galaxy-commits May 2014

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commit/galaxy-central: greg: Add appropriate entries into the Tool Shed's repository registry for newly created repositories and undeleted and undeprecated repositories.
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/155be7ce7910/ Changeset: 155be7ce7910 User: greg Date: 2014-05-21 21:37:27 Summary: Add appropriate entries into the Tool Shed's repository registry for newly created repositories and undeleted and undeprecated repositories. Affected #: 5 files diff -r a769e22480662ec5d1205816bd162b6cfa6649f7 -r 155be7ce7910c2effb12fff904390401bdd7976b 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 @@ -31,12 +31,6 @@ from tool_shed.galaxy_install import repository_util import tool_shed.galaxy_install.grids.admin_toolshed_grids as admin_toolshed_grids -import pkg_resources - -pkg_resources.require( 'elementtree' ) -from elementtree import ElementTree -from elementtree.ElementTree import Element - log = logging.getLogger( __name__ ) diff -r a769e22480662ec5d1205816bd162b6cfa6649f7 -r 155be7ce7910c2effb12fff904390401bdd7976b lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -367,6 +367,9 @@ repository.deleted = False trans.sa_session.add( repository ) trans.sa_session.flush() + if not repository.deprecated: + # Update the repository registry. + trans.app.repository_registry.add_entry( repository ) count += 1 undeleted_repositories += " %s" % repository.name if count: diff -r a769e22480662ec5d1205816bd162b6cfa6649f7 -r 155be7ce7910c2effb12fff904390401bdd7976b lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1053,6 +1053,8 @@ if mark_deprecated: message = 'The repository %s has been marked as deprecated.' % repository.name else: + # Update the repository registry. + trans.app.repository_registry.add_entry( repository ) message = 'The repository %s has been marked as not deprecated.' % repository.name trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', diff -r a769e22480662ec5d1205816bd162b6cfa6649f7 -r 155be7ce7910c2effb12fff904390401bdd7976b lib/tool_shed/repository_registry.py --- a/lib/tool_shed/repository_registry.py +++ b/lib/tool_shed/repository_registry.py @@ -40,6 +40,29 @@ self.load_viewable_repositories_and_suites_by_category() self.load_repository_and_suite_tuples() + def add_entry( self, repository ): + if repository: + is_valid = self.is_valid( repository ) + for rca in repository.categories: + category = rca.category + category_name = str( category.name ) + self.viewable_repositories_and_suites_by_category[ category_name ] += 1 + if is_valid: + self.viewable_valid_repositories_and_suites_by_category[ category_name ] += 1 + if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: + self.viewable_suites_by_category[ category_name ] += 1 + if is_valid: + self.viewable_valid_suites_by_category[ category_name ] += 1 + certified_level_one_tuple = self.get_certified_level_one_tuple( repository ) + latest_installable_changeset_revision, is_level_one_certified = certified_level_one_tuple + if is_level_one_certified: + self.certified_level_one_viewable_repositories_and_suites_by_category[ category_name ] += 1 + if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: + self.certified_level_one_viewable_suites_by_category[ category_name ] += 1 + self.load_repository_and_suite_tuple( repository ) + if is_level_one_certified: + self.load_certified_level_one_repository_and_suite_tuple( repository ) + def get_certified_level_one_clause_list( self ): certified_level_one_tuples = [] clause_list = [] @@ -60,7 +83,9 @@ """ Return True if the latest installable changeset_revision of the received repository is level one certified. """ - if repository.deleted: + if repository is None: + return ( None, False ) + if repository.deleted or repository.deprecated: return ( None, False ) repo = hg_util.get_repo_for_repository( self.app, repository=repository, repo_path=None, create=False ) # Get the latest installable changeset revision since that is all that is currently configured for testing. @@ -126,33 +151,46 @@ return tuple in self.certified_level_one_repository_and_suite_tuples return False + def is_valid( self, repository ): + if repository and not repository.deleted and not repository.deprecated and repository.downloadable_revisions: + return True + return False + + def load_certified_level_one_repository_and_suite_tuple( self, repository ): + # The received repository has been determined to be level one certified. + name = str( repository.name ) + owner = str( repository.user.username ) + tip_changeset_hash = repository.tip( self.app ) + if tip_changeset_hash != suc.INITIAL_CHANGELOG_HASH: + certified_level_one_tuple = ( name, owner, tip_changeset_hash ) + if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: + self.certified_level_one_suite_tuples.append( certified_level_one_tuple ) + else: + self.certified_level_one_repository_and_suite_tuples.append( certified_level_one_tuple ) + + def load_repository_and_suite_tuple( self, repository ): + name = str( repository.name ) + owner = str( repository.user.username ) + for repository_metadata in repository.metadata_revisions: + changeset_revision = str( repository_metadata.changeset_revision ) + tuple = ( name, owner, changeset_revision ) + self.repository_and_suite_tuples.append( tuple ) + if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: + self.suite_tuples.append( tuple ) + def load_repository_and_suite_tuples( self ): # Load self.certified_level_one_repository_and_suite_tuples and self.certified_level_one_suite_tuples. for repository in self.sa_session.query( model.Repository ) \ .join( model.RepositoryMetadata.table ) \ .filter( or_( *self.certified_level_one_clause_list ) ) \ .join( model.User.table ): - name = str( repository.name ) - owner = str( repository.user.username ) - tip_changeset_hash = repository.tip( self.app ) - certified_level_one_tuple = ( name, owner, tip_changeset_hash ) - if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: - self.certified_level_one_suite_tuples.append( certified_level_one_tuple ) - else: - self.certified_level_one_repository_and_suite_tuples.append( certified_level_one_tuple ) + self.load_certified_level_one_repository_and_suite_tuple( repository ) # Load self.repository_and_suite_tuples and self.suite_tuples for repository in self.sa_session.query( model.Repository ) \ .filter( and_( model.Repository.table.c.deleted == False, model.Repository.table.c.deprecated == False ) ) \ .join( model.User.table ): - name = str( repository.name ) - owner = str( repository.user.username ) - for repository_metadata in repository.metadata_revisions: - changeset_revision = str( repository_metadata.changeset_revision ) - tuple = ( name, owner, changeset_revision ) - self.repository_and_suite_tuples.append( tuple ) - if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: - self.suite_tuples.append( tuple ) + self.load_repository_and_suite_tuple( repository ) def load_viewable_repositories_and_suites_by_category( self ): # Clear all dictionaries just in case they were previously loaded. @@ -165,40 +203,39 @@ self.viewable_valid_repositories_and_suites_by_category = {} self.viewable_valid_suites_by_category = {} for category in self.sa_session.query( model.Category ): + category_name = str( category.name ) if category not in self.certified_level_one_viewable_repositories_and_suites_by_category: - self.certified_level_one_viewable_repositories_and_suites_by_category[ str( category.name ) ] = 0 + self.certified_level_one_viewable_repositories_and_suites_by_category[ category_name ] = 0 if category not in self.certified_level_one_viewable_suites_by_category: - self.certified_level_one_viewable_suites_by_category[ str( category.name ) ] = 0 + self.certified_level_one_viewable_suites_by_category[ category_name ] = 0 if category not in self.viewable_repositories_and_suites_by_category: - self.viewable_repositories_and_suites_by_category[ str( category.name ) ] = 0 + self.viewable_repositories_and_suites_by_category[ category_name ] = 0 if category not in self.viewable_suites_by_category: - self.viewable_suites_by_category[ str( category.name ) ] = 0 + self.viewable_suites_by_category[ category_name ] = 0 if category not in self.viewable_valid_repositories_and_suites_by_category: - self.viewable_valid_repositories_and_suites_by_category[ str( category.name ) ] = 0 + self.viewable_valid_repositories_and_suites_by_category[ category_name ] = 0 if category not in self.viewable_valid_suites_by_category: - self.viewable_valid_suites_by_category[ str( category.name ) ] = 0 + self.viewable_valid_suites_by_category[ category_name ] = 0 for rca in category.repositories: repository = rca.repository - if repository.downloadable_revisions: - is_valid = True - else: - is_valid = False - encoded_repository_id = self.app.security.encode_id( repository.id ) - tip_changeset_hash = repository.tip( self.app ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, - encoded_repository_id, - tip_changeset_hash ) - self.viewable_repositories_and_suites_by_category[ str( category.name ) ] += 1 - if is_valid: - self.viewable_valid_repositories_and_suites_by_category[ str( category.name ) ] += 1 - if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION ]: - self.viewable_suites_by_category[ str( category.name ) ] += 1 + if not repository.deleted and not repository.deprecated: + is_valid = self.is_valid( repository ) + encoded_repository_id = self.app.security.encode_id( repository.id ) + tip_changeset_hash = repository.tip( self.app ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + encoded_repository_id, + tip_changeset_hash ) + self.viewable_repositories_and_suites_by_category[ category_name ] += 1 if is_valid: - self.viewable_valid_suites_by_category[ str( category.name ) ] += 1 - if self.is_level_one_certified( repository_metadata ): - self.certified_level_one_viewable_repositories_and_suites_by_category[ str( category.name ) ] += 1 + self.viewable_valid_repositories_and_suites_by_category[ category_name ] += 1 if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION ]: - self.certified_level_one_viewable_suites_by_category[ str( category.name ) ] += 1 + self.viewable_suites_by_category[ category_name ] += 1 + if is_valid: + self.viewable_valid_suites_by_category[ category_name ] += 1 + if self.is_level_one_certified( repository_metadata ): + self.certified_level_one_viewable_repositories_and_suites_by_category[ category_name ] += 1 + if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION ]: + self.certified_level_one_viewable_suites_by_category[ category_name ] += 1 @property def sa_session( self ): diff -r a769e22480662ec5d1205816bd162b6cfa6649f7 -r 155be7ce7910c2effb12fff904390401bdd7976b lib/tool_shed/util/repository_maintenance_util.py --- a/lib/tool_shed/util/repository_maintenance_util.py +++ b/lib/tool_shed/util/repository_maintenance_util.py @@ -93,6 +93,8 @@ flush_needed = True if flush_needed: trans.sa_session.flush() + # Update the repository registry. + trans.app.repository_registry.add_entry( repository ) message = "Repository %s has been created." % str( repository.name ) return repository, message Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e2fb8fe53e8e/ Changeset: e2fb8fe53e8e Branch: next-stable User: jmchilton Date: 2014-05-21 21:33:24 Summary: Fix admin check in security_check for userless admin keys. ... by removing duplicated check of trans.user, this check is done in trans.user_is_admin if needed. Affected #: 1 file diff -r 65ca3d67f90b6617981cd75663dca2246643c047 -r e2fb8fe53e8ec833881a7e45f7946f09a078c3fd lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -304,7 +304,7 @@ def security_check( self, trans, item, check_ownership=False, check_accessible=False ): """ Security checks for an item: checks if (a) user owns item or (b) item is accessible to user. """ # all items are accessible to an admin - if trans.user and trans.user_is_admin(): + if trans.user_is_admin(): return item # Verify ownership: there is a current user and that user is the same as the item's https://bitbucket.org/galaxy/galaxy-central/commits/fc89661b92dc/ Changeset: fc89661b92dc Branch: next-stable User: jmchilton Date: 2014-05-21 21:33:24 Summary: Fix provenance controller for non-admins. Cannot pass check_accessible=True to get_object with HistoryDatasetAssociations (because item.user is undefined.). Affected #: 2 files diff -r e2fb8fe53e8ec833881a7e45f7946f09a078c3fd -r fc89661b92dcbd9684ac779171235525601d0f4a lib/galaxy/webapps/galaxy/api/provenance.py --- a/lib/galaxy/webapps/galaxy/api/provenance.py +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -5,6 +5,7 @@ from galaxy import web from galaxy.web.base.controller import BaseAPIController, UsesHistoryMixin from paste.httpexceptions import HTTPNotImplemented, HTTPBadRequest +from galaxy.managers import hdas log = logging.getLogger( __name__ ) @@ -12,6 +13,10 @@ class BaseProvenanceController( BaseAPIController, UsesHistoryMixin ): """ """ + def __init__( self, app ): + super( BaseProvenanceController, self ).