Improving analysis listing b

.travis.yml

@@ -20,7 +20,8 @@ before_install:
   - wget ftp://ftp.microbio.me/pub/qiita/ascp-install-3.5.4.102989-linux-64-qiita.sh -O ascp-install-3.5.4.102989-linux-64-qiita.sh
   - chmod +x ascp-install-3.5.4.102989-linux-64-qiita.sh
   - ./ascp-install-3.5.4.102989-linux-64-qiita.sh
-  - if [ ${TRAVIS_PULL_REQUEST} == "false" ]; then openssl aes-256-cbc -K $encrypted_a2e23aea5f14_key -iv $encrypted_a2e23aea5f14_iv -in qiita_core/support_files/config_test_travis.cfg.enc -out qiita_core/support_files/config_test_travis.cfg -d ; fi
+  # once we have ebi testing we should uncomment this line
+  # - if [ ${TRAVIS_PULL_REQUEST} == "false" ]; then openssl aes-256-cbc -K $encrypted_a2e23aea5f14_key -iv $encrypted_a2e23aea5f14_iv -in qiita_core/support_files/config_test_travis.cfg.enc -out qiita_core/support_files/config_test_travis.cfg -d ; fi
 install:
   # install a few of the dependencies that pip would otherwise try to install
   # when intalling scikit-bio

qiita_core/testing.py

@@ -58,5 +58,5 @@ def wait_for_processing_job(job_id):
     """
     job = ProcessingJob(job_id)
     while job.status not in ('success', 'error'):
-        sleep(0.5)
-    sleep(0.5)
+        sleep(1.2)
+    sleep(1.2)

qiita_db/analysis.py

@@ -773,8 +773,7 @@ def build_files(self, merge_duplicated_sample_ids):
             # different stages and possible errors.
             samples = self.samples
             # gettin the info of all the artifacts to save SQL time
-            bioms_info = qdb.util.get_artifacts_bioms_information(
-                samples.keys())
+            bioms_info = qdb.util.get_artifacts_information(samples.keys())
 
             # figuring out if we are going to have duplicated samples, again
             # doing it here cause it's computational cheaper

qiita_db/test/test_util.py

@@ -843,10 +843,10 @@ def test_generate_study_list(self):
         obs_info = qdb.util.generate_study_list([1, 2, 3, 4], False)
         self.assertEqual(obs_info, exp_info)
 
-    def test_get_artifacts_bioms_information(self):
+    def test_get_artifacts_information(self):
         # we are gonna test that it ignores 1 and 2 cause they are not biom,
         # 4 has all information and 7 and 8 don't
-        obs = qdb.util.get_artifacts_bioms_information([1, 2, 4, 7, 8])
+        obs = qdb.util.get_artifacts_information([1, 2, 4, 7, 8])
         # not testing timestamp
         for i in range(len(obs)):
             del obs[i]['timestamp']

qiita_db/util.py

@@ -1324,18 +1324,20 @@ def generate_study_list(study_ids, public_only=False):
     return infolist
 
 
-def get_artifacts_bioms_information(artifact_ids):
-        """Returns processing information about the bioms in the artifact
+def get_artifacts_information(artifact_ids, only_biom=True):
+        """Returns processing information about the artifact ids
 
         Parameters
         ----------
         artifact_ids : list of ints
             The artifact ids to look for. Non-existing ids will be ignored
+        only_biom : bool
+            If true only the biom artifacts are retrieved
 
