def get_most_recently_used_history(self):
"""
Returns the current user's most recently used history (not deleted).
"""
url = self.gi._make_url(self, None)
url = "/".join([url, "most_recently_used"])
return Client._get(self, url=url)
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://[email protected]/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'\nFreeBayes requires g++ and the standard C and C++ development libraries.\nAdditionally, cmake is required for building the BamTools API.\n ', 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'\nCompiling SAMtools requires the ncurses and zlib development libraries.\n ', 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)
def show_invocation_step(self, workflow_id, invocation_id, step_id):
""" See the details of a particular workflow invocation step.
:type workflow_id: str
:param workflow_id: Encoded workflow ID
:type invocation_id: str
:param invocation_id: Encoded workflow invocation ID
:type step_id: str
:param step_id: Encoded workflow invocation step ID
:rtype: dict
:return: The workflow invocation step.
For example::
{u'workflow_step_uuid': u'4060554c-1dd5-4287-9040-8b4f281cf9dc',
u'update_time': u'2015-10-31T22:11:14',
u'job_id': None,
u'state': None,
u'workflow_step_label': None,
u'order_index': 2,
u'action': None,
u'model_class': u'WorkflowInvocationStep',
u'workflow_step_id': u'52e496b945151ee8',
u'id': u'63cd3858d057a6d1'}
"""
url = self._invocation_step_url(workflow_id, invocation_id, step_id)
return Client._get(self, url=url)
def get_libraries(self, library_id=None, name=None, deleted=False):
"""
Get all the libraries or filter for specific one(s) via the provided name or ID.
Provide only one argument: ``name`` or ``library_id``, but not both.
:type library_id: str
:param library_id: filter for library by library id
:type name: str
:param name: If ``name`` is set and multiple names match the given
name, all the libraries matching the argument will be
returned.
:type deleted: bool
:param deleted: If set to ``True``, return libraries that have been
deleted.
:rtype: list
:return: list of dicts each containing basic information about a library.
"""
if library_id is not None and name is not None:
raise ValueError('Provide only one argument between name or library_id, but not both')
libraries = Client._get(self, deleted=deleted)
if library_id is not None:
library = next((_ for _ in libraries if _['id'] == library_id), None)
libraries = [library] if library is not None else []
if name is not None:
libraries = [_ for _ in libraries if _['name'] == name]
return libraries
def show_history(self, history_id, contents=False):
"""
Get details of a given history. By default, just get the history meta
information. If ``contents`` is set to ``True``, get the complete list of
datasets in the given history.
"""
return Client._get(self, id=history_id, contents=contents)
def show_genome(self, id, num=None, chrom=None, low=None, high=None):
"""
Returns information about build <id>
:type id: str
:param id: Genome build ID to use
:type num: str
:param num: num
:type chrom: str
:param chrom: chrom
:type low: str
:param low: low
:type high: str
:param high: high
"""
params = {}
if num:
params["num"] = num
if chrom:
params["chrom"] = chrom
if low:
params["low"] = low
if high:
params["high"] = high
return Client._get(self, id, params)
def get_datatypes(self, extension_only=False, upload_only=False):
"""
Get the list of all installed datatypes.
:rtype: list
:return: A list of datatype names.
For example::
[u'snpmatrix',
u'snptest',
u'tabular',
u'taxonomy',
u'twobit',
u'txt',
u'vcf',
u'wig',
u'xgmml',
u'xml']
"""
params = {}
if extension_only:
params['extension_only'] = True
if upload_only:
params['upload_only'] = True
return Client._get(self, params=params)
def show_history(self, history_id, contents=False, deleted=None, visible=None, details=None, types=None):
"""
Get details of a given history. By default, just get the history meta
information.
:type history_id: str
:param history_id: Encoded history ID to filter on
:type contents: str
:param contents: When true, the complete list of datasets in the given history.
:type deleted: str
:param deleted: Used when contents=True, includes deleted datasets is history dataset list
:type visible: str
:param visible: Used when contents=True, includes only visible datasets is history dataset list
:type details: str
:param details: Used when contents=True, includes dataset details. Set to 'all' for the most information
:type types: str
:param types: ???
