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Commit 900c4949 authored by mjbonifa's avatar mjbonifa
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fix. removed contributing.md from mkdocs

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...@@ -54,7 +54,7 @@ CONFIG_SCHEMA = { ...@@ -54,7 +54,7 @@ CONFIG_SCHEMA = {
"version": { "version": {
"type": "string", "type": "string",
"required": True, "required": True,
"regex": r"^v\d+\.\d+\.\d+$" # Enforces 'vN.N.N' format "regex": r"^v\d+\.\d+\.\d+$", # Enforces 'vN.N.N' format
}, },
"omop": { "omop": {
"type": "dict", "type": "dict",
...@@ -65,9 +65,9 @@ CONFIG_SCHEMA = { ...@@ -65,9 +65,9 @@ CONFIG_SCHEMA = {
"vocabulary_reference": { "vocabulary_reference": {
"type": "string", "type": "string",
"required": True, "required": True,
"regex": r"^https?://.*" # Ensures it's a URL "regex": r"^https?://.*", # Ensures it's a URL
},
}, },
}
}, },
"concept_sets": { "concept_sets": {
"type": "list", "type": "list",
...@@ -82,12 +82,12 @@ CONFIG_SCHEMA = { ...@@ -82,12 +82,12 @@ CONFIG_SCHEMA = {
"schema": { "schema": {
"path": {"type": "string", "required": True}, "path": {"type": "string", "required": True},
"columns": {"type": "dict", "required": True}, "columns": {"type": "dict", "required": True},
"category": {"type": "string"}, # Optional but must be string if present "category": {
"type": "string"
}, # Optional but must be string if present
"actions": { "actions": {
"type": "dict", "type": "dict",
"schema": { "schema": {"divide_col": {"type": "string"}},
"divide_col": {"type": "string"}
},
}, },
}, },
}, },
...@@ -99,6 +99,7 @@ CONFIG_SCHEMA = { ...@@ -99,6 +99,7 @@ CONFIG_SCHEMA = {
} }
} }
class PhenValidationException(Exception): class PhenValidationException(Exception):
"""Custom exception class raised when validation errors in phenotype configuration file""" """Custom exception class raised when validation errors in phenotype configuration file"""
...@@ -320,9 +321,7 @@ def validate(phen_dir): ...@@ -320,9 +321,7 @@ def validate(phen_dir):
logger.debug("YAML structure is valid.") logger.debug("YAML structure is valid.")
else: else:
logger.error(f"YAML structure validation failed: {validator.errors}") logger.error(f"YAML structure validation failed: {validator.errors}")
raise Exception( raise Exception(f"YAML structure validation failed: {validator.errors}")
f"YAML structure validation failed: {validator.errors}"
)
except yaml.YAMLError as e: except yaml.YAMLError as e:
logger.error(f"YAML syntax error: {e}") logger.error(f"YAML syntax error: {e}")
raise e raise e
...@@ -387,7 +386,6 @@ def validate(phen_dir): ...@@ -387,7 +386,6 @@ def validate(phen_dir):
if action not in COL_ACTIONS: if action not in COL_ACTIONS:
validation_errors.append(f"Action {action} is not supported") validation_errors.append(f"Action {action} is not supported")
if len(validation_errors) > 0: if len(validation_errors) > 0:
logger.error(validation_errors) logger.error(validation_errors)
raise PhenValidationException( raise PhenValidationException(
......
site_name: ACMC Documentation
theme:
name: material
features:
- navigation.tabs
- navigation.expand
- content.code.copy
nav:
- Home: index.md
- Installation: installation.md
- Usage: usage.md
- Contributing: contributing.md
- API Reference: api.md
- Tutorials:
- Example 1 - Basic local phenotype: ./tutorials/example1.md
- Example 2 - More complex local phenotype: ./tutorials/example2.md
- Example 3 - Using a remote git repository: ./tutorials/example3.md
- Contributing: contributing.md
- Change Log: changelog.md
- Troubleshooting: troubleshooting.md
repo_url: https://git.soton.ac.uk/meldb/concepts-processing/
plugins:
- search
- mkdocstrings:
handlers:
python:
options:
show_source: false
...@@ -9,13 +9,11 @@ nav: ...@@ -9,13 +9,11 @@ nav:
- Home: index.md - Home: index.md
- Installation: installation.md - Installation: installation.md
- Usage: usage.md - Usage: usage.md
- Contributing: contributing.md
- API Reference: api.md - API Reference: api.md
- Tutorials: - Tutorials:
- Example 1 - Basic local phenotype: ./tutorials/example1.md - Example 1 - Basic local phenotype: ./tutorials/example1.md
- Example 2 - More complex local phenotype: ./tutorials/example2.md - Example 2 - More complex local phenotype: ./tutorials/example2.md
- Example 3 - Using a remote git repository: ./tutorials/example3.md - Example 3 - Using a remote git repository: ./tutorials/example3.md
- Contributing: contributing.md
- Change Log: changelog.md - Change Log: changelog.md
- Troubleshooting: troubleshooting.md - Troubleshooting: troubleshooting.md
repo_url: https://git.soton.ac.uk/meldb/concepts-processing/ repo_url: https://git.soton.ac.uk/meldb/concepts-processing/
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