_histories( strings_displayed=[ "Copy of '%s'" % history5.name ] ) # Make sure the dataset is accessible self.switch_history( id=self.security.encode_id( history5_clone3.id ), name=history5_clone3.name ) # Make sure both datasets are in the history @@ -602,16 +602,16 @@ self.display_history_item( str( hda_2_bed.id ), strings_displayed=[ 'chr1' ] ) # Delete the clone so the next test will be valid self.delete_history( id=self.security.encode_id( history5_clone3.id ) ) - # Check security on clone of history5 for regular_user3 + # Check security on copy of history5 for regular_user3 self.logout() self.login( email=regular_user3.email ) # Shared history5 should be in regular_user2's list of shared histories self.view_shared_histories( strings_displayed=[ history5.name, admin_user.email ] ) # Clone restricted history5 - self.clone_history( self.security.encode_id( history5.id ), + self.copy_history( self.security.encode_id( history5.id ), 'activatable', - strings_displayed_after_submit=[ 'is now included in your previously stored histories.' ] ) + strings_displayed_after_submit=[ 'has been created.' ] ) global history5_clone4 history5_clone4 = ( sa_session.query( galaxy.model.History ) @@ -622,7 +622,7 @@ assert history5_clone4 is not None, "Problem retrieving history5_clone4 from database" # Check list of histories to make sure shared history3 was cloned - self.view_stored_active_histories( strings_displayed=[ "Clone of '%s'" % history5.name ] ) + self.view_stored_active_histories( strings_displayed=[ "Copy of '%s'" % history5.name ] ) # Make sure the dataset is accessible self.switch_history( id=self.security.encode_id( history5_clone4.id ), name=history5_clone4.name ) # Make sure both datasets are in the history Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 15 Jan '13

15 Jan '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b45675d0e019/ changeset: b45675d0e019 user: jmchilton date: 2012-12-18 23:28:09 summary: Add more commonly generated Galaxy runtime files to .hgignore. affected #: 1 file diff -r eae248415389203907b5b951f139a200024ae069 -r b45675d0e0192952e9466d843fe0f17a9a6038d3 .hgignore --- a/.hgignore +++ b/.hgignore @@ -16,6 +16,7 @@ database/community_files database/compiled_templates database/files +database/job_working_directory database/pbs database/tmp database/*.sqlite @@ -23,6 +24,11 @@ # Python bytecode *.pyc +# Tool Shed Runtime Files +community_webapp.log +community_webapp.pid +hgweb.config* + # Config files universe_wsgi.ini reports_wsgi.ini https://bitbucket.org/galaxy/galaxy-central/commits/06cdf8b0b582/ changeset: 06cdf8b0b582 user: dannon date: 2013-01-15 23:09:33 summary: Merged in jmchilton/galaxy-central-hgignore-fixes (pull request #100: Add more commonly generated Galaxy runtime files to .hgignore.) affected #: 1 file diff -r 4bd419751ed3e8cc54913fa37389111a0e7faaa9 -r 06cdf8b0b582c40fa89fc7e398fecacb3943dbfc .hgignore --- a/.hgignore +++ b/.hgignore @@ -16,6 +16,7 @@ database/community_files database/compiled_templates database/files +database/job_working_directory database/pbs database/tmp database/*.sqlite @@ -23,6 +24,11 @@ # Python bytecode *.pyc +# Tool Shed Runtime Files +community_webapp.log +community_webapp.pid +hgweb.config* + # Config files universe_wsgi.ini reports_wsgi.ini Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Make galaxy.tools.Tool a new-style class.
by Bitbucket 15 Jan '13

15 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4bd419751ed3/ changeset: 4bd419751ed3 user: dan date: 2013-01-15 22:46:47 summary: Make galaxy.tools.Tool a new-style class. affected #: 1 file diff -r 52395842f8e65a6484268d3db1e3dbac09d60089 -r 4bd419751ed3e8cc54913fa37389111a0e7faaa9 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -813,7 +813,7 @@ self.attributes['split_size'] = 20 self.attributes['split_mode'] = 'number_of_parts' -class Tool: +class Tool( object ): """ Represents a computational tool that can be executed through Galaxy. """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Change 'clone workflow/visualization' to 'copy workflow/visualization' in user interface and associated code.