"""
params = {}
if contents:
if details:
params["details"] = details
if deleted is not None:
params["deleted"] = deleted
if visible is not None:
params["visible"] = visible
if types is not None:
params["types"] = types.join(",")
return Client._get(self, id=history_id, contents=contents, params=params)
def get_workflows(self, workflow_id=None, name=None, deleted=False):
"""
Get all workflows or filter the specific one(s) via the provided ``name``
or ``workflow_id``. Provide only one argument, ``name`` or ``workflow_id``,
but not both.
If ``name`` is set and multiple names match the given name, all the
workflows matching the argument will be returned.
If ``deleted`` is set to ``True``, return workflows that have been deleted.
Return a list of JSON formatted dicts each containing basic information
about a workflow.
:rtype: list
:return: A list of workflow dicts.
For example::
[{u'id': u'92c56938c2f9b315',
u'name': u'Simple',
u'url': u'/api/workflows/92c56938c2f9b315'}]
"""
workflows = Client._get(self, deleted=deleted)
if name is not None or workflow_id is not None:
filtered_wfs = []
for workflow in workflows:
if name == workflow['name'] or workflow_id == workflow['id']:
filtered_wfs.append(workflow)
# Workflows ID's are unique so break now that the wf was found
if workflow_id is not None:
break
workflows = filtered_wfs
return workflows
def show_job(self, job_id, full_details=False):
"""
Display information on a single job from current user
:type job_id: str
:param job_id: Specific job ID
:type full_details: bool
:param full_details: When ``True``, the complete list of details for the
given job.
:rtype: dict
:return: A description of single job
For example::
{ u'create_time': u'2014-03-01T16:17:29.828624',
u'exit_code': 0,
u'id': u'a799d38679e985db',
u'inputs': { u'input': { u'id': u'ebfb8f50c6abde6d', u'src': u'hda'}},
u'model_class': u'Job',
u'outputs': { u'output': { u'id': u'a799d38679e985db', u'src': u'hda'}},
u'params': { u'chromInfo': u'"/opt/galaxy-central/tool-data/shared/ucsc/chrom/?.len"',
u'dbkey': u'"?"',
u'seq_col': u'"2"',
u'title_col': u'["1"]'},
u'state': u'ok',
u'tool_id': u'tab2fasta',
u'update_time': u'2014-03-01T16:17:31.930728'}
"""
params = {}
if full_details:
params['full'] = full_details
return Client._get(self, id=job_id, params=params)
def get_jobs(self):
"""
Get a list of jobs for current user
:type state: string or list
:param state: limit listing of jobs to those that match one of the included states. If none, all are returned.
Valid Galaxy job states include:
'new', 'upload', 'waiting', 'queued', 'running', 'ok', 'error', 'paused', 'deleted', 'deleted_new'
:type tool_id: string or list
:param tool_id: limit listing of jobs to those that match one of the included tool_ids. If none, all are returned.
:type history_id: string
:param history_id: limit listing of jobs to those that match the history_id. If none, all are returned.
