class AdminRepositoryGrid(RepositoryGrid):
class DeletedColumn(grids.BooleanColumn):
def get_value(self, trans, grid, repository):
if repository.deleted:
return 'yes'
return ''
columns = [
RepositoryGrid.NameColumn(
"Name",
key="name",
link=(lambda item: dict(operation="view_or_manage_repository",
id=item.id)),
attach_popup=True),
RepositoryGrid.HeadsColumn("Heads"),
RepositoryGrid.UserColumn(
"Owner",
model_class=model.User,
link=(lambda item: dict(operation="repositories_by_user",
id=item.id)),
attach_popup=False,
key="User.username"),
RepositoryGrid.DeprecatedColumn("Deprecated",
key="deprecated",
attach_popup=False),
# Columns that are valid for filtering but are not visible.
DeletedColumn("Deleted", key="deleted", attach_popup=False)
]
columns.append(
grids.MulticolFilterColumn("Search repository name",
cols_to_filter=[columns[0]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [operation for operation in RepositoryGrid.operations]
operations.append(
grids.GridOperation("Delete",
allow_multiple=False,
condition=(lambda item: not item.deleted),
async_compatible=False))
operations.append(
grids.GridOperation("Undelete",
allow_multiple=False,
condition=(lambda item: item.deleted),
async_compatible=False))
def build_initial_query(self, trans, **kwd):
return trans.sa_session.query(model.Repository) \
.join(model.User.table)
class ReviewedRepositoriesIOwnGrid(RepositoriesWithReviewsGrid):
title = "Reviewed repositories I own"
columns = [
RepositoriesWithReviewsGrid.NameColumn("Repository name",
key="name",
link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
attach_popup=True),
RepositoriesWithReviewsGrid.WithReviewsRevisionColumn("Reviewed revisions"),
RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn("Revisions for review"),
RepositoriesWithReviewsGrid.ReviewersColumn("Reviewers", attach_popup=False),
RepositoryGrid.DeprecatedColumn("Deprecated")
]
columns.append(grids.MulticolFilterColumn("Search repository name",
cols_to_filter=[columns[0]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [
grids.GridOperation("Inspect repository revisions",
allow_multiple=False,
condition=(lambda item: not item.deleted),
async_compatible=False)
]
def build_initial_query(self, trans, **kwd):
return trans.sa_session.query(model.Repository) \
.join((model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id)) \
.filter(model.Repository.table.c.user_id == trans.user.id) \
.join((model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id)) \
.outerjoin((model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id)) \
.outerjoin((model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id))
class RepositoriesWithoutReviewsGrid(RepositoriesWithReviewsGrid):
# This grid filters out repositories that have been marked as either deprecated or deleted.
title = "Repositories with no reviews"
columns = [
RepositoriesWithReviewsGrid.NameColumn("Repository name",
key="name",
link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
attach_popup=True),
RepositoriesWithReviewsGrid.DescriptionColumn("Synopsis",
key="description",
attach_popup=False),
RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn("Revisions for review"),
RepositoriesWithReviewsGrid.UserColumn("Owner",
model_class=model.User,
attach_popup=False,
key="User.username")
]
columns.append(grids.MulticolFilterColumn("Search repository name, description",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [grids.GridOperation("Inspect repository revisions",
allow_multiple=False,
condition=(lambda item: not item.deleted),
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(),
model.Repository.table.c.deprecated == false(),
model.Repository.reviews == null())) \
.join(model.User.table)
class RepositoriesReadyForReviewGrid(RepositoriesWithoutReviewsGrid):
