Global dicts are only used as value lists, so convert them to lists t…

…o avoid discrepancy between keys (step IDs) on LIMS prod vs stage. Also remove unused list.
kedhammar · Jan 22, 2025 · 9bde49e · 9bde49e
1 parent d0addab
commit 9bde49e
Showing 1 changed file with 19 additions and 22 deletions.
diff --git a/scripts/readscount.py b/scripts/readscount.py
@@ -18,25 +18,22 @@
 
 TIMESTAMP: str = dt.now().strftime("%y%m%d_%H%M%S")
 
-# Master step IDs and names
-DEMULTIPLEX = {
-    "13": "Bcl Conversion & Demultiplexing (Illumina SBS) 4.0",
-    "3205": "ONT Finish Sequencing v3",  # TODO Update this to reflect prod
-    "3105": "Bcl Conversion & Demultiplexing (AVITI) v1.0",  # TODO Update this to reflect prod
-}
-SUMMARY = {
-    "356": "Project Summary 1.3",
-}
-SEQUENCING = {
-    "38": "Illumina Sequencing (Illumina SBS) 4.0",
-    "46": "MiSeq Run (MiSeq) 4.0",
-    "714": "Illumina Sequencing (HiSeq X) 1.0",
-    "1454": "AUTOMATED - NovaSeq Run (NovaSeq 6000 v2.0)",
-    "1908": "Illumina Sequencing (NextSeq) v1.0",
-    "2612": "NovaSeqXPlus Run v1.0",
-    "2955": "ONT Start Sequencing v3.0",  # TODO Update this to reflect prod
-    "3113": "AVITI Run v1.0",  # TODO Update this to reflect prod
-}
+# Step names to look for
+DEMULTIPLEX_STEPS = [
+    "Bcl Conversion & Demultiplexing (Illumina SBS) 4.0",
+    "ONT Finish Sequencing v3",
+    "Bcl Conversion & Demultiplexing (AVITI) v1.0",
+]
+SEQUENCING_STEPS = [
+    "Illumina Sequencing (Illumina SBS) 4.0",
+    "MiSeq Run (MiSeq) 4.0",
+    "Illumina Sequencing (HiSeq X) 1.0",
+    "AUTOMATED - NovaSeq Run (NovaSeq 6000 v2.0)",
+    "Illumina Sequencing (NextSeq) v1.0",
+    "NovaSeqXPlus Run v1.0",
+    "ONT Start Sequencing v3.0",
+    "AVITI Run v1.0",
+]
 
 
 @epp_decorator(script_path=__file__, timestamp=TIMESTAMP)
@@ -138,7 +135,7 @@ def sum_reads(sample, summary):
     # Look for artifacts matching the sample name and expected analyte name in the demultiplexing processeses
     demux_arts = lims.get_artifacts(
         sample_name=sample.name,
-        process_type=list(DEMULTIPLEX.values()),
+        process_type=DEMULTIPLEX_STEPS,
         name=f"{sample.name} (FASTQ reads)",
     )
     if not demux_arts:
@@ -200,13 +197,13 @@ def sum_reads(sample, summary):
         demux_art_parent = demux_art_parents[0]
 
         # Two cases to consider:
-        if demux_art_parent.parent_process.type.name in SEQUENCING.values():
+        if demux_art_parent.parent_process.type.name in SEQUENCING_STEPS:
             # Parent of demux artifact is a sequencing process output (ONT)
             seq_process = demux_art_parent.parent_process
         else:
             # Parent of demux artifact is a sequencing process input (Illumina, AVITI)
             seq_process = lims.get_processes(
-                type=list(SEQUENCING.values()),
+                type=SEQUENCING_STEPS,
                 inputartifactlimsid=demux_art_parent.id,
             )[0]