Patch index parsing (#538)(patch)

### Fixed - Patch the way indexes are parsed in order to comply with the new naming format.
Clinical-Genomics · Oct 1, 2024 · 547e9eb · 547e9eb
1 parent 61875d9
commit 547e9eb
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Showing 20 changed files with 25 additions and 24 deletions.
diff --git a/cg_lims/get/fields.py b/cg_lims/get/fields.py
@@ -67,19 +67,20 @@ def get_artifact_well(artifact: Artifact) -> str:
 
 def get_index_well(artifact: Artifact):
     """Parsing out the index well position from the reagent label string which
-    typically looks like this: 'A05 IDT_10nt_446 (AGCGTGACCT-CCATCCGAGT)'
+    typically looks like this: '44_A05 IDT_10nt_446 (AGCGTGACCT-CCATCCGAGT)'
     """
 
     if artifact.reagent_labels:
         # Assuming one reagent label per artifact (reagent_labels is a list):
-        reagent_label = artifact.reagent_labels[0]
+        reagent_label: str = artifact.reagent_labels[0]
 
         # Getting the index well:
-        index_well_with_zero = reagent_label.split(" ")[0]
+        index_well_with_zero_and_us: str = reagent_label.split(" ")[0]
+        index_well_with_zero: str = index_well_with_zero_and_us.split("_")[1]
 
         # Picking out column and removing zeros by int():
-        index_well_col = int(index_well_with_zero[1:])
-        index_well_row = index_well_with_zero[0]
+        index_well_col: int = int(index_well_with_zero[1:])
+        index_well_row: str = index_well_with_zero[0]
         return f"{index_well_row}{index_well_col}"
     else:
         return "-"