# Repositories that are ready for human review are those that either:
# 1) Have no tools
# 2) Have tools that have been proven to be functionally correct within Galaxy.
# This grid filters out repositories that have been marked as either deprecated or deleted.
title = "Repositories ready for review"
columns = [
RepositoriesWithoutReviewsGrid.NameColumn(
"Repository name",
key="name",
link=(lambda item: dict(operation="view_or_manage_repository",
id=item.id)),
attach_popup=True),
RepositoriesWithoutReviewsGrid.DescriptionColumn("Synopsis",
key="description",
attach_popup=False),
RepositoriesWithoutReviewsGrid.WithoutReviewsRevisionColumn(
"Revisions for review"),
RepositoriesWithoutReviewsGrid.UserColumn("Owner",
model_class=model.User,
attach_popup=False,
key="User.username")
]
columns.append(
grids.MulticolFilterColumn("Search repository name, description",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [
grids.GridOperation("Inspect repository revisions",
allow_multiple=False,
condition=(lambda item: not item.deleted),
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(),
model.Repository.table.c.deprecated == false(),
model.Repository.reviews == null())) \
.join(model.RepositoryMetadata.table) \
.filter(and_(model.RepositoryMetadata.table.c.downloadable == true(),
or_(model.RepositoryMetadata.table.c.includes_tools == false(),
and_(model.RepositoryMetadata.table.c.includes_tools == true(),
model.RepositoryMetadata.table.c.tools_functionally_correct == true())))) \
.join(model.User.table)
class AdminController(BaseUIController, Admin):
user_list_grid = admin_grids.UserGrid()
role_list_grid = admin_grids.RoleGrid()
group_list_grid = admin_grids.GroupGrid()
manage_category_grid = admin_grids.ManageCategoryGrid()
repository_grid = admin_grids.AdminRepositoryGrid()
repository_metadata_grid = admin_grids.RepositoryMetadataGrid()
delete_operation = grids.GridOperation(
"Delete",
condition=(lambda item: not item.deleted),
allow_multiple=True)
undelete_operation = grids.GridOperation(
"Undelete",
condition=(lambda item: item.deleted and not item.purged),
allow_multiple=True)
purge_operation = grids.GridOperation(
"Purge",
condition=(lambda item: item.deleted and not item.purged),
allow_multiple=True)
@web.expose
@web.require_admin
def browse_repositories(self, trans, **kwd):
# We add parameters to the keyword dict in this method in order to rename the param
# with an "f-" prefix, simulating filtering by clicking a search link. We have
# to take this approach because the "-" character is illegal in HTTP requests.
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "view_or_manage_repository":
return trans.response.send_redirect(
web.url_for(controller='repository',
action='browse_repositories',
**kwd))
elif operation == "edit_repository":
return trans.response.send_redirect(
web.url_for(controller='repository',
action='edit_repository',
**kwd))
elif operation == "repositories_by_user":
# Eliminate the current filters if any exist.
for k, v in list(kwd.items()):
if k.startswith('f-'):
del kwd[k]
if 'user_id' in kwd:
user = suc.get_user(trans.app, kwd['user_id'])
kwd['f-email'] = user.email
del kwd['user_id']
else:
# The received id is the repository id, so we need to get the id of the user
# that uploaded the repository.
repository_id = kwd.get('id', None)
repository = repository_util.get_repository_in_tool_shed(
trans.app, repository_id)
kwd['f-email'] = repository.user.email
elif operation == "repositories_by_category":
# Eliminate the current filters if any exist.
for k, v in list(kwd.items()):
if k.startswith('f-'):
del kwd[k]
category_id = kwd.get('id', None)
category = suc.get_category(trans.app, category_id)
kwd['f-Category.name'] = category.name
elif operation == "receive email alerts":
if kwd['id']:
kwd['caller'] = 'browse_repositories'
return trans.response.send_redirect(
web.url_for(controller='repository',
action='set_email_alerts',
**kwd))
else:
del kwd['operation']
elif operation == 'delete':
return self.delete_repository(trans, **kwd)
elif operation == "undelete":
return self.undelete_repository(trans, **kwd)
# The changeset_revision_select_field in the RepositoryGrid performs a refresh_on_change
# which sends in request parameters like changeset_revison_1, changeset_revision_2, etc. One
# of the many select fields on the grid performed the refresh_on_change, so we loop through
# all of the received values to see which value is not the repository tip. If we find it, we
# know the refresh_on_change occurred, and we have the necessary repository id and change set
# revision to pass on.
for k, v in kwd.items():
changeset_revision_str = 'changeset_revision_'
if k.startswith(changeset_revision_str):
repository_id = trans.security.encode_id(
int(k.lstrip(changeset_revision_str)))
repository = repository_util.get_repository_in_tool_shed(
trans.app, repository_id)
if repository.tip() != v:
return trans.response.send_redirect(
web.url_for(controller='repository',
action='browse_repositories',
operation='view_or_manage_repository',
id=trans.security.encode_id(repository.id),
changeset_revision=v))
# Render the list view
return self.repository_grid(trans, **kwd)
@web.expose
@web.require_admin
def browse_repository_metadata(self, trans, **kwd):
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "delete":
return self.delete_repository_metadata(trans, **kwd)
if operation == "view_or_manage_repository_revision":
# The received id is a RepositoryMetadata object id, so we need to get the
# associated Repository and redirect to view_or_manage_repository with the
# changeset_revision.
repository_metadata = metadata_util.get_repository_metadata_by_id(
trans.app, kwd['id'])
repository = repository_metadata.repository
kwd['id'] = trans.security.encode_id(repository.id)
kwd['changeset_revision'] = repository_metadata.changeset_revision
kwd['operation'] = 'view_or_manage_repository'
return trans.response.send_redirect(
web.url_for(controller='repository',
action='browse_repositories',
**kwd))
return self.repository_metadata_grid(trans, **kwd)
@web.expose
@web.require_admin
def create_category(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
name = kwd.get('name', '').strip()
description = kwd.get('description', '').strip()
if kwd.get('create_category_button', False):
if not name or not description:
message = 'Enter a valid name and a description'
status = 'error'
elif suc.get_category_by_name(trans.app, name):
message = 'A category with that name already exists'
status = 'error'
else:
# Create the category
category = trans.app.model.Category(name=name,
description=description)
trans.sa_session.add(category)
trans.sa_session.flush()
