Source code for bioblend.toolshed.repositories
"""
Interaction with a Tool Shed instance
"""
from six.moves.urllib.parse import urljoin
from bioblend.galaxy.client import Client
from bioblend.util import attach_file
[docs]class ToolShedClient(Client):
def __init__(self, toolshed_instance):
self.module = 'repositories'
super(ToolShedClient, self).__init__(toolshed_instance)
[docs] def get_repositories(self):
"""
Get a list of all the repositories in a Galaxy Tool Shed
:rtype: list
:return: Returns a list of dictionaries containing information about
repositories present in the Tool Shed.
For example::
[{u'times_downloaded': 0, u'user_id': u'5cefd48bc04af6d4',
u'description': u'Order Contigs', u'deleted': False,
u'deprecated': False, u'private': False,
u'url': u'/api/repositories/287bd69f724b99ce',
u'owner': u'billybob', u'id': u'287bd69f724b99ce',
u'name': u'best_tool_ever'}]
.. versionchanged:: 0.4.1
Changed method name from ``get_tools`` to ``get_repositories`` to
better align with the Tool Shed concepts
"""
return Client._get(self)
[docs] def show_repository(self, toolShed_id):
"""
Display information of a repository from Tool Shed
:type toolShed_id: string
:param toolShed_id: Encoded toolShed ID
:rtype: dictionary
:return: Information about the tool
For example::
{{u'times_downloaded': 0, u'user_id': u'5cefd48bc04af6d4',
u'description': u'Order Contigs', u'deleted': False,
u'deprecated': False, u'private': False,
u'url': u'/api/repositories/287bd69f724b99ce',
u'owner': u'billybob', u'id': u'287bd69f724b99ce',
u'name': u'best_tool_ever'}
.. versionchanged:: 0.4.1
Changed method name from ``show_tool`` to ``show_repository`` to
better align with the Tool Shed concepts
"""
return Client._get(self, id=toolShed_id)
[docs] def get_ordered_installable_revisions(self, name, owner):
"""
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.
:type name: string
:param name: the name of the repository
:type owner: string
:param owner: the owner of the repository
:rtype: list
:return: List of changeset revision hash string from oldest to newest
"""
url = self.url + '/get_ordered_installable_revisions'
params = {}
params['name'] = name
params['owner'] = owner
r = Client._get(self, url=url, params=params)
return r
[docs] def get_repository_revision_install_info(self, name, owner, changeset_revision):
"""
Return a list of dictionaries of metadata about a certain changeset
revision for a single tool.
:type name: string
:param name: the name of the repository
:type owner: string
:param owner: the owner of the repository
:type changeset_revision: string
:param changeset_revision: the changset_revision of the RepositoryMetadata
object associated with the repository
:rtype: List of dictionaries
:return: Returns a list of the following dictionaries:
- a dictionary defining the repository
- a dictionary defining the repository revision (RepositoryMetadata)
- a dictionary including the additional information required to
install the repository
For example::
[{u'times_downloaded': 269, u'user_id': u'1de29d50c3c44272', u'description': u'Galaxy Freebayes Bayesian genetic variant detector tool', u'deleted': False, u'deprecated': False, u'private': False, u'long_description': u'Galaxy Freebayes Bayesian genetic variant detector tool originally included in the Galaxy code distribution but migrated to the tool shed.', u'url': u'/api/repositories/491b7a3fddf9366f', u'owner': u'devteam', u'id': u'491b7a3fddf9366f', u'name': u'freebayes'},
{u'repository_id': u'491b7a3fddf9366f', u'has_repository_dependencies': False, u'includes_tools_for_display_in_tool_panel': True, u'url': u'/api/repository_revisions/504be8aaa652c154', u'malicious': False, u'includes_workflows': False, u'downloadable': True, u'includes_tools': True, u'changeset_revision': u'd291dc763c4c', u'id': u'504be8aaa652c154', u'includes_tool_dependencies': True, u'includes_datatypes': False}, {u'freebayes': [u'Galaxy Freebayes Bayesian genetic variant detector tool', u'http://takadonet@toolshed.g2.bx.psu.edu/repos/devteam/freebayes', u'd291dc763c4c', u'9', u'devteam', {},