diff --git a/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454624.xml b/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454624.xml
@@ -11,6 +11,6 @@
     </location>
     <working-flag>true</working-flag>
     <sample uri="http://127.0.0.1:8000/api/v2/samples/ACC7892A1" limsid="ACC7892A1" />
-    <reagent-label name="A01 UDP0001 (GAACTGAGCG-TCGTGGAGCG)" />
+    <reagent-label name="01_A01 UDP0001 (GAACTGAGCG-TCGTGGAGCG)" />
     <workflow-stages />
 </art:artifact>
diff --git a/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454625.xml b/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454625.xml
@@ -11,6 +11,6 @@
     </location>
     <working-flag>true</working-flag>
     <sample uri="http://127.0.0.1:8000/api/v2/samples/ACC7892A5" limsid="ACC7892A5" />
-    <reagent-label name="A02 UDP0009 (GACTGAGTAG-GTTGATAGTG)" />
+    <reagent-label name="09_A02 UDP0009 (GACTGAGTAG-GTTGATAGTG)" />
     <workflow-stages />
 </art:artifact>
diff --git a/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454626.xml b/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454626.xml
@@ -11,6 +11,6 @@
     </location>
     <working-flag>true</working-flag>
     <sample uri="http://127.0.0.1:8000/api/v2/samples/ACC7892A9" limsid="ACC7892A9" />
-    <reagent-label name="A03 UDP0017 (GAGAATGGTT-TCGGCAGCAA)" />
+    <reagent-label name="17_A03 UDP0017 (GAGAATGGTT-TCGGCAGCAA)" />
     <workflow-stages />
 </art:artifact>
diff --git a/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454627.xml b/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454627.xml
@@ -11,6 +11,6 @@
     </location>
     <working-flag>true</working-flag>
     <sample uri="http://127.0.0.1:8000/api/v2/samples/ACC7892A13" limsid="ACC7892A13" />
-    <reagent-label name="A04 UDP0025 (AACCATAGAA-GGCGAGATGG)" />
+    <reagent-label name="25_A04 UDP0025 (AACCATAGAA-GGCGAGATGG)" />
     <workflow-stages />
 </art:artifact>
diff --git a/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454628.xml b/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454628.xml
@@ -11,6 +11,6 @@
     </location>
     <working-flag>true</working-flag>
     <sample uri="http://127.0.0.1:8000/api/v2/samples/ACC7892A16" limsid="ACC7892A16" />
-    <reagent-label name="A05 UDP0033 (TGATTATACG-GTCGATTACA)" />
+    <reagent-label name="33_A05 UDP0033 (TGATTATACG-GTCGATTACA)" />
     <workflow-stages />
 </art:artifact>
diff --git a/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454629.xml b/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454629.xml
@@ -11,6 +11,6 @@
     </location>
     <working-flag>true</working-flag>
     <sample uri="http://127.0.0.1:8000/api/v2/samples/ACC7892A57" limsid="ACC7892A57" />
-    <reagent-label name="A06 UDP0041 (ACTCGGCAAT-GACAACTGAA)" />
+    <reagent-label name="41_A06 UDP0041 (ACTCGGCAAT-GACAACTGAA)" />
     <workflow-stages />
 </art:artifact>
diff --git a/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454630.xml b/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454630.xml
@@ -11,6 +11,6 @@
     </location>
     <working-flag>true</working-flag>
     <sample uri="http://127.0.0.1:8000/api/v2/samples/ACC7892A64" limsid="ACC7892A64" />
-    <reagent-label name="A07 UDP0049 (AGTGTTGCAC-CTGGTACACG)" />
+    <reagent-label name="49_A07 UDP0049 (AGTGTTGCAC-CTGGTACACG)" />
     <workflow-stages />
 </art:artifact>
diff --git a/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454631.xml b/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454631.xml
@@ -11,6 +11,6 @@
     </location>
     <working-flag>true</working-flag>
     <sample uri="http://127.0.0.1:8000/api/v2/samples/ACC7892A65" limsid="ACC7892A65" />
-    <reagent-label name="A08 UDP0057 (TCTATCCTAA-CGTCGACTGG)" />
+    <reagent-label name="57_A08 UDP0057 (TCTATCCTAA-CGTCGACTGG)" />
     <workflow-stages />
 </art:artifact>
diff --git a/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454632.xml b/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454632.xml
@@ -11,6 +11,6 @@
     </location>
     <working-flag>true</working-flag>
     <sample uri="http://127.0.0.1:8000/api/v2/samples/ACC7892A70" limsid="ACC7892A70" />
-    <reagent-label name="A09 UDP0065 (TAATGTGTCT-GTAAGGCATA)" />
+    <reagent-label name="65_A09 UDP0065 (TAATGTGTCT-GTAAGGCATA)" />
     <workflow-stages />
 </art:artifact>
diff --git a/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454633.xml b/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454633.xml
@@ -11,6 +11,6 @@
     </location>
     <working-flag>true</working-flag>
     <sample uri="http://127.0.0.1:8000/api/v2/samples/ACC7892A73" limsid="ACC7892A73" />
-    <reagent-label name="A10 UDP0073 (CCTGCGGAAC-ATCATAGGCT)" />
+    <reagent-label name="73_A10 UDP0073 (CCTGCGGAAC-ATCATAGGCT)" />
     <workflow-stages />
 </art:artifact>
diff --git a/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454634.xml b/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454634.xml
@@ -11,6 +11,6 @@
     </location>
     <working-flag>true</working-flag>
     <sample uri="http://127.0.0.1:8000/api/v2/samples/ACC7892A78" limsid="ACC7892A78" />
-    <reagent-label name="A11 UDP0081 (TGTCGCTGGT-TCGTCTGACT)" />
+    <reagent-label name="81_A11 UDP0081 (TGTCGCTGGT-TCGTCTGACT)" />
     <workflow-stages />
 </art:artifact>
diff --git a/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454635.xml b/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454635.xml
@@ -11,6 +11,6 @@
     </location>
     <working-flag>true</working-flag>
     <sample uri="http://127.0.0.1:8000/api/v2/samples/ACC7892A81" limsid="ACC7892A81" />
-    <reagent-label name="A12 UDP0089 (GTCCGTAAGC-CGTGTATCTT)" />
+    <reagent-label name="89_A12 UDP0089 (GTCCGTAAGC-CGTGTATCTT)" />
     <workflow-stages />
 </art:artifact>
diff --git a/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454636.xml b/tests/fixtures/hamilton_sars_cov2_indexing_step/artifacts/2-1454636.xml
@@ -11,6 +11,6 @@
     </location>
     <working-flag>true</working-flag>
     <sample uri="http://127.0.0.1:8000/api/v2/samples/ACC7892A92" limsid="ACC7892A92" />
-    <reagent-label name="B01 UDP0002 (AGGTCAGATA-CTACAAGATA)" />
+    <reagent-label name="02_B01 UDP0002 (AGGTCAGATA-CTACAAGATA)" />
     <workflow-stages />
 </art:artifact>
diff --git a/tests/fixtures/make_kapa_csv_missing_udfs/artifacts/2-1155129.xml b/tests/fixtures/make_kapa_csv_missing_udfs/artifacts/2-1155129.xml
@@ -10,7 +10,7 @@
 </location>
 <working-flag>true</working-flag>
 <sample uri="http://127.0.0.1:8000/api/v2/samples/ACC7271A5" limsid="ACC7271A5"/>
-<reagent-label name="A02 IDT_10nt_652 (ACAACCAACT-ACCATCTTGT)"/>
+<reagent-label name="09_A02 IDT_10nt_652 (ACAACCAACT-ACCATCTTGT)"/>
 <udf:field type="Numeric" name="Amount (ng)">375</udf:field>
 <udf:field type="Numeric" name="Volume of sample (ul)">15</udf:field>
 <udf:field type="Numeric" name="Concentration (nM)">103.464487677</udf:field>

