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docs: generate hierarchical code review orchestrator reports
google-labs-jules[bot] Mar 30, 2026
baae4a8
chore: clean up local pytest artifacts
google-labs-jules[bot] Mar 30, 2026
9b8fcd0
Fix pre-existing CI errors (lint, root-hygiene, etc.)
google-labs-jules[bot] Mar 30, 2026
cd1c745
Fix CI errors in python files and docs
google-labs-jules[bot] Mar 30, 2026
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Fix missing directory and file errors in CI architecture tests
google-labs-jules[bot] Apr 2, 2026
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4 changes: 2 additions & 2 deletions .claude/agents/ORCHESTRATION.md
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Expand Up @@ -346,7 +346,7 @@ py-audit-bot (baseline, scope=seed + enricher pipelines)
| `.claude/agents/py-*.md` | Π‘ΠΏΠ΅Ρ†ΠΈΡ„ΠΈΠΊΠ°Ρ†ΠΈΠΈ субагСнтов для Claude Code CLI |
| `.claude/rules/ai-selfreview-rules.md` | ΠŸΡ€Π°Π²ΠΈΠ»Π° автоматичСской самопровСрки ΠΊΠΎΠ΄Π° |
| `docs/00-project/RULES.md` | АрхитСктурныС ΠΏΡ€Π°Π²ΠΈΠ»Π° ΠΏΡ€ΠΎΠ΅ΠΊΡ‚Π° |
| `docs/02-architecture/decisions/` | ADR-001..ADR-040 |
| `docs/02-architecture/decisions/` | ADR-001..ADR-050 |
| `docs/00-project/glossary.md` | ВСрминология |
| `tests/architecture/` | АвтоматичСскиС ΠΏΡ€ΠΎΠ²Π΅Ρ€ΠΊΠΈ ΠΈΠ½Π²Π°Ρ€ΠΈΠ°Π½Ρ‚ΠΎΠ² |
| `docs/00-project/ai/agents/scripts/py-config-bot-1.py` | АвтоматичСская ΠΏΡ€ΠΎΠ²Π΅Ρ€ΠΊΠ° ΠΊΠΎΠ½Ρ„ΠΈΠ³ΠΎΠ² |
Expand Down Expand Up @@ -395,7 +395,7 @@ py-audit-bot (baseline, scope=seed + enricher pipelines)
| **ChEMBL** | βœ… Schema validation | β€” | βœ… Golden data, contracts | βœ… Field reference | βœ… Error repro | β€” |
| **PubMed** | β€” | βœ… Coverage eval | βœ… Test data | β€” | β€” | βœ… Citations |
| **bioRxiv** | β€” | βœ… Trends, research | βœ… Preprint test data | β€” | β€” | βœ… Context |
| **Open Targets** | βœ… Target validation | βœ… Data availability | β€” | βœ… Join key validation | β€” | β€” |
| **OpenAlex** | βœ… Target validation | βœ… Data availability | β€” | βœ… Join key validation | β€” | β€” |
| **Mermaid Chart** | βœ… Arch diagrams | β€” | β€” | β€” | β€” | βœ… All diagrams |
| **BioRender** | β€” | β€” | β€” | β€” | β€” | βœ… Scientific figs |

Expand Down
8 changes: 4 additions & 4 deletions .claude/agents/py-audit-bot.md
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Expand Up @@ -36,13 +36,13 @@ model: opus
- НазначСниС: ETL-Ρ„Ρ€Π΅ΠΉΠΌΠ²ΠΎΡ€ΠΊ для Π΄Π°Π½Π½Ρ‹Ρ… биоактивности ΠΈΠ· Π½Π°ΡƒΡ‡Π½Ρ‹Ρ… Π±Π°Π· Π΄Π°Π½Π½Ρ‹Ρ…
- АрхитСктура: Hexagonal (Ports & Adapters) + Medallion (Bronzeβ†’Silverβ†’Gold) + DDD
- Deployment: Local-Only (ADR-010) β€” Π±Π΅Π· Docker/Redis
- Π’Π΅ΠΊΡƒΡ‰Π΅Π΅ состояниС: 40 ADR (ADR-001..ADR-040), всС Accepted
- Π’Π΅ΠΊΡƒΡ‰Π΅Π΅ состояниС: 50 ADR (ADR-001..ADR-050), всС Accepted

**ΠšΠ»ΡŽΡ‡Π΅Π²Ρ‹Π΅ Ρ„Π°ΠΉΠ»Ρ‹:**
- Domain Ports: `src/bioetl/domain/ports/`
- Adapters: `src/bioetl/infrastructure/adapters/{provider}/`
- Pipelines: `src/bioetl/application/pipelines/`
- Configs: `configs/pipelines/{provider}/{entity}.yaml`
- Configs: `configs/entities/{provider}/{entity}.yaml`
- ADR: `docs/02-architecture/decisions/`
- RULES.md: `docs/00-project/RULES.md`
- Self-review rules: `.claude/rules/ai-selfreview-rules.md`
Expand Down Expand Up @@ -333,11 +333,11 @@ code_review:
3. Π‘Ρ€Π°Π²Π½ΠΈΡ‚ΡŒ с domain entity ΠΈ Pandera schema