         Returns
         -------
         dict
-            The info of the bioms if artifact_type is BIOM or None if not.
+            The info of the artifacts
         """
         if not artifact_ids:
             return {}
@@ -1348,10 +1350,13 @@ def get_artifacts_bioms_information(artifact_ids):
                        array_agg(parent_info.command_parameters),
                        array_agg(filepaths.filepath),
                        qiita.find_artifact_roots(a.artifact_id) AS root_id
-                FROM qiita.artifact a
+                FROM qiita.artifact a"""
+        if only_biom:
+            sql += """
                 JOIN qiita.artifact_type at ON (
                     a.artifact_type_id = at .artifact_type_id
-                        AND artifact_type = 'BIOM')
+                        AND artifact_type = 'BIOM')"""
+        sql += """
                 LEFT JOIN qiita.parent_artifact pa ON (
                     a.artifact_id = pa.artifact_id)
                 LEFT JOIN qiita.data_type dt USING (data_type_id)

qiita_pet/handlers/analysis_handlers/sharing_handlers.py

@@ -30,7 +30,7 @@ def _get_shared_for_study(self, analysis, callback):
     @execute_as_transaction
     def _share(self, analysis, user, callback):
         user = User(user)
-        add_message('Analysis <a href="%s/analysis/results/%d">\'%s\'</a> '
+        add_message('Analysis <a href="%s/analysis/description/%d">\'%s\'</a> '
                     'has been shared with you.' %
                     (qiita_config.portal_dir, analysis.id, analysis.name),
                     [user])

qiita_pet/handlers/analysis_handlers/tests/test_sharing_handlers.py

@@ -45,9 +45,9 @@ def test_get(self):
         self.assertEqual(a.shared_with, [u])
 
         # Make sure shared message added to the system
-        self.assertEqual('Analysis <a href="/analysis/results/1">\'SomeAnalys'
-                         'is\'</a> has been shared with you.',
-                         u.messages()[0][1])
+        self.assertEqual(
+            'Analysis <a href="/analysis/description/1">\'SomeAnalysis\'</a> '
+            'has been shared with you.', u.messages()[0][1])
 
     def test_get_no_access(self):
         args = {'selected': 'demo@microbio.me', 'id': 2}

qiita_pet/handlers/api_proxy/__init__.py

@@ -31,7 +31,7 @@
 from .artifact import (artifact_graph_get_req, artifact_types_get_req,
                        artifact_post_req, artifact_get_req,
                        artifact_status_put_req, artifact_get_prep_req,
-                       artifact_patch_request, artifact_get_biom_info)
+                       artifact_patch_request, artifact_get_info)
 from .ontology import ontology_patch_handler
 from .processing import (
     list_commands_handler_get_req, process_artifact_handler_get_req,
@@ -53,7 +53,7 @@
            'prep_template_get_req', 'study_delete_req',
            'study_prep_get_req', 'sample_template_get_req',
            'artifact_graph_get_req', 'artifact_types_get_req',
-           'artifact_post_req', 'artifact_get_biom_info',
+           'artifact_post_req', 'artifact_get_info',
            'sample_template_meta_cats_get_req',
            'sample_template_samples_get_req', 'prep_template_samples_get_req',
            'sample_template_category_get_req', 'new_prep_template_get_req',

qiita_pet/handlers/api_proxy/artifact.py

@@ -22,7 +22,7 @@
 from qiita_db.user import User
 from qiita_db.metadata_template.prep_template import PrepTemplate
 from qiita_db.util import (
-    get_mountpoint, get_visibilities, get_artifacts_bioms_information)
+    get_mountpoint, get_visibilities, get_artifacts_information)
 from qiita_db.software import Command, Parameters
 from qiita_db.processing_job import ProcessingJob
 
@@ -110,7 +110,7 @@ def artifact_get_prep_req(user_id, artifact_ids):
 
 
 @execute_as_transaction
-def artifact_get_biom_info(user_id, artifact_ids):
+def artifact_get_info(user_id, artifact_ids, only_biom=True):
     """Returns all artifact info for the given artifact_ids
 
     Parameters
@@ -119,6 +119,8 @@ def artifact_get_biom_info(user_id, artifact_ids):
         user making the request
     artifact_ids : list of int
         list of artifact ids
+    only_biom : bool
+        If true only the biom artifacts are retrieved
 
     Returns
     -------
@@ -130,7 +132,7 @@ def artifact_get_biom_info(user_id, artifact_ids):
     """
     artifact_info = {}
 