__init__( app ) + self.hdas = hdas.HDAManager() + @web.expose_api def index( self, trans, **kwd ): follow = kwd.get('follow', False) @@ -34,7 +39,11 @@ raise HTTPBadRequest("Cannot Delete Provenance") def _get_provenance(self, trans, item_class_name, item_id, follow=True): - provenance_item = self.get_object( trans, item_id, item_class_name, check_ownership=False, check_accessible=True ) + provenance_item = self.get_object( trans, item_id, item_class_name, check_ownership=False, check_accessible=False) + if item_class_name == "HistoryDatasetAssociation": + self.hdas.check_accessible(trans, provenance_item) + else: + self.security_check(trans, provenance_item, check_accessible=True) out = self._get_record(trans, provenance_item, follow) return out diff -r e2fb8fe53e8ec833881a7e45f7946f09a078c3fd -r fc89661b92dcbd9684ac779171235525601d0f4a test/api/test_history_contents_provenance.py --- /dev/null +++ b/test/api/test_history_contents_provenance.py @@ -0,0 +1,16 @@ +from base import api +from .helpers import DatasetPopulator + + +class TestProvenance( api.ApiTestCase ): + + def setUp( self ): + super( TestProvenance, self ).setUp( ) + self.dataset_populator = DatasetPopulator( self.galaxy_interactor ) + + def test_show_prov( self ): + history_id = self.dataset_populator.new_history() + new_dataset1 = self.dataset_populator.new_dataset( history_id, content='for prov' ) + prov_response = self._get( "histories/%s/contents/%s/provenance" % ( history_id, new_dataset1[ "id" ] ) ) + self._assert_status_code_is( prov_response, 200 ) + self._assert_has_keys( prov_response.json(), "job_id", "id", "stdout", "stderr", "parameters", "tool_id" ) https://bitbucket.org/galaxy/galaxy-central/commits/a769e2248066/ Changeset: a769e2248066 User: jmchilton Date: 2014-05-21 21:33:51 Summary: Merge next-stable. Affected #: 3 files diff -r 2601a535a02267e6af2c43b4a1a3e22ac9e78193 -r a769e22480662ec5d1205816bd162b6cfa6649f7 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -304,7 +304,7 @@ def security_check( self, trans, item, check_ownership=False, check_accessible=False ): """ Security checks for an item: checks if (a) user owns item or (b) item is accessible to user. """ # all items are accessible to an admin - if trans.user and trans.user_is_admin(): + if trans.user_is_admin(): return item # Verify ownership: there is a current user and that user is the same as the item's diff -r 2601a535a02267e6af2c43b4a1a3e22ac9e78193 -r a769e22480662ec5d1205816bd162b6cfa6649f7 lib/galaxy/webapps/galaxy/api/provenance.py --- a/lib/galaxy/webapps/galaxy/api/provenance.py +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -5,6 +5,7 @@ from galaxy import web from galaxy.web.base.controller import BaseAPIController, UsesHistoryMixin from paste.httpexceptions import HTTPNotImplemented, HTTPBadRequest +from galaxy.managers import hdas log = logging.getLogger( __name__ ) @@ -12,6 +13,10 @@ class BaseProvenanceController( BaseAPIController, UsesHistoryMixin ): """ """ + def __init__( self, app ): + super( BaseProvenanceController, self ).__init__( app ) + self.hdas = hdas.HDAManager() + @web.expose_api def index( self, trans, **kwd ): follow = kwd.get('follow', False) @@ -34,7 +39,11 @@ raise HTTPBadRequest("Cannot Delete Provenance") def _get_provenance(self, trans, item_class_name, item_id, follow=True): - provenance_item = self.get_object( trans, item_id, item_class_name, check_ownership=False, check_accessible=True ) + provenance_item = self.get_object( trans, item_id, item_class_name, check_ownership=False, check_accessible=False) + if item_class_name == "HistoryDatasetAssociation": + self.hdas.check_accessible(trans, provenance_item) + else: + self.security_check(trans, provenance_item, check_accessible=True) out = self._get_record(trans, provenance_item, follow) return out diff -r 2601a535a02267e6af2c43b4a1a3e22ac9e78193 -r a769e22480662ec5d1205816bd162b6cfa6649f7 test/api/test_history_contents_provenance.py --- /dev/null +++ b/test/api/test_history_contents_provenance.py @@ -0,0 +1,16 @@ +from base import api +from .helpers import DatasetPopulator + + +class TestProvenance( api.ApiTestCase ): + + def setUp( self ): + super( TestProvenance, self ).setUp( ) + self.dataset_populator = DatasetPopulator( self.galaxy_interactor ) + + def test_show_prov( self ): + history_id = self.dataset_populator.new_history() + new_dataset1 = self.dataset_populator.new_dataset( history_id, content='for