Merge pull request #489 from oicr-gsi/GCGI-1413_move-failed-report-pl…

…ugin-to-summary

Gcgi 1413 move failed report plugin to summary

CHANGELOG.md

@@ -5,6 +5,7 @@
 - GCGI-1481: Fix raw coverage auto-population to exclude normal samples before selection in TAR assay
 - GCGI-1478: More informative logger name for plugin/helper/merger components
 - GCGI-1479: New `--pre-populate` option in `djerba.py` setup mode
+- GCGI-1413: Remove failed report plugin and allow summary plugin to handle failed reports
 - GCGI-1482: Updated total genome segment length constant in percent genome altered calculation
 - GCGI-1480: Updated CGI manager name and email
 - GCGI-1490: Remove input paths from pwgs.analysis results

src/lib/djerba/core/main.py

@@ -576,17 +576,22 @@ def update(self, config_path, json_path, out_dir, archive, pdf, summary_only, fo
         # 1. INI config with core + plugins to update
         # 2. Text file to update summary only
         # The 'summary_only' argument controls which one is used
+        with open(json_path, encoding=cc.TEXT_ENCODING) as in_file:
+            data = json.loads(in_file.read())
         if summary_only:
+            # get failed/not-failed status from input data
+            failed = data[cc.PLUGINS]['summary'][cc.RESULTS]['failed']
+            failed_opt = 'true' if failed else 'false'
+            self.logger.debug('Found report failure status: '+failed_opt)
             # make an appropriate ConfigParser on-the-fly
             config_in = ConfigParser()
             config_in.add_section(cc.CORE)
             config_in.add_section('summary')
             config_in.set('summary', 'summary_file', config_path)
+            config_in.set('summary', 'failed', failed_opt)
             config = self.configure_from_parser(config_in)
         else:
             config = self.configure(config_path)
-        with open(json_path, encoding=cc.TEXT_ENCODING) as in_file:
-            data = json.loads(in_file.read())
         data_new = self.base_extract(config)
         data = self.update_data_from_file(data_new, json_path, force)
         if archive:

src/lib/djerba/plugins/summary/plugin.py

@@ -16,27 +16,34 @@ class main(plugin_base):
     PRIORITY = 400
     PLUGIN_VERSION = '0.1'
     MAKO_TEMPLATE_NAME = 'summary_report_template.html'
-    SUMMARY_TEMPLATE_FILE = 'summary_template.txt'
+    SUMMARY_TEMPLATE_FILE = 'templates/summary_template.txt'
+    FAILED_TEMPLATE_FILE = 'templates/failed_template.txt'
     SUMMARY_FILE = 'summary_file'
     SUMMARY_TEXT = 'summary_text'
+    FAILED = 'failed'
 
     def configure(self, config):
         config = self.apply_defaults(config)
         wrapper = self.get_config_wrapper(config)
+        failed = wrapper.get_my_boolean(self.FAILED)
         if wrapper.my_param_is_null(self.SUMMARY_FILE):
-            summary_template_path = \
-                os.path.join(os.path.dirname(__file__), self.SUMMARY_TEMPLATE_FILE)
-            wrapper.set_my_param(self.SUMMARY_FILE, summary_template_path)
+            if not failed:
+                template_path = os.path.join(os.path.dirname(__file__), self.SUMMARY_TEMPLATE_FILE)
+            elif failed:
+                template_path = os.path.join(os.path.dirname(__file__), self.FAILED_TEMPLATE_FILE)
+            wrapper.set_my_param(self.SUMMARY_FILE, template_path)
         return wrapper.get_config()
 
