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Bug Patterns Reference import https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/devtu-self-evolve/references/bug-patterns.md e2520a96 2026-06-26 prompt accepted upstream false

Bug Patterns Reference

Detailed code-level fix patterns discovered through role-play debug rounds.

Table of Contents

Rounds 52–57 (core patterns)

Rounds 68–78 (API-specific patterns)

Regex Overmatch: Mutation vs Fusion

Tools: civic_search_evidence_items, civic_search_variants Bug IDs: BUG-56A-001

A regex that normalizes GENE1-GENE2 fusion notation can accidentally match GENE-MutationCode (e.g., EGFR-T790M, BRAF-V600E, KRAS-G12C) because mutation codes start with an uppercase letter.

Fix: Use a lambda that checks if the second part matches HGVS protein-change format before applying the substitution:

def _maybe_fuse(m):
    second = m.group(2)
    # Protein-change: single letter + digits + letter/asterisk (e.g. T790M, V600E, G12C)
    if re.match(r"^[A-Z]\d+[A-Z*]?$", second):
        return m.group(0)  # leave unchanged
    return m.group(1) + "::" + second

normalized = re.sub(r"\b([A-Z][A-Z0-9]*)-([A-Z][A-Z0-9]+)\b", _maybe_fuse, mol_profile)

When the input matches the mutation pattern and returns 0 results, add a hint:

elif re.search(r"\b[A-Z][A-Z0-9]*-[A-Z]\d+[A-Z*]?\b", mol_profile):
    space_form = mol_profile.replace("-", " ", 1)
    mp_warn += f" If '{mol_profile}' is a point mutation, try molecular_profile='{space_form}'..."

Silent Parameter Alias

Tools: SYNERGxDB_search_combos Bug IDs: BUG-55A-011

Users pass cancer_type but tool only accepts sample, tissue_name, tissue. Parameter silently dropped → all-tissue results returned with status: "success".

Fix:

sample = (
    arguments.get("sample")
    or arguments.get("tissue_name")
    or arguments.get("tissue")
    or arguments.get("cancer_type")  # ADD aliases here
)

Always-Fires Conditional

Tools: GtoPdb_get_interactions Bug IDs: BUG-55A-002, BUG-55A-003, BUG-55B-001

item.get("approved") on interaction records returns None always (field only exists on /ligands objects). So has_approved was always False → conditional note always fired. Also used wrong category language ("kinase/enzyme") for GPCR targets.

Fix: Remove the conditional check; always emit the note as factual guidance. Use neutral language; embed the queried gene symbol:

if isinstance(data, list) and len(data) > 0:
    _chembl_target = gene_symbol or result.get("queried_target", {}).get("name", "the target")
    result["coverage_note"] = (
        "GtoPdb interactions list pharmacological research compounds — approved "
        "drugs for this target may not be represented. For approved drugs and "
        "clinical compounds, use ChEMBL_get_drug_mechanisms or "
        f"ChEMBL_search_molecules with target_name='{_chembl_target}'."
    )

Silent Normalization

Tools: civic_search_evidence_items, civic_search_variants Bug IDs: BUG-55A-008, BUG-55B-005

CIViC normalizes therapy (lowercase → Title Case) and molecular_profile (BCR-ABL1 → BCR::ABL1) without disclosing the transformation. Users debugging empty results can't see what was tried.

Fix: Track pre-normalization values, add a normalization_note field to the result:

_therapy_normalized_from = None
_mp_normalized_from = None

# When normalizing therapy:
_therapy_normalized_from = therapy
arguments["therapy"] = therapy.title()

# After result is built:
_norm_parts = []
if _therapy_normalized_from:
    _norm_parts.append(f"therapy '{_therapy_normalized_from}' → '{arguments.get('therapy')}' (CIViC uses Title Case)")
if _mp_normalized_from:
    _norm_parts.append(f"molecular_profile '{_mp_normalized_from}' → '{arguments.get('molecular_profile')}' ...")
if _norm_parts:
    result["normalization_note"] = "Input auto-normalized: " + "; ".join(_norm_parts) + "."

Notation / Case Sensitivity

Tools: civic_search_evidence_items Bug IDs: BUG-55B-005 (fusion), BUG-53B-002 (therapy case)

CIViC uses :: for gene fusions (BCR::ABL1 Fusion, EML4::ALK Fusion). Users write hyphenated forms (BCR-ABL1) → 0 results. CIViC therapy names are Title Case ("Sotorasib" not "sotorasib").

