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Add blank lines to the tool_shed repository controller per new dev team coding standards.

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This commit is contained in:
Greg Von Kuster
2013-02-28 11:06:10 -05:00
parent 2cd0ce34b0
commit a562be195b
1 changed files with 154 additions and 2 deletions
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lib/galaxy/webapps/tool_shed/controllers/repository.py
+154 -2
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@@ -27,14 +27,21 @@ 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 ):
def get_value( self, trans, grid, category ):
return category.name
class DescriptionColumn( grids.TextColumn ):
def get_value( self, trans, grid, category ):
return category.description
class RepositoriesColumn( grids.TextColumn ):
def get_value( self, trans, grid, category ):
if category.repositories:
@@ -44,6 +51,7 @@ class CategoryGrid( grids.Grid ):
viewable_repositories += 1
return viewable_repositories
return 0
title = "Categories"
model_class = model.Category
template='/webapps/tool_shed/category/grid.mako'
@@ -69,7 +77,10 @@ class CategoryGrid( grids.Grid ):
preserve_state = False
use_paging = True
class ValidCategoryGrid( CategoryGrid ):
class RepositoriesColumn( grids.TextColumn ):
def get_value( self, trans, grid, category ):
if category.repositories:
@@ -80,6 +91,7 @@ class ValidCategoryGrid( CategoryGrid ):
viewable_repositories += 1
return viewable_repositories
return 0
title = "Categories of valid repositories"
model_class = model.Category
template='/webapps/tool_shed/category/valid_grid.mako'
@@ -106,13 +118,20 @@ class ValidCategoryGrid( CategoryGrid ):
preserve_state = False
use_paging = True
class RepositoryGrid( grids.Grid ):
class NameColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository ):
return escape_html( repository.name )
class MetadataRevisionColumn( grids.GridColumn ):
def __init__( self, col_name ):
grids.GridColumn.__init__( self, col_name )
def get_value( self, trans, grid, repository ):
"""Display a SelectField whose options are the changeset_revision strings of all metadata revisions of this repository."""
# A repository's metadata revisions may not all be installable, as some may contain only invalid tools.
@@ -122,16 +141,26 @@ class RepositoryGrid( grids.Grid ):
elif len( select_field.options ) == 1:
return select_field.options[ 0 ][ 0 ]
return ''
class TipRevisionColumn( grids.GridColumn ):
def __init__( self, col_name ):
grids.GridColumn.__init__( self, col_name )
def get_value( self, trans, grid, repository ):
"""Display the repository tip revision label."""
return escape_html( repository.revision( trans.app ) )
class DescriptionColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository ):
return escape_html( repository.description )
class CategoryColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository ):
rval = '<ul>'
if repository.categories:
@@ -142,34 +171,49 @@ class RepositoryGrid( grids.Grid ):
rval += '<li>not set</li>'
rval += '</ul>'
return rval
class RepositoryCategoryColumn( grids.GridColumn ):
def filter( self, trans, user, query, column_filter ):
"""Modify query to filter by category."""