4. ΠŸΡ€ΠΈ расхоТдСнии β†’ finding `AUD-SCHEMA-*` с severity MUST

### Open Targets β€” валидация Ρ‚Π°Ρ€Π³Π΅Ρ‚ΠΎΠ²
### OpenAlex β€” валидация Ρ‚Π°Ρ€Π³Π΅Ρ‚ΠΎΠ²

| Π‘Ρ†Π΅Π½Π°Ρ€ΠΈΠΉ | Π˜Π½ΡΡ‚Ρ€ΡƒΠΌΠ΅Π½Ρ‚ | ΠŸΠ°Ρ€Π°ΠΌΠ΅Ρ‚Ρ€Ρ‹ | Π Π΅Π·ΡƒΠ»ΡŒΡ‚Π°Ρ‚ |
|----------|------------|-----------|-----------|
| ΠŸΡ€ΠΎΠ²Π΅Ρ€ΠΊΠ° target ID | `Open Targets:search_entities` | `query_strings=["EGFR"]` | Валидация ENSEMBL ID mapping |
| ΠŸΡ€ΠΎΠ²Π΅Ρ€ΠΊΠ° target ID | `OpenAlex:search_entities` | `query_strings=["EGFR"]` | Валидация ENSEMBL ID mapping |

### Mermaid Chart β€” Π°Ρ€Ρ…ΠΈΡ‚Π΅ΠΊΡ‚ΡƒΡ€Π½Ρ‹Π΅ Π΄ΠΈΠ°Π³Ρ€Π°ΠΌΠΌΡ‹

Expand Down
32 changes: 16 additions & 16 deletions .claude/agents/py-config-bot.md
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Expand Up @@ -118,7 +118,7 @@ configs/
### A. Pipeline config (standard)

```yaml
# configs/pipelines/{provider}/{entity}.yaml
# configs/entities/{provider}/{entity}.yaml
pipeline_name: {provider}_{entity}
provider: {provider}
entity_type: {entity}
Expand Down Expand Up @@ -153,7 +153,7 @@ sink:
### B. DQ rules (externalized)

```yaml
# configs/quality/entities/{provider}/{entity}.yaml
# configs/quality/{provider}/{entity}.yaml
entity: {entity}
provider: {provider}
version: "1.0.0"
Expand All @@ -176,7 +176,7 @@ rules:
### C. Filter rules (externalized)

```yaml
# configs/filters/entities/{provider}/{entity}.yaml
# configs/filters/{provider}/{entity}.yaml
entity: {entity}
provider: {provider}
version: "1.0.0"
Expand All @@ -190,7 +190,7 @@ gold_filters:
### D. Composite pipeline config

```yaml
# configs/pipelines/composite/{name}.yaml
# configs/entities/composite/{name}.yaml
composite:
name: composite_{entity}
version: "1.0.0"
Expand Down Expand Up @@ -220,27 +220,27 @@ composite:
```bash
python docs/00-project/ai/agents/scripts/py-config-bot-1.py -v
find configs/ -path "*/{provider}/*" -name "*.yaml" | sort
cat configs/pipelines/_defaults.yaml 2>/dev/null
cat configs/sources/{provider}.yaml 2>/dev/null
cat configs/entities/_defaults.yaml 2>/dev/null
cat configs/providers/{provider}.yaml 2>/dev/null
```

### ПослС создания/измСнСния

```bash
# YAML syntax
python -c "import yaml; yaml.safe_load(open('configs/pipelines/{provider}/{entity}.yaml'))"
python -c "import yaml; yaml.safe_load(open('configs/entities/{provider}/{entity}.yaml'))"

# Gap analysis β€” 0 critical
python docs/00-project/ai/agents/scripts/py-config-bot-1.py -v

# sort_by присутствуСт (ADR-014)
grep -A3 "sort_by" configs/pipelines/{provider}/{entity}.yaml
grep -A3 "sort_by" configs/entities/{provider}/{entity}.yaml

# НСт inline DQ-ΠΏΠΎΡ€ΠΎΠ³ΠΎΠ² (ADR-027)
grep -n "soft_fail_threshold\|hard_fail_threshold" configs/pipelines/{provider}/{entity}.yaml
grep -n "soft_fail_threshold\|hard_fail_threshold" configs/entities/{provider}/{entity}.yaml

# DQ externalized config сущСствуСт
test -f configs/quality/entities/{provider}/{entity}.yaml && echo "OK" || echo "MISSING"
test -f configs/quality/{provider}/{entity}.yaml && echo "OK" || echo "MISSING"
```

---
Expand Down Expand Up @@ -274,7 +274,7 @@ test -f configs/quality/entities/{provider}/{entity}.yaml && echo "OK" || echo "
#### ИзмСнСния
| Π€Π°ΠΉΠ» | ДСйствиС | ОписаниС |
|------|----------|----------|
| `configs/pipelines/chembl/activity.yaml` | created | Новый pipeline config |
| `configs/entities/chembl/activity.yaml` | created | Новый pipeline config |