:rtype: list
:returns: list of dictionaries containing summary job information
For example::
[{ u'create_time': u'2014-03-01T16:16:48.640550',
u'exit_code': 0,
u'id': u'ebfb8f50c6abde6d',
u'model_class': u'Job',
u'state': u'ok',
u'tool_id': u'fasta2tab',
u'update_time': u'2014-03-01T16:16:50.657399'},
{u'create_time': u'2014-03-01T16:05:34.851246',
u'exit_code': 0,
u'id': u'1cd8e2f6b131e891',
u'model_class': u'Job',
u'state': u'ok',
u'tool_id': u'upload1',
u'update_time': u'2014-03-01T16:05:39.558458'}]
"""
return Client._get(self)
def show_job(self, job_id):
"""
Display information on a single job from current user
:type job_id: string
:param job_id: Specific job ID
:rtype: dict
:return: A description of single job
For example::
{ u'create_time': u'2014-03-01T16:17:29.828624',
u'exit_code': 0,
u'id': u'a799d38679e985db',
u'inputs': { u'input': { u'id': u'ebfb8f50c6abde6d', u'src': u'hda'}},
u'model_class': u'Job',
u'outputs': { u'output': { u'id': u'a799d38679e985db', u'src': u'hda'}},
u'params': { u'chromInfo': u'"/opt/galaxy-central/tool-data/shared/ucsc/chrom/?.len"',
u'dbkey': u'"?"',
u'seq_col': u'"2"',
u'title_col': u'["1"]'},
u'state': u'ok',
u'tool_id': u'tab2fasta',
u'update_time': u'2014-03-01T16:17:31.930728'}
"""
return Client._get(self, id=job_id)
def get_current_history(self):
"""
Returns the current user's most recently used history object (not deleted)
"""
url = self.gi._make_url(self, None)
url = '/'.join([url, 'most_recently_used'])
return Client._get(self, url=url)
def show_visualization(self, visual_id):
"""
Display information on a visualization
:type visual_id: string
:param visual_id: Encoded visualization ID
:rtype: dict
:return: A description of visualization
For example::
{u'annotation': None,u'dbkey': u'mm9',
u'id': u'18df9134ea75e49c',
u'latest_revision': { ... },
u'model_class': u'Visualization',
u'revisions': [ u'aa90649bb3ec7dcb',
u'20622bc6249c0c71'],
u'slug': u'visualization-for-grant-1',
u'title': u'Visualization For Grant',
u'type': u'trackster',
u'url': u'/u/azaron/v/visualization-for-grant-1',
u'user_id': u'21e4aed91386ca8b'}
"""
return Client._get(self, id=visual_id)
def show_quota(self, quota_id, deleted=False):
"""
Display information on a quota
:type quota_id: string
:param quota_id: Encoded quota ID
:type deleted: Boolean
:param deleted: Search for quota in list of ones already marked as deleted
:rtype: dict
:return: A description of quota
For example::
{ u'bytes': 107374182400,
u'default': [],
u'description': u'just testing',
u'display_amount': u'100.0 GB',
u'groups': [],
u'id': u'0604c8a56abe9a50',
u'model_class': u'Quota',
u'name': u'test ',
u'operation': u'=',
u'users': []}
"""
return Client._get(self, id=quota_id, deleted=deleted)
def get_histories(self, history_id=None, name=None, deleted=False):
"""
Get all histories or filter the specific one(s) via the provided
``name`` or ``history_id``. Provide only one argument, ``name`` or
``history_id``, but not both.
If ``deleted`` is set to ``True``, return histories that have been
deleted.
:type history_id: str
:param history_id: Encoded history ID to filter on
:type name: str
:param name: Name of history to filter on
:rtype: list
:return: Return a list of history element dicts. If more than one
history matches the given ``name``, return the list of all the
histories with the given name
"""
if history_id is not None and name is not None:
raise ValueError('Provide only one argument between name or history_id, but not both')
histories = Client._get(self, deleted=deleted)
if history_id is not None:
history = next((_ for _ in histories if _['id'] == history_id), None)
histories = [history] if history is not None else []
elif name is not None:
histories = [_ for _ in histories if _['name'] == name]
return histories
def show_repository(self, toolShed_id):
"""
Display information of a repository from Tool Shed
:type toolShed_id: str
:param toolShed_id: Encoded Tool Shed ID
:rtype: dict
:return: Information about the tool.
For example::
{u'category_ids': [u'c1df3132f6334b0e', u'f6d7b0037d901d9b'],
u'deleted': False,
u'deprecated': False,
u'description': u'Order Contigs',
u'homepage_url': u'',
u'id': u'287bd69f724b99ce',
u'long_description': u'',
u'name': u'best_tool_ever',
u'owner': u'billybob',
u'private': False,
u'remote_repository_url': u'',
u'times_downloaded': 0,
u'type': u'unrestricted',
u'url': u'/api/repositories/287bd69f724b99ce',
u'user_id': u'5cefd48bc04af6d4'}
.. 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)
def get_sniffers(self):
"""
Displays a collection (list) of sniffers.
:rtype: list
:return: A list of individual sniffers.
