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This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for galaxy.webapps.tool_shed.api.repositories
import json
import logging
import os
import tarfile
from collections import namedtuple
from time import strftime
from six import StringIO
from sqlalchemy import and_, false
from webob.compat import cgi_FieldStorage
from galaxy import (
util,
web
)
from galaxy.exceptions import (
ActionInputError,
ConfigDoesNotAllowException,
InsufficientPermissionsException,
MalformedId,
ObjectNotFound,
RequestParameterInvalidException,
RequestParameterMissingException
)
from galaxy.util import checkers
from galaxy.web import (
_future_expose_api as expose_api,
_future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless,
_future_expose_api_raw_anonymous_and_sessionless as expose_api_raw_anonymous_and_sessionless
)
from galaxy.web.base.controller import (
BaseAPIController,
HTTPBadRequest
)
from galaxy.webapps.tool_shed.search.repo_search import RepoSearch
from tool_shed.capsule import capsule_manager
from tool_shed.dependencies import attribute_handlers
from tool_shed.metadata import repository_metadata_manager
from tool_shed.repository_types import util as rt_util
from tool_shed.util import (
basic_util,
commit_util,
encoding_util,
hg_util,
metadata_util,
repository_content_util,
repository_util,
tool_util
)
log = logging.getLogger(__name__)
[docs]class RepositoriesController(BaseAPIController):
"""RESTful controller for interactions with repositories in the Tool Shed."""
[docs] @web.expose_api
def add_repository_registry_entry(self, trans, payload, **kwd):
"""
POST /api/repositories/add_repository_registry_entry
Adds appropriate entries to the repository registry for the repository defined by the received name and owner.
:param key: the user's API key
The following parameters are included in the payload.
:param tool_shed_url (required): the base URL of the Tool Shed containing the Repository
:param name (required): the name of the Repository
:param owner (required): the owner of the Repository
"""
response_dict = {}
if not trans.user_is_admin:
response_dict['status'] = 'error'
response_dict['message'] = "You are not authorized to add entries to this Tool Shed's repository registry."
return response_dict
tool_shed_url = payload.get('tool_shed_url', '')
if not tool_shed_url:
raise HTTPBadRequest(detail="Missing required parameter 'tool_shed_url'.")
tool_shed_url = tool_shed_url.rstrip('/')
name = payload.get('name', '')
if not name:
raise HTTPBadRequest(detail="Missing required parameter 'name'.")
owner = payload.get('owner', '')
if not owner:
raise HTTPBadRequest(detail="Missing required parameter 'owner'.")
repository = repository_util.get_repository_by_name_and_owner(self.app, name, owner)
if repository is None:
error_message = 'Cannot locate repository with name %s and owner %s,' % (str(name), str(owner))
log.debug(error_message)
response_dict['status'] = 'error'
response_dict['message'] = error_message
return response_dict
# Update the repository registry.
self.app.repository_registry.add_entry(repository)
response_dict['status'] = 'ok'
response_dict['message'] = 'Entries for repository %s owned by %s have been added to the Tool Shed repository registry.' \
% (name, owner)
return response_dict
[docs] @web.expose_api_anonymous
def get_ordered_installable_revisions(self, trans, name=None, owner=None, **kwd):
"""
GET /api/repositories/get_ordered_installable_revisions
:param name: the name of the Repository
:param owner: the owner of the Repository
Returns the ordered list of changeset revision hash strings that are associated with installable revisions.
As in the changelog, the list is ordered oldest to newest.
"""
# Example URL: http://localhost:9009/api/repositories/get_ordered_installable_revisions?name=add_column&owner=test
if name is None:
name = kwd.get('name', None)
if owner is None:
owner = kwd.get('owner', None)
tsr_id = kwd.get('tsr_id', None)
if None not in [name, owner]:
# Get the repository information.
repository = repository_util.get_repository_by_name_and_owner(self.app, name, owner)
if repository is None:
trans.response.status = 404
return {'status': 'error', 'message': 'No repository named %s found with owner %s' % (name, owner)}
elif tsr_id is not None:
repository = repository_util.get_repository_in_tool_shed(self.app, tsr_id)
else:
error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: "
error_message += "invalid parameters received."
