linkml-reference-validator 0.1.7__tar.gz → 0.2.0__tar.gz

{linkml_reference_validator-0.1.7 → linkml_reference_validator-0.2.0}/.github/workflows/claude.yml

@@ -31,7 +31,7 @@ jobs:
           fetch-depth: 1
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
             
       - name: Install python tools
         run: |

{linkml_reference_validator-0.1.7 → linkml_reference_validator-0.2.0}/.github/workflows/dragon-ai.yml

@@ -29,7 +29,7 @@ jobs:
         
       - name: Check for qualifying mention
         id: check
-        uses: actions/github-script@v6
+        uses: actions/github-script@v8
         with:
           github-token: ${{ secrets.PAT_FOR_PR }}  # Use PAT instead of default token
           script: |
@@ -131,7 +131,7 @@ jobs:
           ls -alt ${{ env.TOOLS_DIR }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
           
       - name: Install python tools
         run: |

{linkml_reference_validator-0.1.7 → linkml_reference_validator-0.2.0}/.gitignore

@@ -141,3 +141,4 @@ dmypy.json
 .idea
 # Local vscode editor config
 .vscode
+.cursor

{linkml_reference_validator-0.1.7 → linkml_reference_validator-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: linkml_reference_validator
-Version: 0.1.7
+Version: 0.2.0
 Summary: Validation of supporting text from references and publications
 Author-email: Chris Mungall <cjmungall@lbl.gov>
 License-Expression: Apache-2.0
@@ -891,6 +891,32 @@ linkml-reference-validator validate text "text" UNKNOWN:12345
 # ✗ Valid: False (WARNING) - Could not fetch reference
 ```
 
+#### `source_extra_fields` (per-source JSONPath map)
+
+Capture additional fields from reference API responses and append them to cached content so they are included in validation. Keys are source prefixes (e.g. `clinicaltrials`, `PMID`, `DOI`, `GEO`); values map a field name to a JSONPath expression into the raw API response. Prefer paths to a single value (string/number). If the path selects a list, its elements are converted to strings and joined with spaces. If it selects an object or other type, its string representation is used.
+
+**Example:**
+
+Save as `my-config.yaml`:
+
+```yaml
+validation:
+  source_extra_fields:
+    clinicaltrials:
+      eligibility: "$.protocolSection.eligibilityModule.eligibilityCriteria"
+      outcomes: "$.protocolSection.outcomesModule.primaryOutcomes"
+```
+
+Pass this config when fetching so the cache includes these sections: use `--config my-config.yaml` with `cache reference` or `validate`. Captured field names are stored in `extra_fields_captured` in the cache frontmatter.
+
+```bash
+# Fetch and cache a trial with extra fields (eligibility, outcomes)
+linkml-reference-validator cache reference clinicaltrials:NCT00000001 --config my-config.yaml
+
+# Validate text against the cached content (including extra sections)
+linkml-reference-validator validate text "Inclusion: age >= 18" clinicaltrials:NCT00001372 --config my-config.yaml
+```
+
 ### Cache Directory
 
 Default: `references_cache/` in current directory

{linkml_reference_validator-0.1.7 → linkml_reference_validator-0.2.0}/README.md

@@ -871,6 +871,32 @@ linkml-reference-validator validate text "text" UNKNOWN:12345
 # ✗ Valid: False (WARNING) - Could not fetch reference
 ```
 
+#### `source_extra_fields` (per-source JSONPath map)
+
+Capture additional fields from reference API responses and append them to cached content so they are included in validation. Keys are source prefixes (e.g. `clinicaltrials`, `PMID`, `DOI`, `GEO`); values map a field name to a JSONPath expression into the raw API response. Prefer paths to a single value (string/number). If the path selects a list, its elements are converted to strings and joined with spaces. If it selects an object or other type, its string representation is used.
+
+**Example:**
+
+Save as `my-config.yaml`:
+
+```yaml
+validation:
+  source_extra_fields:
+    clinicaltrials:
+      eligibility: "$.protocolSection.eligibilityModule.eligibilityCriteria"
+      outcomes: "$.protocolSection.outcomesModule.primaryOutcomes"
+```
+
+Pass this config when fetching so the cache includes these sections: use `--config my-config.yaml` with `cache reference` or `validate`. Captured field names are stored in `extra_fields_captured` in the cache frontmatter.
+
+```bash
+# Fetch and cache a trial with extra fields (eligibility, outcomes)
+linkml-reference-validator cache reference clinicaltrials:NCT00000001 --config my-config.yaml
+
+# Validate text against the cached content (including extra sections)
+linkml-reference-validator validate text "Inclusion: age >= 18" clinicaltrials:NCT00001372 --config my-config.yaml
+```
+
 ### Cache Directory
 
 Default: `references_cache/` in current directory