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Command-Line Interface (CLI)

MedCo provides a client command-line interface (CLI) to interact with the medco-connector APIs.

Prerequisites

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.

How to use

To show the CLI manual, run:

For a start, you can use the credentials of the default user: username:test password:test

concept-children

You can use this command to browse the MedCo ontology by getting the children of a concept, both concepts and modifiers.

For example:

modifier-children

You can use this command to browse the MedCo ontology by getting the children of a modifier.

For example:

concept-info

You can use this command to get information about a MedCo concept, including the associated metadata.

For example:

modifier-info

You can use this command to get information about a MedCo modifier, including the associated metadata.

For example:

query

You can use this command to query the MedCo network.

This is the syntax of an example query using the pre-loaded .

You will get something like that:

Query terms can be composed using the logical operators NOT, AND and OR.

Note that, in the queries, the OR operator has the highest priority, so1 AND NOT 2 OR 3 AND 2 is factorised as (1) AND (NOT (2 OR 3)) AND (2)

To each group of OR-ed terms you can also add a timing option ("any", "samevisit", "sameinstancenum") that will override the globally set timing option. For example:

1 AND NOT 2 OR 3 samevisit AND 2

Each query term is composed is composed of two mandatory fields, the type field and the content field, and an optional field, the constraint field, all separated by ::.

type::content[::constraint]

Possible values of the type field are: enc, clr, file.

When the type field is equal to enc, the content field contains the concept ID. The constraint field is not present in this case.
When the type field is equal to clr, the content field contains the concept field (containing the concept path) and, possibly, the modifier field, which in turn contains the modifier key and applied path fields, all separated by :. The optional constraint field can be present, containing the operator, type and value fields separated by :. The constraint field applies either to the concept or, if the modifier field is present, to the modifier. The possible types are NUMBER and TEXT. The possible operators for numbers are: EQ (equals), NE (not equal), GT (greater than), LT (less than), GE (greater than or equal), LE (less than or equal), BETWEEN (between, in this case the value field is in the format "x and y"). The possible operators for TEXT are LIKE[exact], LIKE[begin], LIKE[contains] and LIKE[end].

ga-get-values

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 .

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.

ga-get-variant

You can use this command to get the variant ID of a certain genomic annotation.

To do some tests, you may want to .

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.

survival-analysis

You can run this command to get information useful to run survival analysis. The relative time points are computed as the difference between absolute dates of start concept and end concept.

Start and concept are determined by the name of the access table concatenated to the full path of the concept.

The default cohort identifier -1 corresponds to test data loaded for end-to-end testing. All future cohort identifiers will be positive integers. Cohorts can be created after a successful MedCo Explore query.

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 only three types of genomic annotations are available: variant_name, protein_change and hugo_gene_symbol.

Command-Line Interface (CLI)

MedCo provides a client command-line interface (CLI) to interact with the medco-connector APIs.

Prerequisites

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.

How to use

To show the CLI manual, run:

For a start, you can use the credentials of the default user: username:test password:test

concept-children

You can use this command to browse the MedCo ontology by getting the children of a concept, both concepts and modifiers.

For example:

modifier-children

You can use this command to browse the MedCo ontology by getting the children of a modifier.

For example:

concept-info

You can use this command to get information about a MedCo concept, including the associated metadata.

For example:

modifier-info

You can use this command to get information about a MedCo modifier, including the associated metadata.

For example:

query

You can use this command to query the MedCo network.

This is the syntax of an example query using the pre-loaded .

You will get something like that:

Query terms can be composed using the logical operators NOT, AND and OR.

Note that, in the queries, the OR operator has the highest priority, so1 AND NOT 2 OR 3 AND 2 is factorised as (1) AND (NOT (2 OR 3)) AND (2)

To each group of OR-ed terms you can also add a timing option ("any", "samevisit", "sameinstancenum") that will override the globally set timing option. For example:

1 AND NOT 2 OR 3 samevisit AND 2

Each query term is composed is composed of two mandatory fields, the type field and the content field, and an optional field, the constraint field, all separated by ::.

type::content[::constraint]

Possible values of the type field are: enc, clr, file.

When the type field is equal to enc, the content field contains the concept ID. The constraint field is not present in this case.
When the type field is equal to clr, the content field contains the concept field (containing the concept path) and, possibly, the modifier field, which in turn contains the modifier key and applied path fields, all separated by :. The optional constraint field can be present, containing the operator, type and value fields separated by :. The constraint field applies either to the concept or, if the modifier field is present, to the modifier. The possible types are NUMBER and TEXT. The possible operators for numbers are: EQ (equals), NE (not equal), GT (greater than), LT (less than), GE (greater than or equal), LE (less than or equal), BETWEEN (between, in this case the value field is in the format "x and y"). The possible operators for TEXT are LIKE[exact], LIKE[begin], LIKE[contains] and LIKE[end].

ga-get-values

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 .

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:

ga-get-variant

You can use this command to get the variant ID of a certain genomic annotation.

To do some tests, you may want to .

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:

survival-analysis

You can run this command to get information useful to run survival analysis. The relative time points are computed as the difference between absolute dates of start concept and end concept.

Start and concept are determined by the name of the access table concatenated to the full path of the concept.

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 only three types of genomic annotations are available: variant_name, protein_change and hugo_gene_symbol.

Command-Line Interface (CLI)

hashtagPrerequisites

hashtagHow to use

hashtagconcept-children

hashtagmodifier-children

hashtagconcept-info

hashtagmodifier-info

hashtagquery

hashtagga-get-values

hashtagga-get-variant

hashtagsurvival-analysis

Command-Line Interface (CLI)

hashtagPrerequisites

hashtagHow to use

hashtagconcept-children

hashtagmodifier-children

hashtagconcept-info

hashtagmodifier-info

hashtagquery

hashtagga-get-values

hashtagga-get-variant

hashtagsurvival-analysis

Prerequisites

How to use

concept-children

modifier-children

concept-info

modifier-info

query

ga-get-values

ga-get-variant

survival-analysis

Prerequisites

How to use

concept-children

modifier-children

concept-info

modifier-info

query

ga-get-values

ga-get-variant

survival-analysis