Merge pull request #2035 from antgonza/user-jobs

adding User.jobs()

Author: josenavas

qiita_db/processing_job.py

@@ -850,6 +850,25 @@ def outputs(self):
                 name: qdb.artifact.Artifact(aid)
                 for aid, name in qdb.sql_connection.TRN.execute_fetchindex()}
 
+    @property
+    def processing_job_worflow(self):
+        """The processing job worflow
+
+        Returns
+        -------
+        ProcessingWorkflow
+            The processing job workflow the job
+        """
+        with qdb.sql_connection.TRN:
+            sql = """SELECT processing_job_workflow_id
+                     FROM qiita.processing_job_workflow_root
+                     WHERE processing_job_id = %s"""
+            qdb.sql_connection.TRN.add(sql, [self.id])
+            r = qdb.sql_connection.TRN.execute_fetchindex()
+
+            return (qdb.processing_job.ProcessingWorkflow(r[0][0]) if r
+                    else None)
+
 
 class ProcessingWorkflow(qdb.base.QiitaObject):
     """Models a workflow defined by the user

qiita_db/test/test_processing_job.py

@@ -629,6 +629,18 @@ def test_outputs(self):
             [afp for _, afp, _ in
                 qdb.artifact.Artifact(exp_artifact_count).filepaths])
 
+    def test_processing_job_worflow(self):
+        # testing None
+        job = qdb.processing_job.ProcessingJob(
+            "063e553b-327c-4818-ab4a-adfe58e49860")
+        self.assertIsNone(job.processing_job_worflow)
+
+        # testing actual workflow
+        job = qdb.processing_job.ProcessingJob(
+            "b72369f9-a886-4193-8d3d-f7b504168e75")
+        self.assertEqual(job.processing_job_worflow,
+                         qdb.processing_job.ProcessingWorkflow(1))
+
 
 @qiita_test_checker()
 class ProcessingWorkflowTests(TestCase):

qiita_db/test/test_user.py

@@ -450,5 +450,16 @@ def test_user_artifacts(self):
                                     qdb.artifact.Artifact(7)]}
         self.assertEqual(obs, exp)
 
+    def test_jobs(self):
+        PJ = qdb.processing_job.ProcessingJob
+        # generates expected jobs
+        jobs = qdb.user.User('shared@foo.bar').jobs()
+        self.assertEqual(jobs, [
+            PJ('d19f76ee-274e-4c1b-b3a2-a12d73507c55'),
+            PJ('b72369f9-a886-4193-8d3d-f7b504168e75')])
+
+        # no jobs
+        self.assertEqual(qdb.user.User('admin@foo.bar').jobs(), [])
+
 if __name__ == "__main__":
     main()

qiita_db/user.py

@@ -55,6 +55,7 @@ class User(qdb.base.QiitaObject):
     private_analyses
     shared_analyses
     unread_messages
+    jobs
 
     Methods
     -------
@@ -660,6 +661,27 @@ def delete_messages(self, messages):
             qdb.sql_connection.TRN.add(sql)
             qdb.sql_connection.TRN.execute()
 
+    def jobs(self):
+        """Return jobs created by the user
+
+        Parameters
+        ----------
+
+        Returns
+        -------
+        list of ProcessingJob
+
+        """
+        with qdb.sql_connection.TRN:
+            sql_info = [self._id]
+            sql = """SELECT processing_job_id
+                     FROM qiita.processing_job
+                     WHERE email = %s
+                     ORDER BY heartbeat DESC"""
+            qdb.sql_connection.TRN.add(sql, sql_info)
+            return [qdb.processing_job.ProcessingJob(p[0])
+                    for p in qdb.sql_connection.TRN.execute_fetchindex()]
+
 
 def validate_email(email):
     """Validates an email

qiita_pet/handlers/api_proxy/__init__.py

@@ -38,6 +38,7 @@
     list_options_handler_get_req, workflow_handler_post_req,
     workflow_handler_patch_req, workflow_run_post_req,
     job_ajax_get_req)
+from .user import (user_jobs_get_req)
 
 __version__ = "0.2.0-dev"
 
@@ -64,4 +65,4 @@
            'workflow_handler_patch_req', 'workflow_run_post_req',
            'job_ajax_get_req', 'artifact_patch_request',
            'sample_template_patch_request',
-           'get_sample_template_processing_status']
+           'get_sample_template_processing_status', 'user_jobs_get_req']