# Update the Tool Shed's repository registry.
trans.app.repository_registry.add_category_entry(category)
message = "Category '%s' has been created" % escape(
category.name)
status = 'done'
trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=message,
status=status))
return trans.fill_template(
'/webapps/tool_shed/category/create_category.mako',
name=name,
description=description,
message=message,
status=status)
@web.expose
@web.require_admin
def delete_repository(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
id = kwd.get('id', None)
if id:
# Deleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id.
ids = util.listify(id)
count = 0
deleted_repositories = ""
for repository_id in ids:
repository = repository_util.get_repository_in_tool_shed(
trans.app, repository_id)
if repository:
if not repository.deleted:
# Mark all installable repository_metadata records as not installable.
for repository_metadata in repository.downloadable_revisions:
repository_metadata.downloadable = False
trans.sa_session.add(repository_metadata)
# Mark the repository admin role as deleted.
repository_admin_role = repository.admin_role
if repository_admin_role is not None:
repository_admin_role.deleted = True
trans.sa_session.add(repository_admin_role)
repository.deleted = True
trans.sa_session.add(repository)
trans.sa_session.flush()
# Update the repository registry.
trans.app.repository_registry.remove_entry(repository)
count += 1
deleted_repositories += " %s " % repository.name
if count:
message = "Deleted %d %s: %s" % (
count, inflector.cond_plural(
len(ids), "repository"), escape(deleted_repositories))
else:
message = "All selected repositories were already marked deleted."
else:
message = "No repository ids received for deleting."
status = 'error'
trans.response.send_redirect(
web.url_for(controller='admin',
action='browse_repositories',
message=util.sanitize_text(message),
status=status))
@web.expose
@web.require_admin
def delete_repository_metadata(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
id = kwd.get('id', None)
if id:
ids = util.listify(id)
count = 0
for repository_metadata_id in ids:
repository_metadata = metadata_util.get_repository_metadata_by_id(
trans.app, repository_metadata_id)
trans.sa_session.delete(repository_metadata)
trans.sa_session.flush()
count += 1
if count:
message = "Deleted %d repository metadata %s" % (
count, inflector.cond_plural(len(ids), "record"))
else:
message = "No repository metadata ids received for deleting."
status = 'error'
trans.response.send_redirect(
web.url_for(controller='admin',
action='browse_repository_metadata',
message=util.sanitize_text(message),
status=status))
@web.expose
@web.require_admin
def edit_category(self, trans, **kwd):
'''Handle requests to edit TS category name or description'''
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
id = kwd.get('id', None)
if not id:
message = "No category ids received for editing"
trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=message,
status='error'))
category = suc.get_category(trans.app, id)
original_category_name = str(category.name)
original_category_description = str(category.description)
if kwd.get('edit_category_button', False):
flush_needed = False
new_name = kwd.get('name', '').strip()
new_description = kwd.get('description', '').strip()
if original_category_name != new_name:
if not new_name:
message = 'Enter a valid name'
status = 'error'
elif original_category_name != new_name and suc.get_category_by_name(
trans.app, new_name):
message = 'A category with that name already exists'
status = 'error'
else:
category.name = new_name
flush_needed = True
if original_category_description != new_description:
category.description = new_description
if not flush_needed:
flush_needed = True
if flush_needed:
trans.sa_session.add(category)
trans.sa_session.flush()
if original_category_name != new_name:
# Update the Tool Shed's repository registry.
trans.app.repository_registry.edit_category_entry(
original_category_name, new_name)
message = "The information has been saved for category '%s'" % escape(
category.name)
status = 'done'
return trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=message,
status=status))
return trans.fill_template(
'/webapps/tool_shed/category/edit_category.mako',
category=category,
message=message,
status=status)
@web.expose
@web.require_admin
def manage_categories(self, trans, **kwd):
if 'f-free-text-search' in kwd:
# Trick to enable searching repository name, description from the CategoryGrid.
# What we've done is rendered the search box for the RepositoryGrid on the grid.mako
# template for the CategoryGrid. See ~/templates/webapps/tool_shed/category/grid.mako.
# Since we are searching repositories and not categories, redirect to browse_repositories().
return trans.response.send_redirect(
web.url_for(controller='admin',
action='browse_repositories',
**kwd))
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "create":
return trans.response.send_redirect(
web.url_for(controller='admin',
action='create_category',
**kwd))
elif operation == "delete":
return trans.response.send_redirect(
web.url_for(controller='admin',
action='mark_category_deleted',
**kwd))
elif operation == "undelete":
return trans.response.send_redirect(
web.url_for(controller='admin',
action='undelete_category',
**kwd))
elif operation == "purge":
return trans.response.send_redirect(
web.url_for(controller='admin',
action='purge_category',
**kwd))
elif operation == "edit":
return trans.response.send_redirect(
web.url_for(controller='admin',
action='edit_category',
**kwd))
return self.manage_category_grid(trans, **kwd)
@web.expose
@web.require_admin
def regenerate_statistics(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
if 'regenerate_statistics_button' in kwd:
trans.app.shed_counter.generate_statistics()
message = "Successfully regenerated statistics"
return trans.fill_template('/webapps/tool_shed/admin/statistics.mako',
message=message,
status=status)
@web.expose
@web.require_admin
def manage_role_associations(self, trans, **kwd):
"""Manage users, groups and repositories associated with a role."""
