Merge branch 'release/v1.3.2'

admin.py

@@ -35,10 +35,14 @@ class RunErrorsAdmin (admin.ModelAdmin):
 class RunStatesAdmin (admin.ModelAdmin):
     list_display = ('runStateName',)
 
+class SamplesInProjectAdmin (admin.ModelAdmin):
+    list_display = ('project_id','sampleName','barcodeName','pfClusters','percentInProject','yieldMb','qualityQ30')
+
 
 admin.site.register(RunningParameters , RunningParametersAdmin)
 admin.site.register(RunProcess , RunProcessAdmin)
 admin.site.register(LibraryKit,LibraryKitAdmin)
 admin.site.register(Projects, ProjectsAdmin)
 admin.site.register(RunErrors, RunErrorsAdmin)
 admin.site.register(RunStates, RunStatesAdmin)
+admin.site.register(SamplesInProject, SamplesInProjectAdmin)

cron.py

@@ -2,7 +2,7 @@
 from django.conf import settings
 #from django.contrib.auth.models import User
 
-from .wetlab_config import *
+from iSkyLIMS_wetlab import wetlab_config
 from .utils.update_run_state import search_update_new_runs, search_not_completed_run
 
 from .utils.generic_functions import  open_log
@@ -47,10 +47,11 @@ def looking_for_new_runs ():
     '''
     working_path = settings.MEDIA_ROOT
     os.chdir(working_path)
-    logger=open_log()
+    config_file = os.path.join(settings.BASE_DIR,'iSkyLIMS_wetlab',  wetlab_config.LOGGING_CONFIG_FILE )
+    logger=open_log(config_file)
     logger.info('###########---Start Crontab-----############')
     logger.info('Start searching for new/updating runs')
-    
+
     new_runs_updated, run_with_error = search_update_new_runs ()
     logger.info('------- Printing summary for search_update_new_runs -----')
     if len (new_runs_updated) > 0:
@@ -125,7 +126,7 @@ def delete_invalid_run ():
         print ('deleted run' , run_found)
     all_runs = RunProcess.objects.all()
     sample_sheet_valid_files = []
-    
+
     for run in all_runs:
         sample_sheet_valid_files.append(os.path.basename(run.get_sample_file()))
     sample_sheet_folder = os.path.join(settings.MEDIA_ROOT, os.path.dirname(run.get_sample_file()))

static/iSkyLIMS_wetlab/css/styles/a11y-dark.css

@@ -0,0 +1,99 @@
+/* a11y-dark theme */
+/* Based on the Tomorrow Night Eighties theme: https://github.com/isagalaev/highlight.js/blob/master/src/styles/tomorrow-night-eighties.css */
+/* @author: ericwbailey */
+
+/* Comment */
+.hljs-comment,
+.hljs-quote {
+  color: #d4d0ab;
+}
+
+/* Red */
+.hljs-variable,
+.hljs-template-variable,
+.hljs-tag,
+.hljs-name,
+.hljs-selector-id,
+.hljs-selector-class,
+.hljs-regexp,
+.hljs-deletion {
+  color: #ffa07a;
+}
+
+/* Orange */
+.hljs-number,
+.hljs-built_in,
+.hljs-builtin-name,
+.hljs-literal,
+.hljs-type,
+.hljs-params,
+.hljs-meta,
+.hljs-link {
+  color: #f5ab35;
+}
+
+/* Yellow */
+.hljs-attribute {
+  color: #ffd700;
+}
+
+/* Green */
+.hljs-string,
+.hljs-symbol,
+.hljs-bullet,
+.hljs-addition {
+  color: #abe338;
+}
+
+/* Blue */
+.hljs-title,
+.hljs-section {
+  color: #00e0e0;
+}
+
+/* Purple */
+.hljs-keyword,
+.hljs-selector-tag {
+  color: #dcc6e0;
+}
+
+.hljs {
+  display: block;
+  overflow-x: auto;
+  background: #2b2b2b;
+  color: #f8f8f2;
+  padding: 0.5em;
+}
+
+.hljs-emphasis {
+  font-style: italic;
+}
+
+.hljs-strong {
+  font-weight: bold;
+}
+
+@media screen and (-ms-high-contrast: active) {
+  .hljs-addition,
+  .hljs-attribute,
+  .hljs-built_in,
+  .hljs-builtin-name,
+  .hljs-bullet,
+  .hljs-comment,
+  .hljs-link,
+  .hljs-literal,
+  .hljs-meta,
+  .hljs-number,
+  .hljs-params,
+  .hljs-string,
+  .hljs-symbol,
+  .hljs-type,
+  .hljs-quote {
+        color: highlight;
+    }
+
+    .hljs-keyword,
+    .hljs-selector-tag {
+        font-weight: bold;
+    }
+}