-    artifact_info = get_artifacts_bioms_information(artifact_ids)
+    artifact_info = get_artifacts_information(artifact_ids, only_biom)
 
     return {'status': 'success', 'msg': '', 'data': artifact_info}
 

qiita_pet/handlers/api_proxy/prep_template.py

@@ -122,16 +122,19 @@ def prep_template_ajax_get_req(user_id, prep_id):
                 alert_msg = (job.log.msg.replace('\n', '</br>')
                              if job.log is not None else "")
             else:
-                redis_info = loads(r_client.get(job_id))
-                processing = redis_info['status_msg'] == 'Running'
-                success = redis_info['status_msg'] == 'Success'
-                if redis_info['return'] is not None:
-                    alert_type = redis_info['return']['status']
-                    alert_msg = redis_info['return']['message'].replace(
-                        '\n', '</br>')
-                else:
-                    alert_type = 'info'
-                    alert_msg = ''
+                alert_type = 'info'
+                alert_msg = ''
+                # this is not actually necessary but in case of a system
+                # failure this will avoid the error
+                ji = r_client.get(job_id)
+                if ji:
+                    redis_info = loads(ji)
+                    processing = redis_info['status_msg'] == 'Running'
+                    success = redis_info['status_msg'] == 'Success'
+                    if redis_info['return'] is not None:
+                        alert_type = redis_info['return']['status']
+                        alert_msg = redis_info['return']['message'].replace(
+                            '\n', '</br>')
 
             if processing:
                 alert_type = 'info'

qiita_pet/handlers/api_proxy/tests/test_artifact.py

@@ -26,7 +26,7 @@
 from qiita_pet.handlers.api_proxy.artifact import (
     artifact_get_req, artifact_status_put_req, artifact_graph_get_req,
     artifact_types_get_req, artifact_post_req, artifact_patch_request,
-    artifact_get_prep_req, artifact_get_biom_info)
+    artifact_get_prep_req, artifact_get_info)
 
 
 class TestArtifactAPIReadOnly(TestCase):
@@ -219,8 +219,8 @@ def test_artifact_get_prep_req(self):
                'message': 'User does not have access to study'}
         self.assertEqual(obs, exp)
 
-    def test_artifact_get_biom_info(self):
-        obs = artifact_get_biom_info('test@foo.bar', [5, 6, 7])
+    def test_artifact_get_info(self):
+        obs = artifact_get_info('test@foo.bar', [5, 6, 7])
         data = [
             {'files': ['1_study_1001_closed_reference_otu_table_Silva.biom'],
              'target_subfragment': ['V4'], 'algorithm': (

qiita_pet/handlers/study_handlers/__init__.py

@@ -21,8 +21,7 @@
                          ListOptionsHandler, WorkflowHandler,
                          WorkflowRunHandler, JobAJAX)
 from .artifact import (ArtifactGraphAJAX, NewArtifactHandler,
-                       ArtifactAdminAJAX, ArtifactGetSamples,
-                       ArtifactGetBIOMInfo)
+                       ArtifactAdminAJAX, ArtifactGetSamples, ArtifactGetInfo)
 from .sample_template import SampleTemplateAJAX, SampleAJAX
 
 __all__ = ['ListStudiesHandler', 'StudyApprovalList', 'ShareStudyAJAX',
@@ -36,4 +35,4 @@
            'DataTypesMenuAJAX', 'StudyFilesAJAX', 'PrepTemplateSummaryAJAX',
            'WorkflowHandler', 'WorkflowRunHandler',
            'JobAJAX', 'AutocompleteHandler', 'StudyGetTags', 'StudyTags',
-           'ArtifactGetSamples', 'ArtifactGetBIOMInfo']
+           'ArtifactGetSamples', 'ArtifactGetInfo']

qiita_pet/handlers/study_handlers/artifact.py

@@ -15,7 +15,7 @@
 from qiita_pet.handlers.api_proxy import (
     artifact_graph_get_req, artifact_types_get_req, artifact_post_req,
     artifact_status_put_req, artifact_get_req, artifact_get_prep_req,
-    artifact_get_biom_info)
+    artifact_get_info)
 from qiita_core.util import execute_as_transaction
 from qiita_core.qiita_settings import qiita_config
 