log.debug(error_message)
return []
return [revision[1] for revision in repository.installable_revisions(self.app, sort_revisions=True)]
[docs] @web.expose_api_anonymous
def get_repository_revision_install_info(self, trans, name, owner, changeset_revision, **kwd):
"""
GET /api/repositories/get_repository_revision_install_info
:param name: the name of the Repository
:param owner: the owner of the Repository
:param changeset_revision: the changeset_revision of the RepositoryMetadata object associated with the Repository
Returns a list of the following dictionaries::
- a dictionary defining the Repository. For example:
{
"deleted": false,
"deprecated": false,
"description": "add_column hello",
"id": "f9cad7b01a472135",
"long_description": "add_column hello",
"name": "add_column",
"owner": "test",
"private": false,
"times_downloaded": 6,
"url": "/api/repositories/f9cad7b01a472135",
"user_id": "f9cad7b01a472135"
}
- a dictionary defining the Repository revision (RepositoryMetadata). For example:
{
"changeset_revision": "3a08cc21466f",
"downloadable": true,
"has_repository_dependencies": false,
"has_repository_dependencies_only_if_compiling_contained_td": false,
"id": "f9cad7b01a472135",
"includes_datatypes": false,
"includes_tool_dependencies": false,
"includes_tools": true,
"includes_tools_for_display_in_tool_panel": true,
"includes_workflows": false,
"malicious": false,
"repository_id": "f9cad7b01a472135",
"url": "/api/repository_revisions/f9cad7b01a472135",
"valid_tools": [{u'add_to_tool_panel': True,
u'description': u'data on any column using simple expressions',
u'guid': u'localhost:9009/repos/enis/sample_repo_1/Filter1/2.2.0',
u'id': u'Filter1',
u'name': u'Filter',
u'requirements': [],
u'tests': [{u'inputs': [[u'input', u'1.bed'], [u'cond', u"c1=='chr22'"]],
u'name': u'Test-1',
u'outputs': [[u'out_file1', u'filter1_test1.bed']],
u'required_files': [u'1.bed', u'filter1_test1.bed']}],
u'tool_config': u'database/community_files/000/repo_1/filtering.xml',
u'tool_type': u'default',
u'version': u'2.2.0',
u'version_string_cmd': None}]
}
- a dictionary including the additional information required to install the repository. For example:
{
"add_column": [
"add_column hello",
"http://test@localhost:9009/repos/test/add_column",
"3a08cc21466f",
"1",
"test",
{},
{}
]
}
"""
# Example URL:
# http://<xyz>/api/repositories/get_repository_revision_install_info?name=<n>&owner=<o>&changeset_revision=<cr>
if name and owner and changeset_revision:
# Get the repository information.
repository = repository_util.get_repository_by_name_and_owner(self.app, name, owner)
if repository is None:
log.debug('Cannot locate repository %s owned by %s' % (str(name), str(owner)))
return {}, {}, {}
encoded_repository_id = trans.security.encode_id(repository.id)
repository_dict = repository.to_dict(view='element',
value_mapper=self.__get_value_mapper(trans))
repository_dict['url'] = web.url_for(controller='repositories',
action='show',
id=encoded_repository_id)
# Get the repository_metadata information.
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(self.app,
encoded_repository_id,
changeset_revision)
if repository_metadata is None:
# The changeset_revision column in the repository_metadata table has been updated with a new
# value value, so find the changeset_revision to which we need to update.
new_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(self.app, repository, changeset_revision)
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(self.app,
encoded_repository_id,
new_changeset_revision)
changeset_revision = new_changeset_revision
if repository_metadata is not None:
encoded_repository_metadata_id = trans.security.encode_id(repository_metadata.id)
repository_metadata_dict = repository_metadata.to_dict(view='collection',
value_mapper=self.__get_value_mapper(trans))
repository_metadata_dict['url'] = web.url_for(controller='repository_revisions',
action='show',
id=encoded_repository_metadata_id)
if 'tools' in repository_metadata.metadata:
repository_metadata_dict['valid_tools'] = repository_metadata.metadata['tools']
# Get the repo_info_dict for installing the repository.
repo_info_dict, \
includes_tools, \
includes_tool_dependencies, \
includes_tools_for_display_in_tool_panel, \
has_repository_dependencies, \
has_repository_dependencies_only_if_compiling_contained_td = \
repository_util.get_repo_info_dict(self.app,
trans.user,
encoded_repository_id,
changeset_revision)
return repository_dict, repository_metadata_dict, repo_info_dict
else:
log.debug("Unable to locate repository_metadata record for repository id %s and changeset_revision %s" %
(str(repository.id), str(changeset_revision)))
return repository_dict, {}, {}
else:
debug_msg = "Error in the Tool Shed repositories API in get_repository_revision_install_info: "
debug_msg += "Invalid name %s or owner %s or changeset_revision %s received." % \
(str(name), str(owner), str(changeset_revision))
log.debug(debug_msg)
return {}, {}, {}
[docs] @web.expose_api_anonymous
def get_installable_revisions(self, trans, **kwd):
"""
GET /api/repositories/get_installable_revisions
:param tsr_id: the encoded toolshed ID of the repository
Returns a list of lists of changesets, in the format [ [ 0, fbb391dc803c ], [ 1, 9d9ec4d9c03e ], [ 2, 9b5b20673b89 ], [ 3, e8c99ce51292 ] ].
"""
# Example URL: http://localhost:9009/api/repositories/get_installable_revisions?tsr_id=9d37e53072ff9fa4
tsr_id = kwd.get('tsr_id', None)
if tsr_id is not None:
repository = repository_util.get_repository_in_tool_shed(self.app, tsr_id)
else:
error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: "
error_message += "missing or invalid parameter received."
log.debug(error_message)
return []
return repository.installable_revisions(self.app)
def __get_value_mapper(self, trans):
value_mapper = {'id': trans.security.encode_id,
'repository_id': trans.security.encode_id,
'user_id': trans.security.encode_id}
return value_mapper
[docs] @web.expose_api
def import_capsule(self, trans, payload, **kwd):
"""
POST /api/repositories/new/import_capsule
Import a repository capsule into the Tool Shed.
:param key: the user's API key
The following parameters are included in the payload.
:param tool_shed_url (required): the base URL of the Tool Shed into which the capsule should be imported.
:param capsule_file_name (required): the name of the capsule file.