#### ВСрификация
```bash
Expand Down Expand Up @@ -304,12 +304,12 @@ python docs/00-project/ai/agents/scripts/py-config-bot-1.py -v
| Поля Activity | `ChEMBL:get_bioactivity` | `molecule_chembl_id="CHEMBL25"` | Поля для activity config |
| Поля Target | `ChEMBL:target_search` | `gene_symbol="EGFR"` | Поля для target config |

### Open Targets β€” reference для composite config
### OpenAlex β€” reference для composite config

| Π‘Ρ†Π΅Π½Π°Ρ€ΠΈΠΉ | Π˜Π½ΡΡ‚Ρ€ΡƒΠΌΠ΅Π½Ρ‚ | ΠŸΠ°Ρ€Π°ΠΌΠ΅Ρ‚Ρ€Ρ‹ | Π Π΅Π·ΡƒΠ»ΡŒΡ‚Π°Ρ‚ |
|----------|------------|-----------|-----------|
| Available fields | `Open Targets:get_open_targets_graphql_schema` | β€” | Поля для composite merge |
| Join key validation | `Open Targets:search_entities` | `query_strings=["EGFR"]` | ΠŸΡ€ΠΎΠ²Π΅Ρ€ΠΊΠ° join keys |
| Available fields | `OpenAlex:get_open_targets_graphql_schema` | β€” | Поля для composite merge |
| Join key validation | `OpenAlex:search_entities` | `query_strings=["EGFR"]` | ΠŸΡ€ΠΎΠ²Π΅Ρ€ΠΊΠ° join keys |
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⚠️ Potential issue | 🟑 Minor

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
# Check if OpenAlex MCP tools are documented elsewhere with correct names
rg -n "OpenAlex:" .claude/agents/ --type md -C2

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 1584

🏁 Script executed:

#!/bin/bash
# Search for MCP tool definitions or schemas
find . -type f \( -name "*.json" -o -name "*.yaml" -o -name "*.yml" -o -name "*.ts" -o -name "*.js" -o -name "*.py" \) | head -50 | xargs grep -l "OpenAlex" 2>/dev/null || true

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 207

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#!/bin/bash
# Look for any mcp server or tools definitions
fd -e json -e yaml -e yml | xargs grep -l "tools\|Tool" 2>/dev/null | head -20

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 1014

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#!/bin/bash
# Check the actual structure and content of .claude directory
find .claude -type f | head -20

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 780

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#!/bin/bash
# Search for tool definitions more broadly
rg "get_open_targets|query_open_targets|search_entities" --type-list | head -5
rg "get_open_targets|query_open_targets|search_entities" . -C3 | head -100

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 470

🏁 Script executed:

#!/bin/bash
# Search for tool implementations in Python files
rg "get_open_targets|query_open_targets|search_entities" . --type py -C3

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 63

🏁 Script executed:

#!/bin/bash
# Look for tools directory and OpenAlex implementations
find . -type d -name "*tool*" -o -name "*mcp*" 2>/dev/null | head -20
ls -la src/ 2>/dev/null | head -20

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 811

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#!/bin/bash
# Check for OpenAlex in Python files more broadly
rg "OpenAlex" . --type py -C2 | head -100

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#!/bin/bash
# Check if there's an actual MCP tools manifest or tools.json
find . -name "*tools*" -type f | grep -E "\.(json|yaml|yml)$"

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#!/bin/bash
