lib

Guide to using scripts in /lib:

biosample_complete.sh

Generates a TSV file (hopefully) adhering to the biosampleMeta schema as defined in https://github.com/FDA-ARGOS/data.argosdb/blob/main/schema/v1.4/core/biosampleMeta_HIVE.json

The TSV returned contains one row per SRA id associated with the biosample.

Required parameters:

• -f: Path to text file of bioSample IDs (one ID per line)
• -n: Path to NGS QC file (must be TSV format)

Optional parameters:

• -b: BCO ID
• -s: schema version
• -d: debug (if -d is not set, the output directory will contain intermediate xml and tsv files)

Example usage:

./biosample_complete.sh -f biosample_ids.txt -n ngsQC_HIVE.tsv -b ARGOS_000028 -s v1.12

lib

For scripts and sutch

Validating a data file against a schema:

Assume you wanted to validate a flie of the typeSRA_ngsQC(this same process should work for any of the types we have defined).

• The data file is /data_files/test_SRA_ngsQC.tsv
• The schema for a SRA_ngsQC data file is /schema/v0.5/non-core/SRA_ngsQC.json

For illitstration purposes cell T6 in our example data file has been modified. The schema says that the value has to be less than 1, as gc_ content is a percentage. The example data sheet has a value of 10.63682374 in that cell, and the following error shoudl be thrown:

Line 5 failed. '10.63682374' does not match '^[+-]?([0]+\\.?[0-9]*|\\.[0-9]+)$

From the project root run:

> python lib/dictionary_utils.py validate -i data_files/test_SRA_ngsQC.tsv -s schema/v0.5/non-core/SRA_ngsQC.json

Validating a data file against a schema with remote files:

Both the schema [-s] and input file [-i] values can take a URL, assuming they are formatted correctly and resolvable.

For Example:

>  python lib/dictionary_utils.py validate -i https://raw.githubusercontent.com/FDA-ARGOS/data.argosdb/v0.5/data_files/test_SRA_ngsQC.tsv -s https://raw.githubusercontent.com/FDA-ARGOS/data.argosdb/v0.5/schema/v0.5/non-core/SRA_ngsQC.json

should give you the same results.