Merge pull request #79 from UMCUGenetics/release/v1.9.0

v1.9.0

.github/workflows/python.yml

@@ -5,40 +5,39 @@ name: Python (flake8, pytest)
 
 on:
   push:
-    branches: [main, develop]
+    branches: [master, develop]
   pull_request:
-    branches: [main, develop]
+    branches: [master, develop]
 
 jobs:
   build:
-
     runs-on: ubuntu-20.04
     strategy:
       fail-fast: false
       matrix:
         python-version: [3.6]
 
     steps:
-    - uses: actions/checkout@v3
-      with:
-        fetch-depth: 0
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: "Install Apache package"
-      run: sudo apt install -y apache2-dev
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        pytest
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: "Install Apache package"
+        run: sudo apt install -y apache2-dev
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install flake8 pytest
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest
+        run: |
+          pytest

clarity_epp.py

@@ -48,8 +48,8 @@ def export_hamilton(args):
 
 def export_illumina(args):
     """Export (updated) illumina samplesheet."""
-    clarity_epp.export.illumina.update_samplesheet(
-        lims, args.process_id, args.artifact_id, args.output_file, args.conversion_tool
+    clarity_epp.export.illumina.create_samplesheet(
+        lims, args.process_id, args.output_file
     )
 
 
@@ -287,13 +287,9 @@ def placement_pipetting(args):
     parser_export_hamilton.set_defaults(func=export_hamilton)
 
     parser_export_illumina = subparser_export.add_parser(
-        'illumina', help='Export updated illumina samplesheet', parents=[output_parser]
+        'illumina', help='Export illumina samplesheet', parents=[output_parser]
     )
     parser_export_illumina.add_argument('process_id', help='Clarity lims process id')
-    parser_export_illumina.add_argument('artifact_id', help='Clarity lims samplesheet artifact id')
-    parser_export_illumina.add_argument(
-        '-c', '--conversion_tool', choices=['bcl2fastq', 'bclconvert'], default='bcl2fastq', help='Illumina conversion tool'
-    )
     parser_export_illumina.set_defaults(func=export_illumina)
 
     parser_export_labels = subparser_export.add_parser('labels', help='Export container labels', parents=[output_parser])

clarity_epp/__init__.py

@@ -38,8 +38,8 @@ def get_sample_artifacts_from_pool(lims, pool_artifact):
                 # Check if sample_artifact with 2 samples are from the same person
                 if len(sample_artifact.samples) == 2:
                     if (
-                        'Dx Persoons ID' in sample_artifact.samples[0].udf or
-                        'Dx Persoons ID' in sample_artifact.samples[1].udf or
+                        'Dx Persoons ID' in sample_artifact.samples[0].udf and
+                        'Dx Persoons ID' in sample_artifact.samples[1].udf and
                         sample_artifact.samples[0].udf['Dx Persoons ID'] == sample_artifact.samples[1].udf['Dx Persoons ID']
                     ):
                         sample_artifacts.append(sample_artifact)

clarity_epp/export/bioanalyzer.py

@@ -16,7 +16,7 @@ def samplesheet(lims, process_id, output_file):
     }
 
     # Get sample placement
-    for placement, artifact in process.output_containers()[0].placements.iteritems():
+    for placement, artifact in process.output_containers()[0].placements.items():
         placement = ''.join(placement.split(':'))
         plate[placement]['name'] = artifact.name
         plate[placement]['comment'] = ''

clarity_epp/export/hamilton.py

@@ -11,7 +11,7 @@ def samplesheet_filling_out(lims, process_id, output_file):
     process = Process(lims, id=process_id)
     well_plate = {}
 
-    for placement, artifact in process.output_containers()[0].placements.iteritems():
+    for placement, artifact in process.output_containers()[0].placements.items():
         placement = ''.join(placement.split(':'))
         well_plate[placement] = artifact.samples[0].udf['Dx Fractienummer']
 
@@ -29,7 +29,7 @@ def samplesheet_purify(lims, process_id, output_file):
     parent_process_barcode = process.parent_processes()[0].output_containers()[0].name
     well_plate = {}
 
-    for placement, artifact in process.output_containers()[0].placements.iteritems():
+    for placement, artifact in process.output_containers()[0].placements.items():
         placement = ''.join(placement.split(':'))
         well_plate[placement] = artifact.samples[0].udf['Dx Fractienummer']