Merge pull request #3157 from antgonza/wet-lab-admin

charles-cowart · web-flow · commit df4ad9a09e08 · 2021-11-01T11:56:57.000-07:00
[WIP] adding a new wet-lab admin user
diff --git a/qiita_db/handlers/artifact.py b/qiita_db/handlers/artifact.py
@@ -199,6 +199,26 @@ def post(self):
 
 
 class ArtifactTypeHandler(OauthBaseHandler):
+    @authenticate_oauth
+    def get(self):
+        """Returns the artifact types and their local mountpoint location
+
+        Returns
+        -------
+        dict
+            'artifact_type': local mountpoint
+        """
+        atypes = dict()
+        for atype in qdb.util.get_artifact_types():
+            mountpoints = qdb.util.get_mountpoint(atype)
+            if mountpoints:
+                # [0][1]: get latest/active and the actual location
+                atypes[atype] = mountpoints[0][1]
+        # add the upload location
+        atypes['uploads'] = qdb.util.get_mountpoint('uploads')[0][1]
+
+        self.write(atypes)
+
     @authenticate_oauth
     def post(self):
         """Creates a new artifact type
diff --git a/qiita_db/handlers/tests/test_artifact.py b/qiita_db/handlers/tests/test_artifact.py
@@ -287,6 +287,22 @@ def test_post(self):
                         data=data)
         self.assertEqual(obs.code, 200)
 
+    def test_get(self):
+        obs = self.get('/qiita_db/artifacts/types/', headers=self.header)
+        self.assertEqual(obs.code, 200)
+
+        basedir = qdb.util.get_db_files_base_dir()
+        exp = {
+            "SFF": f"{basedir}/SFF",
+            "FASTA": f"{basedir}/FASTA",
+            "FASTA_Sanger": f"{basedir}/FASTA_Sanger",
+            "Demultiplexed": f"{basedir}/Demultiplexed",
+            "FASTQ": f"{basedir}/FASTQ",
+            "per_sample_FASTQ": f"{basedir}/per_sample_FASTQ",
+            "BIOM": f"{basedir}/BIOM",
+            "uploads": f"{basedir}/uploads"}
+        self.assertDictEqual(loads(obs.body), exp)
+
 
 class APIArtifactHandlerTests(OauthTestingBase):
     def setUp(self):
diff --git a/qiita_db/support_files/patches/84.sql b/qiita_db/support_files/patches/84.sql
@@ -0,0 +1,3 @@
+-- October 21, 2021
+-- adding a new user level: wet-lab admin
+INSERT INTO qiita.user_level (name, description) VALUES ('wet-lab admin', 'Can access the private jobs');
diff --git a/qiita_pet/handlers/admin_processing_job.py b/qiita_pet/handlers/admin_processing_job.py
@@ -19,7 +19,7 @@
 
 class AdminProcessingJobBaseClass(BaseHandler):
     def _check_access(self):
-        if self.current_user.level not in {'admin', 'dev'}:
+        if self.current_user.level not in {'admin', 'wet-lab admin'}:
             raise HTTPError(403, reason="User %s doesn't have sufficient "
                             "privileges to view error page" %
                             self.current_user.email)
@@ -62,7 +62,11 @@ def get(self):
                 for job in cmd.processing_jobs:
                     if job.hidden:
                         continue
-                    msg = '' if job.status != 'error' else job.log.msg
+                    msg = ''
+                    if job.status == 'error':
+                        msg = job.log.msg
+                    elif job.status == 'running':
+                        msg = job.step
                     msg = msg.replace('\n', '</br>')
                     outputs = []
                     if job.status == 'success':
diff --git a/qiita_pet/handlers/artifact_handlers/base_handlers.py b/qiita_pet/handlers/artifact_handlers/base_handlers.py
@@ -41,7 +41,7 @@ def check_artifact_access(user, artifact):
     QiitaHTTPError
         If the user doesn't have access to the given artifact
     """
-    if user.level == 'admin':
+    if user.level in ('admin', 'wet-lab admin'):
         return
     if artifact.visibility != 'public':
         study = artifact.study
diff --git a/qiita_pet/support_files/doc/source/dev/rest.rst b/qiita_pet/support_files/doc/source/dev/rest.rst
@@ -32,6 +32,9 @@ the important parts of the values are described in the Parameters column.
 +--------+-----------------------------------------------------------------------------------+-----------------------------------------+-----------------------------------------------------+----------------------------+
 |GET     | ``/qiita_db/jobs/<job_id>``                                                       |                                         | Get the job information                             | JobHandler                 |
 +--------+-----------------------------------------------------------------------------------+-----------------------------------------+-----------------------------------------------------+----------------------------+
+|GET     | ``/qiita_db/artifacts/types/``                                                    |                                         | Retrieves the available artifact types and their    | ArtifactTypeHandler        |
+|        |                                                                                   |                                         | local mount point                                   |                            |
++--------+-----------------------------------------------------------------------------------+-----------------------------------------+-----------------------------------------------------+----------------------------+
 |POST    | ``/qiita_db/artifacts/types/``                                                    | ``name: str``, ``description: str``,    | Creates a new artifact type                         | ArtifactTypeHandler        |
 |        |                                                                                   | ``can_be_submitted_to_ebi: bool``,      |                                                     |                            |
 |        |                                                                                   | ``can_be_submitted_to_vamps: bool``,    |                                                     |                            |
diff --git a/qiita_pet/templates/admin_processing_job.html b/qiita_pet/templates/admin_processing_job.html
@@ -74,7 +74,7 @@
                '</b>: ');
 