role_id = kwd.get('id', None)
role = repository_util.get_role_by_id(trans.app, role_id)
# We currently only have a single role associated with a repository, the repository admin role.
repository_role_association = role.repositories[0]
repository = repository_role_association.repository
associations_dict = repository_util.handle_role_associations(
trans.app, role, repository, **kwd)
in_users = associations_dict.get('in_users', [])
out_users = associations_dict.get('out_users', [])
in_groups = associations_dict.get('in_groups', [])
out_groups = associations_dict.get('out_groups', [])
message = associations_dict.get('message', '')
status = associations_dict.get('status', 'done')
return trans.fill_template('/webapps/tool_shed/role/role.mako',
in_admin_controller=True,
repository=repository,
role=role,
in_users=in_users,
out_users=out_users,
in_groups=in_groups,
out_groups=out_groups,
message=message,
status=status)
@web.expose
@web.require_admin
def reset_metadata_on_selected_repositories_in_tool_shed(
self, trans, **kwd):
rmm = repository_metadata_manager.RepositoryMetadataManager(
trans.app, trans.user)
if 'reset_metadata_on_selected_repositories_button' in kwd:
message, status = rmm.reset_metadata_on_selected_repositories(
**kwd)
else:
message = escape(util.restore_text(kwd.get('message', '')))
status = kwd.get('status', 'done')
repositories_select_field = rmm.build_repository_ids_select_field(
name='repository_ids',
multiple=True,
display='checkboxes',
my_writable=False)
return trans.fill_template(
'/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako',
repositories_select_field=repositories_select_field,
message=message,
status=status)
@web.expose
@web.require_admin
def undelete_repository(self, trans, **kwd):
message = escape(kwd.get('message', ''))
id = kwd.get('id', None)
if id:
# Undeleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id.
ids = util.listify(id)
count = 0
undeleted_repositories = ""
for repository_id in ids:
repository = repository_util.get_repository_in_tool_shed(
trans.app, repository_id)
if repository:
if repository.deleted:
# Inspect all repository_metadata records to determine those that are installable, and mark
# them accordingly.
for repository_metadata in repository.metadata_revisions:
metadata = repository_metadata.metadata
if metadata:
if metadata_util.is_downloadable(metadata):
repository_metadata.downloadable = True
trans.sa_session.add(repository_metadata)
# Mark the repository admin role as not deleted.
repository_admin_role = repository.admin_role
if repository_admin_role is not None:
repository_admin_role.deleted = False
trans.sa_session.add(repository_admin_role)
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:
message = "Undeleted %d %s: %s" % (
count, inflector.cond_plural(
count, "repository"), undeleted_repositories)
else:
message = "No selected repositories were marked deleted, so they could not be undeleted."
else:
message = "No repository ids received for undeleting."
trans.response.send_redirect(
web.url_for(controller='admin',
action='browse_repositories',
message=util.sanitize_text(message),
status='done'))
@web.expose
@web.require_admin
def mark_category_deleted(self, trans, **kwd):
# TODO: We should probably eliminate the Category.deleted column since it really makes no
# sense to mark a category as deleted (category names and descriptions can be changed instead).
# If we do this, and the following 2 methods can be eliminated.
message = escape(kwd.get('message', ''))
id = kwd.get('id', None)
if id:
ids = util.listify(id)
message = "Deleted %d categories: " % len(ids)
for category_id in ids:
category = suc.get_category(trans.app, category_id)
category.deleted = True
trans.sa_session.add(category)
trans.sa_session.flush()
# Update the Tool Shed's repository registry.
trans.app.repository_registry.remove_category_entry(category)
message += " %s " % escape(category.name)
else:
message = "No category ids received for deleting."
trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=util.sanitize_text(message),
status='done'))
@web.expose
@web.require_admin
def purge_category(self, trans, **kwd):
# This method should only be called for a Category that has previously been deleted.
# Purging a deleted Category deletes all of the following from the database:
# - RepoitoryCategoryAssociations where category_id == Category.id
message = escape(kwd.get('message', ''))
id = kwd.get('id', None)
if id:
ids = util.listify(id)
count = 0
purged_categories = ""
message = "Purged %d categories: " % len(ids)
for category_id in ids:
category = suc.get_category(trans.app, category_id)
if category.deleted:
# Delete RepositoryCategoryAssociations
for rca in category.repositories:
trans.sa_session.delete(rca)
trans.sa_session.flush()
purged_categories += " %s " % category.name
message = "Purged %d categories: %s" % (count,
escape(purged_categories))
else:
message = "No category ids received for purging."
trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=util.sanitize_text(message),
status='done'))
@web.expose
@web.require_admin
def undelete_category(self, trans, **kwd):
message = escape(kwd.get('message', ''))
id = kwd.get('id', None)
if id:
ids = util.listify(id)
count = 0
undeleted_categories = ""
for category_id in ids:
category = suc.get_category(trans.app, category_id)
if category.deleted:
category.deleted = False
trans.sa_session.add(category)
trans.sa_session.flush()
# Update the Tool Shed's repository registry.
trans.app.repository_registry.add_category_entry(category)
count += 1
undeleted_categories += " %s" % category.name
message = "Undeleted %d categories: %s" % (
count, escape(undeleted_categories))
else:
message = "No category ids received for undeleting."
trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=util.sanitize_text(message),
status='done'))
class RepositoryMetadataGrid(grids.Grid):
class IdColumn(grids.IntegerColumn):
def get_value(self, trans, grid, repository_metadata):
return repository_metadata.id
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, repository_metadata):
return escape(repository_metadata.repository.name)
class OwnerColumn(grids.TextColumn):
def get_value(self, trans, grid, repository_metadata):
return escape(repository_metadata.repository.user.username)
class RevisionColumn(grids.TextColumn):
def get_value(self, trans, grid, repository_metadata):
repository = repository_metadata.repository
return hg_util.get_revision_label(trans.app,
repository,
repository_metadata.changeset_revision,
include_date=True,
include_hash=True)
class ToolsColumn(grids.TextColumn):
def get_value(self, trans, grid, repository_metadata):
tools_str = '0'
if repository_metadata:
metadata = repository_metadata.metadata
if metadata:
if 'tools' in metadata:
# We used to display the following, but grid was too cluttered.
# for tool_metadata_dict in metadata[ 'tools' ]:
# tools_str += '%s <b>%s</b><br/>' % ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] )
return '%d' % len(metadata['tools'])
return tools_str
class DatatypesColumn(grids.TextColumn):
def get_value(self, trans, grid, repository_metadata):
datatypes_str = '0'
if repository_metadata:
metadata = repository_metadata.metadata
if metadata:
if 'datatypes' in metadata:
# We used to display the following, but grid was too cluttered.
# for datatype_metadata_dict in metadata[ 'datatypes' ]:
# datatypes_str += '%s<br/>' % datatype_metadata_dict[ 'extension' ]
return '%d' % len(metadata['datatypes'])
return datatypes_str
class WorkflowsColumn(grids.TextColumn):
def get_value(self, trans, grid, repository_metadata):
workflows_str = '0'
if repository_metadata:
metadata = repository_metadata.metadata
if metadata:
if 'workflows' in metadata:
# We used to display the following, but grid was too cluttered.
# workflows_str += '<b>Workflows:</b><br/>'
# metadata[ 'workflows' ] is a list of tuples where each contained tuple is
# [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
# workflow_tups = metadata[ 'workflows' ]
# workflow_metadata_dicts = [ workflow_tup[1] for workflow_tup in workflow_tups ]
# for workflow_metadata_dict in workflow_metadata_dicts:
# workflows_str += '%s<br/>' % workflow_metadata_dict[ 'name' ]
return '%d' % len(metadata['workflows'])
return workflows_str
class DeletedColumn(grids.BooleanColumn):
def get_value(self, trans, grid, repository_metadata):
if repository_metadata.repository.deleted:
return 'yes'
return ''
class DeprecatedColumn(grids.BooleanColumn):
def get_value(self, trans, grid, repository_metadata):
if repository_metadata.repository.deprecated:
return 'yes'
return ''
class MaliciousColumn(grids.BooleanColumn):
def get_value(self, trans, grid, repository_metadata):
if repository_metadata.malicious:
return 'yes'
return ''
# Grid definition
title = "Repository Metadata"
model_class = model.RepositoryMetadata
default_sort_key = "name"
use_hide_message = False
columns = [
IdColumn("Id",
visible=False,
attach_popup=False),
NameColumn("Name",
key="name",
model_class=model.Repository,
link=(lambda item: dict(operation="view_or_manage_repository_revision", id=item.id)),
attach_popup=True),
OwnerColumn("Owner", attach_popup=False),
RevisionColumn("Revision", attach_popup=False),
ToolsColumn("Tools", attach_popup=False),
DatatypesColumn("Datatypes", attach_popup=False),
WorkflowsColumn("Workflows", attach_popup=False),
DeletedColumn("Deleted", attach_popup=False),
DeprecatedColumn("Deprecated", attach_popup=False),
MaliciousColumn("Malicious", attach_popup=False)
]
columns.append(grids.MulticolFilterColumn("Search repository name",
cols_to_filter=[columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [grids.GridOperation("Delete",
allow_multiple=False,
allow_popup=True,
async_compatible=False,
confirm="Repository metadata records cannot be recovered after they are deleted. Click OK to delete the selected items.")]