"""
# Get the information about the capsule to be imported from the payload.
tool_shed_url = payload.get('tool_shed_url', '')
if not tool_shed_url:
raise HTTPBadRequest(detail="Missing required parameter 'tool_shed_url'.")
capsule_file_name = payload.get('capsule_file_name', '')
if not capsule_file_name:
raise HTTPBadRequest(detail="Missing required parameter 'capsule_file_name'.")
capsule_file_path = os.path.abspath(capsule_file_name)
capsule_dict = dict(error_message='',
encoded_file_path=None,
status='ok',
tar_archive=None,
uploaded_file=None,
capsule_file_name=None)
if os.path.getsize(os.path.abspath(capsule_file_name)) == 0:
log.debug('Your capsule file %s is empty.' % str(capsule_file_name))
return {}
try:
# Open for reading with transparent compression.
tar_archive = tarfile.open(capsule_file_path, 'r:*')
except tarfile.ReadError as e:
log.debug('Error opening capsule file %s: %s' % (str(capsule_file_name), str(e)))
return {}
irm = capsule_manager.ImportRepositoryManager(self.app,
trans.request.host,
trans.user,
trans.user_is_admin)
capsule_dict['tar_archive'] = tar_archive
capsule_dict['capsule_file_name'] = capsule_file_name
capsule_dict = irm.extract_capsule_files(**capsule_dict)
capsule_dict = irm.validate_capsule(**capsule_dict)
status = capsule_dict.get('status', 'error')
if status == 'error':
log.debug('The capsule contents are invalid and cannot be imported:<br/>%s' %
str(capsule_dict.get('error_message', '')))
return {}
encoded_file_path = capsule_dict.get('encoded_file_path', None)
if encoded_file_path is None:
log.debug('The capsule_dict %s is missing the required encoded_file_path entry.' % str(capsule_dict))
return {}
file_path = encoding_util.tool_shed_decode(encoded_file_path)
manifest_file_path = os.path.join(file_path, 'manifest.xml')
# The manifest.xml file has already been validated, so no error_message should be returned here.
repository_info_dicts, error_message = irm.get_repository_info_from_manifest(manifest_file_path)
# Determine the status for each exported repository archive contained within the capsule.
repository_status_info_dicts = irm.get_repository_status_from_tool_shed(repository_info_dicts)
# Generate a list of repository name / import results message tuples for display after the capsule is imported.
import_results_tups = []
# Only create repositories that do not yet exist and that the current user is authorized to create. The
# status will be None for repositories that fall into the intersection of these 2 categories.
for repository_status_info_dict in repository_status_info_dicts:
# Add the capsule_file_name and encoded_file_path to the repository_status_info_dict.
repository_status_info_dict['capsule_file_name'] = capsule_file_name
repository_status_info_dict['encoded_file_path'] = encoded_file_path
import_results_tups = irm.create_repository_and_import_archive(repository_status_info_dict,
import_results_tups)
irm.check_status_and_reset_downloadable(import_results_tups)
basic_util.remove_dir(file_path)
# NOTE: the order of installation is defined in import_results_tups, but order will be lost
# when transferred to return_dict.
return_dict = {}
for import_results_tup in import_results_tups:
ok, name_owner, message = import_results_tup
name, owner = name_owner
key = 'Archive of repository "%s" owned by "%s"' % (str(name), str(owner))
val = message.replace('<b>', '"').replace('</b>', '"')
return_dict[key] = val
return return_dict
[docs] @expose_api_raw_anonymous_and_sessionless
def index(self, trans, deleted=False, owner=None, name=None, **kwd):
"""
GET /api/repositories
Displays a collection of repositories with optional criteria.
:param q: (optional)if present search on the given query will be performed
:type q: str
:param page: (optional)requested page of the search
:type page: int
:param page_size: (optional)requested page_size of the search
:type page_size: int
:param jsonp: (optional)flag whether to use jsonp format response, defaults to False
:type jsonp: bool
:param callback: (optional)name of the function to wrap callback in
used only when jsonp is true, defaults to 'callback'
:type callback: str
:param deleted: (optional)displays repositories that are or are not set to deleted.
:type deleted: bool
:param owner: (optional)the owner's public username.
:type owner: str
:param name: (optional)the repository name.
:type name: str
:param tool_ids: (optional) a tool GUID to find the repository for
:param tool_ids: str
:returns dict: object containing list of results
Examples:
GET http://localhost:9009/api/repositories
GET http://localhost:9009/api/repositories?q=fastq
"""
repository_dicts = []
deleted = util.asbool(deleted)
q = kwd.get('q', '')
if q:
page = kwd.get('page', 1)
page_size = kwd.get('page_size', 10)
try:
page = int(page)
page_size = int(page_size)
except ValueError:
raise RequestParameterInvalidException('The "page" and "page_size" parameters have to be integers.')