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ls -la src/tools/

Repository: SatoryKono/BioactivityDataAcquisition

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#!/bin/bash
# Search for any MCP tool registration or configuration
rg "tools" .claude/agents/ --type md -B2 -A2 | head -100

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🏁 Script executed:

#!/bin/bash
# Look for references to "open_targets" in the codebase
rg "open_targets" . --type-list 2>/dev/null || rg "open_targets" .

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 63

🏁 Script executed:

#!/bin/bash
# Check context around the OpenAlex references in py-config-bot.md
cat -n .claude/agents/py-config-bot.md | sed -n '300,320p'

Repository: SatoryKono/BioactivityDataAcquisition

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#!/bin/bash
# Check if these are actual tool definitions or just documentation references
# Look for any tool registry or manifest that might define these
find . -type f -name "*.json" -o -name "*.yaml" -o -name "*.yml" | xargs grep -l "search_entities\|get_open_targets\|query_open_targets" 2>/dev/null || echo "No tool definitions found"

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 106

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#!/bin/bash
# Check the broader context of py-config-bot.md to understand if these are proposed/documented tools
cat -n .claude/agents/py-config-bot.md | head -50

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Length of output: 2238

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#!/bin/bash
# Look at py-plan-bot.md to see the context of the tool references there
cat -n .claude/agents/py-plan-bot.md | sed -n '200,225p'

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 1409

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#!/bin/bash
# Search for any documentation about what these tool names should be
rg "OpenAlex" .claude/agents/ --type md -B5 -A5 | head -150

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 8117

Tool names contain potential naming inconsistency in documentation.

The referenced tool names OpenAlex:get_open_targets_graphql_schema and OpenAlex:search_entities mix namespace "OpenAlex" with method names containing "open_targets" (also see OpenAlex:query_open_targets_graphql in py-plan-bot.md). This suggests either outdated naming carried over from an earlier "Open Targets" API, or a documentation error. Consider clarifying and standardizing these tool references across .claude/agents documentation.

πŸ€– Prompt for AI Agents 
Verify each finding against the current code and only fix it if needed.

In @.claude/agents/py-config-bot.md around lines 307 - 312, Update the
documentation to use a consistent tool naming convention for the OpenAlex tools:
replace mixed/ambiguous references like OpenAlex:get_open_targets_graphql_schema
and OpenAlex:search_entities with the canonical tool names used elsewhere (e.g.,
OpenAlex:query_open_targets_graphql if that is the intended name), and ensure
all mentions across .claude/agents (including py-plan-bot.md) match the chosen
canonical names; search for occurrences of get_open_targets, query_open_targets,
and search_entities and standardize them to a single agreed identifier, updating
the table rows and any example parameter sets accordingly.