For example::
[u'galaxy.datatypes.tabular:Vcf',
u'galaxy.datatypes.binary:TwoBit',
u'galaxy.datatypes.binary:Bam',
u'galaxy.datatypes.binary:Sff',
u'galaxy.datatypes.xml:Phyloxml',
u'galaxy.datatypes.xml:GenericXml',
u'galaxy.datatypes.sequence:Maf',
u'galaxy.datatypes.sequence:Lav',
u'galaxy.datatypes.sequence:csFasta']
"""
url = self.gi._make_url(self)
url = '/'.join([url, "sniffers"])
return Client._get(self, url=url)
def get_current_user(self):
"""
Returns the user id associated with this Galaxy connection
"""
url = self.gi._make_url(self, None)
url = '/'.join([url, 'current'])
return Client._get(self, url=url)
def get_folders(self, library_id, folder_id=None, name=None, deleted=False):
"""
Get all the folders or filter specific one(s) via the provided ``name``
or ``folder_id`` in data library with id ``library_id``. Provide only one
argument: ``name`` or ``folder_id``, but not both.
If ``name`` is set and multiple names match the given name, all the
folders matching the argument will be returned.
If ``deleted`` is set to ``True``, return folders that have been deleted.
Return a list of JSON formatted dicts each containing basic information
about a folder.
"""
library_contents = Client._get(self, id=library_id, contents=True)
folders = []
filtered_folders = []
for content in library_contents:
if content['type'] == 'folder':
folders.append(content)
if name == content['name'] or folder_id == content['id']:
filtered_folders.append(content)
if folder_id is not None and filtered_folders:
break
if name is not None or folder_id is not None:
folders = filtered_folders
return folders
def get_folders(self, library_id, folder_id=None, name=None, deleted=False):
"""
Get all the folders or filter specific one(s) via the provided ``name``
or ``folder_id`` in data library with id ``library_id``. Provide only one
argument: ``name`` or ``folder_id``, but not both.
If ``name`` is set and multiple names match the given name, all the
folders matching the argument will be returned.
If ``deleted`` is set to ``True``, return folders that have been deleted.
Return a list of JSON formatted dicts each containing basic information
about a folder.
"""
if folder_id is not None and name is not None:
raise ValueError('Provide only one argument between name or folder_id, but not both')
library_contents = Client._get(self, id=library_id, contents=True)
if folder_id is not None:
folder = next((_ for _ in library_contents if _['type'] == 'folder' and _['id'] == folder_id), None)
folders = [folder] if folder is not None else []
elif name is not None:
folders = [_ for _ in library_contents if _['type'] == 'folder' and _['name'] == name]
else:
folders = [_ for _ in library_contents if _['type'] == 'folder']
return folders
def show_dataset_collection(self, history_id, dataset_collection_id):
"""
Get details about a given history dataset collection.
"""
url = self.gi._make_url(self, history_id, contents=True)
url = '/'.join([url, "dataset_collections", dataset_collection_id])
return Client._get(self, url=url)
def __show_item(self, library_id, item_id):
"""
Get details about a given library item.
"""
url = self.gi._make_url(self, library_id, contents=True)
url = '/'.join([url, item_id])
return Client._get(self, url=url)
def show_repository_revision(self, metadata_id):
'''
Returns a dictionary that includes information about a specified repository
revision.
:type metadata_id: str
: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)
def show_data_table(self, data_table_id):
"""
Display information on a single data_table
:type data_table_id: str
:param data_table_id: ID of the data table
:rtype: dict
:return: A description of data_table and its content
For example::
{
"columns": ["value", "dbkey", "name", "path"],
"fields": [
[
"test id", "test", "test name",
"/opt/galaxy-dist/tool-data/test/seq/test id.fa"
]
],
"model_class": "TabularToolDataTable",
"name": "all_fasta"
}
"""
return Client._get(self, id=data_table_id)
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'category_ids': [u'c1df3132f6334b0e', u'f6d7b0037d901d9b'],
u'deleted': False,
u'deprecated': False,
u'description': u'Order Contigs',
u'homepage_url': u'',
u'id': u'287bd69f724b99ce',
u'name': u'best_tool_ever',
u'owner': u'billybob',
u'private': False,
u'remote_repository_url': u'',
u'times_downloaded': 0,
u'type': u'unrestricted',
u'url': u'/api/repositories/287bd69f724b99ce',
u'user_id': u'5cefd48bc04af6d4'}]
.. 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)
def get_datatypes(self, extension_only=False, upload_only=False):
"""
Displays a collection (list) of datatypes.