qiita_pet/handlers/api_proxy/tests/test_user.py

@@ -0,0 +1,71 @@
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+from unittest import TestCase, main
+from os.path import exists, isdir
+from os import remove
+from shutil import rmtree
+
+from qiita_core.util import qiita_test_checker
+import qiita_db as qdb
+from qiita_pet.handlers.api_proxy.user import (user_jobs_get_req)
+
+
+@qiita_test_checker()
+class TestSUserAPI(TestCase):
+    def setUp(self):
+        self._clean_up_files = []
+
+    def tearDown(self):
+        for fp in self._clean_up_files:
+            if exists(fp):
+                if isdir(fp):
+                    rmtree(fp)
+                else:
+                    remove(fp)
+
+    def test_user_jobs_get_req(self):
+        obs = user_jobs_get_req(qdb.user.User('shared@foo.bar'))
+        exp = {
+            'status': 'success',
+            'message': '',
+            'jobs': [
+                {'id': 'd19f76ee-274e-4c1b-b3a2-a12d73507c55',
+                 'status': 'error',
+                 'heartbeat': '2015-11-22 21:30:00',
+                 'params': {
+                    'reference': 1,
+                    'similarity': 0.97,
+                    'sortmerna_e_value': 1,
+                    'sortmerna_max_pos': 10000,
+                    'input_data': 2,
+                    'threads': 1,
+                    'sortmerna_coverage': 0.97},
+                 'name': 'Pick closed-reference OTUs',
+                 'processing_job_workflow_id': ''},
+                {'id': 'b72369f9-a886-4193-8d3d-f7b504168e75',
+                 'status': 'success',
+                 'heartbeat': '2015-11-22 21:15:00',
+                 'params': {
+                    'max_barcode_errors': 1.5,
+                    'sequence_max_n': 0,
+                    'max_bad_run_length': 3,
+                    'phred_offset': u'auto',
+                    'rev_comp': False,
+                    'phred_quality_threshold': 3,
+                    'input_data': 1,
+                    'rev_comp_barcode': False,
+                    'rev_comp_mapping_barcodes': True,
+                    'min_per_read_length_fraction': 0.75,
+                    'barcode_type': u'golay_12'},
+                 'name': 'Split libraries FASTQ',
+                 'processing_job_workflow_id': 1}]}
+        self.assertEqual(obs, exp)
+
+
+if __name__ == '__main__':
+    main()

qiita_pet/handlers/api_proxy/user.py

@@ -0,0 +1,49 @@
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+from __future__ import division
+
+from qiita_core.util import execute_as_transaction
+
+
+@execute_as_transaction
+def user_jobs_get_req(user):
+    """Gets the json of jobs
+
+    Parameters
+    ----------
+    prep_id : int
+        PrepTemplate id to get info for
+    user_id : str
+        User requesting the sample template info
+
+    Returns
+    -------
+    dict of objects
+    {'status': status,
+     'message': message,
+     'template': {sample: {column: value, ...}, ...}
+    """
+
+    response = []
+    for j in user.jobs():
+        name = j.command.name
+        hb = j.heartbeat
+        hb = "" if hb is None else hb.strftime("%Y-%m-%d %H:%M:%S")
+        pjw = j.processing_job_worflow
+        wid = '' if pjw is None else pjw.id
+        response.append({
+            'id': j.id,
+            'name': name,
+            'params': j.parameters.values,
+            'status': j.status,
+            'heartbeat': hb,
+            'processing_job_workflow_id': wid})
+
+    return {'status': 'success',
+            'message': '',
+            'jobs': response}

qiita_pet/handlers/user_handlers.py

@@ -3,6 +3,7 @@
 from wtforms import Form, StringField, validators
 
 from qiita_pet.handlers.base_handlers import BaseHandler
+from qiita_pet.handlers.api_proxy import user_jobs_get_req
 from qiita_db.user import User
 from qiita_db.logger import LogEntry
 from qiita_db.exceptions import QiitaDBUnknownIDError, QiitaDBError
@@ -185,3 +186,10 @@ def post(self):
 
         self.render("user_messages.html",
                     messages=self.current_user.messages())
+
+
+class UserJobs(BaseHandler):
+    @authenticated
+    def get(self):
+        response = user_jobs_get_req(self.current_user)
+        self.write(response)

qiita_pet/test/test_user_handlers.py

@@ -53,5 +53,11 @@ def test_post_profile(self):
         response = self.post('/profile/', post_args)
         self.assertEqual(response.code, 200)
 
+
+class TestUserJobsHandler(TestHandlerBase):
+    def test_get(self):
+        response = self.get('/user/jobs/')
+        self.assertEqual(response.code, 200)
+
 if __name__ == "__main__":
     main()

qiita_pet/webserver.py

@@ -17,7 +17,7 @@
     AuthCreateHandler, AuthLoginHandler, AuthLogoutHandler, AuthVerifyHandler)
 from qiita_pet.handlers.user_handlers import (
     ChangeForgotPasswordHandler, ForgotPasswordHandler, UserProfileHandler,
-    UserMessagesHander)
+    UserMessagesHander, UserJobs)
 from qiita_pet.handlers.analysis_handlers import (
     SelectCommandsHandler, AnalysisWaitHandler, AnalysisResultsHandler,
     ShowAnalysesHandler, ResultsHandler, SelectedSamplesHandler,
@@ -88,6 +88,7 @@ def __init__(self):
             (r"/auth/reset/(.*)", ChangeForgotPasswordHandler),
             (r"/profile/", UserProfileHandler),
             (r"/user/messages/", UserMessagesHander),
+            (r"/user/jobs/", UserJobs),
             (r"/results/(.*)", ResultsHandler,
              {"path": RES_PATH}),
             (r"/static/(.*)", tornado.web.StaticFileHandler,