Disable make processed data private

qiita_db/metadata_template/__init__.py

@@ -9,8 +9,11 @@
 from .sample_template import SampleTemplate
 from .prep_template import PrepTemplate
 from .util import load_template_to_dataframe
-from .constants import TARGET_GENE_DATA_TYPES
+from .constants import (TARGET_GENE_DATA_TYPES, SAMPLE_TEMPLATE_COLUMNS,
+                        PREP_TEMPLATE_COLUMNS,
+                        PREP_TEMPLATE_COLUMNS_TARGET_GENE)
 
 
 __all__ = ['SampleTemplate', 'PrepTemplate', 'load_template_to_dataframe',
-           'TARGET_GENE_DATA_TYPES']
+           'TARGET_GENE_DATA_TYPES', 'SAMPLE_TEMPLATE_COLUMNS',
+           'PREP_TEMPLATE_COLUMNS', 'PREP_TEMPLATE_COLUMNS_TARGET_GENE']

qiita_db/metadata_template/test/test_prep_template.py

@@ -32,8 +32,8 @@
                            get_count)
 from qiita_db.metadata_template.prep_template import PrepTemplate, PrepSample
 from qiita_db.metadata_template.sample_template import SampleTemplate, Sample
-from qiita_db.metadata_template.constants import (
-    PREP_TEMPLATE_COLUMNS, PREP_TEMPLATE_COLUMNS_TARGET_GENE)
+from qiita_db.metadata_template import (PREP_TEMPLATE_COLUMNS,
+                                        PREP_TEMPLATE_COLUMNS_TARGET_GENE)
 
 
 class BaseTestPrepSample(TestCase):

qiita_pet/handlers/study_handlers/description_handlers.py

@@ -22,7 +22,8 @@
 from qiita_db.data import RawData, PreprocessedData, ProcessedData
 from qiita_db.ontology import Ontology
 from qiita_db.metadata_template import (PrepTemplate, SampleTemplate,
-                                        load_template_to_dataframe)
+                                        load_template_to_dataframe,
+                                        SAMPLE_TEMPLATE_COLUMNS)
 from qiita_db.util import convert_to_id, get_mountpoint
 from qiita_db.exceptions import (QiitaDBUnknownIDError, QiitaDBColumnError,
                                  QiitaDBExecutionError, QiitaDBDuplicateError,
@@ -624,6 +625,18 @@ def display_template(self, study, user, msg, msg_level, full_access,
         user_level = user.level
         sample_template_exists = SampleTemplate.exists(study.id)
 
+        if sample_template_exists:
+            st = SampleTemplate(study.id)
+            missing_cols = st.check_restrictions(
+                [SAMPLE_TEMPLATE_COLUMNS['qiita_main']])
+            allow_approval = len(missing_cols) == 0
+            approval_deny_msg = (
+                "Processed data approval request is disabled due to missing "
+                "columns in the sample template: %s" % ', '.join(missing_cols))
+        else:
+            allow_approval = False
+            approval_deny_msg = ""
+
         # The general information of the study can be changed if the study is
         # not public or if the user is an admin, in which case they can always
         # modify the information of the study
@@ -638,6 +651,8 @@ def display_template(self, study, user, msg, msg_level, full_access,
                     show_edit_btn=show_edit_btn,
                     show_data_tabs=sample_template_exists,
                     full_access=full_access,
+                    allow_approval=allow_approval,
+                    approval_deny_msg=approval_deny_msg,
                     top_tab=top_tab,
                     sub_tab=sub_tab,
                     prep_tab=prep_tab)

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>

qiita_pet/templates/study_description.html

@@ -607,7 +607,7 @@ <h2><i>{{study_alias}}</i></h2>
     <!-- Show the preprocessed data tab -->
     {% module PreprocessedDataTab(study, full_access) %}
     <!-- Show the processed data tab -->
-    {% module ProcessedDataTab(study, full_access) %}
+    {% module ProcessedDataTab(study, full_access, allow_approval, approval_deny_msg) %}
   {% end %}
 </div>
 

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/processed_data_info_tab.html

@@ -15,7 +15,11 @@
     {% end %}
   </table>
   {% if btn_to_show == 'request_approval' %}
-    <a class="btn btn-default glyphicon glyphicon-eye-open" onClick="request_approval({{pd_id}});" style="word-spacing: -10px;"> Request making this data private</a>
+    {% if allow_approval %}
+      <a class="btn btn-default glyphicon glyphicon-eye-open" onClick="request_approval({{pd_id}});" style="word-spacing: -10px;"> Request making this data private</a>
+    {% else %}
+      <b>{{ approval_deny_msg }}</b>
+    {% end %}
   {% elif btn_to_show == 'approve' %}
     <a class="btn btn-success glyphicon glyphicon-thumbs-up" onClick="approve_study({{pd_id}});" style="word-spacing: -10px;"> Approve this data to be private</a>
   {% elif btn_to_show == 'make_public' %}

qiita_pet/templates/study_description_templates/processed_data_tab.html

@@ -23,7 +23,7 @@
       </div>
       <!-- Create one tab pane for each processed data -->
       {% for pd_id, pd, _ in available_processed_data %}
-        {% module ProcessedDataInfoTab(study_id, pd) %}
+        {% module ProcessedDataInfoTab(study_id, pd, allow_approval, approval_deny_msg) %}
       {% end %}
     </div>
   {% else %}

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/processed_data_tab.py

@@ -13,19 +13,22 @@
 
 
 class ProcessedDataTab(BaseUIModule):
-    def render(self, study, full_access):
+    def render(self, study, full_access, allow_approval, approval_deny_msg):
         pd_gen = (ProcessedData(pd_id) for pd_id in study.processed_data())
         avail_pd = [(pd.id, pd, STATUS_STYLER[pd.status]) for pd in pd_gen
                     if full_access or pd.status == 'public']
 
         return self.render_string(
             "study_description_templates/processed_data_tab.html",
             available_processed_data=avail_pd,
-            study_id=study.id)
+            study_id=study.id,
+            allow_approval=allow_approval,
+            approval_deny_msg=approval_deny_msg)
 
 
 class ProcessedDataInfoTab(BaseUIModule):
-    def render(self, study_id, processed_data):
+    def render(self, study_id, processed_data, allow_approval,
+               approval_deny_msg):
         user = self.current_user
         # The request approval, approve processed data and make public buttons
         # are mutually exclusive. Only one of them will be shown, depending on
@@ -65,4 +68,6 @@ def render(self, study_id, processed_data):
             filepaths=filepaths,
             is_local_request=is_local_request,
             btn_to_show=btn_to_show,
-            show_revert_btn=show_revert_btn)
+            show_revert_btn=show_revert_btn,
+            allow_approval=allow_approval,
+            approval_deny_msg=approval_deny_msg)

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):