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Commit 5e730492 authored by mjbonifa's avatar mjbonifa
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(docs) testing mkdocs and readthedocs integratino

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<a id="__init__"></a>
# \_\_init\_\_
<a id="__main__"></a>
# \_\_main\_\_
<a id="util"></a>
# util
<a id="logging_config"></a>
# logging\_config
<a id="logging_config.setup_logger"></a>
#### setup\_logger
```python
def setup_logger(log_level: int = logging.INFO)
```
Sets up logger as a singleton outputing to file and sysout syserr
<a id="logging_config.set_log_level"></a>
#### set\_log\_level
```python
def set_log_level(log_level: int)
```
Sets the log level for the acmc logger
<a id="main"></a>
# main
<a id="main.trud_install"></a>
#### trud\_install
```python
def trud_install(args: argparse.Namespace)
```
Handle the `trud install` command.
<a id="main.omop_install"></a>
#### omop\_install
```python
def omop_install(args: argparse.Namespace)
```
Handle the `omop install` command.
<a id="main.omop_clear"></a>
#### omop\_clear
```python
def omop_clear(args: argparse.Namespace)
```
Handle the `omop clear` command.
<a id="main.omop_delete"></a>
#### omop\_delete
```python
def omop_delete(args: argparse.Namespace)
```
Handle the `omop delete` command.
<a id="main.phen_init"></a>
#### phen\_init
```python
def phen_init(args: argparse.Namespace)
```
Handle the `phen init` command.
<a id="main.phen_fork"></a>
#### phen\_fork
```python
def phen_fork(args: argparse.Namespace)
```
Handle the `phen fork` command.
<a id="main.phen_validate"></a>
#### phen\_validate
```python
def phen_validate(args: argparse.Namespace)
```
Handle the `phen validate` command.
<a id="main.phen_map"></a>
#### phen\_map
```python
def phen_map(args: argparse.Namespace)
```
Handle the `phen map` command.
<a id="main.phen_export"></a>
#### phen\_export
```python
def phen_export(args: argparse.Namespace)
```
Handle the `phen copy` command.
<a id="main.phen_publish"></a>
#### phen\_publish
```python
def phen_publish(args: argparse.Namespace)
```
Handle the `phen publish` command.
<a id="main.phen_copy"></a>
#### phen\_copy
```python
def phen_copy(args: argparse.Namespace)
```
Handle the `phen copy` command.
<a id="main.phen_diff"></a>
#### phen\_diff
```python
def phen_diff(args: argparse.Namespace)
```
Handle the `phen diff` command.
<a id="omop"></a>
# omop
OMOP Module
================
This module provides functionality to manage OMOP vocabularies.
<a id="omop.install"></a>
#### install
```python
def install(omop_zip_file: str, version: str)
```
Installs the OMOP release csv files in a file-based sql database
<a id="omop.write_version_file"></a>
#### write\_version\_file
```python
def write_version_file(version: str)
```
Writes the OMOP vocaburaries and version to a file
<a id="omop.clear"></a>
#### clear
```python
def clear(db_path: Path)
```
Clears the OMOP sql database
<a id="omop.delete"></a>
#### delete
```python
def delete(db_path: Path)
```
Deletes the OMOP sql database
<a id="parse"></a>
# parse
<a id="parse.CodesError"></a>
## CodesError Objects
```python
class CodesError()
```
A class used in InvalidCodesException to report an error if a code parser check fails
<a id="parse.InvalidCodesException"></a>
## InvalidCodesException Objects
```python
class InvalidCodesException(Exception)
```
Custom exception class raised when invalid codes are found that cannot be resolved by processing
<a id="parse.Proto"></a>
## Proto Objects
```python
class Proto()
```
Define checks as list of 3 tuple: (Message, Condition, Process)
- Message = The name of the condition (what is printed and logged)
- Condition = True if Passed, and False if Failed
- Process = Aims to resolve all issues that stop condition from passing (Do not change index!)
<a id="parse.Proto.raise_exception"></a>
#### raise\_exception
```python
def raise_exception(ex: Exception)
```
Raises an exception inside a lambda function. Python does not allow using raise statement inside lambda because lambda can only contain expressions, not statements. Using raise_exception not raise_ as it's more explict
<a id="parse.Proto.process"></a>
#### process
```python
def process(codes: pd.DataFrame,
codes_file: Path) -> Tuple[pd.DataFrame, list]
```
identify issues that do not pass and fix them with define/d process
<a id="parse.Proto.verify"></a>
#### verify
```python
def verify(codes: pd.DataFrame, codes_file: Path)
```
verify codes in codes file
<a id="parse.Read2"></a>
## Read2 Objects
```python
class Read2(Proto)
```
This Read2 class extends Proto, adding custom validation checks for a dataset of "Read2" codes. It ensures that the dataset is loaded, validates the codes based on several rules, and applies corrections or logs errors when necessary.
<a id="parse.CodeTypeParser"></a>
## CodeTypeParser Objects
```python
class CodeTypeParser()
```
A class used in InvalidCodesException to report an error if a code parser check fails
<a id="phen"></a>
# phen
Phenotype Module
================
This module provides functionality for managing phenotypes.