     def extract(self, config):
         wrapper = self.get_config_wrapper(config)
         summary_path = wrapper.get_my_string(self.SUMMARY_FILE)
+        failed = wrapper.get_my_boolean(self.FAILED)
         with open(summary_path, encoding=core_constants.TEXT_ENCODING) as in_file:
             summary_text = in_file.read()
         self.logger.debug('Read summary from {0}: "{1}"'.format(summary_path, summary_text))
         data = self.get_starting_plugin_data(wrapper, self.PLUGIN_VERSION)
         data[core_constants.RESULTS][self.SUMMARY_TEXT] = summary_text
+        data[core_constants.RESULTS][self.FAILED] = failed
         filename = 'results_summary.txt'
         self.workspace.write_string(filename, summary_text)
         self.logger.debug('Wrote summary to {0}'.format(self.workspace.abs_path(filename)))
@@ -49,6 +56,7 @@ def specify_params(self):
         for key in discovered:
             self.add_ini_discovered(key)
         self.set_ini_default(core_constants.ATTRIBUTES, 'clinical')
+        self.set_ini_default(self.FAILED, False)
         self.set_priority_defaults(self.PRIORITY)
 
     def render(self, data):

src/lib/djerba/plugins/summary/summary_report_template.html

@@ -3,11 +3,17 @@
   from djerba.util.html import html_builder
   from djerba.plugins.summary.plugin import main as summary
   SUMMARY_TEXT = results.get(summary.SUMMARY_TEXT)
+  FAILED = results.get(summary.FAILED)
 %>
 
   <!-- results summary -->
   ${html_builder().section_cells_begin("<h2>Results Summary</h2>","main")}
-
-    ${html_builder().markdown_to_html(SUMMARY_TEXT)}
-
+
+  % if not FAILED:
+      ${html_builder().markdown_to_html(SUMMARY_TEXT)}
+  % elif FAILED:
+      <p style="border-width:3px; border-style:solid; border-color:#FF0000; padding: 1em;" ${html_builder().markdown_to_html(SUMMARY_TEXT)}</p>
+  % endif
+
   ${html_builder().section_cells_end()}
+

src/lib/djerba/plugins/summary/templates/failed_template.txt

@@ -0,0 +1 @@
+The patient has been diagnosed with ... and has been referred for the OICR Genomics ... assay through the ... study. A quality failure report for this sample is being issued due to the informatically inferred tumour purity of ...% which is below the reportable threshold of 30% for the assay \ is being issued due to failed extraction \ is being issued as the quantity of extracted DNA/RNA from tissue material was below the lower quantifiable range and therefore below the minimum input amount for this assay (minimums of 25ng for DNA and 50ng for RNA)...

src/lib/djerba/plugins/summary/test/failed.ini

@@ -0,0 +1,4 @@
+[core]
+
+[summary]
+failed = True

src/lib/djerba/plugins/summary/test/plugin_test.py

@@ -25,10 +25,21 @@ def testSummary(self):
         params = {
             self.INI: 'summary.ini',
             self.JSON: json_location,
-            self.MD5: '155e22cc02a45e04dc9058112354367c'
+            self.MD5: '1599ec66c80c2607e71a1dea9d53aacf'
         }
         self.run_basic_test(test_source_dir, params)
 
+    def testFailedSummary(self):
+        test_source_dir = os.path.realpath(os.path.dirname(__file__))
+        json_location = os.path.join(self.data_dir_root, "plugins", "summary", "report_json", "failed.json")
+        params = {
+            self.INI: 'failed.ini',
+            self.JSON: json_location,
+            self.MD5: 'abf18dc395150bf990a0b24b1cf9b422'
+        }
+        self.run_basic_test(test_source_dir, params)
+
+
     def testSummaryWithCustomText(self):
         test_source_dir = os.path.realpath(os.path.dirname(__file__))
         summary_path = os.path.join(test_source_dir, 'custom_summary.txt')
@@ -43,7 +54,7 @@ def testSummaryWithCustomText(self):
         params = {
             self.INI: ini_path,
             self.JSON: json_location,
-            self.MD5: 'cebbb53b9b074131e309dca71704a896'
+            self.MD5: 'b58589404184cd4b8d1a88f276f096b7'
         }
         self.run_basic_test(test_source_dir, params)
 

src/test/core/simple_report_for_update.json

@@ -43,6 +43,7 @@
             ],
             "merge_inputs": {},
             "results": {
+		"failed": false,
                 "summary_text": "Summary text goes here"
             }
         }