:rtype: list
:return: A list of dicts with details on individual datatypes.
For example::
[ u'snpmatrix',
u'snptest',
u'tabular',
u'taxonomy',
u'twobit',
u'txt',
u'vcf',
u'wig',
u'xgmml',
u'xml']
"""
params = {}
if extension_only:
params['extension_only'] = True
if upload_only:
params['upload_only'] = True
return Client._get(self, params=params)
def has_jobs_in_states(gi, history_id, states):
params = {"history_id": history_id}
jobs_url = gi._make_url(gi.jobs)
jobs = Client._get(gi.jobs, params=params, url=jobs_url)
target_jobs = [j for j in jobs if j["state"] in states]
return len(target_jobs) > 0
def get_workflow_inputs(self, workflow_id, label):
"""
Get a list of workflow input IDs that match the given label.
If no input matches the given label, an empty list is returned.
"""
wf = Client._get(self, id=workflow_id)
inputs = wf['inputs']
return [id for id in inputs if inputs[id]['label'] == label]
def get_ftp_files(self, deleted=False):
"""
Get a list of local files.
:rtype: list
:return: A list of dicts with details on individual files on FTP
"""
return Client._get(self)
def show_repository(self, toolShed_id):
"""
Get details of a given Tool Shed repository as it is installed on this
Galaxy instance.
:type toolShed_id: str
:param toolShed_id: Encoded toolShed ID
:rtype: dict
:return: Information about the tool
For example::
{u'changeset_revision': u'b17455fb6222',
u'ctx_rev': u'8',
u'owner': u'aaron',
u'status': u'Installed',
u'url': u'/api/tool_shed_repositories/82de4a4c7135b20a'}
.. 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)
def get_histories(self, history_id=None, name=None, deleted=False):
"""
Get all histories or filter the specific one(s) via the provided ``name``
or ``history_id``. Provide only one argument, ``name`` or ``history_id``,
but not both.
If ``deleted`` is set to ``True``, return histories that have been deleted.
Return a list of history element dicts. If more than one history
matches the given ``name``, return the list of all the histories with the
given name.
"""
histories = Client._get(self, deleted=deleted)
if name is not None or history_id is not None:
filtered_hists = []
for history in histories:
if name == history['name'] or history_id == history['id']:
filtered_hists.append(history)
# History ID's are unique so break now that the hist was found
if history_id is not None:
break
histories = filtered_hists
return histories
def get_visualizations(self):
"""
Get a list of visualizations
:rtype: list
:return: A list of dicts with details on individual visualizations.
For example::
[{ u'dbkey': u'eschColi_K12',
u'id': u'df1c7c96fc427c2d',
u'title': u'AVTest1',
u'type': u'trackster',
u'url': u'/api/visualizations/df1c7c96fc427c2d'},
{ u'dbkey': u'mm9',
u'id': u'a669f50f8bf55b02',
u'title': u'Bam to Bigwig',
u'type': u'trackster',
u'url': u'/api/visualizations/a669f50f8bf55b02'}]
"""
results = Client._get(self)
return results
def get_sniffers(self):
"""
Get the list of all installed sniffers.
:rtype: list
:return: A list of sniffer names.
