Metadata Tool

Make a QC report for metadata & sync all metadata to a database (e.g. MySQL/PostgreSQL/SQLite)

Features

• AutoDetect table schema based on the metadata tables.
• Sync all metadata tables to a specified database (Such as MySQL/PostgreSQL/SQLite).
• Send a notification on updated status to dingtalk group.
• Generate Interactive QC report for a set of metadata tables.
• Validate fields in the metadata tables based on a set of custom-defined and predefined schema, please access the biodata-validator project for more details.
• Please submit a pull request if you have any ideas.

Get Started for Users

Prepare your metadata

Please follow the SEQC DataHub repo or the DataHub repo to learn how to prepare the metadata.

.
├── project
│   └── project_20220226.csv
├── donor
│   └── donor_20220226.csv
├── biospecimen
│   └── biospecimen_20220316.csv
├── reference_materials
│   └── reference_materials_20220226.csv
├── library
│   ├── CBCGA_library_20220304.csv
│   ├── FDUVAZ_4family_library_20220304.csv
│   ├── Pool4project_library_20220304.csv
│   ├── Quartet_library_20220304.csv
│   ├── published_library_20220304.csv
│   └── published_ma_library_20220304.csv
├── sequencing
│   ├── CBCGA_sequencing_20220306.csv
│   ├── FDUVAZ_4family_sequencing_20220306.csv
│   ├── Pool4project_sequencin_202200306.csv
│   ├── Quartet_sequencing_20220306.csv
│   ├── published_ma_sequencing_20220306.csv
│   └── published_sequencing_20220306.csv
├── datafile
│   ├── CBCGA_datafile_20220306.csv
│   ├── FDUVAZ_4family_datafile_20220306.csv
│   ├── GSE47774_datafile_20220306.csv
│   ├── Pool4project_datafile_20220306.csv
│   ├── Quartet_datafile_20220226.csv
│   ├── otherGEO_datafile_20220306.csv
│   └── published_ma_datafile_20220306.csv

How to use it?

java -jar metadata-tool-0.1.0-standalone.jar -h
# MetadataTool - For metadata QC & QA.

# Usage: metadata-tool [options]

# Options:
#   -d, --data-dir PATH  Data Directory
#   -v, --version        Show version
#   -D, --debug          Show debug messages
#   -m, --enable-syncdb  Enable sync to database.
#   -n, --enable-notify  Enable notify user by dingtalk
#   -h, --help

# Please refer to the manual page for more information.

Get Started for Developers

Clone the repo

git clone https://github.com/metadata-tool.git
cd metadata-tool

Make an uberjar

lein uberjar

Unittest

lein test

Contributing

Comming soon...

License

Copyright © 2022 Jingcheng Yang

Distributed under the Eclipse Public License either version 1.0 or (at your option) any later version.