def build_initial_query(self, trans, **kwd):
return trans.sa_session.query(model.RepositoryMetadata) \
.join(model.Repository.table)
class GroupGrid(grids.Grid):
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, group):
return str(group.name)
class StatusColumn(grids.GridColumn):
def get_value(self, trans, grid, group):
if group.deleted:
return "deleted"
return ""
class RolesColumn(grids.GridColumn):
def get_value(self, trans, grid, group):
if group.roles:
return len(group.roles)
return 0
class UsersColumn(grids.GridColumn):
def get_value(self, trans, grid, group):
if group.members:
return len(group.members)
return 0
title = "Groups"
model_class = model.Group
default_sort_key = "name"
columns = [
NameColumn("Name",
key="name",
link=(lambda item: dict(operation="Manage users and roles", id=item.id)),
attach_popup=True),
UsersColumn("Users", attach_popup=False),
RolesColumn("Roles", attach_popup=False),
StatusColumn("Status", attach_popup=False),
# Columns that are valid for filtering but are not visible.
grids.DeletedColumn("Deleted",
key="deleted",
visible=False,
filterable="advanced")
]
columns.append(grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0]],
key="free-text-search",
visible=False,
filterable="standard"))
global_actions = [
grids.GridAction("Add new group",
dict(controller='admin', action='groups', operation='create'))
]
operations = [grids.GridOperation("Rename",
condition=(lambda item: not item.deleted),
allow_multiple=False,
url_args=dict(action="rename_group")),
grids.GridOperation("Delete",
condition=(lambda item: not item.deleted),
allow_multiple=True,
url_args=dict(action="mark_group_deleted")),
grids.GridOperation("Undelete",
condition=(lambda item: item.deleted),
allow_multiple=True,
url_args=dict(action="undelete_group")),
grids.GridOperation("Purge",
condition=(lambda item: item.deleted),
allow_multiple=True,
url_args=dict(action="purge_group"))]
standard_filters = [
grids.GridColumnFilter("Active", args=dict(deleted=False)),
grids.GridColumnFilter("Deleted", args=dict(deleted=True)),
grids.GridColumnFilter("All", args=dict(deleted='All'))
]
use_paging = False
class UserGrid(grids.Grid):
class UserLoginColumn(grids.TextColumn):
def get_value(self, trans, grid, user):
return escape(user.email)
class UserNameColumn(grids.TextColumn):
def get_value(self, trans, grid, user):
if user.username:
return escape(user.username)
return 'not set'
class GroupsColumn(grids.GridColumn):
def get_value(self, trans, grid, user):
if user.groups:
return len(user.groups)
return 0
class RolesColumn(grids.GridColumn):
def get_value(self, trans, grid, user):
if user.roles:
return len(user.roles)
return 0
class ExternalColumn(grids.GridColumn):
def get_value(self, trans, grid, user):
if user.external:
return 'yes'
return 'no'
class LastLoginColumn(grids.GridColumn):
def get_value(self, trans, grid, user):
if user.galaxy_sessions:
return self.format(user.galaxy_sessions[0].update_time)
return 'never'
class StatusColumn(grids.GridColumn):
def get_value(self, trans, grid, user):
if user.purged:
return "purged"
elif user.deleted:
return "deleted"
return ""
class EmailColumn(grids.GridColumn):
def filter(self, trans, user, query, column_filter):
if column_filter == 'All':
return query
return query.filter(and_(model.Tool.table.c.user_id == model.User.table.c.id,
model.User.table.c.email == column_filter))
title = "Users"
model_class = model.User
default_sort_key = "email"
