https://github.com/intermine/intermine-ws-java-docs
Examples for using the InterMine Java client
https://github.com/intermine/intermine-ws-java-docs
Last synced: 5 months ago
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Examples for using the InterMine Java client
- Host: GitHub
- URL: https://github.com/intermine/intermine-ws-java-docs
- Owner: intermine
- License: lgpl-2.1
- Created: 2019-07-03T08:56:24.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2021-04-22T09:10:01.000Z (over 4 years ago)
- Last Synced: 2025-03-13T02:16:08.453Z (10 months ago)
- Language: Java
- Size: 14 MB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# InterMine Webservice Client Examples
This Java client library is for use with Web services
attached to InterMine data-warehouses. It abstracts
and simplifies techniques for making structured
queries on remote databases using the InterMine
REST interface.
## Documentation
* [client source code](https://github.com/intermine/intermine-ws-java/)
* [javadoc](http://intermine.org/intermine-ws-java/javadoc/)
## Autogenerated Code
The easiest way to use the client is to run a query in a mine, and autogenerate the code you need to run that query in the client. You can get example Java web service API code either from a Template Query or the QueryBuilder:
* From the QueryBuilder - after creating or editing a query, click the "Java" link in the Actions section below the query details.
* From a Template Query form - click the "Java" link below the template form.
## Examples
We provide the following sample programs to demonstrate ways to use the services:
### Query client
The QueryClient demonstrates the use of the InterMine Query Web Service.
This resource can be used to perform arbitrary, complex queries over
the full set of data in the InterMine data warehouse.
This example displays the first 100 Drosophila melanogaster genes sorted by the FlyBase identifier.
```
./gradlew execute -PmainClass=samples.QueryClient
```
### Template client
The TemplateClient demonstrates the use of the InterMine Template Web Service.
This resource can be used to automate access to the predefined queries
which an InterMine data warehouse has made available.
This example returns the first 100 predicted orthologues between two organisms sorted by FlyBase gene identifier.
```
./gradlew execute -PmainClass=samples.TemplateClient
```
### List client
The ListClient demonstrates the use of the InterMine List Web Service.
This example fetches all public lists containing the FBgn0000606 gene.
```
./gradlew execute -PmainClass=samples.ListClient
```
### Overlaps example
This example demonstrates how you can query for overlapping features for the given coordinates.
```
./gradlew execute -PmainClass=samples.OverlapsExample --args="2L:14615455..14619002 2R:5866646..5868384 3R:2578486..2580016"
```
### GenesFinder client
The GenesFinder demonstrates the use of command line arguments,
with a query client fetching Genes or
SequenceFeatures located at specific positions with some tolerance. You can use
the included sample-input.txt to try this client:
```
./gradlew execute -PmainClass=samples.GenesFinder --args="--sample-data"
```