Fixing broken search field. (#255)

Extended manual for bug report workflow.

HISTORY.rst

@@ -12,6 +12,8 @@ End-User Summary
 - Fixing Kiosk mode of VarFish.
 - Fixing displaying of beacon information in results table.
 - Fixing broken flags & comments popup for structural variants.
+- Fixing broken search field.
+- Extended manual for bug report workflow.
 
 Full Change List
 ================
@@ -23,6 +25,8 @@ Full Change List
 - Mapping kiosk jobs to import queue.
 - Fixing displaying of beacon information in results table.
 - Fixing broken flags & comments popup for structural variants.
+- Fixing broken search field.
+- Extended manual for bug report workflow.
 
 -------
 v0.23.9

docs_manual/bug_reports.rst

@@ -0,0 +1,155 @@
+.. _bug_reports:
+
+================================
+Bug Reports and Feature Requests
+================================
+
+We do organize bug reports and feature request in the
+`Github issue tracker <https://github.com/bihealth/varfish-server/issues/new/choose>`_.
+Please choose the template that fits best what you want to report and fill out
+the questions to help us decide on how to approach the task.
+
+-----------
+Bug Reports
+-----------
+
+The template for bug reports has the following form (an up-to-date form is located in the Github issue tracker)::
+
+    **Describe the bug**
+    A clear and concise description of what the bug is.
+
+    **To Reproduce**
+    Steps to reproduce the behavior:
+    1. Go to '...'
+    2. Click on '....'
+    3. Scroll down to '....'
+    4. See error
+
+    **Expected behavior**
+    A clear and concise description of what you expected to happen.
+
+    **Screenshots**
+    If applicable, add screenshots to help explain your problem.
+
+    **Desktop (please complete the following information):**
+     - OS: [e.g. iOS]
+     - Browser [e.g. chrome, safari]
+     - Version [e.g. 22]
+
+    **Smartphone (please complete the following information):**
+     - Device: [e.g. iPhone6]
+     - OS: [e.g. iOS8.1]
+     - Browser [e.g. stock browser, safari]
+     - Version [e.g. 22]
+
+    **Additional context**
+    Add any other context about the problem here.
+
+^^^^^^^^^^^^^^^^^^^
+Root Cause Analysis
+^^^^^^^^^^^^^^^^^^^
+
+In the following, a root cause analysis (RCA) needs to be done. The ticket will get an answer with the title
+**Root Cause Analysis** and a thorough description of what might cause the bug.
+
+^^^^^^^^^^^^^^^^^^^
+Resolution Proposal
+^^^^^^^^^^^^^^^^^^^
+
+When the root cause is determined, a solution needs to be proposed, following this form::
+
+    **Resolution Proposal**
+
+    e.g. The component X needs to be changed to Y so Z is not executed when M occurs.
+
+    **Affected Components**
+
+    e.g. VarFish server
+
+    **Affected Modules/Files**
+
+    e.g. variants module or queries.py
+
+    **Required Architectural Changes**
+
+    e.g. Function F needs to be moved to X.
+
+    **Resolution Sketch**
+
+    e.g. Change X in F. Then do Y.
+
+
+^^^^^^^^^^^^^^^^^^
+Fix & Pull Request
+^^^^^^^^^^^^^^^^^^
+
+1. Create new branch (name starts with issue number), e.g. ``123-fix-for-issue``
+2. Create pull request in "Draft" state
+3. Fix problem, ideally in a test-driven way, remove "Draft" state
+
+^^^^^^^^^^^^^^
+Review & Merge
+^^^^^^^^^^^^^^
+
+1. Perform code review
+2. Ensure fix is documented in changelog (link to bug and PR #ids)
+
+----------------
+Feature Requests
+----------------
+
+A feature request follows the same workflow as a bug request (an up-to-date form is located in the Github issue tracker)::
+
+    **Is your feature request related to a problem? Please describe.**
+    A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+    **Describe the solution you'd like**
+    A clear and concise description of what you want to happen.
+
+    **Describe alternatives you've considered**
+    A clear and concise description of any alternative solutions or features you've considered.
+
+    **Additional context**
+    Add any other context or screenshots about the feature request here.
+
+
+^^^^^^
+Design
+^^^^^^
+
+In the following, the design of the feature needs to be specified::
+
+    **Implementation Proposal**
+
+    e.g. The component X needs to be changed to Y so Z is not executed when M occurs.
+
+    **Affected Components**
+
+    e.g. VarFish server
+
+    **Affected Modules/Files**
+
+    e.g. variants module or queries.py
+
+    **Required Architectural Changes**
+
+    e.g. Function F needs to be moved to X.
+
+    **Implementation Sketch**
+
+    e.g. Change X in F. Then do Y.
+
+^^^^^^^^^^^^^^^^
+Implement & Test
+^^^^^^^^^^^^^^^^
+
+1. Create feature branch, named starting with issue ID
+2. Perform implementation, ideally in a test-driven way
+3. Tests and documentation must be augmented/updated as well
+
+^^^^^^^^^^^^^^
+Review & Merge
+^^^^^^^^^^^^^^
+
+1. Perform code review
+2. Ensure change is documented in changelog (link to feature issue and PR #ids)