static/iSkyLIMS_wetlab/css/styles/a11y-light.css

@@ -0,0 +1,99 @@
+/* a11y-light theme */
+/* Based on the Tomorrow Night Eighties theme: https://github.com/isagalaev/highlight.js/blob/master/src/styles/tomorrow-night-eighties.css */
+/* @author: ericwbailey */
+
+/* Comment */
+.hljs-comment,
+.hljs-quote {
+  color: #696969;
+}
+
+/* Red */
+.hljs-variable,
+.hljs-template-variable,
+.hljs-tag,
+.hljs-name,
+.hljs-selector-id,
+.hljs-selector-class,
+.hljs-regexp,
+.hljs-deletion {
+  color: #d91e18;
+}
+
+/* Orange */
+.hljs-number,
+.hljs-built_in,
+.hljs-builtin-name,
+.hljs-literal,
+.hljs-type,
+.hljs-params,
+.hljs-meta,
+.hljs-link {
+  color: #aa5d00;
+}
+
+/* Yellow */
+.hljs-attribute {
+  color: #aa5d00;
+}
+
+/* Green */
+.hljs-string,
+.hljs-symbol,
+.hljs-bullet,
+.hljs-addition {
+  color: #008000;
+}
+
+/* Blue */
+.hljs-title,
+.hljs-section {
+  color: #007faa;
+}
+
+/* Purple */
+.hljs-keyword,
+.hljs-selector-tag {
+  color: #7928a1;
+}
+
+.hljs {
+  display: block;
+  overflow-x: auto;
+  background: #fefefe;
+  color: #545454;
+  padding: 0.5em;
+}
+
+.hljs-emphasis {
+  font-style: italic;
+}
+
+.hljs-strong {
+  font-weight: bold;
+}
+
+@media screen and (-ms-high-contrast: active) {
+  .hljs-addition,
+  .hljs-attribute,
+  .hljs-built_in,
+  .hljs-builtin-name,
+  .hljs-bullet,
+  .hljs-comment,
+  .hljs-link,
+  .hljs-literal,
+  .hljs-meta,
+  .hljs-number,
+  .hljs-params,
+  .hljs-string,
+  .hljs-symbol,
+  .hljs-type,
+  .hljs-quote {
+        color: highlight;
+    }
+
+    .hljs-keyword,
+    .hljs-selector-tag {
+        font-weight: bold;
+    }
+}

static/iSkyLIMS_wetlab/css/styles/agate.css

@@ -0,0 +1,108 @@
+/*!
+ * Agate by Taufik Nurrohman <https://github.com/tovic>
+ * ----------------------------------------------------
+ *
+ * #ade5fc
+ * #a2fca2
+ * #c6b4f0
+ * #d36363
+ * #fcc28c
+ * #fc9b9b
+ * #ffa
+ * #fff
+ * #333
+ * #62c8f3
+ * #888
+ *
+ */
+
+.hljs {
+  display: block;
+  overflow-x: auto;
+  padding: 0.5em;
+  background: #333;
+  color: white;
+}
+
+.hljs-name,
+.hljs-strong {
+  font-weight: bold;
+}
+
+.hljs-code,
+.hljs-emphasis {
+  font-style: italic;
+}
+
+.hljs-tag {
+  color: #62c8f3;
+}
+
+.hljs-variable,
+.hljs-template-variable,
+.hljs-selector-id,
+.hljs-selector-class {
+  color: #ade5fc;
+}
+
+.hljs-string,
+.hljs-bullet {
+  color: #a2fca2;
+}
+
+.hljs-type,
+.hljs-title,
+.hljs-section,
+.hljs-attribute,
+.hljs-quote,
+.hljs-built_in,
+.hljs-builtin-name {
+  color: #ffa;
+}
+
+.hljs-number,
+.hljs-symbol,
+.hljs-bullet {
+  color: #d36363;
+}
+
+.hljs-keyword,
+.hljs-selector-tag,
+.hljs-literal {
+  color: #fcc28c;
+}
+
+.hljs-comment,
+.hljs-deletion,
+.hljs-code {
+  color: #888;
+}
+
+.hljs-regexp,
+.hljs-link {
+  color: #c6b4f0;
+}
+
+.hljs-meta {
+  color: #fc9b9b;
+}
+
+.hljs-deletion {
+  background-color: #fc9b9b;
+  color: #333;
+}
+
+.hljs-addition {
+  background-color: #a2fca2;
+  color: #333;
+}
+
+.hljs a {
+  color: inherit;
+}
+
+.hljs a:focus,
+.hljs a:hover {
+  color: inherit;
+  text-decoration: underline;
+}