by Bitbucket 15 Jan '13

15 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/52395842f8e6/ changeset: 52395842f8e6 user: jgoecks date: 2013-01-15 22:16:55 summary: Change 'clone workflow/visualization' to 'copy workflow/visualization' in user interface and associated code. affected #: 4 files diff -r f93113b8e4771c31aed6dd39aba38d09e11ffb31 -r 52395842f8e65a6484268d3db1e3dbac09d60089 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -190,7 +190,7 @@ grids.GridOperation( "Open", allow_multiple=False, url_args=get_url_args ), grids.GridOperation( "Open in Circster", allow_multiple=False, condition=( lambda item: item.type == 'trackster' ), url_args=dict( action='circster' ) ), grids.GridOperation( "Edit Attributes", allow_multiple=False, url_args=dict( action='edit') ), - grids.GridOperation( "Copy", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False, url_args=dict( action='clone') ), + grids.GridOperation( "Copy", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False, url_args=dict( action='copy') ), grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), async_compatible=True, confirm="Are you sure you want to delete this visualization?" ), ] @@ -352,7 +352,7 @@ @web.expose @web.require_login() - def clone(self, trans, id, *args, **kwargs): + def copy(self, trans, id, *args, **kwargs): visualization = self.get_visualization( trans, id, check_ownership=False ) user = trans.get_user() owner = ( visualization.user == user ) @@ -360,15 +360,15 @@ if not owner: new_title += " shared by %s" % visualization.user.email - cloned_visualization = visualization.copy( user=trans.user, title=new_title ) + copied_viz = visualization.copy( user=trans.user, title=new_title ) # Persist session = trans.sa_session - session.add( cloned_visualization ) + session.add( copied_viz ) session.flush() # Display the management page - trans.set_message( 'Copy created with name "%s"' % cloned_visualization.title ) + trans.set_message( 'Created new visualization with name "%s"' % copied_viz.title ) return self.list( trans ) @web.expose diff -r f93113b8e4771c31aed6dd39aba38d09e11ffb31 -r 52395842f8e65a6484268d3db1e3dbac09d60089 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -51,7 +51,7 @@ operations = [ grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), grids.GridOperation( "Run", condition=( lambda item: not item.deleted ), async_compatible=False ), - grids.GridOperation( "Clone", condition=( lambda item: not item.deleted ), async_compatible=False ), + grids.GridOperation( "Copy", condition=( lambda item: not item.deleted ), async_compatible=False ), grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), async_compatible=False ), grids.GridOperation( "Sharing", condition=( lambda item: not item.deleted ), async_compatible=False ), grids.GridOperation( "Delete", condition=( lambda item: item.deleted ), async_compatible=True ), @@ -499,8 +499,8 @@ @web.expose @web.require_login( "use Galaxy workflows" ) - def clone( self, trans, id ): - # Get workflow to clone. + def copy( self, trans, id ): + # Get workflow to copy. stored = self.get_stored_workflow( trans, id, check_ownership=False ) user = trans.get_user() if stored.user == user: @@ -511,11 +511,11 @@ error( "Workflow is not owned by or shared with current user" ) owner = False - # Clone. + # Copy. new_stored = model.StoredWorkflow() - new_stored.name = "Clone of '%s'" % stored.name + new_stored.name = "Copy of '%s'" % stored.name new_stored.latest_workflow = stored.latest_workflow - # Clone annotation. + # Copy annotation. annotation_obj = self.get_item_annotation_obj( trans.sa_session, stored.user, stored ) if annotation_obj: self.add_item_annotation( trans.sa_session, trans.get_user(), new_stored, annotation_obj.annotation ) @@ -528,7 +528,7 @@ session.add( new_stored ) session.flush() # Display the management page - trans.set_message( 'Clone created with name "%s"' % new_stored.name ) + trans.set_message( 'Created new workflow with name "%s"' % new_stored.name ) return self.list( trans ) @web.expose diff -r f93113b8e4771c31aed6dd39aba38d09e11ffb31 -r 52395842f8e65a6484268d3db1e3dbac09d60089 templates/visualization/list.mako --- a/templates/visualization/list.mako +++ b/templates/visualization/list.mako @@ -48,7 +48,7 @@ <td><div popupmenu="shared-${i}-popup"><a class="action-button" href="${h.url_for( action='display_by_username_and_slug', username=visualization.user.username, slug=visualization.slug)}" target="_top">View</a> - <a class="action-button" href="${h.url_for( action='clone', id=trans.security.encode_id(visualization.id) )}">Copy</a> + <a class="action-button" href="${h.url_for( action='copy', id=trans.security.encode_id(visualization.id) )}">Copy</a></div></td></tr> diff -r f93113b8e4771c31aed6dd39aba38d09e11ffb31 -r 52395842f8e65a6484268d3db1e3dbac09d60089 templates/workflow/list.mako --- a/templates/workflow/list.mako +++ b/templates/workflow/list.mako @@ -67,7 +67,7 @@ <a class="action-button" href="${h.url_for( controller='root', action='index', workflow_id=trans.security.encode_id( workflow.id ) )}" target="_parent">Run</a><a class="action-button" href="${h.url_for( controller='workflow', action='sharing', id=trans.security.encode_id( workflow.id ) )}">Share or Publish</a><a class="action-button" href="${h.url_for( controller='workflow', action='export', id=trans.security.encode_id( workflow.id ) )}">Download or Export</a> - <a class="action-button" href="${h.url_for( controller='workflow', action='clone', id=trans.security.encode_id( workflow.id ) )}">Clone</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='copy', id=trans.security.encode_id( workflow.id ) )}">Copy</a><a class="action-button" href="${h.url_for( controller='workflow', action='rename', id=trans.security.encode_id( workflow.id ) )}">Rename</a><a class="action-button" href="${h.url_for( controller='workflow', action='display_by_id', id=trans.security.encode_id( workflow.id ) )}" target="_top">View</a><a class="action-button" confirm="Are you sure you want to delete workflow '${h.to_unicode( workflow.name ) | h}'?" href="${h.url_for( controller='workflow', action='delete', id=trans.security.encode_id( workflow.id ) )}">Delete</a> @@ -102,7 +102,7 @@ <div popupmenu="shared-${i}-popup"><a class="action-button" href="${h.url_for( controller='workflow', action='display_by_username_and_slug', username=workflow.user.username, slug=workflow.slug )}" target="_top">View</a><a class="action-button" href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">Run</a> - <a class="action-button" href="${h.url_for( controller='workflow', action='clone', id=trans.security.encode_id( workflow.id ) )}">Clone</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='copy', id=trans.security.encode_id( workflow.id ) )}">Copy</a><a class="action-button" confirm="Are you sure you want to remove the shared workflow '${h.to_unicode( workflow.name ) | h}'?" href="${h.url_for( controller='workflow', action='sharing', unshare_me=True, id=trans.security.encode_id( workflow.id ))}">Remove</a></div></td> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Change 'clone history' to 'copy history' in user interface and associated code.