docs_manual/index.rst

@@ -143,6 +143,7 @@ Currently, the main focus is on small/sequence variants called from high-througp
     :titlesonly:
 
     contributors
+    bug_reports
     history
     glossary
     dev_docker

variants/templates/variants/_search_item.html

@@ -8,7 +8,7 @@
   {# Name & link column #}
   <td>
     <div class="sodar-overflow-container">
-      {% highlight_search_term item.name search_term as item_display_name %}
+      {% highlight_search_term item.name search_terms as item_display_name %}
       <a href="{{ item.get_absolute_url }}">
         {% autoescape off %}{{ item_display_name }}{% endautoescape %}
       </a>
@@ -29,7 +29,7 @@
   <td class="sodar-overflow-container">
     {% autoescape off %}
       {% for entry in item.pedigree %}
-        {% highlight_search_term entry.patient|only_source_name search_term %}{% if not forloop.last %}, {% endif %}
+        {% highlight_search_term entry.patient|only_source_name search_terms %}{% if not forloop.last %}, {% endif %}
       {% endfor %}
     {% endautoescape %}
   </td>

variants/tests/test_ui.py

@@ -472,9 +472,12 @@ def test_variant_filter_case_display_loading(self):
         self.compile_url_and_login(
             {"project": self.case.project.sodar_uuid, "case": self.case.sodar_uuid}
         )
-        # find & hit button
+        # Wait until button is a submit button.
+        WebDriverWait(self.selenium, self.wait_time).until(
+            wait_for_the_attribute_value((By.ID, "submitFilter"), "data-event-type", "submit")
+        )
+        # Click button.
         button = self.selenium.find_element_by_id("submitFilter")
-        self.assertEqual(button.get_attribute("data-event-type"), "submit")
         button.click()
         WebDriverWait(self.selenium, self.wait_time).until(
             ec.presence_of_element_located((By.ID, "logger"))
@@ -490,10 +493,12 @@ def test_variant_filter_case_display_cancel(self):
         self.compile_url_and_login(
             {"project": self.case.project.sodar_uuid, "case": self.case.sodar_uuid}
         )
-        # find & hit button
-        time.sleep(5)
+        # Wait until button is a submit button.
+        WebDriverWait(self.selenium, self.wait_time).until(
+            wait_for_the_attribute_value((By.ID, "submitFilter"), "data-event-type", "submit")
+        )
+        # Find & hit button.
         button = self.selenium.find_element_by_id("submitFilter")
-        self.assertEqual(button.get_attribute("data-event-type"), "submit")
         button.click()
         WebDriverWait(self.selenium, self.wait_time).until(
             ec.presence_of_element_located((By.ID, "logger"))
@@ -751,9 +756,12 @@ def test_variant_joint_filter_display_loading(self):
         """Test if submitting the filter initiates the loading response."""
         # login
         self.compile_url_and_login({"project": self.project.sodar_uuid})
+        # Wait until button is a submit button.
+        WebDriverWait(self.selenium, self.wait_time).until(
+            wait_for_the_attribute_value((By.ID, "submitFilter"), "data-event-type", "submit")
+        )
         # find & hit button
         button = self.selenium.find_element_by_id("submitFilter")
-        self.assertEqual(button.get_attribute("data-event-type"), "submit")
         button.click()
         WebDriverWait(self.selenium, self.wait_time).until(
             ec.presence_of_element_located((By.ID, "logger"))
@@ -767,9 +775,12 @@ def test_variant_joint_filter_display_cancel(self):
         """Test if submitting the filter can be canceled."""
         # login
         self.compile_url_and_login({"project": self.project.sodar_uuid})
+        # Wait until button is a submit button.
+        WebDriverWait(self.selenium, self.wait_time).until(
+            wait_for_the_attribute_value((By.ID, "submitFilter"), "data-event-type", "submit")
+        )
         # find & hit button
         button = self.selenium.find_element_by_id("submitFilter")
-        self.assertEqual(button.get_attribute("data-event-type"), "submit")
         button.click()
         WebDriverWait(self.selenium, self.wait_time).until(
             ec.presence_of_element_located((By.ID, "logger"))