Ebi improvements pet

qiita_db/metadata_template/prep_template.py

@@ -700,3 +700,24 @@ def ebi_experiment_accessions(self, value):
             If a sample in `value` already has an accession number
         """
         self._update_accession_numbers('ebi_experiment_accession', value)
+
+    @property
+    def is_submitted_to_ebi(self):
+        """Gets if the prep template has been submitted to EBI or not
+
+        Returns
+        -------
+        bool
+            True if the prep template has been submitted to EBI,
+            false otherwise
+        """
+        with TRN:
+            sql = """SELECT EXISTS(
+                        SELECT sample_id, ebi_experiment_accession
+                        FROM qiita.{0}
+                        WHERE {1}=%s
+                            AND ebi_experiment_accession IS NOT NULL)
+                  """.format(self._table, self._id_column)
+            TRN.add(sql, [self.id])
+            is_submitted = TRN.execute_fetchlast()
+        return is_submitted

qiita_db/metadata_template/test/test_prep_template.py

@@ -1414,6 +1414,12 @@ def f():
             pt.ebi_experiment_accessions = exp_acc
         npt.assert_warns(QiitaDBWarning, f)
 
+    def test_is_submitted_to_ebi(self):
+        self.assertTrue(self.tester.is_submitted_to_ebi)
+        pt = PrepTemplate.create(self.metadata, self.test_study,
+                                 self.data_type)
+        self.assertFalse(pt.is_submitted_to_ebi)
+
 
 EXP_PREP_TEMPLATE = (
     'sample_name\tbarcode\tcenter_name\tcenter_project_name\t'

qiita_pet/templates/study_description_templates/prep_template_info_tab.html

@@ -61,6 +61,13 @@ <h4 class="modal-title" id="myModalLabel">Choose preprocessing parameters</h4>
         {% end %}
       </td>
     </tr>
+    {% if ebi_link %}
+    <tr>
+      <td>
+        <b>EBI accession:</b> {% raw ebi_link %}
+      </td>
+    </tr>
+    {% end %}
     <tr>
       <td style="padding: 5px;">
         <a class="btn btn-primary" href="/metadata_summary/?study_id={{study_id}}&prep_template={{pt_id}}">

qiita_pet/templates/study_description_templates/prep_template_tab.html

@@ -4,9 +4,10 @@
     <!-- Nav tab: adding prep template -->
     <li class="active"><a href="#add_prep_template_tab" role="tab" data-toggle="tab">Add prep template</a></li>
     <!-- Nav tabs: one for each prep template available -->
-  {% for pt_id, pt_data_type, _, (class_icon1, class_icon2, color) in available_prep_templates %}
+  {% for pt_id, pt_data_type, _, (class_icon1, class_icon2, color), ebi in available_prep_templates %}
     <li><a href="#prep_template_info_{{pt_id}}" role="tab" data-toggle="tab">
-      {{pt_data_type}} (ID: {{pt_id}})&nbsp;
+      {{pt_data_type}} (ID: {{pt_id}})&nbsp;&nbsp;
+      {% if ebi %} EBI {% end %}
         <div class="{{class_icon1}}" style="color: {{color}};"></div>
         <div class="{{class_icon2}}" style="color: {{color}};"></div>
       <button class="close" title="Remove this prep template" type="button" onclick="delete_prep_template('{{pt_data_type}}', {{pt_id}})">&nbsp; ×</button>
@@ -72,7 +73,7 @@
     </div>
 
     <!-- Show Prep template info tabs -->
-    {% for _, _, pt, _ in available_prep_templates %}
+    {% for _, _, pt, _, _ in available_prep_templates %}
       {% module PrepTemplateInfoTab(study, pt, full_access, ena_terms, user_defined_terms) %}
     {% end %}
 

qiita_pet/templates/study_description_templates/preprocessed_data_info_tab.html

@@ -79,9 +79,9 @@ <h4 class="modal-title" id="myModalLabel">Choose processing parameters</h4>
 
