drug-discovery-prompts/upstream/mims-harvard-ToolUniverse/skills/devtu-code-optimization/references/api-fixes.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
API-Specific Fix Reference		import	https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/devtu-code-optimization/references/api-fixes.md	e2520a96	2026-06-26	prompt	accepted	upstream	false

API-Specific Fix Reference

Patterns discovered through rounds 52–78 of role-play debugging.

Quick Lookup Table

Tool/API	Issue	Fix
GtoPdb	?name=AR returns 13+ targets	Use ?geneSymbol=AR first, fall back to ?name=
GtoPdb	Multi-word names return 0	Add multi_word_hint suggesting first word only
CIViC	Fusion notation BCR-ABL1 → 0 results	Normalize - → :: (but not for mutations like T790M)
CIViC	Therapy lowercase → 0 results	Auto .title() and disclose in normalization_note
CIViC	query + variant_name — one silently wins	Apply AND logic client-side
CancerPrognosis	expression_units wrong	Prefer profile_name from API over inference from profile_id
CancerPrognosis	study_note wrong when explicit	Detect explicit specification, use different message
SYNERGxDB	cancer_type param silently ignored	Add alias handling for cancer_type, tissue_name, tissue
GTEx	gtex_v10 returns empty	Default to gtex_v8; note limitation when v10 requested
ENCODE	ChIP-seq → 0 results	Map to TF ChIP-seq
ClinVar	[variant_id] field → error	Use [uid]
KEGG find_genes	organism param ignored	Use /find/{organism}/{keyword} not /find/genes/{keyword}
MetabolomicsWorkbench	exactmass broken	Use moverz/REFMET/{mass}/M/{tolerance}
BindingDB	getLigands typo	Use getLinds (actual API typo in URL)
PharmGKB	pharmgkbid → 404	Use clinpgxid from CPIC response
CPIC	Warfarin 0 recommendations	Route to /algorithm endpoint
CPIC	Bare value in PostgREST	Prepend eq. prefix
HPA	ppi column → error	Remove; use enhanced/supported/approved
HMDB	No public API	Return status: error explaining alternatives
RegulomeDB	assembly=hg19 wrong	Use genome=GRCh38
DGIdb	interaction_types/sources ignored	Filter client-side
GxA	geneId param ignored	Filter client-side
MetaboLights	size/page ignored	Paginate client-side
RCSB	type: null in schema	Use ["array", "null"]
ProteomeXchange	title accessed as dict	Access as plain string

Detailed Patterns

GtoPdb Gene Symbol Disambiguation (Feature-54B-001)

# Try precise geneSymbol first
gs_resp = request_with_retry(f"{base_url}/targets?geneSymbol={gene_symbol}")
if gs_resp.status_code == 200 and gs_resp.json():
    target_id = gs_resp.json()[0]["targetId"]
else:
    # Fall back to name (may return multiple)
    name_resp = request_with_retry(f"{base_url}/targets?name={gene_symbol}")
    ...

CIViC Fusion vs Mutation Regex (Feature-56A-001)

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

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

def _postgrest_eq(value):
    v = str(value)
    return v if v.startswith("eq.") else f"eq.{v}"

params["genesymbol"] = _postgrest_eq(gene_symbol)

ENCODE Assay Title Alias (Feature-73B)

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

GTEx Dataset Safety (Feature-69A-001)

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

Broken API Response

# Wrong: return stub success data
# Right:
return {
    "status": "error",
    "message": "HMDB has no public REST API. Use MetabolomicsWorkbench or ChEBI instead."
}