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https://github.com/galaxyproject/galaxy.git
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Relocate the tool shed's ShedCounter.
This commit is contained in:
Greg Von Kuster
@@ -1,7 +1,6 @@
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import sys, os, tempfile, shutil, logging, string, urllib2
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import galaxy.tools.data
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from datetime import date, datetime, timedelta
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from time import strftime, gmtime
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from galaxy import util
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from galaxy.web import url_for
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from galaxy.web.form_builder import SelectField
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@@ -40,85 +39,6 @@ NOT_TOOL_CONFIGS = [ 'datatypes_conf.xml', 'tool_dependencies.xml' ]
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VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" )
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TOOL_SHED_ADMIN_CONTROLLER = 'TOOL_SHED_ADMIN_CONTROLLER'
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class ShedCounter( object ):
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def __init__( self, model ):
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# TODO: Enhance the ShedCounter to retrieve information from the db instead of displaying what's currently in memory.
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self.model = model
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self.generation_time = strftime( "%b %d, %Y", gmtime() )
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self.repositories = 0
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#self.new_repositories = 0
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self.deleted_repositories = 0
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self.invalid_tools = 0
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self.valid_tools = 0
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self.workflows = 0
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self.proprietary_datatypes = 0
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self.total_clones = 0
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self.generate_statistics()
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@property
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def sa_session( self ):
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"""Returns a SQLAlchemy session"""
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return self.model.context
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def generate_statistics( self ):
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self.repositories = 0
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#self.new_repositories = 0
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self.deleted_repositories = 0
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self.invalid_tools = 0
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self.valid_tools = 0
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self.workflows = 0
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self.proprietary_datatypes = 0
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self.total_clones = 0
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for repository in self.sa_session.query( self.model.Repository ):
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self.repositories += 1
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self.total_clones += repository.times_downloaded
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is_deleted = repository.deleted
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#is_new = repository.is_new
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#if is_deleted and is_new:
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if is_deleted:
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self.deleted_repositories += 1
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# self.new_repositories += 1
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#elif is_deleted:
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# self.deleted_repositories += 1
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#elif is_new:
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# self.new_repositories += 1
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else:
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processed_guids = []
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processed_invalid_tool_configs = []
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processed_relative_workflow_paths = []
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processed_datatypes = []
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# A repository's metadata_revisions are those that ignore the value of the repository_metadata.downloadable column.
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for metadata_revision in repository.metadata_revisions:
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metadata = metadata_revision.metadata
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if 'tools' in metadata:
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tool_dicts = metadata[ 'tools' ]
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for tool_dict in tool_dicts:
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if 'guid' in tool_dict:
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guid = tool_dict[ 'guid' ]
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if guid not in processed_guids:
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self.valid_tools += 1
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processed_guids.append( guid )
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if 'invalid_tools' in metadata:
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invalid_tool_configs = metadata[ 'invalid_tools' ]
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for invalid_tool_config in invalid_tool_configs:
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if invalid_tool_config not in processed_invalid_tool_configs:
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self.invalid_tools += 1
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processed_invalid_tool_configs.append( invalid_tool_config )
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if 'datatypes' in metadata:
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datatypes = metadata[ 'datatypes' ]
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for datatypes_dict in datatypes:
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if 'extension' in datatypes_dict:
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extension = datatypes_dict[ 'extension' ]
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if extension not in processed_datatypes:
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self.proprietary_datatypes += 1
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processed_datatypes.append( extension )
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if 'workflows' in metadata:
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workflows = metadata[ 'workflows' ]
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for workflow_tup in workflows:
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relative_path, exported_workflow_dict = workflow_tup
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if relative_path not in processed_relative_workflow_paths:
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self.workflows += 1
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processed_relative_workflow_paths.append( relative_path )
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self.generation_time = strftime( "%b %d, %Y", gmtime() )
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def add_to_shed_tool_config( app, shed_tool_conf_dict, elem_list ):
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# A tool shed repository is being installed so change the shed_tool_conf file. Parse the config file to generate the entire list
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# of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have
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@@ -13,7 +13,7 @@ from galaxy.model.orm import *
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from galaxy.model.orm.ext.assignmapper import *
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from galaxy.model.custom_types import *
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from galaxy.util.bunch import Bunch
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from galaxy.util.shed_util import ShedCounter
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from galaxy.webapps.community.util.shed_statistics import *
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from galaxy.webapps.community.util.hgweb_config import *
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from galaxy.webapps.community.security import CommunityRBACAgent
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@@ -0,0 +1,80 @@
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from time import strftime, gmtime
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class ShedCounter( object ):
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def __init__( self, model ):
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# TODO: Enhance the ShedCounter to retrieve information from the db instead of displaying what's currently in memory.
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self.model = model
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self.generation_time = strftime( "%b %d, %Y", gmtime() )
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self.repositories = 0
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#self.new_repositories = 0
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self.deleted_repositories = 0
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self.invalid_tools = 0
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self.valid_tools = 0
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self.workflows = 0
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self.proprietary_datatypes = 0
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self.total_clones = 0
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self.generate_statistics()
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@property
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def sa_session( self ):
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"""Returns a SQLAlchemy session"""
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return self.model.context
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def generate_statistics( self ):
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self.repositories = 0
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#self.new_repositories = 0
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self.deleted_repositories = 0
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self.invalid_tools = 0
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self.valid_tools = 0
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self.workflows = 0
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self.proprietary_datatypes = 0
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self.total_clones = 0
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for repository in self.sa_session.query( self.model.Repository ):
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self.repositories += 1
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self.total_clones += repository.times_downloaded
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is_deleted = repository.deleted
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#is_new = repository.is_new
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#if is_deleted and is_new:
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if is_deleted:
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self.deleted_repositories += 1
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# self.new_repositories += 1
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#elif is_deleted:
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# self.deleted_repositories += 1
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#elif is_new:
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# self.new_repositories += 1
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else:
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processed_guids = []
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processed_invalid_tool_configs = []
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processed_relative_workflow_paths = []
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processed_datatypes = []
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# A repository's metadata_revisions are those that ignore the value of the repository_metadata.downloadable column.
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for metadata_revision in repository.metadata_revisions:
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metadata = metadata_revision.metadata
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if 'tools' in metadata:
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tool_dicts = metadata[ 'tools' ]
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for tool_dict in tool_dicts:
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if 'guid' in tool_dict:
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guid = tool_dict[ 'guid' ]
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if guid not in processed_guids:
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self.valid_tools += 1
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processed_guids.append( guid )
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if 'invalid_tools' in metadata:
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invalid_tool_configs = metadata[ 'invalid_tools' ]
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for invalid_tool_config in invalid_tool_configs:
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if invalid_tool_config not in processed_invalid_tool_configs:
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self.invalid_tools += 1
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processed_invalid_tool_configs.append( invalid_tool_config )
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if 'datatypes' in metadata:
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datatypes = metadata[ 'datatypes' ]
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for datatypes_dict in datatypes:
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if 'extension' in datatypes_dict:
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extension = datatypes_dict[ 'extension' ]
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if extension not in processed_datatypes:
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self.proprietary_datatypes += 1
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processed_datatypes.append( extension )
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if 'workflows' in metadata:
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workflows = metadata[ 'workflows' ]
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for workflow_tup in workflows:
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relative_path, exported_workflow_dict = workflow_tup
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if relative_path not in processed_relative_workflow_paths:
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self.workflows += 1
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processed_relative_workflow_paths.append( relative_path )
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self.generation_time = strftime( "%b %d, %Y", gmtime() )
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