return_jsonp = util.asbool(kwd.get('jsonp', False))
callback = kwd.get('callback', 'callback')
search_results = self._search(trans, q, page, page_size)
if return_jsonp:
response = str('%s(%s);' % (callback, json.dumps(search_results)))
else:
response = json.dumps(search_results)
return response
tool_ids = kwd.get('tool_ids', None)
if tool_ids is not None:
tool_ids = util.listify(tool_ids)
repository_found = []
all_metadata = dict()
for tool_id in tool_ids:
# A valid GUID looks like toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeMatrix/1.1.0
shed, _, owner, name, tool, version = tool_id.split('/')
clause_list = [and_(self.app.model.Repository.table.c.deprecated == false(),
self.app.model.Repository.table.c.deleted == false(),
self.app.model.Repository.table.c.name == name,
self.app.model.User.table.c.username == owner,
self.app.model.Repository.table.c.user_id == self.app.model.User.table.c.id)]
repository = trans.sa_session.query(self.app.model.Repository).filter(*clause_list).first()
for changeset, changehash in repository.installable_revisions(self.app):
metadata = metadata_util.get_current_repository_metadata_for_changeset_revision(self.app, repository, changehash)
tools = metadata.metadata['tools']
for tool in tools:
if tool['guid'] in tool_ids:
repository_found.append('%d:%s' % (int(changeset), changehash))
metadata = metadata_util.get_current_repository_metadata_for_changeset_revision(self.app, repository, changehash)
if metadata is None:
continue
metadata_dict = metadata.to_dict(value_mapper={'id': self.app.security.encode_id, 'repository_id': self.app.security.encode_id})
metadata_dict['repository'] = repository.to_dict(value_mapper={'id': self.app.security.encode_id})
if metadata.has_repository_dependencies:
metadata_dict['repository_dependencies'] = metadata_util.get_all_dependencies(self.app, metadata, processed_dependency_links=[])
else:
metadata_dict['repository_dependencies'] = []
if metadata.includes_tool_dependencies:
metadata_dict['tool_dependencies'] = repository.get_tool_dependencies(self.app, changehash)
else:
metadata_dict['tool_dependencies'] = {}
if metadata.includes_tools:
metadata_dict['tools'] = metadata.metadata['tools']
all_metadata['%s:%s' % (int(changeset), changehash)] = metadata_dict
if repository_found is not None:
all_metadata['current_changeset'] = repository_found[0]
# all_metadata[ 'found_changesets' ] = repository_found
return json.dumps(all_metadata)
return '{}'
clause_list = [and_(self.app.model.Repository.table.c.deprecated == false(),
self.app.model.Repository.table.c.deleted == deleted)]
if owner is not None:
clause_list.append(and_(self.app.model.User.table.c.username == owner,
self.app.model.Repository.table.c.user_id == self.app.model.User.table.c.id))
if name is not None:
clause_list.append(self.app.model.Repository.table.c.name == name)
for repository in trans.sa_session.query(self.app.model.Repository) \
.filter(*clause_list) \
.order_by(self.app.model.Repository.table.c.name):
repository_dict = repository.to_dict(view='collection',
value_mapper=self.__get_value_mapper(trans))
repository_dict['category_ids'] = \
[trans.security.encode_id(x.category.id) for x in repository.categories]
repository_dicts.append(repository_dict)
return json.dumps(repository_dicts)
def _search(self, trans, q, page=1, page_size=10):
"""
Perform the search over TS repositories.
Note that search works over the Whoosh index which you have
to pre-create with scripts/tool_shed/build_ts_whoosh_index.sh manually.
Also TS config option toolshed_search_on has to be True and
whoosh_index_dir has to be specified.
"""
conf = self.app.config
if not conf.toolshed_search_on:
raise ConfigDoesNotAllowException('Searching the TS through the API is turned off for this instance.')
if not conf.whoosh_index_dir:
raise ConfigDoesNotAllowException('There is no directory for the search index specified. Please contact the administrator.')
search_term = q.strip()
if len(search_term) < 3:
raise RequestParameterInvalidException('The search term has to be at least 3 characters long.')
repo_search = RepoSearch()
Boosts = namedtuple('Boosts', ['repo_name_boost',
'repo_description_boost',
'repo_long_description_boost',
'repo_homepage_url_boost',
'repo_remote_repository_url_boost',
'repo_owner_username_boost'])
boosts = Boosts(float(conf.get('repo_name_boost', 0.9)),
float(conf.get('repo_description_boost', 0.6)),
float(conf.get('repo_long_description_boost', 0.5)),
float(conf.get('repo_homepage_url_boost', 0.3)),
float(conf.get('repo_remote_repository_url_boost', 0.2)),
float(conf.get('repo_owner_username_boost', 0.3)))
results = repo_search.search(trans,
search_term,
page,
page_size,
boosts)
results['hostname'] = web.url_for('/', qualified=True)
return results
[docs] @web.expose_api
def remove_repository_registry_entry(self, trans, payload, **kwd):
"""
POST /api/repositories/remove_repository_registry_entry
Removes appropriate entries from the repository registry for the repository defined by the received name and owner.
:param key: the user's API key
The following parameters are included in the payload.
:param tool_shed_url (required): the base URL of the Tool Shed containing the Repository
:param name (required): the name of the Repository
:param owner (required): the owner of the Repository
"""
response_dict = {}
if not trans.user_is_admin:
response_dict['status'] = 'error'
response_dict['message'] = "You are not authorized to remove entries from this Tool Shed's repository registry."
return response_dict
tool_shed_url = payload.get('tool_shed_url', '')
if not tool_shed_url:
raise HTTPBadRequest(detail="Missing required parameter 'tool_shed_url'.")
tool_shed_url = tool_shed_url.rstrip('/')
name = payload.get('name', '')
if not name:
raise HTTPBadRequest(detail="Missing required parameter 'name'.")
owner = payload.get('owner', '')
if not owner:
raise HTTPBadRequest(detail="Missing required parameter 'owner'.")
repository = repository_util.get_repository_by_name_and_owner(self.app, name, owner)
if repository is None:
error_message = 'Cannot locate repository with name %s and owner %s,' % (str(name), str(owner))
log.debug(error_message)
response_dict['status'] = 'error'
response_dict['message'] = error_message
return response_dict
# Update the repository registry.
self.app.repository_registry.remove_entry(repository)
response_dict['status'] = 'ok'
response_dict['message'] = 'Entries for repository %s owned by %s have been removed from the Tool Shed repository registry.' \
% (name, owner)
return response_dict
[docs] @web.expose_api
def repository_ids_for_setting_metadata(self, trans, my_writable=False, **kwd):
"""
GET /api/repository_ids_for_setting_metadata
Displays a collection (list) of repository ids ordered for setting metadata.
