Disabling preprocessing if there are missing columns

Author: josenavas

qiita_db/metadata_template/__init__.py

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

qiita_pet/templates/study_description_templates/prep_template_panel.html

@@ -88,7 +88,11 @@ <h4 class="panel-title">
       <br/>
       {% if not preprocessed_data or preprocessing_status.startswith('failed') %}
         {% if study_status == 'sandbox' %}
-          <a class="btn btn-primary glyphicon glyphicon-play" data-toggle="modal" data-target="#preprocess-modal-view-{{prep_id}}" style="word-spacing: -10px;"> Preprocess</a>
+          {% if show_preprocess_btn %}
+            <a class="btn btn-primary glyphicon glyphicon-play" data-toggle="modal" data-target="#preprocess-modal-view-{{prep_id}}" style="word-spacing: -10px;"> Preprocess</a>
+          {% else %}
+            <b>{{ no_preprocess_msg }}</b>
+          {% end %}
         {% end %}
           <br>
           <i>Status:</i> {{preprocessing_status}}

qiita_pet/templates/study_description_templates/raw_data_editor_tab.html

@@ -73,7 +73,7 @@ <h4>Add prep template to this raw data</h4>
         <h4>Prep templates uploaded</h4>
         <div class="panel-group" id="prep-accordion-{{raw_data_id}}">
           {% for prep in available_prep_templates %}
-            {% module PrepTemplatePanel(prep, study_id, is_editable, ena_terms, study_status, user_defined_terms) %}
+            {% module PrepTemplatePanel(prep, study_id, is_editable, ena_terms, study_status, user_defined_terms, raw_data_files) %}
           {% end %}
         </div>
       </td>

qiita_pet/uimodules/raw_data_tab.py

@@ -16,7 +16,8 @@
 from qiita_db.study import Study
 from qiita_db.data import RawData
 from qiita_db.ontology import Ontology
-from qiita_db.metadata_template import PrepTemplate
+from qiita_db.metadata_template import (PrepTemplate, TARGET_GENE_DATA_TYPES,
+                                        PREP_TEMPLATE_COLUMNS_TARGET_GENE)
 from qiita_db.parameters import (Preprocessed454Params,
                                  PreprocessedIlluminaParams)
 from qiita_pet.util import STATUS_STYLER
@@ -166,7 +167,7 @@ def render(self, study, raw_data, full_access):
 
 class PrepTemplatePanel(BaseUIModule):
     def render(self, prep, study_id, is_editable, ena_terms,
-               study_status, user_defined_terms):
+               study_status, user_defined_terms, raw_data_files):
         # Check if the request came from a local source
         is_local_request = self._is_local()
 
@@ -203,6 +204,23 @@ def render(self, prep, study_id, is_editable, ena_terms,
                     if 'qiime' in basename(fp) else "Prep template")
         filepaths = [(id_, fp, _fp_type(fp)) for id_, fp in filepaths]
 
+        # Check if the template have all the required columns for preprocessing
+        if prep.data_type() in TARGET_GENE_DATA_TYPES:
+            key = ('demultiplex_multiple' if len(raw_data_files) > 2
+                   else 'demultiplex')
+            missing_cols = prep.check_restrictions(
+                [PREP_TEMPLATE_COLUMNS_TARGET_GENE[key]])
+            show_preprocess_btn = len(missing_cols) == 0
+            if not show_preprocess_btn:
+                no_preprocess_msg = (
+                    "Preprocessing disabled due to missing columns in the "
+                    "prep template: %s" % ', '.join(missing_cols))
+            else:
+                no_preprocess_msg = None
+        else:
+            show_preprocess_btn = True
+            no_preprocess_msg = None
+
         return self.render_string(
             "study_description_templates/prep_template_panel.html",
             prep_id=prep_id,
@@ -220,7 +238,9 @@ def render(self, prep, study_id, is_editable, ena_terms,
             ena_terms=ena_terms,
             study_status=study_status,
             user_defined_terms=user_defined_terms,
-            preprocess_options=preprocess_options)
+            preprocess_options=preprocess_options,
+            show_preprocess_btn=show_preprocess_btn,
+            no_preprocess_msg=no_preprocess_msg)
 
 
 class EditInvestigationType(BaseUIModule):