by Bitbucket 15 Jan '13

15 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f93113b8e477/ changeset: f93113b8e477 user: jgoecks date: 2013-01-15 16:48:35 summary: Change 'clone history' to 'copy history' in user interface and associated code. affected #: 5 files diff -r ec543816a2a2b6fea98e3353e65f9e9c30d62cbe -r f93113b8e4771c31aed6dd39aba38d09e11ffb31 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -150,7 +150,7 @@ ] operations = [ grids.GridOperation( "View", allow_multiple=False, target="_top" ), - grids.GridOperation( "Clone" ), + grids.GridOperation( "Copy" ), grids.GridOperation( "Unshare" ) ] standard_filters = [] @@ -400,13 +400,13 @@ # Display history. history = self.get_history( trans, ids[0], False) return self.display_by_username_and_slug( trans, history.user.username, history.slug ) - elif operation == "clone": + elif operation == "copy": if not ids: - message = "Select a history to clone" + message = "Select a history to copy" return self.shared_list_grid( trans, status='error', message=message, **kwargs ) - # When cloning shared histories, only copy active datasets - new_kwargs = { 'clone_choice' : 'active' } - return self.clone( trans, ids, **new_kwargs ) + # When copying shared histories, only copy active datasets + new_kwargs = { 'copy_choice' : 'active' } + return self.copy( trans, ids, **new_kwargs ) elif operation == 'unshare': if not ids: message = "Select a history to unshare" @@ -957,7 +957,7 @@ def share( self, trans, id=None, email="", **kwd ): # If a history contains both datasets that can be shared and others that cannot be shared with the desired user, # then the entire history is shared, and the protected datasets will be visible, but inaccessible ( greyed out ) - # in the cloned history + # in the copyd history params = util.Params( kwd ) user = trans.get_user() # TODO: we have too many error messages floating around in here - we need @@ -1270,15 +1270,16 @@ return trans.show_message( "<p>%s" % change_msg, refresh_frames=['history'] ) @web.expose - @web.require_login( "clone shared Galaxy history" ) - def clone( self, trans, id=None, **kwd ): - """Clone a list of histories""" + @web.require_login( "copy shared Galaxy history" ) + def copy( self, trans, id=None, **kwd ): + """Copy one or more histories""" params = util.Params( kwd ) - # If clone_choice was not specified, display form passing along id + # If copy_choice was not specified, display form passing along id # argument - clone_choice = params.get( 'clone_choice', None ) - if not clone_choice: - return trans.fill_template( "/history/clone.mako", id_argument=id ) + copy_choice = params.get( 'copy_choice', None ) + if not copy_choice: + return trans.fill_template( "/history/copy.mako", id_argument=id ) + # Extract histories for id argument, defaulting to current if id is None: histories = [ trans.history ] @@ -1296,20 +1297,20 @@ if trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ) \ .filter_by( user=user, history=history ) \ .count() == 0: - return trans.show_error_message( "The history you are attempting to clone is not owned by you or shared with you. " ) + return trans.show_error_message( "The history you are attempting to copy is not owned by you or shared with you. " ) owner = False - name = "Clone of '%s'" % history.name + name = "Copy of '%s'" % history.name if not owner: name += " shared by '%s'" % history.user.email - if clone_choice == 'activatable': + if copy_choice == 'activatable': new_history = history.copy( name=name, target_user=user, activatable=True ) - elif clone_choice == 'active': + elif copy_choice == 'active': name += " (active items only)" new_history = history.copy( name=name, target_user=user ) if len( histories ) == 1: - msg = 'Clone with name "<a href="%s" target="_top">%s</a>" is now included in your previously stored histories.' % ( url_for( controller="history", action="switch_to_history", hist_id=trans.security.encode_id( new_history.id ) ) , new_history.name ) + msg = 'New history "<a href="%s" target="_top">%s</a>" has been created.' % ( url_for( controller="history", action="switch_to_history", hist_id=trans.security.encode_id( new_history.id ) ) , new_history.name ) else: - msg = '%d cloned histories are now included