---

Expand Down Expand Up @@ -338,8 +338,8 @@ python docs/00-project/ai/agents/scripts/py-config-bot-1.py -v

| Бсылка | ОписаниС | Verification |
|--------|----------|-------------|
| [ADR-014] | Deterministic Writes: sort_by обязатСлСн Π² Silver sink | `find configs/pipelines/ -name "*.yaml" -exec grep -L "sort_by" {} \;` |
| [ADR-014] | Deterministic Writes: sort_by обязатСлСн Π² Silver sink | `find configs/entities/ -name "*.yaml" -exec grep -L "sort_by" {} \;` |
| [ADR-025] | Pipeline Config Unification | `python docs/00-project/ai/agents/scripts/py-config-bot-1.py -v` |
| [ADR-026] | Composite Pipeline Pattern: seed/enrichers/merge | Review composite config structure |
| [ADR-027] | DQ Rules Externalization: no inline thresholds | `grep -rn "soft_fail_threshold" src/bioetl/ --include="*.py"` |
| [ADR-028] | Filter Rules Externalization | `grep -rn "gold_filters" configs/pipelines/ --include="*.yaml"` |
| [ADR-028] | Filter Rules Externalization | `grep -rn "gold_filters" configs/entities/ --include="*.yaml"` |
4 changes: 2 additions & 2 deletions .claude/agents/py-doc-bot.md
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Expand Up @@ -42,7 +42,7 @@ model: sonnet
- НазначСниС: ETL-Ρ„Ρ€Π΅ΠΉΠΌΠ²ΠΎΡ€ΠΊ для Π΄Π°Π½Π½Ρ‹Ρ… биоактивности ΠΈΠ· Π½Π°ΡƒΡ‡Π½Ρ‹Ρ… Π±Π°Π· Π΄Π°Π½Π½Ρ‹Ρ…
- АрхитСктура: Hexagonal (Ports & Adapters) + Medallion (Bronze->Silver->Gold) + DDD
- Deployment: Local-Only (ADR-010) β€” Π±Π΅Π· Docker/Redis
- Π’Π΅ΠΊΡƒΡ‰Π΅Π΅ состояниС: 40 ADR (ADR-001..ADR-040), всС Π² статусС Accepted
- Π’Π΅ΠΊΡƒΡ‰Π΅Π΅ состояниС: 50 ADR (ADR-001..ADR-050), всС Π² статусС Accepted

**ΠšΠ»ΡŽΡ‡Π΅Π²Ρ‹Π΅ Ρ„Π°ΠΉΠ»Ρ‹:**

Expand All @@ -52,7 +52,7 @@ model: sonnet
| Adapters | `src/bioetl/infrastructure/adapters/{provider}/` |
| Pipelines | `src/bioetl/application/pipelines/` |
| Bootstrap | `src/bioetl/composition/bootstrap/` |
| Configs | `configs/pipelines/{provider}/{entity}.yaml` |
| Configs | `configs/entities/{provider}/{entity}.yaml` |
| ADR | `docs/02-architecture/decisions/` |
| RULES.md | `docs/00-project/RULES.md` |
| Glossary | `docs/00-project/glossary.md` |
Expand Down
2 changes: 1 addition & 1 deletion .claude/agents/py-doc-swarm.md
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Expand Up @@ -53,7 +53,7 @@ model: opus
- АрхитСктура: Hexagonal (Ports & Adapters) + Medallion (Bronzeβ†’Silverβ†’Gold) + DDD
- Deployment: Local-Only (ADR-010) β€” Π±Π΅Π· Docker/Redis