prov' ) + prov_response = self._get( "histories/%s/contents/%s/provenance" % ( history_id, new_dataset1[ "id" ] ) ) + self._assert_status_code_is( prov_response, 200 ) + self._assert_has_keys( prov_response.json(), "job_id", "id", "stdout", "stderr", "parameters", "tool_id" ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/65ca3d67f90b/ Changeset: 65ca3d67f90b Branch: next-stable User: greg Date: 2014-05-21 21:06:41 Summary: Enhance the Tool Shed API to be able to retrieve an API key for an authenticated user. Affected #: 2 files diff -r a8904f154c5a1d94d8180c75683992a4123caef2 -r 65ca3d67f90b6617981cd75663dca2246643c047 lib/galaxy/webapps/tool_shed/api/authenticate.py --- /dev/null +++ b/lib/galaxy/webapps/tool_shed/api/authenticate.py @@ -0,0 +1,94 @@ +""" +API key retrieval through BaseAuth +Sample usage: + +curl --user zipzap@foo.com:password http://localhost:9009/api/authenticate/baseauth + +Returns: +{ + "api_key": <some api key> +} +""" +import logging +from base64 import b64decode +from paste.httpexceptions import HTTPBadRequest +from urllib import unquote + +from galaxy import web +from galaxy.exceptions import ObjectNotFound +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import CreatesApiKeysMixin + +log = logging.getLogger( __name__ ) + + +class AuthenticationController( BaseAPIController, CreatesApiKeysMixin ): + + @web.expose_api_anonymous + def get_api_key( self, trans, **kwd ): + """ + def get_api_key( self, trans, **kwd ) + * GET /api/authenticate/baseauth + returns an API key for authenticated user based on BaseAuth headers + + :returns: api_key in json format + :rtype: dict + + :raises: ObjectNotFound, HTTPBadRequest + """ + email, password = self._decode_baseauth( trans.environ.get( 'HTTP_AUTHORIZATION' ) ) + user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).all() + if ( len( user ) is not 1 ): + # DB is inconsistent and we have more users with same email + raise ObjectNotFound + else: + user = user[ 0 ] + is_valid_user = user.check_password( password ) + if ( is_valid_user ): + if user.api_keys: + key = user.api_keys[ 0 ].key + else: + key = self.create_api_key( trans, user ) + return dict( api_key=key ) + else: + trans.response.status = 500 + return "invalid password" + + def _decode_baseauth( self, encoded_str ): + """ + Decode an encrypted HTTP basic authentication string. Returns a tuple of + the form (email, password), and raises a HTTPBadRequest exception if + nothing could be decoded. + + :param encoded_str: BaseAuth string encoded base64 + :type encoded_str: string + + :returns: email of the user + :rtype: string + :returns: password of the user + :rtype: string + + :raises: HTTPBadRequest + """ + split = encoded_str.strip().split( ' ' ) + # If split is only one element, try to decode the email and password directly. + if len( split ) == 1: + try: + email, password = b64decode( split[ 0 ] ).split( ':' ) + except: + raise HTTPBadRequest + # If there are only two elements, check the first and ensure it says + # 'basic' so that we know we're about to decode the right thing. If not, + # bail out. + elif len( split ) == 2: + if split[ 0 ].strip().lower() == 'basic': + try: + email, password = b64decode( split[ 1 ] ).split( ':' ) + except: + raise HTTPBadRequest + else: + raise HTTPBadRequest + # If there are more than 2 elements, something crazy must be happening. Bail. + else: + raise HTTPBadRequest + return unquote( email ), unquote( password ) diff -r a8904f154c5a1d94d8180c75683992a4123caef2 -r 65ca3d67f90b6617981cd75663dca2246643c047 lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -80,6 +80,11 @@ webapp.add_route( '/repos/*path_info', controller='hg', action='handle_request', path_info='/' ) # Add the web API. # A good resource for RESTful services - http://routes.readthedocs.org/en/latest/restful.html webapp.add_api_controllers( 'galaxy.webapps.tool_shed.api', app ) + webapp.mapper.connect( 'api_key_retrieval', + '/api/authenticate/baseauth/', + controller='authenticate', + action='get_api_key', + conditions=dict( method=[ "GET" ] ) ) webapp.mapper.resource( 'category', 'categories', controller='categories', https://bitbucket.org/galaxy/galaxy-central/commits/2601a535a022/ Changeset: 2601a535a022 User: davebgx Date: 2014-05-21 21:10:01 Summary: Merge with next-stable. Affected #: 0 files 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.

