Merge pull request #12 from vladsavelyev/fixes-v1-22-3

Minor fixes
NationalGenomicsInfrastructure · Jul 15, 2024 · 7956ec0 · 7956ec0
2 parents 03bc773 + 0f761fd
commit 7956ec0
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Showing 4 changed files with 22 additions and 14 deletions.
diff --git a/.gitignore b/.gitignore
@@ -57,3 +57,5 @@ docs/_build/
 
 # PyBuilder
 target/
+
+.idea
diff --git a/multiqc_ngi/multiqc_ngi.py b/multiqc_ngi/multiqc_ngi.py
@@ -83,11 +83,9 @@ def __init__(self):
                 return None
 
             # Run WGS Piper specific cleanup
-            for f in report.prep_ordered_search_files_list('piper_ngi')[1]:
-                if 'piper_ngi' in f[1].split(os.sep):
-                    log.info("Looks like WGS data - cleaning up report")
-                    self.ngi_wgs_cleanup()
-                    break
+            if 'piper_ngi' in report.files:
+                log.info("Looks like WGS data - cleaning up report")
+                self.ngi_wgs_cleanup()
 
             # Are we using the dummy test data?
             self.couch = None
@@ -539,20 +537,20 @@ def push_statusdb_multiqc_data(self):
 
     def connect_statusdb(self):
         """ Connect to statusdb """
+        conf_file = os.path.join(os.environ.get('HOME'), '.ngi_config', 'statusdb.yaml')
         try:
-            conf_file = os.path.join(os.environ.get('HOME'), '.ngi_config', 'statusdb.yaml')
             with open(conf_file, "r") as f:
                 sdb_config = yaml.safe_load(f)
                 log.debug("Got MultiQC_NGI statusdb config from the home directory.")
         except IOError:
-            log.debug("Could not open the MultiQC_NGI statusdb config file {conf_file}")
+            log.debug(f"Could not open the MultiQC_NGI statusdb config file {conf_file}")
             try:
                 with open(os.environ['STATUS_DB_CONFIG'], "r") as f:
                     sdb_config = yaml.safe_load(f)
                     log.debug(f"Got MultiQC_NGI statusdb config from $STATUS_DB_CONFIG: {os.environ['STATUS_DB_CONFIG']}")
             except (KeyError, IOError):
                 log.debug("Could not get the MultiQC_NGI statusdb config file from env STATUS_DB_CONFIG")
-                log.warn("Could not find a statusdb config file")
+                log.warning("Could not find a statusdb config file")
                 return None
         try:
             couch_user = sdb_config['statusdb']['username']
@@ -568,7 +566,7 @@ def connect_statusdb(self):
         try:
             requests.get(server_url, timeout=3)
         except (requests.exceptions.Timeout, requests.exceptions.ConnectionError):
-            log.warn("Cannot contact statusdb - skipping NGI metadata stuff")
+            log.warning("Cannot contact statusdb - skipping NGI metadata stuff")
             return None
 
         return Server(server_url)

diff --git a/multiqc_ngi/templates/genstat/header.html b/multiqc_ngi/templates/genstat/header.html
@@ -10,6 +10,14 @@
 
 <h1 id="page_title">{{ config.title }} : MultiQC Report</h1>
 
-<p>Report generated on {{ config.creation_date }} based on data in
-    <code id="mqc_analysis_path">{{ config.analysis_dir |join('</code>
-    and <code id="mqc_analysis_path">') }}</code></p>
+<p>Report generated on {{ config.creation_date }} based on data in:
+{% if report.analysis_files | length == 1 %}
+  <code class="mqc_analysis_path">{{ report.analysis_files[0] }}</code>
+{% else %}
+  <ul>
+    {% for d in report.analysis_files %}
+    <li><code class="mqc_analysis_path">{{ d }}</code></li>
+    {%  endfor %}
+  </ul>
+{% endif %}
+</p>
diff --git a/multiqc_ngi/templates/ngi/header.html b/multiqc_ngi/templates/ngi/header.html
@@ -65,10 +65,10 @@ <h4>JavaScript Disabled</h4>
 
 <div id="analysis_dirs_wrapper">
   <p>Report generated on {{ config.creation_date }} based on data in:
-  {% if config.analysis_dir | length == 1 %}<code class="mqc_analysis_path">{{ config.analysis_dir[0] }}</code>
+  {% if report.analysis_files | length == 1 %}<code class="mqc_analysis_path">{{ report.analysis_files[0] }}</code>
   {% else %}
   <ul>
-    {% for d in config.analysis_dir %}
+    {% for d in report.analysis_files %}
     <li><code class="mqc_analysis_path">{{ d }}</code></li>
     {%  endfor %}
   </ul>