3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/da044e190f11/ Changeset: da044e190f11 User: martenson Date: 2015-02-23 15:44:51+00:00 Summary: fix toolshed auth API returning double converted json allow sessionless key retrieval Affected #: 1 file diff -r 67222d8cb3a54c7a3dc28accc8f16ff502fe547b -r da044e190f11d33a8556aa60ff563f1e801abf6d lib/galaxy/webapps/tool_shed/api/authenticate.py --- a/lib/galaxy/webapps/tool_shed/api/authenticate.py +++ b/lib/galaxy/webapps/tool_shed/api/authenticate.py @@ -13,13 +13,14 @@ from galaxy import web from galaxy.webapps.galaxy.api.authenticate import AuthenticationController +from galaxy.web import _future_expose_api_raw_anonymous_and_sessionless as expose_api_raw_anonymous_and_sessionless log = logging.getLogger( __name__ ) class ToolShedAuthenticationController( AuthenticationController ): - @web.expose_api_anonymous + @expose_api_raw_anonymous_and_sessionless def get_tool_shed_api_key( self, trans, **kwd ): """ def get_api_key( self, trans, **kwd ) https://bitbucket.org/galaxy/galaxy-central/commits/d06aa2582d93/ Changeset: d06aa2582d93 User: martenson Date: 2015-02-23 15:54:52+00:00 Summary: Return more specific API auth errors Affected #: 1 file diff -r da044e190f11d33a8556aa60ff563f1e801abf6d -r d06aa2582d9353a39fe7e6afccfa34d58464551f lib/galaxy/webapps/galaxy/api/authenticate.py --- a/lib/galaxy/webapps/galaxy/api/authenticate.py +++ b/lib/galaxy/webapps/galaxy/api/authenticate.py @@ -45,9 +45,11 @@ 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 exceptions.ObjectNotFound() + if ( len( user ) == 0 ): + raise exceptions.ObjectNotFound( 'The user does not exist.' ) + elif ( len( user ) > 1 ): + # DB is inconsistent and we have more users with the same email. + raise exceptions.InconsistentDatabase( 'An error occured, please contact your administrator.' ) else: user = user[0] is_valid_user = user.check_password( password ) @@ -55,7 +57,7 @@ key = self.api_keys_manager.get_or_create_api_key( user ) return dict( api_key=key ) else: - raise exceptions.AuthenticationFailed() + raise exceptions.AuthenticationFailed( 'Invalid password.' ) def _decode_baseauth( self, encoded_str ): """ https://bitbucket.org/galaxy/galaxy-central/commits/cc3c4f51d1ea/ Changeset: cc3c4f51d1ea User: jmchilton Date: 2015-02-18 16:34:23+00:00 Summary: Tool diagnostic API endpoints. It is easy to get Galaxy's database and shed tool files out of sync and the results are bad. I don't think this is new but I may have made it worse this cycle by trying to slowly walk back Galaxy's use of the database to track lineages (e.g. https://bitbucket.org/galaxy/galaxy-central/commits/08f8850853d004bf8a456...). New API endpoints include: /api/configuration/dynamic_tool_confs /api/configuration/tool_lineages /api/<tool_id>/diagnostics Affected #: 6 files diff -r d06aa2582d9353a39fe7e6afccfa34d58464551f -r cc3c4f51d1ea571608b017c1d1fc8100f6ad9e35 lib/galaxy/tools/toolbox/lineages/interface.py --- a/lib/galaxy/tools/toolbox/lineages/interface.py +++ b/lib/galaxy/tools/toolbox/lineages/interface.py @@ -40,3 +40,9 @@ externally). """ return self.version is None + + def to_dict(self): + return dict( + id=self.id, + version=self.version, + ) diff -r d06aa2582d9353a39fe7e6afccfa34d58464551f -r cc3c4f51d1ea571608b017c1d1fc8100f6ad9e35 lib/galaxy/tools/toolbox/lineages/stock.py --- a/lib/galaxy/tools/toolbox/lineages/stock.py +++ b/lib/galaxy/tools/toolbox/lineages/stock.py @@ -38,6 +38,13 @@ # method for comparing tool versions. return sorted( versions, key=_to_loose_version ) + def to_dict(self): + return dict( + tool_id=self.tool_id, + tool_versions=list(self.tool_versions), + lineage_type='stock', + ) + def _to_loose_version( tool_lineage_version ): version = str( tool_lineage_version.version ) diff -r d06aa2582d9353a39fe7e6afccfa34d58464551f -r cc3c4f51d1ea571608b017c1d1fc8100f6ad9e35 lib/galaxy/tools/toolbox/lineages/tool_shed.py --- a/lib/galaxy/tools/toolbox/lineages/tool_shed.py +++ b/lib/galaxy/tools/toolbox/lineages/tool_shed.py @@ -8,9 +8,11 @@ """ Representation of tool lineage derived from tool shed repository installations. """ - def __init__(self, app, tool_version): + def __init__(self, app, tool_version, tool_shed_repository=None): self.app = app self.tool_version_id = tool_version.id + # Only used for logging + self._tool_shed_repository = tool_shed_repository @staticmethod def from_tool( app, tool, tool_shed_repository ): @@ -36,6 +38,16 @@ def get_versions( self, reverse=False ): return map( ToolLineageVersion.from_guid, self.get_version_ids( reverse=reverse ) ) + def to_dict(self): + tool_shed_repository = self._tool_shed_repository + rval = dict( + tool_version_id=self.tool_version_id, + tool_versions=map(lambda v: v.to_dict(), self.get_versions()), + tool_shed_repository=tool_shed_repository if tool_shed_repository is not None else None, + lineage_type='tool_shed', + ) + return