if column_filter == "All":
return query
return query.filter( model.Category.name == column_filter )
class UserColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository ):
if repository.user:
return escape_html( repository.user.username )
return 'no user'
class EmailColumn( grids.TextColumn ):
def filter( self, trans, user, query, column_filter ):
if column_filter == 'All':
return query
return query.filter( and_( model.Repository.table.c.user_id == model.User.table.c.id,
model.User.table.c.email == column_filter ) )
class EmailAlertsColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository ):
if trans.user and repository.email_alerts and trans.user.email in json.from_json_string( repository.email_alerts ):
return 'yes'
return ''
class DeprecatedColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository ):
if repository.deprecated:
return 'yes'
return ''
# Grid definition
title = "Repositories"
model_class = model.Repository
template='/webapps/tool_shed/repository/grid.mako'
@@ -217,6 +261,7 @@ class RepositoryGrid( grids.Grid ):
num_rows_per_page = 50
preserve_state = False
use_paging = True
def build_initial_query( self, trans, **kwd ):
return trans.sa_session.query( model.Repository ) \
.filter( and_( model.Repository.table.c.deleted == False,
@@ -225,6 +270,7 @@ class RepositoryGrid( grids.Grid ):
.outerjoin( model.RepositoryCategoryAssociation.table ) \
.outerjoin( model.Category.table )
class RepositoriesByUserGrid( RepositoryGrid ):
title = "Repositories by user"
columns = [
@@ -248,6 +294,7 @@ class RepositoriesByUserGrid( RepositoryGrid ):
num_rows_per_page = 50
preserve_state = False
use_paging = True
def build_initial_query( self, trans, **kwd ):
decoded_user_id = trans.security.decode_id( kwd[ 'user_id' ] )
return trans.sa_session.query( model.Repository ) \
@@ -258,6 +305,7 @@ class RepositoriesByUserGrid( RepositoryGrid ):
.outerjoin( model.RepositoryCategoryAssociation.table ) \
.outerjoin( model.Category.table )
class RepositoriesIOwnGrid( RepositoryGrid ):
title = "Repositories I own"
columns = [
@@ -287,6 +335,7 @@ class RepositoriesIOwnGrid( RepositoryGrid ):
allow_multiple=False,
condition=( lambda item: not item.deleted and item.deprecated ),
async_compatible=False ) ]
def build_initial_query( self, trans, **kwd ):
return trans.sa_session.query( model.Repository ) \
.filter( and_( model.Repository.table.c.deleted == False,
@@ -295,6 +344,7 @@ class RepositoriesIOwnGrid( RepositoryGrid ):
.outerjoin( model.RepositoryCategoryAssociation.table ) \
.outerjoin( model.Category.table )
class DeprecatedRepositoriesIOwnGrid( RepositoriesIOwnGrid ):
title = "Deprecated repositories I own"
columns = [
@@ -314,6 +364,7 @@ class DeprecatedRepositoriesIOwnGrid( RepositoriesIOwnGrid ):
key="free-text-search",
visible=False,
filterable="standard" ) )
def build_initial_query( self, trans, **kwd ):
return trans.sa_session.query( model.Repository ) \
.filter( and_( model.Repository.table.c.deleted == False,
@@ -323,6 +374,7 @@ class DeprecatedRepositoriesIOwnGrid( RepositoriesIOwnGrid ):
.outerjoin( model.RepositoryCategoryAssociation.table ) \
.outerjoin( model.Category.table )
class EmailAlertsRepositoryGrid( RepositoryGrid ):
columns = [
RepositoryGrid.NameColumn( "Name",
@@ -352,6 +404,7 @@ class EmailAlertsRepositoryGrid( RepositoryGrid ):
grids.GridAction( "User preferences", dict( controller='user', action='index', cntrller='repository' ) )
]
class MyWritableRepositoriesGrid( RepositoryGrid ):
# This grid filters out repositories that have been marked as either deprecated or deleted.
columns = [
@@ -386,6 +439,7 @@ class MyWritableRepositoriesGrid( RepositoryGrid ):
allow_multiple=False,
condition=( lambda item: not item.deleted ),
async_compatible=False ) ]
def build_initial_query( self, trans, **kwd ):
# TODO: improve performance by adding a db table associating users with repositories for which they have write access.
username = trans.user.username
@@ -408,8 +462,11 @@ class MyWritableRepositoriesGrid( RepositoryGrid ):
return trans.sa_session.query( model.Repository ) \
.filter( model.Repository.table.c.id < 0 )
class ValidRepositoryGrid( RepositoryGrid ):
# This grid filters out repositories that have been marked as either deleted or deprecated.
class CategoryColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository ):
rval = '<ul>'
@@ -421,15 +478,21 @@ class ValidRepositoryGrid( RepositoryGrid ):
rval += '<li>not set</li>'
rval += '</ul>'
return rval
class RepositoryCategoryColumn( grids.GridColumn ):
def filter( self, trans, user, query, column_filter ):
"""Modify query to filter by category."""
