diff env/lib/python3.9/site-packages/bioblend/galaxy/jobs/__init__.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/bioblend/galaxy/jobs/__init__.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,221 @@
+"""
+Contains possible interactions with the Galaxy Jobs
+"""
+from bioblend.galaxy.client import Client
+
+
+class JobsClient(Client):
+
+    def __init__(self, galaxy_instance):
+        self.module = 'jobs'
+        super().__init__(galaxy_instance)
+
+    def get_jobs(self):
+        """
+        Get the list of jobs of the current user.
+
+        :rtype: list
+        :return: list of dictionaries containing summary job information.
+          For example::
+
+            [{'create_time': '2014-03-01T16:16:48.640550',
+              'exit_code': 0,
+              'id': 'ebfb8f50c6abde6d',
+              'model_class': 'Job',
+              'state': 'ok',
+              'tool_id': 'fasta2tab',
+              'update_time': '2014-03-01T16:16:50.657399'},
+             {'create_time': '2014-03-01T16:05:34.851246',
+              'exit_code': 0,
+              'id': '1cd8e2f6b131e891',
+              'model_class': 'Job',
+              'state': 'ok',
+              'tool_id': 'upload1',
+              'update_time': '2014-03-01T16:05:39.558458'}]
+        """
+        return self._get()
+
+    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::
+
+            {'create_time': '2014-03-01T16:17:29.828624',
+             'exit_code': 0,
+             'id': 'a799d38679e985db',
+             'inputs': {'input': {'id': 'ebfb8f50c6abde6d', 'src': 'hda'}},
+             'model_class': 'Job',
+             'outputs': {'output': {'id': 'a799d38679e985db', 'src': 'hda'}},
+             'params': {'chromInfo': '"/opt/galaxy-central/tool-data/shared/ucsc/chrom/?.len"',
+                        'dbkey': '"?"',
+                        'seq_col': '"2"',
+                        'title_col': '["1"]'},
+             'state': 'ok',
+             'tool_id': 'tab2fasta',
+             'update_time': '2014-03-01T16:17:31.930728'}
+        """
+        params = {}
+        if full_details:
+            params['full'] = full_details
+
+        return self._get(id=job_id, params=params)
+
+    def _build_for_rerun(self, job_id):
+        """
+        Get details of a given job that can be used to rerun the corresponding tool.
+
+        :type job_id: str
+        :param job_id: job ID
+
+        :rtype: dict
+        :return: A description of the given job, with all parameters required to rerun.
+
+        """
+        url = '/'.join((self._make_url(job_id), 'build_for_rerun'))
+        return self._get(url=url)
+
+    def rerun_job(self, job_id, remap=False, tool_inputs_update=None, history_id=None):
+        """
+        Rerun a job.
+
+        :type job_id: str
+        :param job_id: job ID
+
+        :type remap: bool
+        :param remap: when ``True``, the job output(s) will be remapped onto the dataset(s)
+          created by the original job; if other jobs were waiting for this job to finish
+          successfully, they will be resumed using the new outputs of this tool run. When
+          ``False``, new job output(s) will be created. Note that if Galaxy does not permit
+          remapping for the job in question, specifying ``True`` will result in an error.
+
+        :type tool_inputs_update: dict
+        :param tool_inputs_update: dictionary specifying any changes which should be
+          made to tool parameters for the rerun job.
+
+        :type history_id: str
+        :param history_id: ID of the history in which the job should be executed; if
+          not specified, the same history will be used as the original job run.
+
+        :rtype: dict
+        :return: Information about outputs and the rerun job
+        .. note::
+          This method can only be used with Galaxy ``release_20.09`` or later.
+        """
+        job_rerun_params = self._build_for_rerun(job_id)
+        job_inputs = job_rerun_params['state_inputs']
+
+        if remap:
+            if not job_inputs['job_remap']:
+                raise ValueError('remap was set to True, but this job is not remappable.')
+            job_inputs['rerun_remap_job_id'] = job_id
+
+        if tool_inputs_update:
+            for input_param, input_value in tool_inputs_update.items():
+                job_inputs[input_param] = input_value
+        url = '/'.join((self.gi.url, 'tools'))
+        payload = {
+            "history_id": history_id if history_id else job_rerun_params['history_id'],
+            "tool_id": job_rerun_params['id'],
+            "inputs": job_inputs,
+            "input_format": '21.01'
+        }
+        return self._post(url=url, payload=payload)
+
+    def get_state(self, job_id):
+        """
+        Display the current state for a given job of the current user.
+
+        :type job_id: str
+        :param job_id: job ID
+
+        :rtype: str
+        :return: state of the given job among the following values: `new`,
+          `queued`, `running`, `waiting`, `ok`. If the state cannot be
+          retrieved, an empty string is returned.
+
+        .. versionadded:: 0.5.3
+        """
+        return self.show_job(job_id).get('state', '')
+
+    def search_jobs(self, job_info):
+        """
+        Return jobs for the current user based payload content.
+
+        :type job_info: dict
+        :param job_info: dictionary containing description of the requested job.
+          This is in the same format as a request to POST /api/tools would take
+          to initiate a job
+
+        :rtype: list
+        :return: list of dictionaries containing summary job information of
+          the jobs that match the requested job run
+
+        This method is designed to scan the list of previously run jobs and find
+        records of jobs that had the exact some input parameters and datasets.
+        This can be used to minimize the amount of repeated work, and simply
+        recycle the old results.
+
+        """
+
+        payload = job_info
+        url = self._make_url() + '/search'
+        return self._post(url=url, payload=payload)
+
+    def get_metrics(self, job_id):
+        """
+        Return job metrics for a given job.
+
+        :type job_id: str
+        :param job_id: job ID
+
+        :rtype: list
+        :return: list containing job metrics
+
+        .. note::
+          Calling ``show_job()`` with ``full_details=True`` also returns the
+          metrics for a job if the user is an admin. This method allows to fetch
+          metrics even as a normal user as long as the Galaxy instance has the
+          ``expose_potentially_sensitive_job_metrics`` option set to ``true`` in
+          the ``config/galaxy.yml`` configuration file.
+        """
+        url = self._make_url(module_id=job_id) + '/metrics'
+        return self._get(url=url)
+
+    def report_error(self, job_id, dataset_id, message, email=None):
+        """
+        Report an error for a given job and dataset.
+
+        :type job_id: str
+        :param job_id: job ID
+
+        :type dataset_id: str
+        :param dataset_id: Dataset ID
+
+        :type message: str
+        :param message: Error message
+
+        :type email: str
+        :param email: Email to submit error report to
+
+        :rtype: dict
+        :return: dict containing job error reply
+        """
+        payload = {
+            "message": message,
+            "dataset_id": dataset_id,
+        }
+        if email is not None:
+            payload["email"] = email
+
+        url = self._make_url(module_id=job_id) + '/error'
+        return self._post(url=url, payload=payload)