:param key: the API key of the Tool Shed user.
:param my_writable (optional): if the API key is associated with an admin user in the Tool Shed, setting this param value
to True will restrict resetting metadata to only repositories that are writable by the user
in addition to those repositories of type tool_dependency_definition. This param is ignored
if the current user is not an admin user, in which case this same restriction is automatic.
"""
if trans.user_is_admin:
my_writable = util.asbool(my_writable)
else:
my_writable = True
handled_repository_ids = []
repository_ids = []
rmm = repository_metadata_manager.RepositoryMetadataManager(self.app, trans.user)
query = rmm.get_query_for_setting_metadata_on_repositories(my_writable=my_writable, order=False)
# Make sure repositories of type tool_dependency_definition are first in the list.
for repository in query:
if repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids:
repository_ids.append(trans.security.encode_id(repository.id))
# Now add all remaining repositories to the list.
for repository in query:
if repository.type != rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids:
repository_ids.append(trans.security.encode_id(repository.id))
return repository_ids
[docs] @web.expose_api
def reset_metadata_on_repositories(self, trans, payload, **kwd):
"""
PUT /api/repositories/reset_metadata_on_repositories
Resets all metadata on all repositories in the Tool Shed in an "orderly fashion". Since there are currently only two
repository types (tool_dependecy_definition and unrestricted), the order in which metadata is reset is repositories of
type tool_dependecy_definition first followed by repositories of type unrestricted, and only one pass is necessary. If
a new repository type is introduced, the process will undoubtedly need to be revisited. To facilitate this order, an
in-memory list of repository ids that have been processed is maintained.
:param key: the API key of the Tool Shed user.
The following parameters can optionally be included in the payload.
:param my_writable (optional): if the API key is associated with an admin user in the Tool Shed, setting this param value
to True will restrict resetting metadata to only repositories that are writable by the user
in addition to those repositories of type tool_dependency_definition. This param is ignored
if the current user is not an admin user, in which case this same restriction is automatic.
:param encoded_ids_to_skip (optional): a list of encoded repository ids for repositories that should not be processed.
:param skip_file (optional): A local file name that contains the encoded repository ids associated with repositories to skip.
This param can be used as an alternative to the above encoded_ids_to_skip.
"""
def handle_repository(trans, rmm, repository, results):
log.debug("Resetting metadata on repository %s" % str(repository.name))
try:
rmm.set_repository(repository)
rmm.reset_all_metadata_on_repository_in_tool_shed()
rmm_invalid_file_tups = rmm.get_invalid_file_tups()
if rmm_invalid_file_tups:
message = tool_util.generate_message_for_invalid_tools(self.app,
rmm_invalid_file_tups,
repository,
None,
as_html=False)
results['unsuccessful_count'] += 1
else:
message = "Successfully reset metadata on repository %s owned by %s" % \
(str(repository.name), str(repository.user.username))
results['successful_count'] += 1
except Exception as e:
message = "Error resetting metadata on repository %s owned by %s: %s" % \
(str(repository.name), str(repository.user.username), str(e))
results['unsuccessful_count'] += 1
status = '%s : %s' % (str(repository.name), message)
results['repository_status'].append(status)
return results
rmm = repository_metadata_manager.RepositoryMetadataManager(app=self.app,
user=trans.user,
resetting_all_metadata_on_repository=True,
updating_installed_repository=False,
persist=False)
start_time = strftime("%Y-%m-%d %H:%M:%S")
results = dict(start_time=start_time,
repository_status=[],
successful_count=0,
unsuccessful_count=0)
handled_repository_ids = []
encoded_ids_to_skip = payload.get('encoded_ids_to_skip', [])
skip_file = payload.get('skip_file', None)
if skip_file and os.path.exists(skip_file) and not encoded_ids_to_skip:
# Load the list of encoded_ids_to_skip from the skip_file.
# Contents of file must be 1 encoded repository id per line.
lines = open(skip_file, 'rb').readlines()
for line in lines:
if line.startswith('#'):
# Skip comments.
continue
encoded_ids_to_skip.append(line.rstrip('\n'))
if trans.user_is_admin:
my_writable = util.asbool(payload.get('my_writable', False))
else:
my_writable = True
query = rmm.get_query_for_setting_metadata_on_repositories(my_writable=my_writable, order=False)
# First reset metadata on all repositories of type repository_dependency_definition.
for repository in query:
encoded_id = trans.security.encode_id(repository.id)
if encoded_id in encoded_ids_to_skip:
log.debug("Skipping repository with id %s because it is in encoded_ids_to_skip %s" %
(str(repository.id), str(encoded_ids_to_skip)))
elif repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids:
results = handle_repository(trans, rmm, repository, results)
# Now reset metadata on all remaining repositories.
for repository in query:
encoded_id = trans.security.encode_id(repository.id)
if encoded_id in encoded_ids_to_skip:
log.debug("Skipping repository with id %s because it is in encoded_ids_to_skip %s" %
(str(repository.id), str(encoded_ids_to_skip)))
elif repository.type != rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids:
results = handle_repository(trans, rmm, repository, results)
stop_time = strftime("%Y-%m-%d %H:%M:%S")
results['stop_time'] = stop_time
return json.dumps(results, sort_keys=True, indent=4)
[docs] @web.expose_api
def reset_metadata_on_repository(self, trans, payload, **kwd):
"""
PUT /api/repositories/reset_metadata_on_repository
Resets all metadata on a specified repository in the Tool Shed.