       if (status === 'running' || status === 'queued') {
-        out.push(row[0] + ' <i>' + row[3] + '</i>')
+        out.push(row[0] + '</br> <i>' + row[3] + '</i>')
       }
       else {
         // We write a callback attribute on the link to be able to display a
diff --git a/qiita_pet/templates/artifact_ajax/artifact_summary.html b/qiita_pet/templates/artifact_ajax/artifact_summary.html
@@ -143,7 +143,7 @@ <h4 style="color: #FF2222;">This artifact is being deleted</h4>
 
         {% if artifact_type == 'BIOM' and not is_from_analysis %}
           <input type="button" class="btn btn-default btn-sm" value="Add to Analysis" onclick="send_samples_to_analysis(this, [{{artifact_id}}]);">
-        {% else %}
+        {% elif artifact_type != 'job-output-folder' %}
           <a class="btn btn-default btn-sm" id="process-btn"><span class="glyphicon glyphicon-play"></span> Process</a>
         {% end %}
 
@@ -182,7 +182,7 @@ <h4 style="color: #FF2222;">This artifact is being deleted</h4>
   </div>
 </div>
 
-{% if files %}
+{% if files and artifact_type != 'job-output-folder' %}
 <div class='row'>
   <div class='col-md-12'>
     <b>Available files:</b>
diff --git a/qiita_pet/templates/sitebase.html b/qiita_pet/templates/sitebase.html
@@ -374,15 +374,17 @@
                 </ul>
               </li>
                 {% set user_level = user.level %}
-                {% if user_level == 'admin' %}
+                {% if user_level in ('admin', 'wet-lab admin') %}
               <li class="dropdown">
                 <a href="#" data-toggle="dropdown" class="dropdown-toggle">Admin<b class="caret"></b></a>
                 <ul class="dropdown-menu">
                   {% if qiita_config.portal == "QIITA" %}
-                  <li><a href="{% raw qiita_config.portal_dir %}/admin/error/">View Errors</a></li>
-                  <li><a href="{% raw qiita_config.portal_dir %}/admin/approval/">View Studies awaiting approval</a></li>
-                  <li><a href="{% raw qiita_config.portal_dir %}/admin/portals/studies/">Edit study portal connections</a></li>
-                  <li><a href="{% raw qiita_config.portal_dir %}/admin/processing_jobs/">Processing Jobs</a></li>
+                    {% if user_level == 'admin' %}
+                      <li><a href="{% raw qiita_config.portal_dir %}/admin/error/">View Errors</a></li>
+                      <li><a href="{% raw qiita_config.portal_dir %}/admin/approval/">View Studies awaiting approval</a></li>
+                      <li><a href="{% raw qiita_config.portal_dir %}/admin/portals/studies/">Edit study portal connections</a></li>
+                    {% end %}
+                    <li><a href="{% raw qiita_config.portal_dir %}/admin/processing_jobs/">Processing Jobs</a></li>
                   {% else %}
                   <li><a href="/">Admin tasks can only be done in the main Qiita portal</a></li>
                   {% end %}

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+-- October 21, 2021`
	`2`	`+-- adding a new user level: wet-lab admin`
	`3`	`+INSERT INTO qiita.user_level (name, description) VALUES ('wet-lab admin', 'Can access the private jobs');`
Original file line number	Diff line number	Diff line change
`@@ -74,7 +74,7 @@`
`74`	`74`	`'</b>: ');`
`75`	`75`
`76`	`76`	`if (status === 'running' \|\| status === 'queued') {`
`77`		`- out.push(row[0] + ' <i>' + row[3] + '</i>')`
	`77`	`+ out.push(row[0] + '</br> <i>' + row[3] + '</i>')`
`78`	`78`	`}`
`79`	`79`	`else {`
`80`	`80`	`// We write a callback attribute on the link to be able to display a`