feat: progress parsing pattern

model/src/progress.test.ts

@@ -0,0 +1,68 @@
+import { test } from 'vitest';
+import { ProgressPattern } from './progress';
+
+// Applying correction & sorting alignments by UMI: 0%
+// Alignment: 0%
+// Alignment: 30.2%  ETA: 00:00:02
+// Alignment: 60.4%  ETA: 00:00:01
+//
+//
+// Applying correction & sorting alignments by UMI: 15.2%
+// Writing result: 0%
+//
+
+test.for([
+  {
+    input: 'Applying correction & sorting alignments by UMI: 0%',
+    expected: {
+      stage: 'Applying correction & sorting alignments by UMI',
+      progress: '0',
+      eta: undefined
+    }
+  },
+  {
+    input: 'Alignment: 0%',
+    expected: {
+      stage: 'Alignment',
+      progress: '0',
+      eta: undefined
+    }
+  },
+  {
+    input: 'Alignment: 60.4%  ETA: 00:00:01',
+    expected: {
+      stage: 'Alignment',
+      progress: '60.4',
+      eta: '00:00:01'
+    }
+  },
+  {
+    input: 'Alignment: 100%  ETA: 00:00:00',
+    expected: {
+      stage: 'Alignment',
+      progress: '100',
+      eta: '00:00:00'
+    }
+  },
+  {
+    input: 'Final sorting: 95.2%',
+    expected: {
+      stage: 'Final sorting',
+      progress: '95.2',
+      eta: undefined
+    }
+  },
+  {
+    input: 'Initialization: progress unknown',
+    expected: {
+      stage: 'Initialization',
+      progress: undefined,
+      eta: undefined
+    }
+  }
+])('parsing progress for: $input', ({ input, expected }, { expect }) => {
+  const match = input.match(ProgressPattern);
+  expect(match).toBeDefined();
+  const { stage, progress, eta } = match?.groups!;
+  expect({ stage, progress, eta }).toMatchObject(expected);
+});

model/src/progress.ts

@@ -0,0 +1,2 @@
+export const ProgressPattern =
+  /(?<stage>[^:]*)\:(?: *(?<progress>[0-9.]+)\%)?(?: *ETA\: *(?<eta>.+))?/;

test/assets/expected_results/mixcr.sh

@@ -5,4 +5,4 @@ set -e
 mixcr exportPreset --preset-name milab-human-dna-xcr-7genes-multiplex -f preset.json
 
 # --add-step assembleContigs 
-mixcr analyze milab-human-dna-xcr-7genes-multiplex -f ../small_data_R1.fastq.gz ../small_data_R2.fastq.gz result
+mixcr analyze milab-human-dna-xcr-7genes-multiplex -f ../small_data_R1.fastq.gz ../small_data_R2.fastq.gz result > log.txt