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commit/galaxy-central: greg: Enhance the Tool Shed API to be able to retrieve an API key for an authenticated user.
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/55cefad9d53c/ Changeset: 55cefad9d53c User: greg Date: 2014-05-21 21:06:41 Summary: Enhance the Tool Shed API to be able to retrieve an API key for an authenticated user. Affected #: 2 files diff -r ffe1fed76848569754c81c59fdba999d488782c9 -r 55cefad9d53cdb16d0fb04bef60ea43c73e512b0 lib/galaxy/webapps/tool_shed/api/authenticate.py --- /dev/null +++ b/lib/galaxy/webapps/tool_shed/api/authenticate.py @@ -0,0 +1,94 @@ +""" +API key retrieval through BaseAuth +Sample usage: + +curl --user zipzap@foo.com:password http://localhost:9009/api/authenticate/baseauth + +Returns: +{ + "api_key": <some api key> +} +""" +import logging +from base64 import b64decode +from paste.httpexceptions import HTTPBadRequest +from urllib import unquote + +from galaxy import web +from galaxy.exceptions import ObjectNotFound +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import CreatesApiKeysMixin + +log = logging.getLogger( __name__ ) + + +class AuthenticationController( BaseAPIController, CreatesApiKeysMixin ): + + @web.expose_api_anonymous + def get_api_key( self, trans, **kwd ): + """ + def get_api_key( self, trans, **kwd ) + * GET /api/authenticate/baseauth + returns an API key for authenticated user based on BaseAuth headers + + :returns: api_key in json format + :rtype: dict + + :raises: ObjectNotFound, HTTPBadRequest + """ + email, password = self._decode_baseauth( trans.environ.get( 'HTTP_AUTHORIZATION' ) ) + user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).all() + if ( len( user ) is not 1 ): + # DB is inconsistent and we have more users with same email + raise ObjectNotFound + else: + user = user[ 0 ] + is_valid_user = user.check_password( password ) + if ( is_valid_user ): + if user.api_keys: + key = user.api_keys[ 0 ].key + else: + key = self.create_api_key( trans, user ) + return dict( api_key=key ) + else: + trans.response.status = 500 + return "invalid password" + + def _decode_baseauth( self, encoded_str ): + """ + Decode an encrypted HTTP basic authentication string. Returns a tuple of + the form (email, password), and raises a HTTPBadRequest exception if + nothing could be decoded. + + :param encoded_str: BaseAuth string encoded base64 + :type encoded_str: string + + :returns: email of the user + :rtype: string + :returns: password of the user + :rtype: string + + :raises: HTTPBadRequest + """ + split = encoded_str.strip().split( ' ' ) + # If split is only one element, try to decode the email and password directly. + if len( split ) == 1: + try: + email, password = b64decode( split[ 0 ] ).split( ':' ) + except: + raise HTTPBadRequest + # If there are only two elements, check the first and ensure it says + # 'basic' so that we know we're about to decode the right thing. If not, + # bail out. + elif len( split ) == 2: + if split[ 0 ].strip().lower() == 'basic': + try: + email, password = b64decode( split[ 1 ] ).split( ':' ) + except: + raise HTTPBadRequest + else: + raise HTTPBadRequest + # If there are more than 2 elements, something crazy must be happening. Bail. + else: + raise HTTPBadRequest + return unquote( email ), unquote( password ) diff -r ffe1fed76848569754c81c59fdba999d488782c9 -r 55cefad9d53cdb16d0fb04bef60ea43c73e512b0 lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -80,6 +80,11 @@ webapp.add_route( '/repos/*path_info', controller='hg', action='handle_request', path_info='/' ) # Add the web API. # A good resource for RESTful services - http://routes.readthedocs.org/en/latest/restful.html webapp.add_api_controllers( 'galaxy.webapps.tool_shed.api', app ) + webapp.mapper.connect( 'api_key_retrieval', + '/api/authenticate/baseauth/', + controller='authenticate', + action='get_api_key', + conditions=dict( method=[ "GET" ] ) ) webapp.mapper.resource( 'category', 'categories', controller='categories', 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.

