Disabling EBI submission if there are missing columns

Author: josenavas

qiita_db/metadata_template/__init__.py

@@ -9,8 +9,10 @@
 from .sample_template import SampleTemplate
 from .prep_template import PrepTemplate
 from .util import load_template_to_dataframe
-from .constants import TARGET_GENE_DATA_TYPES, SAMPLE_TEMPLATE_COLUMNS
+from .constants import (TARGET_GENE_DATA_TYPES, SAMPLE_TEMPLATE_COLUMNS,
+                        PREP_TEMPLATE_COLUMNS)
 
 
 __all__ = ['SampleTemplate', 'PrepTemplate', 'load_template_to_dataframe',
-           'TARGET_GENE_DATA_TYPES', 'SAMPLE_TEMPLATE_COLUMNS']
+           'TARGET_GENE_DATA_TYPES', 'SAMPLE_TEMPLATE_COLUMNS',
+           'PREP_TEMPLATE_COLUMNS']

qiita_pet/handlers/study_handlers/ebi_handlers.py

@@ -13,7 +13,9 @@
 from qiita_ware.demux import stats as demux_stats
 from qiita_ware.dispatchable import submit_to_ebi
 from qiita_db.data import PreprocessedData
-from qiita_db.metadata_template import PrepTemplate, SampleTemplate
+from qiita_db.metadata_template import (PrepTemplate, SampleTemplate,
+                                        SAMPLE_TEMPLATE_COLUMNS,
+                                        PREP_TEMPLATE_COLUMNS)
 from qiita_db.study import Study
 from qiita_db.exceptions import QiitaDBUnknownIDError
 from qiita_pet.handlers.base_handlers import BaseHandler
@@ -58,11 +60,33 @@ def display_template(self, preprocessed_data_id, msg, msg_level):
             stats.append(('Number of sequences', demux_file_stats.n))
             msg_level = 'success'
 
+        # Check if the templates have all the required columns for EBI
+        pt_missing_cols = prep_template.check_restrictions(
+            [PREP_TEMPLATE_COLUMNS['EBI']])
+        st_missing_cols = sample_template.check_restrictions(
+            [SAMPLE_TEMPLATE_COLUMNS['EBI']])
+        allow_submission = (len(pt_missing_cols) == 0 and
+                            len(st_missing_cols) == 0)
+
+        if not allow_submission:
+            msg_list = ["Submission to EBI disabled due to missing columns:"]
+            if len(pt_missing_cols) > 0:
+                msg_list.append("Columns missing in prep template: %s"
+                                % ', '.join(pt_missing_cols))
+            if len(st_missing_cols) > 0:
+                msg_list.append("Columns missing in sample template: %s"
+                                % ', '.join(st_missing_cols))
+            ebi_disabled_msg = "<br/>".join(msg_list)
+        else:
+            ebi_disabled_msg = None
+
         self.render('ebi_submission.html',
                     study_title=study.title, stats=stats, message=msg,
                     study_id=study.id, level=msg_level,
                     preprocessed_data_id=preprocessed_data_id,
-                    investigation_type=prep_template.investigation_type)
+                    investigation_type=prep_template.investigation_type,
+                    allow_submission=allow_submission,
+                    ebi_disabled_msg=ebi_disabled_msg)
 
     @authenticated
     def get(self, preprocessed_data_id):

qiita_pet/templates/ebi_submission.html

@@ -28,14 +28,18 @@ <h1>Submission summary for study: <b>{{study_title}}</b></h1>
     <br/><br/>
     {% if investigation_type %}
       {% if level != 'danger' and maintenance is None %}
-        <br/>
-        What kind of submission do you want to do?
-        <select name="submission_type">
-          <option value="ADD">ADD</option>
-          <option value="MODIFY">MODIFY</option>
-        </select>
-        <br/><br/>
-        <input type="submit" class="btn btn-primary" value="Submit to EBI">
+        {% if allow_submission %}
+            <br/>
+            What kind of submission do you want to do?
+            <select name="submission_type">
+                <option value="ADD">ADD</option>
+                <option value="MODIFY">MODIFY</option>
+            </select>
+            <br/><br/>
+            <input type="submit" class="btn btn-primary" value="Submit to EBI">
+        {% else %}
+            <b>{% raw ebi_disabled_msg %}
+        {% end %}
       {% end %}
     {% else %}
       <b>You need to set an investigation type to continue!</b>