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cmdcolinclaude
cmdcolin
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claude
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Enhance python-apollo diagnostic to capture actual errors
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Lines changed: 58 additions & 29 deletions

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‎.github/workflows/python-apollo.yml‎

Lines changed: 58 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -74,62 +74,91 @@ jobs:
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cd python-apollo
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export ARROW_GLOBAL_CONFIG_PATH=$(pwd)/test-data/local-apollo2-arrow.yml
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python3 -c "
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import traceback, json, sys
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import traceback, json, sys, logging
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logging.basicConfig(level=logging.DEBUG)
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try:
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from apollo import ApolloInstance
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from apollo import util
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from BCBio import GFF
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wa = ApolloInstance('http://localhost:8080/apollo', 'admin@local.host', 'password')
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print('=== Organisms ===')
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orgs = wa.organisms.get_organisms()
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for o in orgs:
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print(f\" {o.get('commonName')}: sequences={o.get('sequences')}\")
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print()
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print('=== Attempting load_gff3 with full traceback ===')
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print('Installed apollo version:', end=' ')
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import apollo; print(getattr(apollo, '__version__', 'unknown'))
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print('BCBio.GFF available:', end=' ')
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try:
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from BCBio import GFF
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print('yes')
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except ImportError as e:
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print(f'NO - {e}')
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print()
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print('=== Manual GFF3 parsing test ===')
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from BCBio import GFF
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with open('test-data/mrna-top.gff') as f:
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for rec in GFF.parse(f):
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print(f'Record: {rec.id}, features: {len(rec.features)}')
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for feat in rec.features[:2]:
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for feat in rec.features:
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print(f' Feature: {feat.id}, type: {feat.type}, loc: {feat.location}')
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print(f' Sub-features: {[(sf.type, sf.location) for sf in feat.sub_features]}')
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print()
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print('=== Manual addTranscript via python-apollo ===')
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print('=== Replicate load_gff3 step by step ===')
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wa.annotations.set_sequence('test_organism', 'Merlin')
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result = wa.annotations.add_transcripts([{
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'location': {'fmin': 5000, 'fmax': 6000, 'strand': 1},
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'type': {'name': 'mRNA', 'cv': {'name': 'sequence'}},
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'children': [{
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'location': {'fmin': 5000, 'fmax': 6000, 'strand': 1},
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'type': {'name': 'exon', 'cv': {'name': 'sequence'}}
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}]
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}])
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print(f'addTranscript result: {json.dumps(result, indent=2)[:500]}')
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# Parse GFF3 and build Apollo JSON like load_gff3 does
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with open('test-data/mrna-top.gff') as f:
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for rec in GFF.parse(f):
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print(f'Processing record: {rec.id}')
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for feature in rec.features:
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print(f' Feature type: {feature.type}')
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try:
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apollo_data = util.yieldApolloData(feature)
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print(f' Apollo data: {json.dumps(apollo_data, indent=2, default=str)[:1000]}')
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except Exception as e:
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print(f' yieldApolloData FAILED: {e}')
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traceback.print_exc()
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continue
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# Try sending as transcript
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try:
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print(f' Calling add_transcripts...')
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result = wa.annotations.add_transcripts([apollo_data])
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print(f' add_transcripts result: {json.dumps(result, indent=2, default=str)[:500]}')
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except Exception as e:
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print(f' add_transcripts FAILED: {type(e).__name__}: {e}')
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traceback.print_exc()
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print()
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print('=== Test addFeature endpoint ===')
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with open('test-data/mrna-top.gff') as f:
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for rec in GFF.parse(f):
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for feature in rec.features:
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apollo_data = util.yieldApolloData(feature)
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try:
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print(f' Calling add_feature...')
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result = wa.annotations.add_feature(apollo_data)
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print(f' add_feature result: {json.dumps(result, indent=2, default=str)[:500]}')
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except Exception as e:
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print(f' add_feature FAILED: {type(e).__name__}: {e}')
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traceback.print_exc()
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print()
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print('=== Full load_gff3 attempt with traceback ===')
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print('=== Remote API test ===')
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try:
123-
feature_data = wa.annotations.load_gff3('test_organism', 'test-data/mrna-top.gff')
124-
print(f'load_gff3 returned: {feature_data}')
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import tempfile, tarfile, glob
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with tempfile.NamedTemporaryFile(suffix='.tar.gz') as archive:
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with tarfile.open(archive.name, mode='w:gz') as tar:
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for file in glob.glob('test-data/dataset_1_files/data/*'):
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tar.add(file, arcname=file.replace('test-data/dataset_1_files/data/', './'))
148+
print(f' Archive contents:')
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with tarfile.open(archive.name, mode='r:gz') as tar:
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for m in tar.getmembers()[:10]:
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print(f' {m.name}')
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result = wa.remote.add_organism('diag_remote_org', archive)
153+
print(f' add_organism result: {json.dumps(result, indent=2, default=str)[:500]}')
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except Exception as e:
126-
print(f'load_gff3 raised: {type(e).__name__}: {e}')
155+
print(f' remote add_organism FAILED: {type(e).__name__}: {e}')
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traceback.print_exc()
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129158
except Exception as e:
130159
print(f'DIAGNOSTIC FAILED: {type(e).__name__}: {e}')
131160
traceback.print_exc()
132-
" || true
161+
" 2>&1 || true
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echo ""
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echo "=== Apollo ERROR/WARN log lines ==="

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