if column_filter == "All":
return query
return query.filter( model.Category.name == column_filter )
class RevisionColumn( grids.GridColumn ):
def __init__( self, col_name ):
grids.GridColumn.__init__( self, col_name )
def get_value( self, trans, grid, repository ):
"""Display a SelectField whose options are the changeset_revision strings of all download-able revisions of this repository."""
select_field = build_changeset_revision_select_field( trans, repository, downloadable=True )
@@ -462,6 +525,7 @@ class ValidRepositoryGrid( RepositoryGrid ):
visible=False,
filterable="standard" ) )
operations = []
def build_initial_query( self, trans, **kwd ):
if 'id' in kwd:
# The user is browsing categories of valid repositories, so filter the request by the received id, which is a category id.
@@ -484,22 +548,36 @@ class ValidRepositoryGrid( RepositoryGrid ):
.outerjoin( model.Category.table ) \
.filter( model.RepositoryMetadata.table.c.downloadable == True )
class MatchedRepositoryGrid( grids.Grid ):
# This grid filters out repositories that have been marked as deprecated.
class NameColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository_metadata ):
return repository_metadata.repository.name
class DescriptionColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository_metadata ):
return repository_metadata.repository.description
class RevisionColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository_metadata ):
return repository_metadata.changeset_revision
class UserColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository_metadata ):
if repository_metadata.repository.user:
return repository_metadata.repository.user.username
return 'no user'
# Grid definition
title = "Matching repositories"
model_class = model.RepositoryMetadata
@@ -524,6 +602,7 @@ class MatchedRepositoryGrid( grids.Grid ):
num_rows_per_page = 50
preserve_state = False
use_paging = True
def build_initial_query( self, trans, **kwd ):
match_tuples = kwd.get( 'match_tuples', [] )
clause_list = []
@@ -545,6 +624,7 @@ class MatchedRepositoryGrid( grids.Grid ):
return trans.sa_session.query( model.RepositoryMetadata ) \
.filter( model.RepositoryMetadata.id < 0 )
class InstallMatchedRepositoryGrid( MatchedRepositoryGrid ):
columns = [ col for col in MatchedRepositoryGrid.columns ]
# Override the NameColumn
@@ -552,6 +632,7 @@ class InstallMatchedRepositoryGrid( MatchedRepositoryGrid ):
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=False )
class RepositoryController( BaseUIController, common_util.ItemRatings ):
install_matched_repository_grid = InstallMatchedRepositoryGrid()
@@ -594,6 +675,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
action='browse_repositories',
**kwd ) )
return self.category_grid( trans, **kwd )
@web.expose
def browse_invalid_tools( self, trans, **kwd ):
params = util.Params( kwd )
@@ -634,6 +716,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
invalid_tools_dict=invalid_tools_dict,
message=message,
status=status )
@web.expose
def browse_repositories( self, trans, **kwd ):
# We add params to the keyword dict in this method in order to rename the param with an "f-" prefix, simulating filtering by clicking a search
@@ -705,6 +788,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
id=trans.security.encode_id( repository.id ),
changeset_revision=selected_changeset_revision ) )
return self.repository_grid( trans, **kwd )
@web.expose
def browse_repositories_by_user( self, trans, **kwd ):
"""Display the list of repositories owned by a specified user."""
@@ -735,6 +819,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
user = suc.get_user( trans, kwd[ 'user_id' ] )
self.repositories_by_user_grid.title = "Repositories owned by %s" % user.username
return self.repositories_by_user_grid( trans, **kwd )
@web.expose
def browse_repository( self, trans, id, **kwd ):
params = util.Params( kwd )
@@ -754,6 +839,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
is_malicious=is_malicious,
message=message,
status=status )
@web.expose
def browse_valid_categories( self, trans, **kwd ):