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commit/galaxy-central: dan: merge next-stable
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ffe1fed76848/ Changeset: ffe1fed76848 User: dan Date: 2014-05-21 20:24:51 Summary: merge next-stable Affected #: 1 file diff -r 6f2455ab4acbce667ff5155fd85fef4d3dacc9cc -r ffe1fed76848569754c81c59fdba999d488782c9 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -16,9 +16,10 @@ self._data_table_name = data_table_name self._static_chrom_info_path = app.config.len_file_path # A dbkey can be listed multiple times, but with different names, so we can't use dictionaries for lookups - self._static_dbkeys = [] if load_old_style: self._static_dbkeys = list( dbnames ) + else: + self._static_dbkeys = [] def get_genome_build_names( self, trans=None ): # FIXME: how to deal with key duplicates? @@ -34,7 +35,7 @@ datasets = trans.sa_session.query( self._app.model.HistoryDatasetAssociation ) \ .filter_by( deleted=False, history_id=trans.history.id, extension="len" ) for dataset in datasets: - rval.append( (dataset.dbkey, dataset.name) ) + rval.append( ( dataset.dbkey, "%s (%s) [History]" % ( dataset.name, dataset.dbkey ) ) ) user = trans.get_user() if user and 'dbkeys' in user.preferences: user_keys = from_json_string( user.preferences['dbkeys'] ) 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.

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commit/galaxy-central: dan: Provide a visual clue that those odd len files as dbkeys are from the history.
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a8904f154c5a/ Changeset: a8904f154c5a Branch: next-stable User: dan Date: 2014-05-21 20:24:05 Summary: Provide a visual clue that those odd len files as dbkeys are from the history. Affected #: 1 file diff -r 6ee45090d5b1ff8e0cd0497930aa0618133c612d -r a8904f154c5a1d94d8180c75683992a4123caef2 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -16,9 +16,10 @@ self._data_table_name = data_table_name self._static_chrom_info_path = app.config.len_file_path # A dbkey can be listed multiple times, but with different names, so we can't use dictionaries for lookups - self._static_dbkeys = [] if load_old_style: self._static_dbkeys = list( dbnames ) + else: + self._static_dbkeys = [] def get_genome_build_names( self, trans=None ): # FIXME: how to deal with key duplicates? @@ -34,7 +35,7 @@ datasets = trans.sa_session.query( self._app.model.HistoryDatasetAssociation ) \ .filter_by( deleted=False, history_id=trans.history.id, extension="len" ) for dataset in datasets: - rval.append( (dataset.dbkey, dataset.name) ) + rval.append( ( dataset.dbkey, "%s (%s) [History]" % ( dataset.name, dataset.dbkey ) ) ) user = trans.get_user() if user and 'dbkeys' in user.preferences: user_keys = from_json_string( user.preferences['dbkeys'] ) 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.

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commit/galaxy-central: dan: merge next stable
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6f2455ab4acb/ Changeset: 6f2455ab4acb User: dan Date: 2014-05-21 20:14:06 Summary: merge next stable Affected #: 1 file diff -r eaa335bf43a8b679a2d7f2d5ba701fc2f424a1c2 -r 6f2455ab4acbce667ff5155fd85fef4d3dacc9cc lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -4,7 +4,6 @@ #dbkeys read from disk using builds.txt from galaxy.util import dbnames from galaxy.util.json import from_json_string -from galaxy.util.odict import odict import os.path @@ -16,10 +15,10 @@ self._app = app self._data_table_name = data_table_name self._static_chrom_info_path = app.config.len_file_path - self._static_dbkeys = odict() #need odict to keep ? at top of list + # A dbkey can be listed multiple times, but with different names, so we can't use dictionaries for lookups + self._static_dbkeys = [] if load_old_style: - for key, value in dbnames: - self._static_dbkeys[ key ] = value + self._static_dbkeys = list( dbnames ) def get_genome_build_names( self, trans=None ): # FIXME: how to deal with key duplicates? @@ -42,7 +41,7 @@ for key, chrom_dict in user_keys.iteritems(): rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) # Load old builds.txt static keys - rval.extend( self._static_dbkeys.items() ) + rval.extend( self._static_dbkeys ) #load dbkeys from dbkey data table dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) if dbkey_table is not None: 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.