:param key: the API key of the Tool Shed user.
The following parameters must be included in the payload.
:param repository_id: the encoded id of the repository on which metadata is to be reset.
"""
def handle_repository(trans, start_time, repository):
results = dict(start_time=start_time,
repository_status=[])
try:
rmm = repository_metadata_manager.RepositoryMetadataManager(app=self.app,
user=trans.user,
repository=repository,
resetting_all_metadata_on_repository=True,
updating_installed_repository=False,
persist=False)
rmm.reset_all_metadata_on_repository_in_tool_shed()
rmm_invalid_file_tups = rmm.get_invalid_file_tups()
if rmm_invalid_file_tups:
message = tool_util.generate_message_for_invalid_tools(self.app,
rmm_invalid_file_tups,
repository,
None,
as_html=False)
results['status'] = 'warning'
else:
message = "Successfully reset metadata on repository %s owned by %s" % \
(str(repository.name), str(repository.user.username))
results['status'] = 'ok'
except Exception as e:
message = "Error resetting metadata on repository %s owned by %s: %s" % \
(str(repository.name), str(repository.user.username), str(e))
results['status'] = 'error'
status = '%s : %s' % (str(repository.name), message)
results['repository_status'].append(status)
return results
repository_id = payload.get('repository_id', None)
if repository_id is not None:
repository = repository_util.get_repository_in_tool_shed(self.app, repository_id)
start_time = strftime("%Y-%m-%d %H:%M:%S")
log.debug("%s...resetting metadata on repository %s" % (start_time, str(repository.name)))
results = handle_repository(trans, start_time, repository)
stop_time = strftime("%Y-%m-%d %H:%M:%S")
results['stop_time'] = stop_time
return results
[docs] @expose_api_anonymous_and_sessionless
def show(self, trans, id, **kwd):
"""
GET /api/repositories/{encoded_repository_id}
Returns information about a repository in the Tool Shed.
Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135
:param id: the encoded id of the Repository object
:type id: encoded str
:returns: detailed repository information
:rtype: dict
:raises: ObjectNotFound, MalformedId
"""
try:
trans.security.decode_id(id)
except Exception:
raise MalformedId('The given id is invalid.')
repository = repository_util.get_repository_in_tool_shed(self.app, id)
if repository is None:
raise ObjectNotFound('Unable to locate repository for the given id.')
repository_dict = repository.to_dict(view='element',
value_mapper=self.__get_value_mapper(trans))
# TODO the following property would be better suited in the to_dict method
repository_dict['category_ids'] = \
[trans.security.encode_id(x.category.id) for x in repository.categories]
return repository_dict
[docs] @expose_api_raw_anonymous_and_sessionless
def updates(self, trans, **kwd):
"""
GET /api/repositories/updates
Return a dictionary with boolean values for whether there are updates available
for the repository revision, newer installable revisions available,
the revision is the latest installable revision, and if the repository is deprecated.
:param owner: owner of the repository
:type owner: str
:param name: name of the repository
:type name: str
:param changeset_revision: changeset of the repository
:type changeset_revision: str
:param hexlify: flag whether to hexlify the response (for backward compatibility)
:type changeset: boolean
:returns: information about repository deprecations, updates, and upgrades
:rtype: dict
"""
name = kwd.get('name', None)
owner = kwd.get('owner', None)
changeset_revision = kwd.get('changeset_revision', None)
hexlify_this = util.asbool(kwd.get('hexlify', True))
repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
if repository:
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
trans.security.encode_id(repository.id),
changeset_revision)
tool_shed_status_dict = {}
# Handle repository deprecation.
tool_shed_status_dict['repository_deprecated'] = str(repository.deprecated)
# Handle latest installable revision.
if changeset_revision == repository.tip(trans.app):
tool_shed_status_dict['latest_installable_revision'] = 'True'
else:
next_installable_revision = metadata_util.get_next_downloadable_changeset_revision(trans.app, repository, changeset_revision)
if repository_metadata is None:
if next_installable_revision and next_installable_revision != changeset_revision:
tool_shed_status_dict['latest_installable_revision'] = 'True'
else:
tool_shed_status_dict['latest_installable_revision'] = 'False'
else:
if next_installable_revision and next_installable_revision != changeset_revision:
tool_shed_status_dict['latest_installable_revision'] = 'False'
else:
tool_shed_status_dict['latest_installable_revision'] = 'True'
# Handle revision updates.
if changeset_revision == repository.tip(trans.app):
tool_shed_status_dict['revision_update'] = 'False'
else:
if repository_metadata is None:
tool_shed_status_dict['revision_update'] = 'True'
else:
tool_shed_status_dict['revision_update'] = 'False'