- 5 слоёв: domain (192), application (133), infrastructure (140), composition (54), interfaces (29)
- 310 markdown-Ρ„Π°ΠΉΠ»ΠΎΠ² Π² `docs/`, 40 ADR, 7 ΠΏΡ€ΠΎΠ²Π°ΠΉΠ΄Π΅Ρ€ΠΎΠ²
- 310 markdown-Ρ„Π°ΠΉΠ»ΠΎΠ² Π² `docs/`, 50 ADR, 7 ΠΏΡ€ΠΎΠ²Π°ΠΉΠ΄Π΅Ρ€ΠΎΠ²
- Doc site: MkDocs + Material + mkdocstrings (Google-style docstrings)

**Полная спСцификация:** `.claude/agents/py-doc-swarm-standalone.md`
Expand Down
10 changes: 5 additions & 5 deletions .claude/agents/py-plan-bot.md
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Expand Up @@ -32,7 +32,7 @@ model: opus
- НазначСниС: ETL-Ρ„Ρ€Π΅ΠΉΠΌΠ²ΠΎΡ€ΠΊ для Π΄Π°Π½Π½Ρ‹Ρ… биоактивности ΠΈΠ· Π½Π°ΡƒΡ‡Π½Ρ‹Ρ… Π±Π°Π· Π΄Π°Π½Π½Ρ‹Ρ…
- АрхитСктура: Hexagonal (Ports & Adapters) + Medallion (Bronzeβ†’Silverβ†’Gold) + DDD
- Deployment: Local-Only (ADR-010)
- ΠŸΡ€ΠΎΠ²Π°ΠΉΠ΄Π΅Ρ€Ρ‹: ChEMBL, PubChem, UniProt, PubMed, CrossRef, OpenAlex, SemanticScholar, IUPHAR, Open Targets
- ΠŸΡ€ΠΎΠ²Π°ΠΉΠ΄Π΅Ρ€Ρ‹: ChEMBL, PubChem, UniProt, PubMed, CrossRef, OpenAlex, SemanticScholar, Semantic Scholar, OpenAlex
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⚠️ Potential issue | 🟑 Minor

Duplicate providers in the list.

The provider list contains duplicates and inconsistent naming:

  • "OpenAlex" appears twice
  • "Semantic Scholar" appears as both "SemanticScholar" and "Semantic Scholar"
Proposed fix 
-- ΠŸΡ€ΠΎΠ²Π°ΠΉΠ΄Π΅Ρ€Ρ‹: ChEMBL, PubChem, UniProt, PubMed, CrossRef, OpenAlex, SemanticScholar, Semantic Scholar, OpenAlex
+- ΠŸΡ€ΠΎΠ²Π°ΠΉΠ΄Π΅Ρ€Ρ‹: ChEMBL, PubChem, UniProt, PubMed, CrossRef, OpenAlex, SemanticScholar
πŸ“ Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
- ΠŸΡ€ΠΎΠ²Π°ΠΉΠ΄Π΅Ρ€Ρ‹: ChEMBL, PubChem, UniProt, PubMed, CrossRef, OpenAlex, SemanticScholar, Semantic Scholar, OpenAlex
- ΠŸΡ€ΠΎΠ²Π°ΠΉΠ΄Π΅Ρ€Ρ‹: ChEMBL, PubChem, UniProt, PubMed, CrossRef, OpenAlex, SemanticScholar
πŸ€– Prompt for AI Agents 
Verify each finding against the current code and only fix it if needed.

In @.claude/agents/py-plan-bot.md at line 35, The provider list string
"ΠŸΡ€ΠΎΠ²Π°ΠΉΠ΄Π΅Ρ€Ρ‹: ChEMBL, PubChem, UniProt, PubMed, CrossRef, OpenAlex,
SemanticScholar, Semantic Scholar, OpenAlex" contains duplicates and
inconsistent naming; update that text to remove duplicates and normalize names
(use a single "OpenAlex" and a single "Semantic Scholar" form), e.g.,
"ΠŸΡ€ΠΎΠ²Π°ΠΉΠ΄Π΅Ρ€Ρ‹: ChEMBL, PubChem, UniProt, PubMed, CrossRef, OpenAlex, Semantic
Scholar", ensuring only one entry per provider and consistent
spacing/capitalization.


