https://github.com/hexylena/chado-postgraphql

https://github.com/hexylena/chado-postgraphql

Last synced: 16 days ago
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• Host: GitHub
• URL: https://github.com/hexylena/chado-postgraphql
• Owner: hexylena
• Created: 2017-02-18T02:17:18.000Z (almost 8 years ago)
• Default Branch: master
• Last Pushed: 2018-05-29T17:24:31.000Z (over 6 years ago)
• Last Synced: 2024-10-17T13:58:27.458Z (about 1 month ago)
• Language: PLpgSQL
• Size: 57.6 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Chado-PostGraphQL

Repo for connecting postgraphql to chado. See

[https://github.com/erasche/jbrowse-chado-postgraphql](https://github.com/erasche/jbrowse-chado-postgraphql)

for how this is used.

Some custom SQL is needed to expose two search functions that work well:

```

function find_features(argOrgName varchar, argRefseq text, argSoType text, argFmin int, argFmax int) returns setof feature

function find_sequence(argOrgName varchar, argRefseq text, argFmin int, argFlen int) returns text

```

These two functions allow for 1) fetching top-level features (and then recursing into them using GraphQL), 2) fetching sequence data

The functions need to be loaded from the sql file INTO the database, before launching PostGraphQL.

## Example Queries

Fetch a region of sequence

```graphql

{

  sequence: findSequence(argorgname:"yeast",argrefseq:"chrI", argfmin: 0, argflen: 100) 

}

```

Fetch top level gene features (their names, dbxrefId, and uniquename), as well as the names of their children

```graphql

{

  findFeatures(organismName:"yeast",refseq:"chrI", sotype:"gene", fmin:1, fmax:1000) {

    edges {

      node {

        name

        dbxrefId

        uniquename

        featureRelationshipsByObjectId {

          edges {

            node {

              featureBySubjectId {

                name

              }

            }

          }

        }

      }

    }

  }

}

```

List all Organisms

```graphql

query{

  allOrganisms {

    edges {

      node {

        __id

        organismId

        abbreviation

        genus

        species

        commonName

        infraspecificName

        typeId

        comment

      }

    }

  }

}

```

Creating a new Organism

```graphql

mutation CreateOrganism($input: CreateOrganismInput!) {

	createOrganism(input: $input) {

		clientMutationId

		organism {

			organismId

		}

	}

}

```

data

```json

{

	"input": {

		"clientMutationId": "549b5e7c-0516-4fc9-8944-125401211590",

		"organism": {

			"abbreviation": "abcd",

			"genus": "Abb",

			"species": "cddd",

			"commonName": "asdf",

			"typeId": null,

			"comment": ""

		}

	}

}

```