fix #2902

qiita_db/artifact.py

@@ -50,6 +50,7 @@ class Artifact(qdb.base.QiitaObject):
     -------
     create
     delete
+    being_deleted_by
 
     See Also
     --------
@@ -1412,6 +1413,30 @@ def merging_scheme(self):
 
         return ', '.join(merging_schemes), ', '.join(parent_softwares)
 
+    @property
+    def being_deleted_by(self):
+        """The running job that is deleting this artifact
+
+        Returns
+        -------
+        qiita_db.processing_job.ProcessingJob
+            The running job that is deleting this artifact, None if it
+            doesn't exist
+        """
+
+        with qdb.sql_connection.TRN:
+            sql = """
+                SELECT processing_job_id FROM qiita.artifact_processing_job
+                  LEFT JOIN qiita.processing_job using (processing_job_id)
+                  LEFT JOIN qiita.processing_job_status using (
+                    processing_job_status_id)
+                  LEFT JOIN qiita.software_command using (command_id)
+                  WHERE artifact_id = %s AND name = 'delete_artifact' AND
+                    processing_job_status = 'running'"""
+            qdb.sql_connection.TRN.add(sql, [self.id])
+            res = qdb.sql_connection.TRN.execute_fetchindex()
+        return qdb.processing_job.ProcessingJob(res[0][0]) if res else None
+
     def jobs(self, cmd=None, status=None, show_hidden=False):
         """Jobs that used this artifact as input
 

qiita_db/processing_job.py

@@ -591,6 +591,9 @@ def create(cls, user, parameters, force=False):
                         TTRN.add(sql, [artifact_info, job_id])
                     else:
                         pending[artifact_info[0]][pname] = artifact_info[1]
+                elif pname == 'artifact':
+                    TTRN.add(sql, [parameters.values[pname], job_id])
+
             if pending:
                 sql = """UPDATE qiita.processing_job
                          SET pending = %s

qiita_db/test/test_artifact.py

@@ -21,6 +21,7 @@
 from biom.util import biom_open
 
 from qiita_core.util import qiita_test_checker
+from qiita_core.testing import wait_for_processing_job
 import qiita_db as qdb
 
 
@@ -1114,6 +1115,44 @@ def test_delete_with_jobs(self):
         # Check that the job still exists, so we cap keep track of system usage
         qdb.processing_job.ProcessingJob(job.id)
 
+    def test_being_deleted_by(self):
+        test = qdb.artifact.Artifact.create(
+            self.filepaths_root, "FASTQ", prep_template=self.prep_template)
+        uploads_fp = join(qdb.util.get_mountpoint("uploads")[0][1],
+                          str(test.study.id))
+        self._clean_up_files.extend(
+            [join(uploads_fp, basename(x['fp'])) for x in test.filepaths])
+
+        # verifying that there are no jobs in the list
+        self.assertIsNone(test.being_deleted_by)
+
+        # creating new deleting job
+        qiita_plugin = qdb.software.Software.from_name_and_version(
+            'Qiita', 'alpha')
+        cmd = qiita_plugin.get_command('delete_artifact')
+        params = qdb.software.Parameters.load(
+            cmd, values_dict={'artifact': test.id})
+        job = qdb.processing_job.ProcessingJob.create(
+            qdb.user.User('test@foo.bar'), params, True)
+        job._set_status('running')
+
+        # verifying that there is a job and is the same than above
+        self.assertEqual(job, test.being_deleted_by)
+
+        # let's set it as error and now we should not have it anymore
+        job._set_error('Killed by admin')
+        self.assertIsNone(test.being_deleted_by)
+
+        # now, let's actually remove
+        job = qdb.processing_job.ProcessingJob.create(
+            qdb.user.User('test@foo.bar'), params, True)
+        job.submit()
+        # let's wait for job
+        wait_for_processing_job(job.id)
+
+        with self.assertRaises(qdb.exceptions.QiitaDBUnknownIDError):
+            qdb.artifact.Artifact(test.id)
+
     def test_delete_as_output_job(self):
         fd, fp = mkstemp(suffix='_table.biom')
         self._clean_up_files.append(fp)

qiita_pet/handlers/api_proxy/prep_template.py

@@ -18,6 +18,7 @@
 from qiita_core.qiita_settings import r_client
 from qiita_pet.handlers.api_proxy.util import check_access, check_fp
 from qiita_pet.util import get_network_nodes_edges
+from qiita_db.artifact import Artifact
 from qiita_db.metadata_template.util import load_template_to_dataframe
 from qiita_db.util import convert_to_id, get_files_from_uploads_folders
 from qiita_db.study import Study
@@ -660,11 +661,17 @@ def prep_template_graph_get_req(prep_id, user_id):
     G = artifact.descendants_with_jobs
 
     nodes, edges, wf_id = get_network_nodes_edges(G, full_access)
+    # nodes returns [node_type, node_name, element_id]; here we are looking
+    # for the node_type == artifact, and check by the element/artifact_id if
+    # it's being deleted
+    artifacts_being_deleted = [a[2] for a in nodes if a[0] == 'artifact' and
+                               Artifact(a[2]).being_deleted_by is not None]
 
     return {'edges': edges,
             'nodes': nodes,
             'workflow': wf_id,
             'status': 'success',
+            'artifacts_being_deleted': artifacts_being_deleted,
             'message': ''}
 