in your previously stored histories.' % len( histories ) + msg = 'Copied and created %d new histories.' % len( histories ) return trans.show_ok_message( msg ) @web.expose diff -r ec543816a2a2b6fea98e3353e65f9e9c30d62cbe -r f93113b8e4771c31aed6dd39aba38d09e11ffb31 templates/history/clone.mako --- a/templates/history/clone.mako +++ /dev/null @@ -1,27 +0,0 @@ -<% _=n_ %> -<%inherit file="/base.mako"/> -<%def name="title()">Clone History</%def> - -<div class="toolForm"> - <div class="toolFormTitle">Clone History</div> - <div class="toolFormBody"> - <form action="${h.url_for( controller='history', action='clone' )}" method="post" > - <div class="form-row"> - %if id_argument is not None: - <input type="hidden" name="id" value="${id_argument}"> - %endif - You can clone the history such that the clone will include all items in the original - history, or you can eliminate the original history's deleted items from the clone. - </div> - <div class="form-row"> - <input type="radio" name="clone_choice" value="activatable"> Clone all history items, including deleted items - </div> - <div class="form-row"> - <input type="radio" name="clone_choice" value="active"> Clone only items that are not deleted - </div> - <div class="form-row"> - <input type="submit" name="clone_choice_button" value="Clone"> - </div> - </form> - </div> -</div> diff -r ec543816a2a2b6fea98e3353e65f9e9c30d62cbe -r f93113b8e4771c31aed6dd39aba38d09e11ffb31 templates/history/copy.mako --- /dev/null +++ b/templates/history/copy.mako @@ -0,0 +1,27 @@ +<% _=n_ %> +<%inherit file="/base.mako"/> +<%def name="title()">Copy History</%def> + +<div class="toolForm"> + <div class="toolFormTitle">Copy History</div> + <div class="toolFormBody"> + <form action="${h.url_for( controller='history', action='copy' )}" method="post" > + <div class="form-row"> + %if id_argument is not None: + <input type="hidden" name="id" value="${id_argument}"> + %endif + You can make a copy of the history that includes all datasets in the original history or just the active + (not deleted) datasets. + </div> + <div class="form-row"> + <input type="radio" name="copy_choice" value="activatable"> Copy all datasets, including deleted ones + </div> + <div class="form-row"> + <input type="radio" name="copy_choice" value="active"> Copy only active (not deleted) datasets + </div> + <div class="form-row"> + <input type="submit" name="copy_choice_button" value="Copy"> + </div> + </form> + </div> +</div> diff -r ec543816a2a2b6fea98e3353e65f9e9c30d62cbe -r f93113b8e4771c31aed6dd39aba38d09e11ffb31 templates/history/options.mako --- a/templates/history/options.mako +++ b/templates/history/options.mako @@ -16,7 +16,7 @@ %if len( history.active_datasets ) > 0: <li><a href="${h.url_for( controller='root', action='history_new' )}">Create</a> a new empty history</li><li><a href="${h.url_for( controller='workflow', action='build_from_current_history' )}">Construct workflow</a> from current history</li> - <li><a href="${h.url_for( controller='history', action='clone', id=trans.security.encode_id( history.id ) )}">Clone</a> current history</li> + <li><a href="${h.url_for( controller='history', action='copy', id=trans.security.encode_id( history.id ) )}">Copy</a> current history</li> %endif <li><a href="${h.url_for( controller='history', action='share' )}" target="galaxy_main">Share</a> current history</div><li><a href="${h.url_for( controller='root', action='history_set_default_permissions' )}">Change default permissions</a> for current history</li> diff -r ec543816a2a2b6fea98e3353e65f9e9c30d62cbe -r f93113b8e4771c31aed6dd39aba38d09e11ffb31 templates/root/index.mako --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -22,8 +22,8 @@ "${_("Create New")}": function() { galaxy_history.location = "${h.url_for( controller='root', action='history_new' )}"; }, - "${_("Clone")}": function() { - galaxy_main.location = "${h.url_for( controller='history', action='clone')}"; + "${_("Copy History")}": function() { + galaxy_main.location = "${h.url_for( controller='history', action='copy')}"; }, "${_("Copy Datasets")}": function() { galaxy_main.location = "${h.url_for( controller='dataset', action='copy_datasets' )}"; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0