Fix (fusion normalization):

import re as _re
mol_profile = arguments.get("molecular_profile")
if mol_profile and isinstance(mol_profile, str):
    normalized_mp = _re.sub(
        r"\b([A-Z][A-Z0-9]*)-([A-Z][A-Z0-9]+)\b",
        r"\1::\2",
        mol_profile,
    )
    if normalized_mp != mol_profile:
        _mp_normalized_from = mol_profile
        arguments = dict(arguments)
        arguments["molecular_profile"] = normalized_mp

Fix (therapy case):

if therapy == therapy.lower() or therapy == therapy.upper():
    _therapy_normalized_from = therapy
    arguments["therapy"] = therapy.title()

Truncation Not Top-Level

Tools: CancerPrognosis_get_gene_expression Bug IDs: BUG-55A-006

Truncation info (e.g., 500 of 1100 samples returned) buried inside data.note string. Researchers reading top-level fields miss it.

Fix: Add top-level flags:

response = {"status": "success", "data": result_data}
if len(values) > max_samples:
    response["truncated"] = True
    response["truncation_note"] = (
        f"Returning {len(values[:max_samples])} of {len(values)} samples. "
        f"Pass max_samples={len(values)} (up to 2000) to retrieve the full dataset."
    )
return response

Gene Symbol Substring Match

Tools: GtoPdb_get_interactions Bug IDs: BUG-54B-001

?name=AR returns all targets containing "AR" (13+ targets). ?geneSymbol=AR is the unambiguous HGNC lookup.

Fix: Try ?geneSymbol= first; fall back to ?name= if nothing returned:

gs_url = f"{base_url}/targets?{urlencode({'geneSymbol': gene_symbol})}"
gs_resp = request_with_retry(...)
if gs_resp.status_code == 200:
    gs_targets = gs_resp.json()
    if gs_targets:
        target_id = gs_targets[0]["targetId"]

# Fall back to ?name= only if geneSymbol returned nothing
if target_id is None:
    lookup_url = f"{base_url}/targets?{urlencode({'name': gene_symbol})}"
    ...

try/except Indentation

Every try: MUST have an except at the exact same indentation level. A common error is placing code after try: at the same level as the try: keyword — Python sees the try block as having no except.

# CORRECT
try:              # 16 spaces
    resp = ...    # 20 spaces (inside try)
    if resp.ok:   # 20 spaces (still inside try)
        ...
except Exception: # 16 spaces — matches try
    pass

# WRONG — SyntaxError
try:              # 16 spaces
    resp = ...    # 20 spaces
if resp.ok:       # 16 spaces — OUTSIDE try, before except!
    ...
except Exception: # 16 spaces — Python: "try without except"
    pass

Multi-Word Search Hints

Tools: GtoPdb_search_targets, GtoPdb_search_ligands Bug IDs: BUG-54B-002

name="androgen receptor" returns empty — GtoPdb text search doesn't reliably match multi-word phrases.

Fix: When count=0 and query has a space, add a hint suggesting first word only:

if result["count"] == 0 and name_q and " " in str(name_q):
    first_word = str(name_q).split()[0]
    result["multi_word_hint"] = (
        f"GtoPdb text search may not match multi-word phrases like '{name_q}'. "
        f"Try a single keyword: name='{first_word}'."
    )

Expression Units Inference

Tools: CancerPrognosis_get_gene_expression Bug IDs: BUG-54A-002

_get_expression_units(profile_id) infers units from the profile ID string. Some studies use misleading suffixes (e.g., aml_ohsu_2022 uses _rna_seq_v2_mrna but stores log2 RPKM).

Fix: Return (profile_id, profile_name) from _get_mrna_profile() and prefer the actual API description over inference:

def _get_expression_units(self, profile_id, profile_name=None):
    if profile_name:
        return profile_name  # Prefer actual API name
    # ... fallback inference from profile_id

Auto-Selected vs Explicit Study

Tools: CancerPrognosis_get_gene_expression Bug IDs: BUG-54A-004

study_note always said "Auto-selected study_id=..." even when user explicitly passed a full study ID like brca_tcga.

Fix: Detect explicit specification and use a different message:

study_was_explicit = (
    cancer == study_id_arg
    and study_id_arg
    and "_" in str(study_id_arg)
    and str(study_id_arg).upper() not in TCGA_STUDY_MAP
    and str(study_id_arg).upper() not in _CANCER_NAME_ALIASES
)
"study_note": (
    f"Using explicitly specified study_id='{study_id}'."
    if study_was_explicit
    else f"Auto-selected study_id='{study_id}'. Use CancerPrognosis_search_studies "
         "to find alternative cohorts for this cancer type."
),

CIViC Therapy + AND Logic

Tools: civic_search_evidence_items, civic_search_variants Bug IDs: BUG-54A-001, BUG-54A-005

  1. When both query and variant_name are provided, one silently wins. Fix: apply AND logic.
  2. When molecular_profile + therapy returns 0, silently fails. Fix: auto-probe without therapy to surface available therapy names.