rval + def get_install_tool_version( app, tool_id ): return app.install_model.context.query( diff -r d06aa2582d9353a39fe7e6afccfa34d58464551f -r cc3c4f51d1ea571608b017c1d1fc8100f6ad9e35 lib/galaxy/webapps/galaxy/api/configuration.py --- a/lib/galaxy/webapps/galaxy/api/configuration.py +++ b/lib/galaxy/webapps/galaxy/api/configuration.py @@ -4,6 +4,8 @@ """ from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +from galaxy.web import _future_expose_api as expose_api +from galaxy.web import require_admin from galaxy.web.base.controller import BaseAPIController from galaxy.managers import base @@ -33,6 +35,13 @@ @expose_api_anonymous def version( self, trans, **kwds ): + """ + GET /api/version + Return a description of the major version of Galaxy (e.g. 15.03). + + :rtype: dict + :returns: dictionary with major version keyed on 'version_major' + """ return {"version_major": self.app.config.version_major } def get_config_dict( self, trans, return_admin=False, view=None, keys=None, default_view='all' ): @@ -52,6 +61,29 @@ view=view, keys=keys, default_view=default_view ) return serialized + @expose_api + @require_admin + def dynamic_tool_confs(self, trans): + confs = self.app.toolbox.dynamic_confs(include_migrated_tool_conf=True) + return map(_tool_conf_to_dict, confs) + + @expose_api + @require_admin + def tool_lineages(self, trans): + rval = [] + for id, tool in self.app.toolbox.tools(): + if hasattr( tool, 'lineage' ): + lineage_dict = tool.lineage.to_dict() + else: + lineage_dict = None + + entry = dict( + id=id, + lineage=lineage_dict + ) + rval.append(entry) + return rval + #TODO: for lack of a manager file for the config. May well be better in config.py? Circ imports? class ConfigSerializer( base.ModelSerializer ): @@ -122,3 +154,10 @@ 'allow_user_creation' : _defaults_to( False ), 'allow_user_deletion' : _defaults_to( False ), }) + + +def _tool_conf_to_dict(conf): + return dict( + config_filename=conf['config_filename'], + tool_path=conf['tool_path'], + ) diff -r d06aa2582d9353a39fe7e6afccfa34d58464551f -r cc3c4f51d1ea571608b017c1d1fc8100f6ad9e35 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -94,6 +94,36 @@ message, status = trans.app.toolbox.reload_tool_by_id( tool_id ) return { status: message } + @_future_expose_api + @web.require_admin + def diagnostics( self, trans, id, **kwd ): + """ + GET /api/tools/{tool_id}/diagnostics + Return diagnostic information to help debug panel + and dependency related problems. + """ + to_dict = lambda x: x.to_dict() + tool = self._get_tool( id, user=trans.user ) + if hasattr( tool, 'lineage' ): + lineage_dict = tool.lineage.to_dict() + else: + lineage_dict = None + tool_shed_dependencies = tool.installed_tool_dependencies + if tool_shed_dependencies: + tool_shed_dependencies_dict = map(to_dict, tool_shed_dependencies) + else: + tool_shed_dependencies_dict = None + tool = self._get_tool( id, user=trans.user ) + return { + "tool_id": tool.id, + "tool_version": tool.version, + "dependency_shell_commands": tool.build_dependency_shell_commands(), + "lineage": lineage_dict, + "requirements": map(to_dict, tool.requirements), + "installed_tool_shed_dependencies": tool_shed_dependencies_dict, + "tool_dir": tool.tool_dir, + } + @_future_expose_api_anonymous def citations( self, trans, id, **kwds ): tool = self._get_tool( id, user=trans.user ) diff -r d06aa2582d9353a39fe7e6afccfa34d58464551f -r cc3c4f51d1ea571608b017c1d1fc8100f6ad9e35 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -210,6 +210,7 @@ webapp.mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) webapp.mapper.connect( '/api/tools/{id:.+?}/build', action='build', controller="tools" ) webapp.mapper.connect( '/api/tools/{id:.+?}/reload', action='reload', controller="tools" ) + webapp.mapper.connect( '/api/tools/{id:.+?}/diagnostics', action='diagnostics', controller="tools" ) webapp.mapper.connect( '/api/tools/{id:.+?}/citations', action='citations', controller="tools" ) webapp.mapper.connect( '/api/tools/{id:.+?}/download', action='download', controller="tools" ) webapp.mapper.connect( '/api/tools/{id:.+?}', action='show', controller="tools" ) @@ -221,6 +222,18 @@ webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) webapp.mapper.connect( '/api/histories/{history_id}/citations', action='citations', controller="histories" ) + webapp.mapper.connect( + 'dynamic_tool_confs', + '/api/configuration/dynamic_tool_confs', + controller="configuration", + action="dynamic_tool_confs" + ) + webapp.mapper.connect( + 'tool_lineages', + '/api/configuration/tool_lineages', + controller="configuration", + action="tool_lineages" + ) webapp.mapper.resource( 'configuration', 'configuration', path_prefix='/api' ) webapp.mapper.connect( "configuration_version", "/api/version", controller="configuration", Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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