 

qiita_pet/handlers/artifact_handlers/base_handlers.py

@@ -234,6 +234,7 @@ def artifact_summary_get_request(user, artifact_id):
             'job': job_info,
             'artifact_timestamp': artifact.timestamp.strftime(
                 "%Y-%m-%d %H:%m"),
+            'being_deleted': artifact.being_deleted_by is not None,
             'errored_summary_jobs': errored_summary_jobs}
 
 
@@ -392,23 +393,30 @@ def artifact_post_req(user, artifact_id):
     artifact = Artifact(artifact_id)
     check_artifact_access(user, artifact)
 
-    analysis = artifact.analysis
+    being_deleted_by = artifact.being_deleted_by
 
-    if analysis:
-        # Do something when deleting in the analysis part to keep track of it
-        redis_key = "analysis_%s" % analysis.id
-    else:
-        pt_id = artifact.prep_templates[0].id
-        redis_key = PREP_TEMPLATE_KEY_FORMAT % pt_id
+    if being_deleted_by is None:
+        analysis = artifact.analysis
 
-    qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
-    cmd = qiita_plugin.get_command('delete_artifact')
-    params = Parameters.load(cmd, values_dict={'artifact': artifact_id})
-    job = ProcessingJob.create(user, params, True)
+        if analysis:
+            # Do something when deleting in the analysis part to keep
+            # track of it
+            redis_key = "analysis_%s" % analysis.id
+        else:
+            pt_id = artifact.prep_templates[0].id
+            redis_key = PREP_TEMPLATE_KEY_FORMAT % pt_id
 
-    r_client.set(redis_key, dumps({'job_id': job.id, 'is_qiita_job': True}))
+        qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
+        cmd = qiita_plugin.get_command('delete_artifact')
+        params = Parameters.load(cmd, values_dict={'artifact': artifact_id})
+        job = ProcessingJob.create(user, params, True)
 
-    job.submit()
+        r_client.set(
+            redis_key, dumps({'job_id': job.id, 'is_qiita_job': True}))
+
+        job.submit()
+    else:
+        job = being_deleted_by
 
     return {'job': job.id}
 

qiita_pet/handlers/artifact_handlers/tests/test_base_handlers.py

@@ -102,7 +102,7 @@ def test_artifact_summary_get_request(self):
              '2125826711', '58B')]
         exp = {'name': 'Raw data 1',
                'artifact_id': 1,
-               'artifact_type': 'FASTQ',
+               'artifact_type': 'FASTQ', 'being_deleted': False,
                'artifact_timestamp': '2012-10-01 09:10',
                'visibility': 'private',
                'editable': True,
@@ -124,7 +124,7 @@ def test_artifact_summary_get_request(self):
         obs = artifact_summary_get_request(user, 1)
         exp = {'name': 'Raw data 1',
                'artifact_id': 1,
-               'artifact_type': 'FASTQ',
+               'artifact_type': 'FASTQ', 'being_deleted': False,
                'artifact_timestamp': '2012-10-01 09:10',
                'visibility': 'private',
                'editable': True,
@@ -154,7 +154,7 @@ def test_artifact_summary_get_request(self):
         obs = artifact_summary_get_request(user, 1)
         exp = {'name': 'Raw data 1',
                'artifact_id': 1,
-               'artifact_type': 'FASTQ',
+               'artifact_type': 'FASTQ', 'being_deleted': False,
                'artifact_timestamp': '2012-10-01 09:10',
                'visibility': 'private',
                'editable': True,
@@ -177,7 +177,7 @@ def test_artifact_summary_get_request(self):
         obs = artifact_summary_get_request(demo_u, 1)
         exp = {'name': 'Raw data 1',
                'artifact_id': 1,
-               'artifact_type': 'FASTQ',
+               'artifact_type': 'FASTQ', 'being_deleted': False,
                'artifact_timestamp': '2012-10-01 09:10',
                'visibility': 'public',
                'editable': False,
@@ -195,7 +195,7 @@ def test_artifact_summary_get_request(self):
         obs = artifact_summary_get_request(user, 1)
         exp = {'name': 'Raw data 1',
                'artifact_id': 1,
-               'artifact_type': 'FASTQ',
+               'artifact_type': 'FASTQ', 'being_deleted': False,
                'artifact_timestamp': '2012-10-01 09:10',
                'visibility': 'sandbox',
                'editable': True,
@@ -219,7 +219,7 @@ def test_artifact_summary_get_request(self):
             (5, '1_seqs.demux (preprocessed demux)', '', '0B')]
         exp = {'name': 'Demultiplexed 1',
                'artifact_id': 2,
-               'artifact_type': 'Demultiplexed',
+               'artifact_type': 'Demultiplexed', 'being_deleted': False,
                'artifact_timestamp': '2012-10-01 10:10',
                'visibility': 'private',
                'editable': True,
@@ -261,7 +261,7 @@ def test_artifact_summary_get_request(self):
         obs = artifact_summary_get_request(user, 8)
         exp = {'name': 'noname',
                'artifact_id': 8,
-               'artifact_type': 'BIOM',
+               'artifact_type': 'BIOM', 'being_deleted': False,
                # this value changes on build so copy from obs
                'artifact_timestamp': obs['artifact_timestamp'],
                'visibility': 'sandbox',