@@ -69,12 +69,13 @@ def get(self):
         self.write(response)
 
 
-class ArtifactGetBIOMInfo(BaseHandler):
+class ArtifactGetInfo(BaseHandler):
     @authenticated
     def get(self):
         aids = map(int, self.request.arguments.get('ids[]', []))
+        only_biom = self.get_argument('only_biom', 'True') == 'True'
 
-        response = artifact_get_biom_info(self.current_user.id, aids)
+        response = artifact_get_info(self.current_user.id, aids, only_biom)
 
         self.write(response)
 

qiita_pet/handlers/study_handlers/tests/test_artifact.py

@@ -158,7 +158,7 @@ def test_get(self):
         self.assertEqual(loads(response.body), exp)
 
 
-class ArtifactGetBIOMInfoTest(TestHandlerBase):
+class ArtifactGetInfoTest(TestHandlerBase):
     def test_get(self):
         response = self.get('/artifact/info/', {'ids[]': [6, 7]})
         self.assertEqual(response.code, 200)

qiita_pet/templates/list_analyses.html

@@ -8,8 +8,74 @@
     {% if analyses %}
       $('#no-analyses').hide()
       $('#analyses-table').dataTable({
-        "order": [[ 2, "desc" ]]
+        "order": [[ 2, "desc" ]],
+        columnDefs: [
+          {"render": function ( data, type, row, meta ) {
+            data = JSON.parse(data);
+            if (data !== null && data !== undefined && data.length != 0){
+              return '<div class="container" style="max-width: 5em;">'+
+                       '<div class="row justify-content-md-center">' +
+                         '<div class="col-md-1 text-center details-control">&nbsp;</div>' +
+                         '<div class="col-md-1 text-center">' + data.length + '</div>' +
+                       '</div>' +
+                     '</div>';
+            } else {
+              return 'No artifacts';
+            }
+          }, targets: [0]}]
       });
+
+      $('#analyses-table tbody').on('click', 'div.details-control', function () {
+          var table = $('#analyses-table').DataTable();
+          var tr = $(this).closest('tr');
+          var row = table.row( tr );
+
+          if ( row.child.isShown() ) {
+            // This row is already open - close it
+            row.child.hide();
+            tr.removeClass('shown');
+          } else {
+            // Open this row
+            // modified from: https://jsfiddle.net/8rejaL88/2/
+            tr.addClass('shown');
+            row.child('<p><center><img src="{% raw qiita_config.portal_dir %}/static/img/waiting.gif" style="display:block;margin-left: auto;margin-right: auto"/></center></p>', 'no-padding' ).show();
+            $.get('/artifact/info/', {ids: JSON.parse(row.data()[0]), only_biom: 'False' })
+              .done(function ( data ) {
+                if (data['status']=='success') {
+                  $('td', row.child()).html(format_biom_rows(data.data, row.index())).show();
+                } else {
+                  bootstrapAlert('ERROR: ' + data['msg'], "danger", 10000);
+                }
+              });
+          }
+      });
+
+      function format_biom_rows(data, row) {
+        var proc_data_table = '<table class="table" cellpadding="0" cellspacing="0" border="0" style="padding-left:0px;width:95%">';
+        proc_data_table += '<tr>';
+        proc_data_table += '<th>Name</th>';
+        proc_data_table += '<th>Processing method</th>';
+        proc_data_table += '<th>Parameters</th>';
+        proc_data_table += '<th>Files</th>';
+        proc_data_table += '</tr>';
+        $.each(data, function (idx, info) {
+          if (typeof info !== 'string' && !(info instanceof String)) {
+            proc_data_table += '<tr>';
+            proc_data_table += '<td>' + info.name + ' (' + info.artifact_id + ' - ' + info.timestamp.split('.')[0] + ')</td>';
+            proc_data_table += '<td>' + info.algorithm + '</td>';
+            var params = '';
+            for (var key in info.parameters) {
+              params += '<i>' + key + '</i>: ' + info.parameters[key] + '<br/>';
+            }
+            proc_data_table += '<td><small>' + params + '</small></td>';
+            proc_data_table += '<td><small>' + info.files.join('<br/>')  + '</small></td>';
+            proc_data_table += '</tr>';
+          }
+        });
+
+        proc_data_table += '</table>';
+        return proc_data_table;
+      }
     {% end %}
   });
 </script>
@@ -37,7 +103,7 @@ <h3><a href="{% raw qiita_config.portal_dir %}/study/list/">Create an analysis</
         {% set _id = analysis.id %}
         <tr>
           <td>
-            {{len(analysis.artifacts)}}
+            {{[ar.id for ar in analysis.artifacts]}}
           </td>
           <td>
             <a href="{% raw qiita_config.portal_dir %}/analysis/description/{{_id}}/">{{analysis.name}}</a>