# The request came from Galaxy, so restrict category links to display only valid repository changeset revisions.
@@ -787,6 +873,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
action='browse_valid_repositories',
**kwd ) )
return self.valid_category_grid( trans, **kwd )
@web.expose
def browse_valid_repositories( self, trans, **kwd ):
galaxy_url = kwd.get( 'galaxy_url', None )
@@ -832,6 +919,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
allow_multiple=False,
async_compatible=False ) ]
return self.valid_repository_grid( trans, **kwd )
def __build_allow_push_select_field( self, trans, current_push_list, selected_value='none' ):
options = []
for user in trans.sa_session.query( trans.model.User ):
@@ -844,6 +932,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
selected_value=selected_value,
refresh_on_change=False,
multiple=True )
def __change_repository_name_in_hgrc_file( self, hgrc_file, new_name ):
config = ConfigParser.ConfigParser()
config.read( hgrc_file )
@@ -852,6 +941,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
new_file = open( hgrc_file, 'wb' )
config.write( new_file )
new_file.close()
@web.expose
def check_for_updates( self, trans, **kwd ):
"""Handle a request from a local Galaxy instance."""
@@ -929,6 +1019,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
url += str( latest_changeset_revision )
url += '&latest_ctx_rev=%s' % str( update_to_ctx.rev() )
return trans.response.send_redirect( url )
@web.expose
def contact_owner( self, trans, id, **kwd ):
params = util.Params( kwd )
@@ -945,6 +1036,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
else:
# Do all we can to eliminate spam.
return trans.show_error_message( "You must be logged in to contact the owner of a repository." )
def __create_hgrc_file( self, trans, repository ):
# At this point, an entry for the repository is required to be in the hgweb.config file so we can call repository.repo_path( trans.app ).
# Since we support both http and https, we set push_ssl to False to override the default (which is True) in the mercurial api. The hg
@@ -962,6 +1054,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
fp.write( '[extensions]\n' )
fp.write( 'hgext.purge=' )
fp.close()
@web.expose
def create_repository( self, trans, **kwd ):
params = util.Params( kwd )
@@ -1040,6 +1133,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
categories=categories,
message=message,
status=status )
@web.expose
@web.require_login( "deprecate repository" )
def deprecate( self, trans, **kwd ):
@@ -1061,6 +1155,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
operation='repositories_i_own',
message=message,
status=status ) )
@web.expose
def display_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ):
params = util.Params( kwd )
@@ -1098,6 +1193,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
changeset_revision=changeset_revision,
message=message,
status='error' ) )
@web.expose
def download( self, trans, repository_id, changeset_revision, file_type, **kwd ):
# Download an archive of the repository files compressed as zip, gz or bz2.
@@ -1118,6 +1214,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
trans.sa_session.flush()
download_url = '/repos/%s/%s/archive/%s' % ( repository.user.username, repository.name, file_type_str )
return trans.response.send_redirect( download_url )
@web.expose
def find_tools( self, trans, **kwd ):
params = util.Params( kwd )
@@ -1204,6 +1301,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
exact_matches_check_box=exact_matches_check_box,
message=message,
status=status )
@web.expose
def find_workflows( self, trans, **kwd ):
params = util.Params( kwd )
@@ -1291,10 +1389,12 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
exact_matches_check_box=exact_matches_check_box,
message=message,
status=status )
@web.expose
def generate_workflow_image( self, trans, workflow_name, repository_metadata_id=None ):
"""Return an svg image representation of a workflow dictionary created when the workflow was exported."""
return workflow_util.generate_workflow_image( trans, workflow_name, repository_metadata_id=repository_metadata_id, repository_id=None )
@web.expose
def get_changeset_revision_and_ctx_rev( self, trans, **kwd ):
"""Handle a request from a local Galaxy instance to retrieve the changeset revision hash to which an installed repository can be updated."""
@@ -1392,6 +1492,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
update_dict[ 'changeset_revision' ] = str( latest_changeset_revision )
update_dict[ 'ctx_rev' ] = str( update_to_ctx.rev() )
return encoding_util.tool_shed_encode( update_dict )
@web.expose
def get_ctx_rev( self, trans, **kwd ):
"""Given a repository and changeset_revision, return the correct ctx.rev() value."""