For example::
[u'galaxy.datatypes.tabular:Vcf',
u'galaxy.datatypes.binary:TwoBit',
u'galaxy.datatypes.binary:Bam',
u'galaxy.datatypes.binary:Sff',
u'galaxy.datatypes.xml:Phyloxml',
u'galaxy.datatypes.xml:GenericXml',
u'galaxy.datatypes.sequence:Maf',
u'galaxy.datatypes.sequence:Lav',
u'galaxy.datatypes.sequence:csFasta']
"""
url = self.gi._make_url(self)
url = '/'.join([url, "sniffers"])
return Client._get(self, url=url)
def show_repository(self, toolShed_id):
"""
Display information of a repository from Tool Shed
:type toolShed_id: str
: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)
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://[email protected]/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'\nFreeBayes requires g++ and the standard C and C++ development libraries.\nAdditionally, cmake is required for building the BamTools API.\n ', 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'\nCompiling SAMtools requires the ncurses and zlib development libraries.\n ', 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)
def show_repository_revision(self, metadata_id):
'''
Returns a dictionary that includes information about a specified
repository revision.
:type metadata_id: str
:param metadata_id: Encoded repository metadata ID
:rtype: dict
:return: Returns a dictionary that includes information about a
specified repository revision.
For example::
{u'changeset_revision': u'7602de1e7f32',
u'do_not_test': False,
u'downloadable': True,
u'has_repository_dependencies': False,
u'id': u'504be8aaa652c154',
u'includes_datatypes': False,
u'includes_tool_dependencies': False,
u'includes_tools': True,
u'includes_tools_for_display_in_tool_panel': True,
u'includes_workflows': False,
u'malicious': False,
u'missing_test_components': True,
u'repository_id': u'491b7a3fddf9366f',
u'test_install_error': False,
u'time_last_tested': None,
u'tool_test_results': {u'missing_test_components': []},
u'tools_functionally_correct': False,
u'url': u'/api/repository_revisions/504be8aaa652c154'}
'''
# 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 = '/'.join([self.gi.url, 'repository_revisions', metadata_id])
return Client._get(self, url=url)
def get_jobs(self):
"""
Get the list of jobs of the current user.
:rtype: list
:returns: list of dictionaries containing summary job information.
For example::
[{u'create_time': u'2014-03-01T16:16:48.640550',
u'exit_code': 0,
u'id': u'ebfb8f50c6abde6d',
u'model_class': u'Job',
u'state': u'ok',
u'tool_id': u'fasta2tab',
u'update_time': u'2014-03-01T16:16:50.657399'},
{u'create_time': u'2014-03-01T16:05:34.851246',
u'exit_code': 0,
u'id': u'1cd8e2f6b131e891',
u'model_class': u'Job',
u'state': u'ok',
u'tool_id': u'upload1',
u'update_time': u'2014-03-01T16:05:39.558458'}]
"""
return Client._get(self)
def show_job(self, job_id, full_details=False):
"""
Get details of a given job of the current user.
:type job_id: str
:param job_id: job ID
:type full_details: bool
:param full_details: when ``True``, the complete list of details for the
given job.
:rtype: dict
:return: A description of the given job.
For example::
{u'create_time': u'2014-03-01T16:17:29.828624',
u'exit_code': 0,
u'id': u'a799d38679e985db',
u'inputs': {u'input': {u'id': u'ebfb8f50c6abde6d',
u'src': u'hda'}},
u'model_class': u'Job',
u'outputs': {u'output': {u'id': u'a799d38679e985db',
u'src': u'hda'}},
u'params': {u'chromInfo': u'"/opt/galaxy-central/tool-data/shared/ucsc/chrom/?.len"',
u'dbkey': u'"?"',
u'seq_col': u'"2"',
u'title_col': u'["1"]'},
u'state': u'ok',
u'tool_id': u'tab2fasta',
u'update_time': u'2014-03-01T16:17:31.930728'}
"""
params = {}
if full_details:
params['full'] = full_details
return Client._get(self, id=job_id, params=params)
def get_quotas(self,deleted=False):
"""
Get a list of quotas
:type deleted: Boolean
:param deleted: Only return quota(s) that have been deleted
:rtype: list
:return: A list of dicts with details on individual quotas.
For example::
[{ u'id': u'0604c8a56abe9a50',
u'model_class': u'Quota',
u'name': u'test ',
u'url': u'/api/quotas/0604c8a56abe9a50'},
{ u'id': u'1ee267091d0190af',
u'model_class': u'Quota',
u'name': u'workshop',
u'url': u'/api/quotas/1ee267091d0190af'}]
"""
return Client._get(self,deleted=deleted)
def get_config(self):
"""
Get a list of attributes about the Galaxy instance. More attributes will
be present if the user is an admin.