qiita_pet/templates/list_studies.html

@@ -130,15 +130,11 @@
         {"targets": [ 2 ], "visible": false},
         // render zero
         {"render": function ( data, type, row, meta ) {
-          var len = 0;
-          if (data !== null && data !== undefined){
-            len = data.length;
-          }
-          if (len != 0){
+          if (data !== null && data !== undefined && data.length != 0){
             return '<div class="container" style="max-width: 5em;">'+
                      '<div class="row justify-content-md-center">' +
                        '<div class="col-md-1 text-center details-control">&nbsp;</div>' +
-                       '<div class="col-md-1 text-center">' + len + '</div>' +
+                       '<div class="col-md-1 text-center">' + data.length + '</div>' +
                      '</div>' +
                    '</div>';
           } else {
@@ -203,15 +199,11 @@
         {"targets": [ 2 ], "visible": false},
         // render zero
         {"render": function ( data, type, row, meta ) {
-          var len = 0;
-          if (data !== null && data !== undefined){
-            len = data.length;
-           }
-          if (len != 0){
+          if (data !== null && data !== undefined && data.length != 0){
             return '<div class="container" style="max-width: 5em;">'+
                      '<div class="row justify-content-md-center">' +
                        '<div class="col-md-1 text-center details-control">&nbsp;</div>' +
-                       '<div class="col-md-1 text-center">' + len + '</div>' +
+                       '<div class="col-md-1 text-center">' + data.length + '</div>' +
                      '</div>' +
                    '</div>';
           } else {

qiita_pet/webserver.py

@@ -30,7 +30,7 @@
     ListCommandsHandler, ListOptionsHandler, PrepTemplateSummaryAJAX,
     PrepTemplateAJAX, NewArtifactHandler, SampleAJAX, StudyDeleteAjax,
     ArtifactAdminAJAX, NewPrepTemplateAjax, DataTypesMenuAJAX, StudyFilesAJAX,
-    ArtifactGetSamples, ArtifactGetBIOMInfo, WorkflowHandler,
+    ArtifactGetSamples, ArtifactGetInfo, WorkflowHandler,
     WorkflowRunHandler, JobAJAX, AutocompleteHandler)
 from qiita_pet.handlers.artifact_handlers import (
     ArtifactSummaryAJAX, ArtifactAJAX, ArtifactSummaryHandler,
@@ -108,7 +108,7 @@ def __init__(self):
             (r"/analysis/description/(.*)/", AnalysisDescriptionHandler),
             (r"/analysis/sharing/", ShareAnalysisAJAX),
             (r"/artifact/samples/", ArtifactGetSamples),
-            (r"/artifact/info/", ArtifactGetBIOMInfo),
+            (r"/artifact/info/", ArtifactGetInfo),
             (r"/moi-ws/", MOIMessageHandler),
             (r"/consumer/", MessageHandler),
             (r"/admin/error/", LogEntryViewerHandler),