{u'freebayes/0.9.6_9608597d12e127c847ae03aa03440ab63992fedf': {u'repository_name': u'freebayes', u'name': u'freebayes', u'readme': u'FreeBayes requires g++ and the standard C and C++ development libraries. Additionally, cmake is required for building the BamTools API.', u'version': u'0.9.6_9608597d12e127c847ae03aa03440ab63992fedf', u'repository_owner': u'devteam', u'changeset_revision': u'd291dc763c4c', u'type': u'package'}, u'samtools/0.1.18': {u'repository_name': u'freebayes', u'name': u'samtools', u'readme': u'Compiling SAMtools requires the ncurses and zlib development libraries.', u'version': u'0.1.18', u'repository_owner': u'devteam', u'changeset_revision': u'd291dc763c4c', u'type': u'package'}}]}]
"""
url = self.url + '/get_repository_revision_install_info'
params = {}
params['name'] = name
params['owner'] = owner
params['changeset_revision'] = changeset_revision
return Client._get(self, url=url, params=params)
[docs] def repository_revisions(
self, downloadable=None, malicious=None,
tools_functionally_correct=None, missing_test_components=None,
do_not_test=None, includes_tools=None, test_install_error=None,
skip_tool_test=None):
"""
Returns a (possibly filtered) list of dictionaries that include information
about all repository revisions. The following parameters can be used to
filter the list.
:type downloadable: Boolean
:param downloadable: Can the tool be downloaded
:type malicious: Boolean
:param malicious:
:type tools_functionally_correct: Boolean
:param tools_functionally_correct:
:type missing_test_components: Boolean
:param missing_test_components:
:type do_not_test: Boolean
:param do_not_test:
:type includes_tools: Boolean
:param includes_tools:
:type test_install_error: Boolean
:param test_install_error:
:type skip_tool_test: Boolean
:param skip_tool_test:
:rtype: List of dictionaries
:return: Returns a (possibly filtered) list of dictionaries that include
information about all repository revisions.
For example::
[{u'repository_id': u'78f2604ff5e65707', u'has_repository_dependencies': False, u'includes_tools_for_display_in_tool_panel': True, u'url': u'/api/repository_revisions/92250afff777a169', u'malicious': False, u'includes_workflows': False, u'downloadable': True, u'includes_tools': True, u'changeset_revision': u'6e26c5a48e9a', u'id': u'92250afff777a169', u'includes_tool_dependencies': False, u'includes_datatypes': False},
{u'repository_id': u'f9662009da7bfce0', u'has_repository_dependencies': False, u'includes_tools_for_display_in_tool_panel': True, u'url': u'/api/repository_revisions/d3823c748ae2205d', u'malicious': False, u'includes_workflows': False, u'downloadable': True, u'includes_tools': True, u'changeset_revision': u'15a54fa11ad7', u'id': u'd3823c748ae2205d', u'includes_tool_dependencies': False, u'includes_datatypes': False}]
"""
# Not using '_make_url' or '_get' to create url since the module id used
# to create url is not the same as needed for this method
url = self.gi.url + '/repository_revisions'
params = {}
# nice and long... my god!
if downloadable:
params['downloadable'] = 'True'
if malicious:
params['malicious'] = 'True'
if tools_functionally_correct:
params['tools_functionally_correct'] = 'True'
if missing_test_components:
params['missing_test_components'] = 'True'
if do_not_test:
params['do_not_test'] = 'True'
if includes_tools:
params['includes_tools'] = 'True'
if test_install_error:
params['test_install_error'] = 'True'
if skip_tool_test:
params['skip_tool_test'] = 'True'
return Client._get(self, url=url, params=params)
[docs] def show_repository_revision(self, metadata_id):
'''
Returns a dictionary that includes information about a specified repository
revision.
:type metadata_id: string
:param metadata_id: Encoded repository metadata ID
:rtype: dictionary
:return: Returns a dictionary that includes information about a specified
repository revision.