qiita_pet/static/js/networkVue.js

@@ -216,7 +216,7 @@ Vue.component('processing-graph', {
         // Clean up the div
         $("#processing-results").empty();
         // Update the artifact node to mark that it is being deleted
-        var node = vm.nodes_ds.get(artifactId);
+        var node = vm.nodes_ds.get(artifactId.toString());
         var node_info = vm.colorScheme['deleting'];
         node.group = 'deleting';
         node.color = node_info;
@@ -985,6 +985,10 @@ Vue.component('processing-graph', {
           // Format node list data
           for(var i = 0; i < data.nodes.length; i++) {
             var node_info = vm.colorScheme[data.nodes[i][4]];
+            if (data.artifacts_being_deleted.includes(data.nodes[i][2])) {
+              data.nodes[i][0] = 'deleting'
+              node_info = vm.colorScheme['deleting']
+            }
             // forcing a string
             data.nodes[i][2] = data.nodes[i][2].toString()
             vm.nodes.push({id: data.nodes[i][2], shape: node_info['shape'], label: formatNodeLabel(data.nodes[i][3]), type: data.nodes[i][1], group: data.nodes[i][0], color: node_info, status: data.nodes[i][4]});

qiita_pet/templates/artifact_ajax/artifact_summary.html

@@ -133,23 +133,28 @@ <h4>
         {% end %}
       {% end %}
       <i id='summary-title'>{{name}}</i><i> (ID: {{artifact_id}}) Visibility: {{visibility}}</i>
-      {% if editable %}
-        <a class="btn btn-default btn-sm" data-toggle="modal" data-target="#update-artifact-name"><span class="glyphicon glyphicon-pencil"></span> Edit name</a>
-      {% end %}
 
-      {% 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}}]);">
+      {% if being_deleted %}
+        <h4 style="color: #FF2222;">This artifact is being deleted</h4>
       {% else %}
-        <a class="btn btn-default btn-sm" id="process-btn"><span class="glyphicon glyphicon-play"></span> Process</a>
-      {% end %}
+        {% if editable %}
+          <a class="btn btn-default btn-sm" data-toggle="modal" data-target="#update-artifact-name"><span class="glyphicon glyphicon-pencil"></span> Edit name</a>
+        {% end %}
 
-      {% if editable %}
-        <a class="btn btn-danger btn-sm" onclick="if (confirm('Are you sure you want to delete artifact {{artifact_id}}?')){ processingNetwork.$refs.procGraph.deleteArtifact({{artifact_id}}) };"><span class="glyphicon glyphicon-trash"></span> Delete</a>
-        {% raw buttons %}
-      {% end %}
+        {% 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 %}
+          <a class="btn btn-default btn-sm" id="process-btn"><span class="glyphicon glyphicon-play"></span> Process</a>
+        {% end %}
 
-      {% if processing_info %}
-        <button class="btn btn-default btn-sm" data-toggle="collapse" data-target="#processing-info"><span class="glyphicon glyphicon-eye-open"></span> Show processing information</a>
+        {% if editable %}
+          <a class="btn btn-danger btn-sm" onclick="if (confirm('Are you sure you want to delete artifact {{artifact_id}}?')){ processingNetwork.$refs.procGraph.deleteArtifact({{artifact_id}}) };"><span class="glyphicon glyphicon-trash"></span> Delete</a>
+          {% raw buttons %}
+        {% end %}
+
+        {% if processing_info %}
+          <button class="btn btn-default btn-sm" data-toggle="collapse" data-target="#processing-info"><span class="glyphicon glyphicon-eye-open"></span> Show processing information</a>
+        {% end %}
       {% end %}
     </h4>
     {% if processing_info %}

qiita_pet/util.py

@@ -188,6 +188,9 @@ def get_network_nodes_edges(graph, full_access, nodes=None, edges=None):
     # n[1] is the object
     for n in graph.nodes():
         if n[0] == 'job':
+            # ignoring internal Jobs
+            if n[1].command.software.name == 'Qiita':
+                continue
             atype = 'job'
             name = n[1].command.name
             status = n[1].status