Merge pull request #10 from UMCUGenetics/develop

v1.1.4
UMCUGenetics · Jan 6, 2020 · 5e2bbd8 · 5e2bbd8
2 parents 6969d19 + e2d7bdb
commit 5e2bbd8
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Showing 4 changed files with 32 additions and 23 deletions.
diff --git a/clarity_epp/qc/qubit.py b/clarity_epp/qc/qubit.py
@@ -1,12 +1,15 @@
 """Qubit QC epp functions."""
 
+import re
+
 from genologics.entities import Process
 
 
 def set_qc_flag(lims, process_id, cutoff=10):
     """Set qubit qc flags based on Dx Concentratie fluorescentie (ng/ul) values."""
     process = Process(lims, id=process_id)
     artifacts = process.result_files()
+    concentration_range = map(float, re.findall('[\d\.]+', process.udf['Concentratiebereik (ng/ul)']))
     samples_measurements = {}
 
     for artifact in artifacts:
@@ -24,14 +27,17 @@ def set_qc_flag(lims, process_id, cutoff=10):
         sample_measurements_average = sum(sample_measurements) / float(len(sample_measurements))
         artifact.udf['Dx Concentratie fluorescentie (ng/ul)'] = sample_measurements_average
 
-        if len(sample_measurements) == 1:
-            artifact.qc_flag = 'PASSED'
-        elif len(sample_measurements) == 2:
-            sample_measurements_difference = abs(sample_measurements[0] - sample_measurements[1])
-            sample_measurements_deviation = sample_measurements_difference / sample_measurements_average
-
-            if sample_measurements_deviation <= 0.1:
+        if concentration_range[0] <= sample_measurements_average <= concentration_range[1]:
+            if len(sample_measurements) == 1:
                 artifact.qc_flag = 'PASSED'
-            else:
-                artifact.qc_flag = 'FAILED'
+            elif len(sample_measurements) == 2:
+                sample_measurements_difference = abs(sample_measurements[0] - sample_measurements[1])
+                sample_measurements_deviation = sample_measurements_difference / sample_measurements_average
+                if sample_measurements_deviation <= 0.1:
+                    artifact.qc_flag = 'PASSED'
+                else:
+                    artifact.qc_flag = 'FAILED'
+        else:
+            artifact.qc_flag = 'FAILED'
+
         artifact.put()
diff --git a/clarity_epp/upload/samples.py b/clarity_epp/upload/samples.py
@@ -101,7 +101,7 @@ def from_helix(lims, email_settings, input_file):
         sample_name = udf_data['Dx Monsternummer']
 
         # Set 'Dx Handmatig' udf
-        if udf_data['Dx Foetus'] or udf_data['Dx Overleden'] or udf_data['Dx Materiaal type'] != 'BL':
+        if udf_data['Dx Foetus'] or udf_data['Dx Overleden'] or udf_data['Dx Materiaal type'] not in ['BL', 'BLHEP', 'BM', 'BMEDTA']:
             udf_data['Dx Handmatig'] = True
         else:
             udf_data['Dx Handmatig'] = False

diff --git a/clarity_epp/upload/tecan.py b/clarity_epp/upload/tecan.py
@@ -1,11 +1,14 @@
 """Tecan results upload epp functions."""
 
+import re
+
 from genologics.entities import Process
 
 
 def results(lims, process_id):
     """Upload tecan results to artifacts."""
     process = Process(lims, id=process_id)
+    concentration_range = map(float, re.findall('[\d\.]+', process.udf['Concentratiebereik (ng/ul)']))
 
     # Parse output file
     for output in process.all_outputs(unique=True):
@@ -86,13 +89,17 @@ def results(lims, process_id):
                 artifact.udf['Dx Concentratie fluorescentie (ng/ul)'] = ng_values[std_number - 1]
             else:
                 # Calculate measurement deviation from average.
-                if len(sample_measurements[artifact.name]) == 1:
-                    artifact.qc_flag = 'PASSED'
-                elif len(sample_measurements[artifact.name]) == 2:
-                    artifact_fluorescence_difference = abs(sample_measurements[artifact.name][0] - sample_measurements[artifact.name][1])
-                    artifact_fluorescence_deviation = artifact_fluorescence_difference / sample_fluorescence
-                    if artifact_fluorescence_deviation <= 0.1:
+                if concentration_range[0] <= sample_concentration <= concentration_range[1]:
+                    if len(sample_measurements[artifact.name]) == 1:
                         artifact.qc_flag = 'PASSED'
-                    else:
-                        artifact.qc_flag = 'FAILED'
+                    elif len(sample_measurements[artifact.name]) == 2:
+                        artifact_fluorescence_difference = abs(sample_measurements[artifact.name][0] - sample_measurements[artifact.name][1])
+                        artifact_fluorescence_deviation = artifact_fluorescence_difference / sample_fluorescence
+                        if artifact_fluorescence_deviation <= 0.1:
+                            artifact.qc_flag = 'PASSED'
+                        else:
+                            artifact.qc_flag = 'FAILED'
+                else:
+                    artifact.qc_flag = 'FAILED'
+
             artifact.put()
diff --git a/clarity_epp/upload/utils.py b/clarity_epp/upload/utils.py
@@ -35,11 +35,7 @@ def transform_sex(value):
 def transform_sample_name(value):
     """Transform legacy name to new sample name."""
     if '/' in value:
-        match = re.search("D(\d\d)/(.+)", value)
-        sample_name = '{year}D{sample_id}'.format(
-            year=datetime.strptime(match.group(1), '%y').year,
-            sample_id=match.group(2).zfill(5)
-        )
+        sample_name = ''.join(value.split('/'))
         return sample_name
     else:
         return value