columns = [
UserLoginColumn("Email",
key="email",
link=(lambda item: dict(operation="information", id=item.id)),
attach_popup=True,
filterable="advanced"),
UserNameColumn("User Name",
key="username",
attach_popup=False,
filterable="advanced"),
GroupsColumn("Groups", attach_popup=False),
RolesColumn("Roles", attach_popup=False),
ExternalColumn("External", attach_popup=False),
LastLoginColumn("Last Login", format=time_ago),
StatusColumn("Status", attach_popup=False),
# Columns that are valid for filtering but are not visible.
EmailColumn("Email",
key="email",
visible=False)
]
columns.append(grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
global_actions = [
grids.GridAction("Create new user",
dict(controller='admin', action='users', operation='create'))
]
operations = [
grids.GridOperation("Manage Roles and Groups",
condition=(lambda item: not item.deleted),
allow_multiple=False,
url_args=dict(action="manage_roles_and_groups_for_user")),
grids.GridOperation("Reset Password",
condition=(lambda item: not item.deleted),
allow_multiple=True,
allow_popup=False,
url_args=dict(action="reset_user_password"))
]
standard_filters = [
grids.GridColumnFilter("Active", args=dict(deleted=False)),
grids.GridColumnFilter("Deleted", args=dict(deleted=True, purged=False)),
grids.GridColumnFilter("Purged", args=dict(purged=True)),
grids.GridColumnFilter("All", args=dict(deleted='All'))
]
use_paging = False
def get_current_item(self, trans, **kwargs):
return trans.user
class RoleGrid(grids.Grid):
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, role):
return escape(str(role.name))
class DescriptionColumn(grids.TextColumn):
def get_value(self, trans, grid, role):
if role.description:
return str(role.description)
return ''
class TypeColumn(grids.TextColumn):
def get_value(self, trans, grid, role):
return str(role.type)
class StatusColumn(grids.GridColumn):
def get_value(self, trans, grid, role):
if role.deleted:
return "deleted"
return ""
class GroupsColumn(grids.GridColumn):
def get_value(self, trans, grid, role):
if role.groups:
return len(role.groups)
return 0
class RepositoriesColumn(grids.GridColumn):
def get_value(self, trans, grid, role):
if role.repositories:
return len(role.repositories)
return 0
class UsersColumn(grids.GridColumn):
def get_value(self, trans, grid, role):
if role.users:
return len(role.users)
return 0
title = "Roles"
model_class = model.Role
default_sort_key = "name"
columns = [
NameColumn("Name",
key="name",
link=(lambda item: dict(operation="Manage role associations", id=item.id)),
attach_popup=True,
filterable="advanced"),
DescriptionColumn("Description",
key='description',
attach_popup=False,
filterable="advanced"),
GroupsColumn("Groups", attach_popup=False),
RepositoriesColumn("Repositories", attach_popup=False),
UsersColumn("Users", attach_popup=False),
# Columns that are valid for filtering but are not visible.
grids.DeletedColumn("Deleted",
key="deleted",
visible=False,
filterable="advanced")
]
columns.append(grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0]],
key="free-text-search",
visible=False,
filterable="standard"))
global_actions = [
grids.GridAction("Add new role",
dict(controller='admin', action='roles', operation='create'))
]
# Repository admin roles currently do not have any operations since they are managed automatically based
# on other events. For example, if a repository is renamed, its associated admin role is automatically
# renamed accordingly and if a repository is deleted its associated admin role is automatically deleted.
operations = [grids.GridOperation("Rename",
condition=(lambda item: not item.deleted and not item.is_repository_admin_role),
allow_multiple=False,
url_args=dict(action="rename_role")),
grids.GridOperation("Delete",
condition=(lambda item: not item.deleted and not item.is_repository_admin_role),
allow_multiple=True,
url_args=dict(action="mark_role_deleted")),
grids.GridOperation("Undelete",
condition=(lambda item: item.deleted and not item.is_repository_admin_role),
allow_multiple=True,
url_args=dict(action="undelete_role")),
grids.GridOperation("Purge",
condition=(lambda item: item.deleted and not item.is_repository_admin_role),
allow_multiple=True,
url_args=dict(action="purge_role"))]
standard_filters = [
grids.GridColumnFilter("Active", args=dict(deleted=False)),
grids.GridColumnFilter("Deleted", args=dict(deleted=True)),
grids.GridColumnFilter("All", args=dict(deleted='All'))
]
use_paging = False
def apply_query_filter(self, trans, query, **kwd):
return query.filter(model.Role.type != model.Role.types.PRIVATE)
class RepositoriesWithReviewsGrid(RepositoryGrid):
# This grid filters out repositories that have been marked as either deprecated or deleted.
class WithReviewsRevisionColumn(grids.GridColumn):
def get_value(self, trans, grid, repository):
# Restrict to revisions that have been reviewed.
if repository.reviews:
rval = ''
repo = repository.hg_repo
for review in repository.reviews:
changeset_revision = review.changeset_revision
rev, label = hg_util.get_rev_label_from_changeset_revision(
repo, changeset_revision)
rval += '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>' % \
(trans.security.encode_id(repository.id), changeset_revision, label)
return rval
return ''
class WithoutReviewsRevisionColumn(grids.GridColumn):
def get_value(self, trans, grid, repository):