 <div class="tab-pane" id="preprocessed_data_info_{{ppd_id}}" style="padding: 10px;">
   <a href="#" onclick="display_tab('prep_template_tab', {{prep_template_id}});">Prep template</a><br/>
-  <b>EBI status:</b> {{ebi_status}}<br/>
-  <b>EBI study accession:</b> {{ebi_study_accession}}<br/>
-  <b>EBI submission accession:</b> {{ebi_submission_accession}}<br/>
+  {% if ebi_link %}
+    <b>EBI accession:</b> {% raw ebi_link %}<br/>
+  {% end %}
   <b>VAMPS status:</b> {{vamps_status}}<br/>
   {% module EditInvestigationType(ena_terms, user_defined_terms, prep_template_id, inv_type, ppd_id) %}
   {% if show_ebi_btn %}

qiita_pet/templates/study_description_templates/preprocessed_data_tab.html

@@ -5,12 +5,14 @@
       <!-- Adding a preprocessed data -->
       <li class="active"><a href="#add_preprocessed_data_tab" role="tab" data-toggle="tab">Add preprocessed data</a></li>
       <!-- Create the tabs for each preprocessed data -->
-      {% for ppd_id, ppd, (class_icon1, class_icon2, color) in available_preprocessed_data %}
-        <li><a href="#preprocessed_data_info_{{ppd_id}}" role="tab" data-toggle="tab">ID: {{ppd_id}}&nbsp;
+      {% for ppd_id, ppd, (class_icon1, class_icon2, color), ebi in available_preprocessed_data %}
+        <li><a href="#preprocessed_data_info_{{ppd_id}}" role="tab" data-toggle="tab">ID: {{ppd_id}}&nbsp;&nbsp;
+          {% if ebi %} EBI {% end %}
           <div class="{{class_icon1}}" style="color: {{color}};"></div>
           <div class="{{class_icon2}}" style="color: {{color}};"></div>
           <button class="close" title="Remove this preprocessed data" type="button" onclick="delete_preprocessed_data({{ppd_id}})">&nbsp; ×</button>
-        </a></li>
+          </a>
+        </li>
       {% end %}
     </ul>
     <!-- Create the tab panes -->
@@ -20,7 +22,7 @@
         <b>Not implemented! Coming soon...</b>
       </div>
       <!-- Create one tab pane for each preprocessed data -->
-      {% for ppd_id, ppd, _ in available_preprocessed_data %}
+      {% for ppd_id, ppd, _, _ in available_preprocessed_data %}
         {% module PreprocessedDataInfoTab(study_id, ppd) %}
       {% end %}
     </div>

qiita_pet/templates/study_description_templates/study_information_tab.html

@@ -8,6 +8,8 @@
   <b>Principal investigator:</b> {% raw principal_investigator %} <br/>
   <b>Samples:</b> {{number_samples_promised}}/{{number_samples_collected}}<br/>
   <b>Metadata:</b> {{metadata_complete}} <br/>
+  <b>EBI status:</b> {{ebi_status}} <br/>
+  <b>EBI accession:</b> {% raw ebi_accession %} <br/>
 
   <hr>
 

qiita_pet/uimodules/prep_template_tab.py

@@ -22,7 +22,7 @@
                                         PREP_TEMPLATE_COLUMNS_TARGET_GENE)
 from qiita_db.parameters import (Preprocessed454Params,
                                  PreprocessedIlluminaParams)
-from qiita_pet.util import STATUS_STYLER, is_localhost
+from qiita_pet.util import STATUS_STYLER, is_localhost, ebi_linkifier
 from qiita_pet.handlers.util import download_link_or_path
 from .base_uimodule import BaseUIModule
 from qiita_core.util import execute_as_transaction
@@ -75,7 +75,8 @@ def _template_generator(study, full_access):
     for pt_id in sorted(study.prep_templates()):
         pt = PrepTemplate(pt_id)
         if full_access or pt.status == 'public':
-            yield (pt.id, pt.data_type(), pt, STATUS_STYLER[pt.status])
+            yield (pt.id, pt.data_type(), pt, STATUS_STYLER[pt.status],
+                   pt.is_submitted_to_ebi)
 
 
 class PrepTemplateTab(BaseUIModule):
@@ -225,6 +226,10 @@ def render(self, study, prep_template, full_access, ena_terms,
 
         preprocessing_status = prep_template.preprocessing_status
 
+        ebi_link = None
+        if prep_template.is_submitted_to_ebi:
+            ebi_link = ebi_linkifier.format(study.ebi_study_accession)
+
         return self.render_string(
             "study_description_templates/prep_template_info_tab.html",
             pt_id=prep_template.id,
@@ -249,7 +254,8 @@ def render(self, study, prep_template, full_access, ena_terms,
             preprocessed_data=preprocessed_data,
             preprocessing_status=preprocessing_status,
             show_preprocess_btn=show_preprocess_btn,
-            no_preprocess_msg=no_preprocess_msg)
+            no_preprocess_msg=no_preprocess_msg,
+            ebi_link=ebi_link)
 
 
 class RawDataInfoDiv(BaseUIModule):