---

Expand Down Expand Up @@ -160,7 +160,7 @@ find configs/ -name "*.yaml" | xargs grep -l "<entity>"

**Workflow для composite pipeline:**
1. Analyze Requirements β€” data sources, target layers, DQ needs
2. Design Pipeline Configuration β€” YAML Π² `configs/pipelines/composite/`
2. Design Pipeline Configuration β€” YAML Π² `configs/entities/composite/`
3. Implement Transformers β€” extend `BaseTransformer`
4. Wire Dependencies β€” factories Π² `composition/factories/`
5. Add Tests β€” unit, integration, architecture
Expand Down Expand Up @@ -204,12 +204,12 @@ find configs/ -name "*.yaml" | xargs grep -l "<entity>"
| Π’Ρ€Π΅Π½Π΄Ρ‹ ΠΏΠΎ ΠΊΠ°Ρ‚Π΅Π³ΠΎΡ€ΠΈΠΈ | `bioRxiv:search_preprints` | `category="bioinformatics"` | ΠšΠΎΠ½Ρ‚Π΅ΠΊΡΡ‚ для planning |
| Бтатистика ΠΏΡƒΠ±Π»ΠΈΠΊΠ°Ρ†ΠΈΠΉ | `bioRxiv:get_content_statistics` | `interval="monthly"` | Capacity planning |

### Open Targets β€” валидация ΠΏΠ»Π°Π½ΠΎΠ² ΠΏΠΎ Ρ‚Π°Ρ€Π³Π΅Ρ‚Π°ΠΌ
### OpenAlex β€” валидация ΠΏΠ»Π°Π½ΠΎΠ² ΠΏΠΎ Ρ‚Π°Ρ€Π³Π΅Ρ‚Π°ΠΌ

| Π‘Ρ†Π΅Π½Π°Ρ€ΠΈΠΉ | Π˜Π½ΡΡ‚Ρ€ΡƒΠΌΠ΅Π½Ρ‚ | ΠŸΠ°Ρ€Π°ΠΌΠ΅Ρ‚Ρ€Ρ‹ | Π Π΅Π·ΡƒΠ»ΡŒΡ‚Π°Ρ‚ |
|----------|------------|-----------|-----------|
| ΠŸΡ€ΠΎΠ²Π΅Ρ€ΠΊΠ° target existence | `Open Targets:search_entities` | `query_strings=["BRCA1"]` | ID resolution |
| ΠžΡ†Π΅Π½ΠΊΠ° data volume | `Open Targets:query_open_targets_graphql` | Query с counts | Capacity planning |
| ΠŸΡ€ΠΎΠ²Π΅Ρ€ΠΊΠ° target existence | `OpenAlex:search_entities` | `query_strings=["BRCA1"]` | ID resolution |
| ΠžΡ†Π΅Π½ΠΊΠ° data volume | `OpenAlex:query_open_targets_graphql` | Query с counts | Capacity planning |
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⚠️ Potential issue | 🟑 Minor

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
# Check for consistent OpenAlex tool naming across agent docs
rg -n "open_targets" .claude/agents/*.md

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 347

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#!/bin/bash
# Search for OpenAlex method definitions and implementations
fd -e py -e js -e ts | xargs grep -l "OpenAlex" | head -20

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 1316

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#!/bin/bash
# Look for method definitions containing the disputed method names
rg "query_open_targets_graphql|get_open_targets_graphql_schema|search_entities" --type py --type js --type ts -B 2 -A 2

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 63

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#!/bin/bash
# Check the structure of the agents directory and look for OpenAlex tool configurations
cat .claude/agents/py-plan-bot.md | head -50

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 1725

🏁 Script executed:

#!/bin/bash
# Look at the OpenAlex adapter implementation
find src -type f -name "*openalex*" -o -name "*open_alex*" | head -20

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 177

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#!/bin/bash
# Search for tool definitions or method signatures in OpenAlex-related files
rg "def.*(" src/tools/openalex* src/infrastructure/adapters/openalex* 2>/dev/null | head -30

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 63

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#!/bin/bash
# Check if "open_targets" exists as a separate tool/integration
rg -i "open.target" src/ --type py | head -20

Repository: SatoryKono/BioactivityDataAcquisition

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#!/bin/bash
# Find the OpenAlex adapter implementation
find src -type d -name "*openalex*"

Repository: SatoryKono/BioactivityDataAcquisition

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#!/bin/bash
# Check the specific lines in py-plan-bot.md
sed -n '200,220p' .claude/agents/py-plan-bot.md

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 1111

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#!/bin/bash
# Look for any tools/providers registry or configuration
rg -i "search_entities|query_open_targets" . --type md --type json --type yaml

