MedCo provides a client command-line interface (CLI) to interact with the medco-connector APIs.
To use the CLI, you must first follow one of the deployment guides. However, the version of the CLI documented here is the one shipped with the Local Development Deployment.
To show the CLI manual, run:
For a start, you can use the credentials of the default user: username:test password:test
You can use this command to query the MedCo network.
This is the syntax of an example query using the pre-loaded default test data.
You will get something like that:
Not that, in the queries, the OR operator has the highest priority, so 1 AND 2 OR 3 AND 2
is factorised as (1) AND (2 OR 3) AND (2)
.
You can use this command to get the values of the genomic annotations that MedCo nodes make available for queries.
To do some tests, you may want to load some data first.
Then, for example, if you want to know which genomic annotations of type "protein_change" containing the string "g32" are available, you can run:
You will get:
The matching is case-insensitive and it is not possible to use wildcards. At the moment, with the loader v0, only three types of genomic annotations are available: variant_name, protein_change and hugo_gene_symbol.
You can use this command to get the variant ID of a certain genomic annotation.
To do some tests, you may want to load some data first.
Then, for example, if you want to know the variant ID of the genomic annotation "HTR5A" of type "hugo_gene_symbol" with zygosity "heterozygous" or "homozygous", you can run:
You will get:
The matching is case-insensitive and it is not possible to use wildcards. If you request the ID of an annotation which is not available (e.g, in the previous, example, "HTR5") you will get an error message. At the moment, with the loader v0, only three types of genomic annotations are available: variant_name, protein_change and hugo_gene_symbol.