@@ -1405,12 +1506,14 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
if ctx:
return str( ctx.rev() )
return ''
@web.json
def get_file_contents( self, trans, file_path ):
# Avoid caching
trans.response.headers['Pragma'] = 'no-cache'
trans.response.headers['Expires'] = '0'
return suc.get_repository_file_contents( file_path )
def get_file_from_changeset_revision( self, repo_files_dir, changeset_revision, file_name, dir ):
"""Return file_name from the received changeset_revision of the repository manifest."""
stripped_file_name = suc.strip_path( file_name )
@@ -1418,11 +1521,13 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
named_tmp_file = suc.get_named_tmpfile_from_ctx( ctx, file_name, dir )
return named_tmp_file
def get_metadata( self, trans, repository_id, changeset_revision ):
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
if repository_metadata and repository_metadata.metadata:
return repository_metadata.metadata
return None
@web.json
def get_readme_files( self, trans, **kwd ):
"""
@@ -1435,6 +1540,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision )
return suc.build_readme_files_dict( repository_metadata.metadata )
@web.json
def get_repository_dependencies( self, trans, **kwd ):
"""Return an encoded dictionary of all repositories upon which the contents of the received repository depends."""
@@ -1459,6 +1565,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
if repository_dependencies:
return encoding_util.tool_shed_encode( repository_dependencies )
return ''
def __get_repository_from_refresh_on_change( self, trans, **kwd ):
# The changeset_revision_select_field in several grids 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,
@@ -1474,6 +1581,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
return v, repository
# This should never be reached - raise an exception?
return v, None
@web.json
def get_repository_information( self, trans, repository_ids, changeset_revisions, **kwd ):
"""
@@ -1517,6 +1625,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
has_repository_dependencies=has_repository_dependencies,
includes_tool_dependencies=includes_tool_dependencies,
repo_info_dicts=repo_info_dicts )
@web.json
def get_required_repo_info_dict( self, trans, encoded_str ):
"""
@@ -1540,6 +1649,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
else:
repo_info_dict = {}
return repo_info_dict
@web.expose
def get_tool_dependencies( self, trans, **kwd ):
"""Handle a request from a Galaxy instance to get the tool_dependencies entry from the metadata for a specified changeset revision."""
@@ -1556,6 +1666,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
if tool_dependencies:
return encoding_util.tool_shed_encode( tool_dependencies )
return ''
@web.expose
def get_tool_dependencies_config_contents( self, trans, **kwd ):
"""Handle a request from a Galaxy instance to get the tool_dependencies.xml file contents for a specified changeset revision."""
@@ -1576,6 +1687,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
tool_dependencies_config_file.close()
return contents
return ''
@web.expose
def get_tool_versions( self, trans, **kwd ):
"""
@@ -1599,6 +1711,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
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 dictionary that contains the information about a repository that is necessary for installing it into a local Galaxy instance."""
@@ -1655,6 +1768,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
includes_workflows=includes_workflows,
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 )
@@ -1685,12 +1799,14 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
current_parent_guid = child_guid
break
return tool_guid_lineage
@web.expose
def help( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
return trans.fill_template( '/webapps/tool_shed/repository/help.mako', message=message, status=status, **kwd )
def __in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ):
found = False
if tool_id and not tool_name and not tool_version:
@@ -1732,10 +1848,12 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
tool_dict_tool_name.find( tool_name ) >= 0 and \
tool_dict_tool_id.find( tool_id ) >= 0 )
return found
def __in_workflow_dict( self, workflow_dict, exact_matches_checked, workflow_name ):
workflow_dict_workflow_name = workflow_dict[ 'name' ].lower()
return ( workflow_name == workflow_dict_workflow_name ) or \
( not exact_matches_checked and workflow_dict_workflow_name.find( workflow_name ) >= 0 )
@web.expose
def index( self, trans, **kwd ):
params = util.Params( kwd )
@@ -1771,6 +1889,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
changeset_revision=changeset_revision,
message=message,
status=status )
@web.expose
def install_repositories_by_revision( self, trans, **kwd ):
"""
@@ -1793,6 +1912,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
'admin_toolshed/prepare_for_install?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \
( web.url_for( '/', qualified=True ), ','.join( util.listify( repository_ids ) ), ','.join( util.listify( changeset_revisions ) ) ) )
return trans.response.send_redirect( url )
@web.expose
def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ):
params = util.Params( kwd )
@@ -1837,6 +1957,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
changeset_revision=changeset_revision,
message=message,
status='error' ) )
def __make_same_length( self, list1, list2 ):
