Merge pull request #273 from include-dcc/issue-231

deprecate custom validator

Author: madanucd

README.md

@@ -37,11 +37,5 @@ The repository structure is organized as follows:
 - Inclusion of over 25 new slots.
 - 5 new enumerations: EnumClinicalDataSourceType, EnumDataCategory, EnumGuidType, EnumParticipantLifespanStage, EnumResearchDomain.
 
-### CLI Enhancements:
 
-- **Validation**: Streamlines data cleaning and validation via the command line (CLI), allowing users to specify the data type and file path. The CLI reads, cleans, and validates data using LinkML-defined models for robust validation. For more details, use:
-
-```bash
-validate-data --help
-```
 

src/data_validation/README.md

@@ -0,0 +1,61 @@
+# LinkML Schema Linting and Validation
+
+This project uses [LinkML](https://linkml.io/) to define schemas and validate tabular data files. Below are the commands used to lint and validate schemas and data using `linkml-lint` and `linkml-validate`.
+
+---
+
+## 🔍 Schema Linting
+
+We use `linkml-lint` to check for syntax and structure issues in the schema.
+
+### 1. Full Linting Check
+
+```bash
+linkml-lint src/linkml/include_schema.yaml
+```
+- **More Info**: [linkml-lint CLI](https://linkml.io/linkml/cli/lint.html)
+
+✅ Data Validation
+-----------------
+
+We use `linkml-validate` to check whether data files conform to their schema definitions.
+
+### 1. Validate `study.csv` against `Study` class
+```bash
+linkml-validate -s src/linkml/include_schema.yaml -C Study src/data/input/study.csv
+```
+### 2. Validate `participant.csv` against `Participant` class
+```bash
+linkml-validate -s src/linkml/include_schema.yaml -C Participant src/data/input/participant.csv
+```
+### 3. Validate `condition.csv` against `Condition` class
+```bash
+linkml-validate -s src/linkml/include_schema.yaml -C Condition src/data/input/condition.csv
+```
+### 4. Validate `biospecimen.csv` against `Biospecimen` class
+```bash
+linkml-validate -s src/linkml/include_schema.yaml -C Biospecimen src/data/input/biospecimen.csv
+```
+### 5. Validate `datafile.csv` against `DataFile` class
+```bash
+linkml-validate -s src/linkml/include_schema.yaml -C DataFile src/data/input/datafile.csv
+```
+
+- **More Info**: [linkml-validate CLI](https://linkml.io/linkml/cli/validate.html) 
+
+### 📤 Saving Validation Logs
+
+To save validation output to a file (e.g., for documentation or reporting), redirect the output of `linkml-validate`:
+
+```bash
+linkml-validate -s src/linkml/include_schema.yaml -C Study src/data/input/study.csv > src/data/output/validation-report.md
+```
+You can change the extension to .csv, .txt, or .json based on your preferred format.
+
+📌 Notes
+    
+- Ensure all required fields are present in your CSV files.
+    
+- Column names in SCV files must match the schema slot names.
+    
+- The schema file (src/linkml/include_schema.yaml) must define all referenced classes (Study, Participant, etc.).