diff --git a/tests/fixtures/make_kapa_csv_missing_udfs/artifacts/2-1155129_other_sample.xml b/tests/fixtures/make_kapa_csv_missing_udfs/artifacts/2-1155129_other_sample.xml
@@ -10,7 +10,7 @@
 </location>
 <working-flag>true</working-flag>
 <sample uri="http://127.0.0.1:8000/api/v2/samples/dummy_sample1" limsid="dummy_sample1"/>
-<reagent-label name="A02 IDT_10nt_652 (ACAACCAACT-ACCATCTTGT)"/>
+<reagent-label name="09_A02 IDT_10nt_652 (ACAACCAACT-ACCATCTTGT)"/>
 <udf:field type="Numeric" name="Amount (ng)">375</udf:field>
 <udf:field type="Numeric" name="Volume of sample (ul)">15</udf:field>
 <udf:field type="Numeric" name="Concentration (nM)">103.464487677</udf:field>

diff --git a/tests/fixtures/make_kapa_csv_missing_udfs/artifacts/2-1155130.xml b/tests/fixtures/make_kapa_csv_missing_udfs/artifacts/2-1155130.xml
@@ -10,7 +10,7 @@
 </location>
 <working-flag>true</working-flag>
 <sample uri="http://127.0.0.1:8000/api/v2/samples/ACC7272A2" limsid="ACC7272A2"/>
-<reagent-label name="A01 IDT_10nt_651 (ATGGTTGACT-GCTTGTGCCA)"/>
+<reagent-label name="01_A01 IDT_10nt_651 (ATGGTTGACT-GCTTGTGCCA)"/>
 <udf:field type="Numeric" name="Amount (ng)">1500</udf:field>
 <udf:field type="Numeric" name="Volume of sample (ul)">5</udf:field>
 <udf:field type="Numeric" name="Concentration (nM)">408.310256999</udf:field>

diff --git a/tests/fixtures/make_kapa_csv_missing_udfs/artifacts/2-1155130_other_sample.xml b/tests/fixtures/make_kapa_csv_missing_udfs/artifacts/2-1155130_other_sample.xml
@@ -10,7 +10,7 @@
 </location>
 <working-flag>true</working-flag>
 <sample uri="http://127.0.0.1:8000/api/v2/samples/dummy_sample2" limsid="dummy_sample2"/>
-<reagent-label name="A01 IDT_10nt_651 (ATGGTTGACT-GCTTGTGCCA)"/>
+<reagent-label name="01_A01 IDT_10nt_651 (ATGGTTGACT-GCTTGTGCCA)"/>
 <udf:field type="Numeric" name="Amount (ng)">1500</udf:field>
 <udf:field type="Numeric" name="Volume of sample (ul)">5</udf:field>
 <udf:field type="Numeric" name="Concentration (nM)">408.310256999</udf:field>

diff --git a/tests/fixtures/test_make_kapa_csv/artifacts/2-1155129.xml b/tests/fixtures/test_make_kapa_csv/artifacts/2-1155129.xml
@@ -10,7 +10,7 @@
 </location>
 <working-flag>true</working-flag>
 <sample uri="http://127.0.0.1:8000/api/v2/samples/ACC7271A5" limsid="ACC7271A5"/>
-<reagent-label name="A02 IDT_10nt_652 (ACAACCAACT-ACCATCTTGT)"/>
+<reagent-label name="09_A02 IDT_10nt_652 (ACAACCAACT-ACCATCTTGT)"/>
 <udf:field type="Numeric" name="Amount (ng)">375</udf:field>
 <udf:field type="Numeric" name="Volume of sample (ul)">15</udf:field>
 <udf:field type="Numeric" name="Concentration (nM)">103.464487677</udf:field>

diff --git a/tests/fixtures/test_make_kapa_csv/artifacts/2-1155130.xml b/tests/fixtures/test_make_kapa_csv/artifacts/2-1155130.xml
@@ -10,7 +10,7 @@
 </location>
 <working-flag>true</working-flag>
 <sample uri="http://127.0.0.1:8000/api/v2/samples/ACC7272A2" limsid="ACC7272A2"/>
-<reagent-label name="A01 IDT_10nt_651 (ATGGTTGACT-GCTTGTGCCA)"/>
+<reagent-label name="01_A01 IDT_10nt_651 (ATGGTTGACT-GCTTGTGCCA)"/>
 <udf:field type="Numeric" name="Amount (ng)">1500</udf:field>
 <udf:field type="Numeric" name="Volume of sample (ul)">5</udf:field>
 <udf:field type="Numeric" name="Concentration (nM)">408.310256999</udf:field>