qiita_pet/uimodules/preprocessed_data_tab.py

@@ -7,6 +7,7 @@
 # -----------------------------------------------------------------------------
 
 from qiita_core.util import execute_as_transaction
+from qiita_db.study import Study
 from qiita_db.data import PreprocessedData
 from qiita_db.metadata_template import PrepTemplate
 from qiita_db.ontology import Ontology
@@ -15,15 +16,16 @@
 from qiita_db.parameters import ProcessedSortmernaParams
 from .base_uimodule import BaseUIModule
 from qiita_pet.util import (generate_param_str, STATUS_STYLER,
-                            is_localhost)
+                            is_localhost, ebi_linkifier)
 
 
 class PreprocessedDataTab(BaseUIModule):
     @execute_as_transaction
     def render(self, study, full_access):
         ppd_gen = (PreprocessedData(ppd_id)
                    for ppd_id in study.preprocessed_data())
-        avail_ppd = [(ppd.id, ppd, STATUS_STYLER[ppd.status])
+        avail_ppd = [(ppd.id, ppd, STATUS_STYLER[ppd.status],
+                      ppd.is_submitted_to_ebi)
                      for ppd in ppd_gen
                      if full_access or ppd.status == 'public']
         return self.render_string(
@@ -37,9 +39,6 @@ class PreprocessedDataInfoTab(BaseUIModule):
     def render(self, study_id, preprocessed_data):
         user = self.current_user
         ppd_id = preprocessed_data.id
-        ebi_status = preprocessed_data.submitted_to_insdc_status()
-        ebi_study_accession = preprocessed_data.ebi_study_accession
-        ebi_submission_accession = preprocessed_data.ebi_submission_accession
         vamps_status = preprocessed_data.submitted_to_vamps_status()
         filepaths = preprocessed_data.get_filepaths()
         is_local_request = is_localhost(self.request.headers['host'])
@@ -76,13 +75,15 @@ def render(self, study_id, preprocessed_data):
         # so we can initialize the interface
         default_params = 1
 
+        ebi_link = None
+        if preprocessed_data.is_submitted_to_ebi:
+            ebi_link = ebi_linkifier.format(
+                Study(study_id).ebi_study_accession)
+
         return self.render_string(
             "study_description_templates/preprocessed_data_info_tab.html",
             ppd_id=ppd_id,
             show_ebi_btn=show_ebi_btn,
-            ebi_status=ebi_status,
-            ebi_study_accession=ebi_study_accession,
-            ebi_submission_accession=ebi_submission_accession,
             filepaths=filepaths,
             is_local_request=is_local_request,
             prep_template_id=prep_template_id,
@@ -95,4 +96,5 @@ def render(self, study_id, preprocessed_data):
             default_params=default_params,
             study_id=preprocessed_data.study,
             processing_status=processing_status,
-            processed_data=processed_data)
+            processed_data=processed_data,
+            ebi_link=ebi_link)

qiita_pet/uimodules/study_information_tab.py

@@ -15,7 +15,7 @@
 from qiita_db.util import get_files_from_uploads_folders, get_data_types
 from qiita_db.study import StudyPerson
 from qiita_db.metadata_template import SampleTemplate
-from qiita_pet.util import linkify, is_localhost
+from qiita_pet.util import linkify, is_localhost, ebi_linkifier
 from .base_uimodule import BaseUIModule
 
 
@@ -62,6 +62,12 @@ def render(self, study):
         show_select_sample = (
             study.status == 'sandbox' or self.current_user.level == 'admin')
 
+        # Ebi information
+        ebi_status = study.ebi_submission_status
+        ebi_accession = study.ebi_study_accession
+        if ebi_accession:
+            ebi_accession = (ebi_linkifier.format(ebi_accession))
+
         return self.render_string(
             "study_description_templates/study_information_tab.html",
             abstract=abstract,
@@ -77,4 +83,6 @@ def render(self, study):
             study_id=study.id,
             sample_templates=sample_templates,
             is_local_request=is_local_request,
-            data_types=data_types)
+            data_types=data_types,
+            ebi_status=ebi_status,
+            ebi_accession=ebi_accession)

qiita_pet/util.py

@@ -39,6 +39,8 @@
     'public':
         ('glyphicon glyphicon-eye-open', 'glyphicon glyphicon-globe', 'green')}
 
+ebi_linkifier = ('<a href="http://www.ebi.ac.uk/ena/data/view/{0}" '
+                 'target="_blank">{0}</a>')
 
 def linkify(link_template, item):
     """Formats a strings into a URL using string replacement