:rtype: list
:return: A list of attributes.
For example::
{u'allow_library_path_paste': False,
u'allow_user_creation': True,
u'allow_user_dataset_purge': True,
u'allow_user_deletion': False,
u'enable_unique_workflow_defaults': False,
u'ftp_upload_dir': u'/SOMEWHERE/galaxy/ftp_dir',
u'ftp_upload_site': u'galaxy.com',
u'library_import_dir': u'None',
u'logo_url': None,
u'support_url': u'http://wiki.g2.bx.psu.edu/Support',
u'terms_url': None,
u'user_library_import_dir': None,
u'wiki_url': u'http://g2.trac.bx.psu.edu/'}
"""
return Client._get(self)
def get_repositories(self):
"""
Get the list of all installed Tool Shed repositories on this Galaxy instance.
:rtype: list
:return: a list of dictionaries containing information about
repositories present in the Tool Shed.
For example::
[{u'changeset_revision': u'4afe13ac23b6',
u'deleted': False,
u'dist_to_shed': False,
u'error_message': u'',
u'name': u'velvet_toolsuite',
u'owner': u'edward-kirton',
u'status': u'Installed'}]
.. versionchanged:: 0.4.1
Changed method name from ``get_tools`` to ``get_repositories`` to
better align with the Tool Shed concepts
.. seealso:: bioblend.galaxy.tools.get_tool_panel()
"""
return Client._get(self)
def show_visualization(self, visual_id):
"""
Get details of a given visualization.
:type visual_id: str
:param visual_id: Encoded visualization ID
:rtype: dict
:return: A description of the given visualization.
For example::
{u'annotation': None,
u'dbkey': u'mm9',
u'id': u'18df9134ea75e49c',
u'latest_revision': { ... },
u'model_class': u'Visualization',
u'revisions': [u'aa90649bb3ec7dcb', u'20622bc6249c0c71'],
u'slug': u'visualization-for-grant-1',
u'title': u'Visualization For Grant',
u'type': u'trackster',
u'url': u'/u/azaron/v/visualization-for-grant-1',
u'user_id': u'21e4aed91386ca8b'}
"""
return Client._get(self, id=visual_id)
def show_form(self, form_id):
"""
Display information on a single form
:type form_id: string
:param form_id: Encoded form ID
:rtype: dict
:return: A description of single form
For example::
{ u'desc': u'here it is ',
u'fields': [],
u'form_definition_current_id': u'f2db41e1fa331b3e',
u'id': u'f2db41e1fa331b3e',
u'layout': [],
u'model_class': u'FormDefinition',
u'name': u'First form',
u'url': u'/api/forms/f2db41e1fa331b3e'}
"""
return Client._get(self, id=form_id)
def get_genomes(self):
"""
Returns a list of installed genomes
"""
genomes = Client._get(self)
return genomes
def show_user(self, user_id, deleted=False):
"""
Display information about a user. If ``deleted`` is set to ``True``,
display information about a deleted user.