Fix (AND logic):

raw_query = arguments.get("query")
raw_variant_name = arguments.get("variant_name") or arguments.get("variant")
_both = raw_query and raw_variant_name and raw_query != raw_variant_name
if _both:
    query_term = raw_query
    _secondary_term = raw_variant_name
else:
    query_term = raw_query or raw_variant_name
    _secondary_term = None

# Later, apply AND filter:
if _secondary_term:
    filtered = [v for v in filtered if _secondary_term.lower() in v.get("name","").lower()]
    result["filter_note"] = f"Applied AND logic for query+variant_name."

Fix (therapy auto-probe):

if mol_profile and therapy and not disease and len(evidence_nodes) == 0:
    probe_args = {k: v for k, v in arguments.items() if k != "therapy"}
    probe_nodes = civic_query(probe_args)
    available_therapies = sorted({
        t.get("name") for node in probe_nodes
        for t in node.get("therapies", []) if t.get("name")
    })
    result["therapy_warning"] = (
        f"No evidence for '{mol_profile}' + therapy='{therapy}'. "
        f"Available therapies: {available_therapies[:10]}"
    )

DGIdb Client-Side Filtering (Feature-68A-001/002)

Tools: DGIdb_get_drug_gene_interactions Pattern: API ignores interaction_types and sources filters server-side → returns everything.

Fix: Fetch all, filter client-side:

if interaction_types:
    results = [r for r in results if r.get("interactionTypes") and
               any(it in interaction_types for it in r["interactionTypes"])]
if sources:
    results = [r for r in results if r.get("source") in sources]
# Always wrap with status
return {"status": "success", "count": len(results), "data": results}

CPIC PostgREST Filter Prefix (Feature-68A-004)

Tools: CPICSearchPairsTool Pattern: PostgREST requires equality filter as eq.VALUE, not bare VALUE.

Fix: Auto-prepend eq. if not already present:

def _postgrest_eq(value):
    v = str(value)
    return v if v.startswith("eq.") else f"eq.{v}"
params["genesymbol"] = _postgrest_eq(gene_symbol)

CPIC Recommendation Join (Feature-68A-006)

Tools: CPIC_get_recommendations Pattern: /recommendation endpoint doesn't include drug name — need to join /drug table.

Fix: Use ?select=*,drug(name) in the URL query string for PostgREST joins.

KEGG Organism-Specific Gene Search (Feature-68B-001)

Tools: kegg_find_genes Pattern: /find/genes/{keyword} ignores organism param → returns all organisms.

Fix: Use /find/{organism}/{keyword}:

url = f"https://rest.kegg.jp/find/{organism}/{keyword}" if organism else f"https://rest.kegg.jp/find/genes/{keyword}"

HPA Deprecated Column (Feature-68B-002)

Tools: HPA_get_protein_expression Pattern: ppi column was deprecated; API returns error listing alternatives (enhanced, supported, approved, uncertain).

Fix: Remove ppi from select list; return error message with alternatives when API responds with column-not-found error.

PDBePISA Operation from Config (Feature-68B-006)

Tools: PDBePISA tools Pattern: operation param exposed as public parameter → users pass wrong values.

Fix: Read operation from the tool's JSON fields config, never expose as public argument.

GTEx Dataset Selection (Feature-69A-001/002)

Tools: GTEx_get_median_gene_expression Pattern: gtex_v10 returns empty for medianGeneExpression endpoint; only gtex_v8 works reliably.

Fix: Always default to gtex_v8. Add note in result:

dataset = arguments.get("dataset", "gtex_v8")
if dataset == "gtex_v10":
    result["dataset_note"] = "gtex_v10 may return empty for this endpoint; gtex_v8 is recommended."

GxA Silent geneId Ignore (Feature-69A-003)

Tools: ExpressionAtlas_get_experiment Pattern: /experiments/{accession} API ignores geneId parameter silently.

Fix: Apply geneId filter client-side on the returned data.

ExpressionAtlas Schema Key Mismatch (Feature-69A-004)

Tools: ExpressionAtlas tools Pattern: return_schema key experiments but code returns baseline_experiments.

Fix: Make key in return_schema match exactly what the code produces. Use baseline_experiments.

Proteins API Human Priority (Feature-69A-007)

Tools: proteins_api_search Pattern: Gene/name searches return non-human results first.

Fix: Add taxid=9606 default for gene and name searches to prioritize human entries.

RCSB Null Type in Schema (Feature-69B-002/010)

Tools: RCSB tools Pattern: return_schema has type: null which is invalid JSON Schema.

Fix: Use ["array", "null"] or ["string", "null"] for nullable types. Also avoid using protein-only PDB IDs as test examples — use IDs that represent the tested operation.