# Handle revision upgrades.
metadata_revisions = [revision[1] for revision in metadata_util.get_metadata_revisions(trans.app, repository)]
num_metadata_revisions = len(metadata_revisions)
for index, metadata_revision in enumerate(metadata_revisions):
if index == num_metadata_revisions:
tool_shed_status_dict['revision_upgrade'] = 'False'
break
if metadata_revision == changeset_revision:
if num_metadata_revisions - index > 1:
tool_shed_status_dict['revision_upgrade'] = 'True'
else:
tool_shed_status_dict['revision_upgrade'] = 'False'
break
return encoding_util.tool_shed_encode(tool_shed_status_dict) if hexlify_this else json.dumps(tool_shed_status_dict)
return encoding_util.tool_shed_encode({}) if hexlify_this else json.dumps({})
[docs] @expose_api_anonymous_and_sessionless
def show_tools(self, trans, id, changeset, **kwd):
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(self.app,
id,
changeset)
if repository_metadata is not None:
encoded_repository_metadata_id = trans.security.encode_id(repository_metadata.id)
repository_metadata_dict = repository_metadata.to_dict(view='collection',
value_mapper=self.__get_value_mapper(trans))
repository_metadata_dict['url'] = web.url_for(controller='repository_revisions',
action='show',
id=encoded_repository_metadata_id)
if 'tools' in repository_metadata.metadata:
repository_metadata_dict['valid_tools'] = repository_metadata.metadata['tools']
# Get the repo_info_dict for installing the repository.
repo_info_dict, \
includes_tools, \
includes_tool_dependencies, \
includes_tools_for_display_in_tool_panel, \
has_repository_dependencies, \
has_repository_dependencies_only_if_compiling_contained_td = \
repository_util.get_repo_info_dict(self.app,
trans.user,
id,
changeset)
return repository_metadata_dict
else:
log.debug("Unable to locate repository_metadata record for repository id %s and changeset_revision %s" %
(str(id), str(changeset)))
return {}
[docs] @expose_api_anonymous_and_sessionless
def metadata(self, trans, id, **kwd):
"""
GET /api/repositories/{encoded_repository_id}/metadata
Returns information about a repository in the Tool Shed.
Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135/metadata
:param id: the encoded id of the Repository object
:returns: A dictionary containing the specified repository's metadata, by changeset,
recursively including dependencies and their metadata.
:not found: Empty dictionary.
"""
try:
trans.security.decode_id(id)
except Exception:
raise MalformedId('The given id is invalid.')
recursive = util.asbool(kwd.get('recursive', 'True'))
all_metadata = {}
repository = repository_util.get_repository_in_tool_shed(self.app, id)
for changeset, changehash in repository.installable_revisions(self.app):
metadata = metadata_util.get_current_repository_metadata_for_changeset_revision(self.app, repository, changehash)
if metadata is None:
continue
metadata_dict = metadata.to_dict(value_mapper={'id': self.app.security.encode_id, 'repository_id': self.app.security.encode_id})
metadata_dict['repository'] = repository.to_dict(value_mapper={'id': self.app.security.encode_id})
if metadata.has_repository_dependencies and recursive:
metadata_dict['repository_dependencies'] = metadata_util.get_all_dependencies(self.app, metadata, processed_dependency_links=[])
else:
metadata_dict['repository_dependencies'] = []
if metadata.includes_tool_dependencies and recursive:
metadata_dict['tool_dependencies'] = repository.get_tool_dependencies(self.app, changehash)
else:
metadata_dict['tool_dependencies'] = {}
if metadata.includes_tools:
metadata_dict['tools'] = metadata.metadata['tools']
all_metadata['%s:%s' % (int(changeset), changehash)] = metadata_dict
return all_metadata
[docs] @expose_api
def update(self, trans, id, **kwd):
"""
PATCH /api/repositories/{encoded_repository_id}
Updates information about a repository in the Tool Shed.
:param id: the encoded id of the Repository object
:param payload: dictionary structure containing::
'name': repo's name (optional)
'synopsis': repo's synopsis (optional)
'description': repo's description (optional)
'remote_repository_url': repo's remote repo (optional)
'homepage_url': repo's homepage url (optional)
'category_ids': list of existing encoded TS category ids
the updated repo should be associated with (optional)
:type payload: dict
:returns: detailed repository information
:rtype: dict
:raises: RequestParameterInvalidException, InsufficientPermissionsException
"""
payload = kwd.get('payload', None)
if not payload:
raise RequestParameterMissingException("You did not specify any payload.")
name = payload.get('name', None)
synopsis = payload.get('synopsis', None)
description = payload.get('description', None)
remote_repository_url = payload.get('remote_repository_url', None)
homepage_url = payload.get('homepage_url', None)
category_ids = payload.get('category_ids', None)
if category_ids is not None:
# We need to know if it was actually passed, and listify turns None into []
category_ids = util.listify(category_ids)
update_kwds = dict(
name=name,
description=synopsis,
long_description=description,
remote_repository_url=remote_repository_url,
homepage_url=homepage_url,
category_ids=category_ids,
)
repo, message = repository_util.update_repository(app=self.app, trans=trans, id=id, **update_kwds)
if repo is None:
if "You are not the owner" in message:
raise InsufficientPermissionsException(message)
else:
raise ActionInputError(message)
repository_dict = repo.to_dict(view='element', value_mapper=self.__get_value_mapper(trans))
repository_dict['category_ids'] = \
[trans.security.encode_id(x.category.id) for x in repo.categories]
return repository_dict
[docs] @expose_api
def create(self, trans, **kwd):
"""
create( self, trans, payload, **kwd )
* POST /api/repositories:
Creates a new repository.