"""
return Client._get(self, id=user_id, deleted=deleted)
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: str
:param name: the name of the repository
:type owner: str
:param owner: the owner of the repository
:type changeset_revision: str
:param changeset_revision: the changeset_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'deleted': False,
u'deprecated': False,
u'description': u'Galaxy Freebayes Bayesian genetic variant detector tool',
u'homepage_url': u'',
u'id': u'491b7a3fddf9366f',
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'name': u'freebayes',
u'owner': u'devteam',
u'private': False,
u'remote_repository_url': u'',
u'times_downloaded': 269,
u'type': u'unrestricted',
u'url': u'/api/repositories/491b7a3fddf9366f',
u'user_id': u'1de29d50c3c44272'},
{u'changeset_revision': u'd291dc763c4c',
u'do_not_test': False,
u'downloadable': True,
u'has_repository_dependencies': False,
u'id': u'504be8aaa652c154',
u'includes_datatypes': False,
u'includes_tool_dependencies': True,
u'includes_tools': True,
u'includes_tools_for_display_in_tool_panel': True,
u'includes_workflows': False,
u'malicious': False,
u'repository_id': u'491b7a3fddf9366f',
u'url': u'/api/repository_revisions/504be8aaa652c154'},
{u'freebayes': [u'Galaxy Freebayes Bayesian genetic variant detector tool',
u'http://testtoolshed.g2.bx.psu.edu/repos/devteam/freebayes',
u'd291dc763c4c',
u'9',
u'devteam',
{},
{u'freebayes/0.9.6_9608597d12e127c847ae03aa03440ab63992fedf': {u'changeset_revision': u'd291dc763c4c',
u'name': u'freebayes',
u'repository_name': u'freebayes',
u'repository_owner': u'devteam',
u'type': u'package',
u'version': u'0.9.6_9608597d12e127c847ae03aa03440ab63992fedf'},
u'samtools/0.1.18': {u'changeset_revision': u'd291dc763c4c',
u'name': u'samtools',
u'repository_name': u'freebayes',
u'repository_owner': u'devteam',
u'type': u'package',
u'version': u'0.1.18'}}]}]
"""
url = '/'.join([self.url, 'get_repository_revision_install_info'])
params = {
'name': name,
'owner': owner,
'changeset_revision': changeset_revision
}
return Client._get(self, url=url, params=params)
def __show_item(self, library_id, item_id):
url = self.gi._make_url(self, library_id, contents=True)
url = '/'.join([url, item_id])
return Client._get(self, url=url)
def _get_extra_files(self, dataset_details):
extra_files_url = "%s/%s/contents/%s/extra_files" % (
self._user_gi._make_url(self._user_gi.histories), self._history_id, dataset_details["id"]
)
extra_files = Client._get(self._user_gi.jobs, url=extra_files_url)
return extra_files
def _raw_get_tool(self, in_panel=None, trackster=None):
params = {}
params['in_panel'] = in_panel
params['trackster'] = trackster
return Client._get(self, params=params)
def show_dataset(self, dataset_id, deleted=False):
"""
Display information about and/or content of a dataset. This can be a
history or a library dataset.
"""
return Client._get(self, id=dataset_id, deleted=deleted)
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).json()
def search_repositories(self, q, page=1, page_size=10):
"""
Search for repositories in a Galaxy Tool Shed
:type q: str
:param q: query string for searching purposes
:type page: int
:param page: page requested
:type page_size: int
:param page_size: page size requested
:rtype: dict
:return: dictionary containing search hits as well as metadata
for the search
example:
{
u'hits':
[
{
u'matched_terms': [],
u'repository':
{
u'approved': u'no',
u'description': u'Convert export file to fastq',
u'full_last_updated': u'2015-01-18 09:48 AM',
u'homepage_url': None,
u'id': u'bdfa208f0cf6504e',
u'last_updated': u'less than a year',
u'long_description': u'This is a simple too to convert Solexas Export files to FASTQ files. The tool installation needs to add a new Export file type, the new class is included in the README file as a patch.',
u'name': u'export_to_fastq',
u'remote_repository_url': None,
u'repo_owner_username': u'louise',
u'times_downloaded': 164
},
u'score': 4.92
},
{
u'matched_terms': [],
u'repository':
{
u'approved': u'no',
u'description': u'Convert BAM file to fastq',
u'full_last_updated': u'2015-04-07 11:57 AM',
u'homepage_url': None,
u'id': u'175812cd7caaf439',
u'last_updated': u'less than a month',
u'long_description': u'Use Picards SamToFastq to convert a BAM file to fastq. Useful for storing reads as BAM in Galaxy and converting to fastq when needed for analysis.',
u'name': u'bam_to_fastq',
u'remote_repository_url': None,
u'repo_owner_username': u'brad-chapman',
u'times_downloaded': 138
},
u'score': 4.14
}
],
u'hostname': u'https://testtoolshed.g2.bx.psu.edu/',
u'page': u'1',
u'page_size': u'2',
u'total_results': u'64'
}
"""
params = dict(q=q, page=page, page_size=page_size)
return Client._get(self, params=params)