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 63

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#!/bin/bash
# List files in OpenAlex adapter
ls -la src/bioetl/infrastructure/adapters/openalex/

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 1384

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#!/bin/bash
# Check for public methods/functions in the OpenAlex adapter
rg "def\s+" src/bioetl/infrastructure/adapters/openalex/ --type py -A 1 | head -50

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 3755

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#!/bin/bash
# Check if "open_targets" is mentioned anywhere in the OpenAlex adapter files
rg "open_target" src/bioetl/infrastructure/adapters/openalex/ -i

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 63

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#!/bin/bash
# Check if "Open Targets" exists as a separate provider/tool
rg -i "open.*target" src/ --type py | grep -v ".pyc"

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 218

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#!/bin/bash
# Check all providers mentioned in the py-plan-bot.md file
grep -E "^\s*-\s+.*:" .claude/agents/py-plan-bot.md | head -20

Repository: SatoryKono/BioactivityDataAcquisition

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#!/bin/bash
# Look at the client.py to see what public methods are exposed
sed -n '1,100p' src/bioetl/infrastructure/adapters/openalex/client.py

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 3286

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#!/bin/bash
# Check if these are meant to be actual method implementations or just documentation examples
# Look for any MCP tool definitions or tool registry
find . -name "tools.json" -o -name "tools.yaml" -o -name "*tools*config*" 2>/dev/null

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 63

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#!/bin/bash
# Check the README or docs for tool naming conventions
find docs -name "*.md" 2>/dev/null | xargs grep -l "OpenAlex\|tool.*naming" 2>/dev/null | head -5

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 278

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#!/bin/bash
# Look at the complete py-plan-bot.md to understand context of these "tools"
wc -l .claude/agents/py-plan-bot.md

Repository: SatoryKono/BioactivityDataAcquisition

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#!/bin/bash
# Look at broader context around the OpenAlex section
sed -n '180,237p' .claude/agents/py-plan-bot.md

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 2214

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#!/bin/bash
# Check if there's any mention of "open_targets" as a separate data source
grep -r "open.target" docs/ .claude/ --ignore-case -i

Repository: SatoryKono/BioactivityDataAcquisition

Length of output: 520

OpenAlex:query_open_targets_graphql incorrectly references a different data source.

The method name OpenAlex:query_open_targets_graphql conflates OpenAlex with Open Targets, which is documented as a separate adapter/pipeline (opentargets). The "open_targets" suffix should not appear in OpenAlex tool names. Ensure consistency with the actual data source naming convention.

πŸ€– Prompt for AI Agents 
Verify each finding against the current code and only fix it if needed.

In @.claude/agents/py-plan-bot.md around lines 207 - 212, The OpenAlex tool name
wrongly includes the Open Targets suffix β€” change all occurrences of
"OpenAlex:query_open_targets_graphql" to a clean OpenAlex name such as
"OpenAlex:query_graphql" (or another consistent OpenAlex-only identifier you
use), and update any doc/table references and tooling metadata that reference
that symbol so they no longer reference the separate "opentargets" adapter;
ensure the symbol rename is applied wherever
"OpenAlex:query_open_targets_graphql" appears.


### PubMed β€” ΠΎΡ†Π΅Π½ΠΊΠ° publication coverage

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