For example::
{u'repository_id': u'491b7a3fddf9366f',
u'has_repository_dependencies': False,
u'includes_tools_for_display_in_tool_panel': True,
u'test_install_error': False,
u'url': u'/api/repository_revisions/504be8aaa652c154',
u'malicious': False,
u'includes_workflows': False,
u'id': u'504be8aaa652c154',
u'do_not_test': False,
u'downloadable': True,
u'includes_tools': True,
u'tool_test_results': {u'missing_test_components': [],,
u'includes_datatypes': False}
'''
# Not using '_make_url' or '_get' to create url since the module id used
# to create url is not the same as needed for this method
# since metadata_id has to be defined, easy to create the url here
url = self.gi.url + '/repository_revisions/' + metadata_id
return Client._get(self, url=url)
[docs] def get_categories(self):
"""
Returns a list of dictionaries that contain descriptions of the
repository categories found on the given Tool Shed instance.
:rtype: list
:return: A list of dictionaries containing information about
repository categories present in the Tool Shed.
For example::
[{u'deleted': False,
u'description': u'Tools for manipulating data',
u'id': u'175812cd7caaf439',
u'model_class': u'Category',
u'name': u'Text Manipulation',
u'url': u'/api/categories/175812cd7caaf439'},]
.. versionadded:: 0.5.2
"""
url = urljoin(self.url, 'categories')
return Client._get(self, url=url)
[docs] def update_repository(self, id, tar_ball_path, commit_message=None):
"""
Update the contents of a tool shed repository with specified tar
ball.
:type id: string
:param id: Encoded repository ID
:type tar_ball_path: string
:param tar_ball_path: Path to file containing tar ball to upload.
:type commit_message: string
:param commit_message: Commit message used for underlying mercurial
repository backing tool shed repository.
:rtype: dict
:return: Returns a dictionary that includes repository content
warnings. Most valid uploads will result in no such
warning and an exception will be raised generally if
there are problems.
For example a successful upload will look like::
{u'content_alert': u'', u'message': u''}
.. versionadded:: 0.5.2
"""
url = self.gi._make_url(self, id) + '/changeset_revision'
payload = {}
if commit_message is not None:
payload['commit_message'] = commit_message
payload["file"] = attach_file(tar_ball_path)
try:
return Client._post(self, id=id, payload=payload, files_attached=True, url=url)
finally:
payload["file"].close()
[docs] def create_repository(self, name, synopsis, description=None, type="unrestricted",
remote_repository_url=None, homepage_url=None,
category_ids=None):
"""
Create a new repository in a Tool Shed
:type name: str
:param name: Name of the repository
:type synopsis: str
:param synopsis: Synopsis of the repository
:type description: str
:param description: Optional description of the repository
:type type: str
:param type: type of the repository. One of "unrestricted",
"repository_suite_definition", or "tool_dependency_definition"
:type remote_repository_url: str
:param remote_repository_url: Remote URL (e.g. github/bitbucket repository)
:type homepage_url: str
:param homepage_url: Upstream's homepage for the project.
:type category_ids: list
:param category_ids: List of encoded category IDs
:rtype: dict
:return: a dictionary containing information about the new repository.
For example::
{
"deleted": false,
"deprecated": false,
"description": "new_synopsis",
"homepage_url": "https://github.com/galaxyproject/",
"id": "8cf91205f2f737f4",
"long_description": "this is some repository",
"model_class": "Repository",
"name": "new_repo_17",
"owner": "qqqqqq",
"private": false,
"remote_repository_url": "https://github.com/galaxyproject/tools-devteam",
"times_downloaded": 0,
"type": "unrestricted",
"user_id": "adb5f5c93f827949"
}
"""
payload = {
'name': name,
'synopsis': synopsis,
}
if description is not None:
payload['description'] = description
if description is not None:
payload['description'] = description
if type is not None:
payload['type'] = type
if remote_repository_url is not None:
payload['remote_repository_url'] = remote_repository_url
if homepage_url is not None:
payload['homepage_url'] = homepage_url
if category_ids is not None:
payload['category_ids[]'] = category_ids
return Client._post(self, payload)