<commit_before># clinvar-submitter

Clojure (java) application for parsing the ClinGen Variant Pathogenicity Interpretation msessages in JSON-LD form and transforming it into a ClinVar Variant submission record. The primary benefits are to improve consistency and reduce time to draft a ClinVar Submission *Variant* sheet. It has features for error checking and warnings, as well as, consistent evidence summary description generation containing the ACMG ISV criterion rules. 

This project consists of

* project.clj - Clojure project and build options.
* [Source code](src) 
** ld.clj - A linked-data utility for providing XPath-like queries agains json-ld input files
** form.clj - A set of ClinVar submssion specific form parsing functions 
** core.clj - A set of input/output procedures for orchestrating the transformation
** report.clj - The functions for writing out the output and run report.
* [Unit Tests](test/clinvar-submitter) 
* [Data files](data)
** Example json files - input interpretation data files 
** Clinvar Submission Template - A copy of the ClinVar Submission Template spreadsheet on which this version of the application is aligned. Also available at the ClinVar website.
* [Developer Documentation](doc)
* combineall.sh - an optional script to combine multiple interpretation json files into a single json file. 

## Setup Environment
This project is managed using [Leiningen](https://leiningen.org/), a tool and style that focuses on project automation and declarative configuration.  See the [tutorial](https://github.com/technomancy/leiningen/blob/stable/doc/TUTORIAL.md) for more information.

This project can be downloaded and run using the `lein run` command-line tool or it can used to build a stand-alone executable file for distribution. In order to perform either of these steps, you must first install the tool following the instructions in the Install section found at [Leiningen](https://leiningen.org/). 

## Executing Conversions
### Command line using 'Lein Run'<commit_msg>fixed readme nested list<commit_after># clinvar-submitter

Clojure (java) application for parsing the ClinGen Variant Pathogenicity Interpretation msessages in JSON-LD form and transforming it into a ClinVar Variant submission record. The primary benefits are to improve consistency and reduce time to draft a ClinVar Submission *Variant* sheet. It has features for error checking and warnings, as well as, consistent evidence summary description generation containing the ACMG ISV criterion rules. 

This project consists of

* project.clj - Clojure project and build options.
* [Source code](src) 
  * ld.clj - A linked-data utility for providing XPath-like queries agains json-ld input files
  * form.clj - A set of ClinVar submssion specific form parsing functions 
  * core.clj - A set of input/output procedures for orchestrating the transformation
  * report.clj - The functions for writing out the output and run report.
* [Unit Tests](test/clinvar-submitter) 
* [Data files](data)
  * Example json files - input interpretation data files 
  * Clinvar Submission Template - A copy of the ClinVar Submission Template spreadsheet on which this version of the application is aligned. Also available at the ClinVar website.
* [Developer Documentation](doc)
* combineall.sh - an optional script to combine multiple interpretation json files into a single json file. 

## Setup Environment
This project is managed using [Leiningen](https://leiningen.org/), a tool and style that focuses on project automation and declarative configuration.  See the [tutorial](https://github.com/technomancy/leiningen/blob/stable/doc/TUTORIAL.md) for more information.

This project can be downloaded and run using the `lein run` command-line tool or it can used to build a stand-alone executable file for distribution. In order to perform either of these steps, you must first install the tool following the instructions in the Install section found at [Leiningen](https://leiningen.org/). 

## Executing Conversions
### Command line using 'Lein Run'
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{'dir': 'git-commits-cleaned', 'id': '3238148', 'n_tokens_mistral': 1023, 'n_tokens_neox': 977, 'n_words': 512}