Merge 12406cc into b9b2caa

qiita-spots · Jan 3, 2017 · 3d429e2 · 3d429e2
2 parents b9b2caa + 12406cc
commit 3d429e2
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Showing 20 changed files with 640 additions and 270 deletions.
diff --git a/qiita_db/processing_job.py b/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 (None if not r
+                    else qdb.processing_job.ProcessingWorkflow(r[0][0]))
+
 
 class ProcessingWorkflow(qdb.base.QiitaObject):
     """Models a workflow defined by the user

diff --git a/qiita_db/test/test_processing_job.py b/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):

diff --git a/qiita_db/test/test_user.py b/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()
diff --git a/qiita_db/user.py b/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

diff --git a/qiita_pet/handlers/api_proxy/__init__.py b/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']
diff --git a/qiita_pet/handlers/api_proxy/tests/test_user.py b/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()
diff --git a/qiita_pet/handlers/api_proxy/user.py b/qiita_pet/handlers/api_proxy/user.py
@@ -0,0 +1,55 @@
+# -----------------------------------------------------------------------------
+# 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, limit=10):
+    """Gets the json of jobs
+
+    Parameters
+    ----------
+    user : User
+        The user from which you want to return all jobs
+    limit : int, optional
+        Maximum jobs to send, negative values will return all
+
+    Returns
+    -------
+    dict of objects
+    {'status': status,
+     'message': message,
+     'template': {{column: value, ...}, ...}
+    """
+
+    response = []
+    cmds = {}
+    for i, j in enumerate(user.jobs()):
+        if i == limit:
+            break
+        cmd = j.command
+        if cmd not in cmds:
+            cmds[cmd] = cmd
+        ccmd = cmds[cmd]
+        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': ccmd.name,
+            'params': j.parameters.values,
+            'status': j.status,
+            'heartbeat': hb,
+            'processing_job_workflow_id': wid})
+
+    return {'status': 'success',
+            'message': '',
+            'jobs': response}
diff --git a/qiita_pet/handlers/user_handlers.py b/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)
diff --git a/qiita_pet/static/css/style.css b/qiita_pet/static/css/style.css
@@ -1,3 +1,17 @@
+div.qiita-main {
+  position: relative;
+  height: 100%;
+  width: 100%;
+}
+
+#qiita-processing {
+  position: absolute;
+  height: 100%;
+  width: 0%;
+  right: 0;
+  top: 0;
+}
+
 #template-content{
   padding: 10px;
   height: 100%;

diff --git a/qiita_pet/static/js/qiita.js b/qiita_pet/static/js/qiita.js
@@ -40,7 +40,6 @@ function show_hide(div) {
 	$('#' + div).toggle();
 }
 
-
 function delete_analysis(aname, analysis_id) {
   if (confirm('Are you sure you want to delete analysis: ' + aname + '?')) {
     var form = $("<form>")
@@ -58,3 +57,19 @@ function delete_analysis(aname, analysis_id) {
     form.submit();
   }
 }
+
+function show_hide_process_list() {
+  if ($("#qiita-main").width() == $("#qiita-main").parent().width()) {
+    $("#qiita-main").width("76%");
+    $("#user-studies-table").width("76%");
+    $("#studies-table").width("76%");
+    $("#qiita-processing").width("24%");
+    $("#qiita-processing").show();
+  } else {
+    $("#qiita-main").width("100%");
+    $("#user-studies-table").width("100%");
+    $("#studies-table").width("100%");
+    $("#qiita-processing").width("0%");
+    $("#qiita-processing").hide();
+  }
+}
diff --git a/qiita_pet/static/vendor/js/vue.min.js b/qiita_pet/static/vendor/js/vue.min.js
diff --git a/qiita_pet/templates/admin_approval.html b/qiita_pet/templates/admin_approval.html
@@ -1,7 +1,5 @@
 {% extends sitebase.html %}
 {% block head %}
-<link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/jquery.dataTables.css" type="text/css">
-<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/jquery.dataTables.min.js" type="text/javascript"></script>
 
 <script type="text/javascript">
 $(document).ready(function() {

diff --git a/qiita_pet/templates/error_log.html b/qiita_pet/templates/error_log.html
@@ -3,10 +3,6 @@
 {% from future.utils import viewitems %}
 {% from qiita_core.qiita_settings import qiita_config %}
 
-<link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/jquery.dataTables.css" type="text/css">
-
-<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/jquery.dataTables.min.js"></script>
-
 <script type="text/javascript">
 $(document).ready(function() {
     $('#error-table').dataTable({"order": [[1, "asc"]]});

diff --git a/qiita_pet/templates/index.html b/qiita_pet/templates/index.html
@@ -3,7 +3,7 @@
 {% end %}
 
 {%block content %}
-<div id="jumbotron" class="jumbotron">
+<div id="jumbotron" class="jumbotron" style="border-radius: 10px; padding: 30px">
   <h1>{% raw portal_styling.index_header%}</h1>
   {% raw portal_styling.index_text%}
 </div>

diff --git a/qiita_pet/templates/list_studies.html b/qiita_pet/templates/list_studies.html
@@ -15,8 +15,6 @@
   cursor: pointer;
 }
 </style>
-<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/jquery.dataTables.min.js"></script>
-<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/jquery.dataTables.plugin.natural.js"></script>
 <script src="{% raw qiita_config.portal_dir %}/static/vendor/js/moi.js"></script>
 <script src="{% raw qiita_config.portal_dir %}/static/vendor/js/select2.min.js"></script>
 <script src="{% raw qiita_config.portal_dir %}/static/js/sharing.js"></script>
@@ -302,6 +300,8 @@ <h3 class="gray-msg">Other Studies</h3>
             </tr>
         </thead>
     </table>
+  </div>
+</div>
 <!--Abstract Modal-->
 <div class="modal fade" tabindex="-1" role="dialog" aria-labelledby="myLargeModalLabel" aria-hidden="true" id="study-abstract-modal">
   <div class="modal-dialog modal-med">

diff --git a/qiita_pet/templates/portals_edit.html b/qiita_pet/templates/portals_edit.html
@@ -1,7 +1,6 @@
 {% extends sitebase.html%}
 
 {%block head%}
-<link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/jquery.dataTables.css" type="text/css">
 <style type="text/css">
   .navlist li
   {
@@ -19,7 +18,6 @@
     white-space: nowrap;
   }
 </style>
-<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/jquery.dataTables.min.js"></script>
 <script type="text/javascript">
 function check_submit(action) {
   //disable submit buttons