# Restrict the options to revisions that have not yet been reviewed.
repository_metadata_revisions = metadata_util.get_repository_metadata_revisions_for_review(
repository, reviewed=False)
if repository_metadata_revisions:
rval = ''
for repository_metadata in repository_metadata_revisions:
rev, label, changeset_revision = \
hg_util.get_rev_label_changeset_revision_from_repository_metadata(trans.app,
repository_metadata,
repository=repository,
include_date=True,
include_hash=False)
rval += '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>' % \
(trans.security.encode_id(repository.id), changeset_revision, label)
return rval
return ''
class ReviewersColumn(grids.TextColumn):
def get_value(self, trans, grid, repository):
rval = ''
if repository.reviewers:
for user in repository.reviewers:
rval += '<a class="view-info" href="repository_reviews_by_user?id=%s">' % trans.security.encode_id(
user.id)
rval += '%s</a> | ' % user.username
if rval[-3:] == ' | ':
rval = rval[:-3]
return rval
class RatingColumn(grids.TextColumn):
def get_value(self, trans, grid, repository):
rval = ''
for review in repository.reviews:
if review.rating:
for index in range(1, 6):
rval += '<input '
rval += 'name="star1-%s" ' % trans.security.encode_id(
review.id)
rval += 'type="radio" '
rval += 'class="community_rating_star star" '
rval += 'disabled="disabled" '
rval += 'value="%s" ' % str(review.rating)
if review.rating > (index - 0.5) and review.rating < (
index + 0.5):
rval += 'checked="checked" '
rval += '/>'
rval += '<br/>'
return rval
class ApprovedColumn(grids.TextColumn):
def get_value(self, trans, grid, repository):
rval = ''
for review in repository.reviews:
if review.approved:
rval += '%s<br/>' % review.approved
return rval
title = "All reviewed repositories"
model_class = model.Repository
template = '/webapps/tool_shed/repository_review/grid.mako'
default_sort_key = "Repository.name"
columns = [
RepositoryGrid.NameColumn(
"Repository name",
key="name",
link=(lambda item: dict(operation="view_or_manage_repository",
id=item.id)),
attach_popup=True),
RepositoryGrid.UserColumn("Owner",
model_class=model.User,
attach_popup=False,
key="User.username"),
WithReviewsRevisionColumn("Reviewed revisions"),
ReviewersColumn("Reviewers", attach_popup=False),
RatingColumn("Rating", attach_popup=False),
ApprovedColumn("Approved", attach_popup=False)
]
columns.append(
grids.MulticolFilterColumn("Search repository name",
cols_to_filter=[columns[0]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [
grids.GridOperation("Inspect repository revisions",
allow_multiple=False,
condition=(lambda item: not item.deleted),
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(),
model.Repository.table.c.deprecated == false())) \
.join((model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id)) \
.join((model.User.table, model.User.table.c.id == model.Repository.table.c.user_id)) \
.outerjoin((model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id)) \
.outerjoin((model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id))
class RepositoryReviewsByUserGrid(grids.Grid):
# This grid filters out repositories that have been marked as deprecated.
class RepositoryNameColumn(grids.TextColumn):
def get_value(self, trans, grid, review):
return escape(review.repository.name)
class RepositoryDescriptionColumn(grids.TextColumn):
def get_value(self, trans, grid, review):
return escape(review.repository.description)
class RevisionColumn(grids.TextColumn):
def get_value(self, trans, grid, review):
encoded_review_id = trans.security.encode_id(review.id)
rval = '<a class="action-button" href="'
if review.user == trans.user:
rval += 'edit_review'
else:
rval += 'browse_review'
revision_label = hg_util.get_revision_label(
trans.app,
review.repository,
review.changeset_revision,
include_date=True,
include_hash=False)
rval += f'?id={encoded_review_id}">{revision_label}</a>'
return rval
class RatingColumn(grids.TextColumn):
def get_value(self, trans, grid, review):
if review.rating:
for index in range(1, 6):
rval = '<input '
rval += 'name="star1-%s" ' % trans.security.encode_id(
review.id)
rval += 'type="radio" '
rval += 'class="community_rating_star star" '
rval += 'disabled="disabled" '
rval += 'value="%s" ' % str(review.rating)
if review.rating > (index -
0.5) and review.rating < (index + 0.5):
rval += 'checked="checked" '
rval += '/>'
return rval
return ''
title = "Reviews by user"
model_class = model.RepositoryReview
template = '/webapps/tool_shed/repository_review/grid.mako'
default_sort_key = 'repository_id'
use_hide_message = False
columns = [
RepositoryNameColumn(
"Repository Name",
model_class=model.Repository,
key="Repository.name",
link=(lambda item: dict(operation="view_or_manage_repository",
id=item.id)),
attach_popup=True),
RepositoryDescriptionColumn("Description",
model_class=model.Repository,
key="Repository.description",
attach_popup=False),
RevisionColumn("Revision", attach_popup=False),
RatingColumn("Rating", attach_popup=False),
]
operations = [
grids.GridOperation("Inspect repository revisions",
allow_multiple=False,
condition=(lambda item: not item.deleted),
async_compatible=False)
]
num_rows_per_page = 50
def build_initial_query(self, trans, **kwd):
user_id = trans.security.decode_id(kwd['id'])
return trans.sa_session.query(model.RepositoryReview) \
.filter(and_(model.RepositoryReview.table.c.deleted == false(),
model.RepositoryReview.table.c.user_id == user_id)) \
.join((model.Repository.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id)) \
.filter(model.Repository.table.c.deprecated == false())