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commit/galaxy-central: davebgx: Add user_info.xml to the .hgignore filters.
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eaa335bf43a8/ Changeset: eaa335bf43a8 User: davebgx Date: 2014-05-21 20:11:26 Summary: Add user_info.xml to the .hgignore filters. Affected #: 1 file diff -r cc9164a8b545afe0d4132f31d627609ba941d1cb -r eaa335bf43a8b679a2d7f2d5ba701fc2f424a1c2 .hgignore --- a/.hgignore +++ b/.hgignore @@ -35,6 +35,7 @@ tool_shed_webapp.log tool_shed_webapp.pid hgweb.config* +lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml # Reports Runtime Files reports_webapp.lock 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.

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commit/galaxy-central: dan: Fix for when a dbkey should be displayed multiple times, but with possibly different names.
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6ee45090d5b1/ Changeset: 6ee45090d5b1 Branch: next-stable User: dan Date: 2014-05-21 20:08:04 Summary: Fix for when a dbkey should be displayed multiple times, but with possibly different names. Affected #: 1 file diff -r 20227293c9fe496cf0995f7c194969e785d5ff1e -r 6ee45090d5b1ff8e0cd0497930aa0618133c612d lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -4,7 +4,6 @@ #dbkeys read from disk using builds.txt from galaxy.util import dbnames from galaxy.util.json import from_json_string -from galaxy.util.odict import odict import os.path @@ -16,10 +15,10 @@ self._app = app self._data_table_name = data_table_name self._static_chrom_info_path = app.config.len_file_path - self._static_dbkeys = odict() #need odict to keep ? at top of list + # A dbkey can be listed multiple times, but with different names, so we can't use dictionaries for lookups + self._static_dbkeys = [] if load_old_style: - for key, value in dbnames: - self._static_dbkeys[ key ] = value + self._static_dbkeys = list( dbnames ) def get_genome_build_names( self, trans=None ): # FIXME: how to deal with key duplicates? @@ -42,7 +41,7 @@ for key, chrom_dict in user_keys.iteritems(): rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) # Load old builds.txt static keys - rval.extend( self._static_dbkeys.items() ) + rval.extend( self._static_dbkeys ) #load dbkeys from dbkey data table dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) if dbkey_table is not None: 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.

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commit/galaxy-central: greg: Make sure a valid object is received when checking certification the Tool Shed's new repository registry.
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cc9164a8b545/ Changeset: cc9164a8b545 User: greg Date: 2014-05-21 18:29:33 Summary: Make sure a valid object is received when checking certification the Tool Shed's new repository registry. Affected #: 1 file diff -r 7eaa7e058c2898b10674b4ca43a0a76e566517c3 -r cc9164a8b545afe0d4132f31d627609ba941d1cb lib/tool_shed/repository_registry.py --- a/lib/tool_shed/repository_registry.py +++ b/lib/tool_shed/repository_registry.py @@ -114,14 +114,17 @@ return ( None, False ) def is_level_one_certified( self, repository_metadata ): - repository = repository_metadata.repository - if repository.deprecated or repository.deleted: - return False - tuple = ( str( repository.name ), str( repository.user.username ), str( repository_metadata.changeset_revision ) ) - if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION ]: - return tuple in self.certified_level_one_suite_tuples - else: - return tuple in self.certified_level_one_repository_and_suite_tuples + if repository_metadata: + repository = repository_metadata.repository + if repository: + if repository.deprecated or repository.deleted: + return False + tuple = ( str( repository.name ), str( repository.user.username ), str( repository_metadata.changeset_revision ) ) + if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION ]: + return tuple in self.certified_level_one_suite_tuples + else: + return tuple in self.certified_level_one_repository_and_suite_tuples + return False def load_repository_and_suite_tuples( self ): # Load self.certified_level_one_repository_and_suite_tuples and self.certified_level_one_suite_tuples. 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.

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