<a id="phen.PhenValidationException"></a>
## PhenValidationException Objects
```python
class PhenValidationException(Exception)
```
Custom exception class raised when validation errors in phenotype configuration file
<a id="phen.construct_git_url"></a>
#### construct\_git\_url
```python
def construct_git_url(remote_url: str)
```
Constructs a git url for github or gitlab including a PAT token environment variable
<a id="phen.create_empty_git_dir"></a>
#### create\_empty\_git\_dir
```python
def create_empty_git_dir(path: Path)
```
Creates a directory with a .gitkeep file so that it's tracked in git
<a id="phen.check_delete_dir"></a>
#### check\_delete\_dir
```python
def check_delete_dir(path: Path, msg: str) -> bool
```
Checks on the command line if a user wants to delete a directory
**Arguments**:
- `path` _Path_ - path of the directory to be deleted
- `msg` _str_ - message to be displayed to the user
**Returns**:
- `Boolean` - True if deleted
<a id="phen.fork"></a>
#### fork
```python
def fork(phen_dir: str, upstream_url: str, upstream_version: str,
new_origin_url: str)
```
Forks an upstream phenotype in a remote repo at a specific version to a local director, and optionally sets to a new remote origin"
**Arguments**:
- `phen_dir` _str_ - local directory path where the upstream repo is to be cloned
- `upstream_url` _str_ - url to the upstream repo
- `upstream_version` _str_ - version in the upstream repo to clone
- `new_origin_url` _str, optional_ - url of the remote repo to set as the new origin. Defaults to None.
**Raises**:
- `ValueError` - if the specified version is not in the upstream repo
- `ValueError` - if the upstream repo is not a valid phenotype repo
- `ValueError` - if there's any other problems with Git
<a id="phen.init"></a>
#### init
```python
def init(phen_dir: str, remote_url: str)
```
Initial phenotype directory as git repo with standard structure
<a id="phen.validate"></a>
#### validate
```python
def validate(phen_dir: str)
```
Validates the phenotype directory is a git repo with standard structure
<a id="phen.read_table_file"></a>
#### read\_table\_file
```python
def read_table_file(path: Path, excel_sheet: str = "")
```
Load Code List File
<a id="phen.preprocess_source_concepts"></a>
#### preprocess\_source\_concepts
```python
def preprocess_source_concepts(
df: pd.DataFrame, concept_set: dict,
code_file_path: Path) -> Tuple[pd.DataFrame, list]
```
Parses each column individually - Order and length will not be preserved!
<a id="phen.translate_codes"></a>
#### translate\_codes
```python
def translate_codes(source_df: pd.DataFrame, target_code_type: str,
concept_name: str) -> pd.DataFrame
```
Translates each source code type the source coding list into a target type and returns all conversions as a concept set
<a id="phen.publish"></a>
#### publish
```python
def publish(phen_dir: str,
msg: str,
remote_url: str,
increment: str = DEFAULT_VERSION_INC)
```
Publishes updates to the phenotype by commiting all changes to the repo directory
<a id="phen.export"></a>
#### export
```python
def export(phen_dir: str, version: str)
```
Exports a phen repo at a specific tagged version into a target directory
<a id="phen.copy"></a>
#### copy
```python
def copy(phen_dir: str, target_dir: str, version: str)
```
Copys a phen repo at a specific tagged version into a target directory
<a id="phen.extract_concepts"></a>
#### extract\_concepts
```python
def extract_concepts(config_data: dict) -> Tuple[dict, Set[str]]
```
Extracts concepts as {name: file_path} dictionary and a name set.
<a id="phen.extract_clean_deepdiff_keys"></a>
#### extract\_clean\_deepdiff\_keys
```python
def extract_clean_deepdiff_keys(diff: dict, key_type: str) -> Set[Any]
```
Extracts clean keys from a DeepDiff dictionary.
**Arguments**:
- `diff`: DeepDiff result dictionary
- `key_type`: The type of change to extract (e.g., "dictionary_item_added", "dictionary_item_removed")
**Returns**:
A set of clean key names
<a id="phen.diff_phen"></a>
#### diff\_phen
```python
def diff_phen(new_phen_path: Path, new_version: str, old_phen_path: Path,
old_version: str, report_path: Path)
```
Compare the differences between two versions of a phenotype
<a id="trud"></a>
# trud
<a id="trud.get_releases"></a>
#### get\_releases
```python
def get_releases(item_id: str, API_KEY: str, latest=False) -> list
```
Retrieve release information for an item from the TRUD API.
<a id="trud.download_release_file"></a>
#### download\_release\_file
```python
def download_release_file(item_id: str, release_ordinal: str, release: dict,
file_json_prefix: str) -> Path
```
Download specified file type for a given release of an item.
<a id="trud.create_map_directories"></a>
#### create\_map\_directories
```python
def create_map_directories()
```
Create map directories.
docs/index.md
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......@@ -9,7 +9,7 @@
- [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)
- [API Reference](./api.md)
- [API Reference](./api/acmc.html)
- [Change Log](./changelog.md)
- [Troubleshooting](./troubleshooting.md)
mkdocs.yml
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......@@ -6,8 +6,16 @@ theme:
nav:
- Home: index.md
- API:
- acmc: api/acmc.html
- Installation: installation.md
- User Guide: user-guide.md
- Usage: usage.md
- Tutorial 1 Basic local phenotype: tutorials/example1.md
- Tutorial 2 More complex local phenotype: tutorials/example2.md
- Tutorial 3 Using a remote git repository: tutorials/example3.md
- API Reference:
- acmc: api/acmc.html
- Change Log: changelog.md
- Troubleshooting: troubleshooting.md
markdown_extensions:
- toc:
......
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