# If either list is 1 item, we'll append to it until its length is the same as the other.
if len( list1 ) == 1:
@@ -1846,6 +1967,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
for i in range( 1, len( list1 ) ):
list2.append( list2[ 0 ] )
return list1, list2
@web.expose
@web.require_login( "manage email alerts" )
def manage_email_alerts( self, trans, **kwd ):
@@ -1877,6 +1999,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
email_alert_repositories=email_alert_repositories,
message=message,
status=status )
@web.expose
@web.require_login( "manage repository" )
def manage_repository( self, trans, id, **kwd ):
@@ -2083,12 +2206,14 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
can_browse_repository_reviews=can_browse_repository_reviews,
message=message,
status=status )
@web.expose
@web.require_login( "review repository revision" )
def manage_repository_reviews_of_revision( self, trans, **kwd ):
return trans.response.send_redirect( web.url_for( controller='repository_review',
action='manage_repository_reviews_of_revision',
**kwd ) )
@web.expose
@web.require_login( "multi select email alerts" )
def multi_select_email_alerts( self, trans, **kwd ):
@@ -2110,6 +2235,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
del kwd[ 'operation' ]
self.email_alerts_repository_grid.title = "Set email alerts for repository changes"
return self.email_alerts_repository_grid( trans, **kwd )
def __new_state( self, trans, all_pages=False ):
"""
Create a new `DefaultToolState` for this tool. It will not be initialized
@@ -2121,12 +2247,14 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
state = galaxy.tools.DefaultToolState()
state.inputs = {}
return state
@web.json
def open_folder( self, trans, folder_path ):
# Avoid caching
trans.response.headers['Pragma'] = 'no-cache'
trans.response.headers['Expires'] = '0'
return suc.open_repository_files_folder( trans, folder_path )
@web.expose
def preview_tools_in_changeset( self, trans, repository_id, **kwd ):
params = util.Params( kwd )
@@ -2173,6 +2301,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
metadata=metadata,
message=message,
status=status )
@web.expose
def previous_changeset_revisions( self, trans, **kwd ):
"""
@@ -2201,6 +2330,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
changeset_hashes_str = ','.join( changeset_hashes )
return changeset_hashes_str
return ''
@web.expose
@web.require_login( "rate repositories" )
def rate_repository( self, trans, **kwd ):
@@ -2240,6 +2370,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
is_malicious=is_malicious,
message=message,
status=status )
@web.expose
def reset_all_metadata( self, trans, id, **kwd ):
# This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template.
@@ -2257,24 +2388,28 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
id=id,
message=message,
status=status ) )
def __search_ids_names( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ):
for i, tool_id in enumerate( tool_ids ):
tool_name = tool_names[ i ]
if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ):
match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
return match_tuples
def __search_ids_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ):
for i, tool_id in enumerate( tool_ids ):
tool_version = tool_versions[ i ]
if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ):
match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
return match_tuples
def __search_names_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ):
for i, tool_name in enumerate( tool_names ):
tool_version = tool_versions[ i ]
if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version ):
match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
return match_tuples
def __search_repository_metadata( self, trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='', all_workflows=False ):
match_tuples = []
ok = True
@@ -2346,6 +2481,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
elif all_workflows and 'workflows' in metadata:
match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
return ok, match_tuples
@web.expose
def select_files_to_delete( self, trans, id, **kwd ):
params = util.Params( kwd )
@@ -2412,6 +2548,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
is_malicious=is_malicious,
message=message,
status=status )
@web.expose
def send_to_owner( self, trans, id, message='' ):
repository = suc.get_repository_in_tool_shed( trans, id )
@@ -2450,6 +2587,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
id=id,
message=message,
status=status ) )
@web.expose
@web.require_login( "set email alerts" )
def set_email_alerts( self, trans, **kwd ):
@@ -2490,6 +2628,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
return trans.response.send_redirect( web.url_for( controller='repository',
action=caller,
**kwd ) )
@web.expose
@web.require_login( "set repository as malicious" )
def set_malicious( self, trans, id, ctx_str, **kwd ):
@@ -2512,6 +2651,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
malicious=malicious,
message=message,
status=status ) )
@web.expose
def sharable_owner( self, trans, owner ):
"""Support for sharable URL for each repository owner's tools, e.g. http://example.org/view/owner."""