Only ``name`` and ``synopsis`` parameters are required.
:param payload: dictionary structure containing::
'name': new repo's name (required)
'synopsis': new repo's synopsis (required)
'description': new repo's description (optional)
'remote_repository_url': new repo's remote repo (optional)
'homepage_url': new repo's homepage url (optional)
'category_ids[]': list of existing encoded TS category ids
the new repo should be associated with (optional)
'type': new repo's type, defaults to ``unrestricted`` (optional)
:type payload: dict
:returns: detailed repository information
:rtype: dict
:raises: RequestParameterMissingException, RequestParameterInvalidException
"""
payload = kwd.get('payload', None)
if not payload:
raise RequestParameterMissingException("You did not specify any payload.")
name = payload.get('name', None)
if not name:
raise RequestParameterMissingException("Missing required parameter 'name'.")
synopsis = payload.get('synopsis', None)
if not synopsis:
raise RequestParameterMissingException("Missing required parameter 'synopsis'.")
description = payload.get('description', '')
remote_repository_url = payload.get('remote_repository_url', '')
homepage_url = payload.get('homepage_url', '')
category_ids = util.listify(payload.get('category_ids[]', ''))
repo_type = payload.get('type', rt_util.UNRESTRICTED)
if repo_type not in rt_util.types:
raise RequestParameterInvalidException('This repository type is not valid')
invalid_message = repository_util.validate_repository_name(self.app, name, trans.user)
if invalid_message:
raise RequestParameterInvalidException(invalid_message)
repo, message = repository_util.create_repository(app=self.app,
name=name,
type=repo_type,
description=synopsis,
long_description=description,
user_id=trans.user.id,
category_ids=category_ids,
remote_repository_url=remote_repository_url,
homepage_url=homepage_url)
repository_dict = repo.to_dict(view='element', value_mapper=self.__get_value_mapper(trans))
repository_dict['category_ids'] = \
[trans.security.encode_id(x.category.id) for x in repo.categories]
return repository_dict
[docs] @web.expose_api
def create_changeset_revision(self, trans, id, payload, **kwd):
"""
POST /api/repositories/{encoded_repository_id}/changeset_revision
Create a new tool shed repository commit - leaving PUT on parent
resource open for updating meta-attributes of the repository (and
Galaxy doesn't allow PUT multipart data anyway
https://trello.com/c/CQwmCeG6).
:param id: the encoded id of the Repository object
The following parameters may be included in the payload.
:param commit_message: hg commit message for update.
"""
# Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135
rdah = attribute_handlers.RepositoryDependencyAttributeHandler(self.app, unpopulate=False)
tdah = attribute_handlers.ToolDependencyAttributeHandler(self.app, unpopulate=False)
repository = repository_util.get_repository_in_tool_shed(self.app, id)
if not (trans.user_is_admin or
self.app.security_agent.user_can_administer_repository(trans.user, repository) or
self.app.security_agent.can_push(self.app, trans.user, repository)):
trans.response.status = 400
return {
"err_msg": "You do not have permission to update this repository.",
}
repo_dir = repository.repo_path(self.app)
upload_point = commit_util.get_upload_point(repository, **kwd)
tip = repository.tip(self.app)
file_data = payload.get('file')
# Code stolen from gx's upload_common.py
if isinstance(file_data, cgi_FieldStorage):
assert not isinstance(file_data.file, StringIO)
assert file_data.file.name != '<fdopen>'
local_filename = util.mkstemp_ln(file_data.file.name, 'upload_file_data_')
file_data.file.close()
file_data = dict(filename=file_data.filename,
local_filename=local_filename)
elif type(file_data) == dict and 'local_filename' not in file_data:
raise Exception('Uploaded file was encoded in a way not understood.')
commit_message = kwd.get('commit_message', 'Uploaded')
uploaded_file = open(file_data['local_filename'], 'rb')
uploaded_file_name = file_data['local_filename']
isgzip = False
isbz2 = False
isgzip = checkers.is_gzip(uploaded_file_name)
if not isgzip:
isbz2 = checkers.is_bz2(uploaded_file_name)
if (isgzip or isbz2):
# Open for reading with transparent compression.
tar = tarfile.open(uploaded_file_name, 'r:*')
else:
tar = tarfile.open(uploaded_file_name)
new_repo_alert = False
remove_repo_files_not_in_tar = True
ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
repository_content_util.upload_tar(
trans,
rdah,
tdah,
repository,
tar,
uploaded_file,
upload_point,
remove_repo_files_not_in_tar,
commit_message,
new_repo_alert
)
if ok:
# Update the repository files for browsing.
hg_util.update_repository(repo_dir)
# Get the new repository tip.
if tip == repository.tip(self.app):
trans.response.status = 400
message = 'No changes to repository.'
ok = False
else:
rmm = repository_metadata_manager.RepositoryMetadataManager(app=self.app,
user=trans.user,
repository=repository)
status, error_message = \
rmm.set_repository_metadata_due_to_new_tip(trans.request.host,
content_alert_str=content_alert_str,
**kwd)
if error_message:
ok = False
trans.response.status = 500
message = error_message
else:
trans.response.status = 500
if os.path.exists(uploaded_file_name):
os.remove(uploaded_file_name)
if not ok:
return {
"err_msg": message
}
else:
return {
"message": message
}