ClinVar Search Field Tags (Feature-70B-004/005)

Tools: ClinVar tools Pattern: [variant_id] is not a valid eSearch field → use [uid]. [disease/phenotype] not valid → use bare condition text (no brackets).

Fix:

# Wrong:
query = f"{variant_id}[variant_id]"
query = f"{condition}[disease/phenotype]"

# Right:
query = f"{variant_id}[uid]"
query = condition  # bare text, NCBI searches all fields

ENCODE Tissue+Organism Filter (Feature-70A-003)

Tools: ENCODE_search_experiments Pattern: Combining tissue + organism filter → HTTP 404.

Fix: Fall back without organism filter when 404 occurs:

try:
    resp = requests.get(url_with_organism)
    if resp.status_code == 404:
        resp = requests.get(url_without_organism)
except Exception:
    ...

GEO Double-Adding Search Terms (Feature-70A-008)

Tools: geo_search_datasets Pattern: Code adds "methylation" to query even when it's already present.

Fix: Check before appending:

if "methylation" not in query.lower():
    query += " methylation"

CPIC Warfarin Algorithm Guideline (Feature-70B-001)

Tools: CPIC_get_recommendations Pattern: Warfarin guideline (ID 100425) uses algorithm endpoint, not /recommendation. Returns 0 rows from recommendation endpoint.

Fix: Detect warfarin (or any guideline that uses algorithm-based dosing) and redirect to /algorithm endpoint or explain in the response.

PharmGKB clinpgxid vs pharmgkbid (Feature-70B-002/011)

Tools: PharmGKB tools Pattern: CPIC list_guidelines returns clinpgxid, but code uses pharmgkbid → 404 from PharmGKB.

Fix: Use clinpgxid from CPIC response when building PharmGKB URLs.

ENCODE ChIP-seq Assay Title (Feature-73B)

Tools: ENCODE_search_experiments Pattern: Querying assay_title=ChIP-seq returns 0; correct value is TF ChIP-seq. Also: organism filter uses wrong nested field name.

Fix: Map user-friendly aliases to ENCODE-specific values:

ASSAY_ALIASES = {"ChIP-seq": "TF ChIP-seq", "CHIP": "TF ChIP-seq"}
assay_title = ASSAY_ALIASES.get(assay_title, assay_title)

RegulomeDB Parameter Names (Feature-73B)

Tools: RegulomeDB tools Pattern: assembly=hg19 is wrong → use genome=GRCh38. Test example rs123456 doesn't exist → use rs4994.

Fix: Update parameter names and test examples to match actual API.

BindingDB API Typo (Feature-73A)

Tools: BindingDB tools Pattern: API endpoint has typo: getLindsByXxx (not getLigandsByXxx). Also response key is bdb.affinities not affinities.

Fix: Use exact typo as in the real API URL. Access response["bdb.affinities"].

ProteomeXchange Title and Instruments (Feature-73A)

Tools: ProteomeXchange tools Pattern: title field is plain string not dict. instruments use {name, accession} not nested terms.

Fix: Access dataset.get("title") directly. For instruments: inst.get("name") not inst["terms"][0]["name"].

MetabolomicsWorkbench moverz URL (Feature-73A/74A)

Tools: MetabolomicsWorkbench tools Pattern: moverz endpoint needs database prefix: /moverz/{database}/{mz}/{adduct}/{tolerance}. Also exactmass endpoint is broken → use moverz/REFMET/{mass}/M/{tolerance}.

Fix:

url = f"https://www.metabolomicsworkbench.org/rest/moverz/REFMET/{mz}/M+H/{tolerance}"

MetaboLights Pagination Ignored (Feature-74A)

Tools: MetaboLights tools Pattern: /ws/studies API silently ignores size and page params → always returns full list.

Fix: Apply pagination client-side after fetching all results:

all_studies = resp.json()
start = page * size
return all_studies[start:start + size]

ChEBI Search Nulls and HTML (Feature-74A)

Tools: ChEBI_search_compounds Pattern: smiles and inchikey always null from search API. Names contain HTML entities (&, <).

Fix: Strip HTML from names using re.sub(r"<[^>]+>", "", name) and html.unescape(name). Don't return null smiles/inchikey — omit them or fetch from detail endpoint.

HMDB No Open API (Feature-74A)

Tools: HMDB tools Pattern: HMDB has no open REST API; tools were returning stub success responses.

Fix: Return {"status": "error", "message": "HMDB does not provide a public REST API. Use MetabolomicsWorkbench or ChEBI instead."}.

PharmGKB relatedGenes Filter (Feature-74B)

Tools: PharmGKB tools Pattern: relatedGenes.id and relatedGenes.symbol filters not supported by API — silently returns all results.

Fix: Return informative message: "relatedGenes filter is not supported by PharmGKB API. Filter results client-side or use gene-specific endpoints instead."

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