@@ -2527,6 +2667,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
else:
return trans.show_error_message( "The tool shed <b>%s</b> contains no repositories owned by <b>%s</b>." % \
( web.url_for( '/', qualified=True ).rstrip( '/' ), str( owner ) ) )
@web.expose
def sharable_repository( self, trans, owner, name ):
"""Support for sharable URL for a specified repository, e.g. http://example.org/view/owner/name."""
@@ -2556,6 +2697,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
else:
return trans.show_error_message( "The tool shed <b>%s</b> contains no repositories named <b>%s</b> with owner <b>%s</b>." % \
( web.url_for( '/', qualified=True ).rstrip( '/' ), str( name ), str( owner ) ) )
@web.expose
def sharable_repository_revision( self, trans, owner, name, changeset_revision ):
"""Support for sharable URL for a specified repository revision, e.g. http://example.org/view/owner/name/changeset_revision."""
@@ -2592,10 +2734,12 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
return trans.response.send_redirect( web.url_for( controller='repository',
action='sharable_owner',
owner=owner ) )
def __stringify( self, list ):
if list:
return ','.join( list )
return ''
@web.expose
def updated_changeset_revisions( self, trans, **kwd ):
"""
@@ -2625,6 +2769,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
changeset_hashes_str = ','.join( changeset_hashes )
return changeset_hashes_str
return ''
def __validate_repository_name( self, name, user ):
# Repository names must be unique for each user, must be at least four characters
# in length and must contain only lower-case letters, numbers, and the '_' character.
@@ -2642,6 +2787,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
if not( VALID_REPOSITORYNAME_RE.match( name ) ):
return "Repository names must contain only lower-case letters, numbers and underscore <b>_</b>."
return ''
@web.expose
def view_changelog( self, trans, id, **kwd ):
params = util.Params( kwd )
@@ -2679,6 +2825,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
is_malicious=is_malicious,
message=message,
status=status )
@web.expose
def view_changeset( self, trans, id, ctx_str, **kwd ):
params = util.Params( kwd )
@@ -2719,6 +2866,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
is_malicious=is_malicious,
message=message,
status=status )
@web.expose
def view_or_manage_repository( self, trans, **kwd ):
repository = suc.get_repository_in_tool_shed( trans, kwd[ 'id' ] )
@@ -2730,6 +2878,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
return trans.response.send_redirect( web.url_for( controller='repository',
action='view_repository',
**kwd ) )
@web.expose
def view_repository( self, trans, id, **kwd ):
params = util.Params( kwd )
@@ -2829,6 +2978,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
can_browse_repository_reviews=can_browse_repository_reviews,
message=message,
status=status )
@web.expose
def view_tool_metadata( self, trans, repository_id, changeset_revision, tool_id, **kwd ):
params = util.Params( kwd )
@@ -2907,6 +3057,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
review_id=review_id,
message=message,
status=status )
@web.expose
def view_workflow( self, trans, workflow_name, repository_metadata_id, **kwd ):
"""Retrieve necessary information about a workflow from the database so that it can be displayed in an svg image."""
@@ -2927,6 +3078,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
metadata=metadata,
message=message,
status=status )
# ----- Utility methods -----
def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True,