Web Services REST API: Difference between revisions

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There are two main ways a programmer can interact with CoGe:
Our web services let you incorporate CoGe's database of organisms, genomes, and other data sets into your web site or pipeline.  You can also run any type of analysis on CoGe.
#Through the web pages via URLs
#Through CoGe's web services API (Application Programming Interface)


==Linking to CoGe==
==Documentation==
* Interactive documentation:  https://genomevolution.org/apidocs
** Live-test API endpoints using simple web interface
** A tad out of date and doesn't include all API endpoints
* Specification document:  http://docs.google.com/document/d/1GXOPIVvyTwoGR2IRjDNmdd2nj_6d8db7jx9hG8RxTDc
** Up-to-date documentation of all API endoints
* [[Embedding CoGe JBrowse in your website]]
* Automated Testing ([http://robotframework.org/ Robot Framework]): https://geco.iplantcollaborative.org/coge/test/log.html


Each web application of CoGe is designed for a particular task, and provides links to other web applications in CoGe.  This is how CoGe's [[Open-ended Analysis Network]] works.  To get information on how to link to a particular web application, please see that application's wiki.  If the information you are seeking is not immediately apparent, please feel free to e-mail [mailto:elyons@berkeley.edu Eric Lyons] and for help.
==Examples==
 
==CoGe Web Services API==
 
We are currently developing public web services for accessing and loading data in CoGe!
 
Here is our draft API specification document:<br>
http://docs.google.com/document/d/1GXOPIVvyTwoGR2IRjDNmdd2nj_6d8db7jx9hG8RxTDc
 
 
The new services won't be available for a few more weeks, but here are some examples of how they will work ...


'''Organism Search'''
'''Organism Search'''
<pre>
<pre>
curl http://genomevolution.org/api/v1/organisms/search/col-0
curl https://genomevolution.org/coge/api/v1/organisms/search/col-0
{
{
   "organisms":
   "organisms":
Line 32: Line 27:
</pre>
</pre>


'''Organism Fetch'''
'''Genome Search'''
<pre>
<pre>
curl http://genomevolution.org/api/v1/organisms/1
curl https://genomevolution.org/coge/api/v1/genomes/search/col-0
{
[
  "id": 1,
    {
  "name": "Arabidopsis thaliana Col-0 (thale cress)",
        "name": "",
  "description": "Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis"
        "chromosome_count": 7,
  “genomes” : [ 16911, ... ]
        "sequence_type": {
}
            "id": "1",
            "description": "unmasked sequence data",
            "name": "unmasked"
        },
        "info": "Arabidopsis thaliana Col-0 (thale cress) (v10.02, id16911): unmasked",
        "description": "",
        "organism": {
            "id": 1,
            "description": "Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis",
            "name": "Arabidopsis thaliana Col-0 (thale cress)"
        },
        "restricted": false,
        "organism_id": 1,
        "version": "10.02",
        "id": 16911,
        "link": ""
    },
    ...
]
</pre>
</pre>


'''Genome Fetch'''
'''Genome Fetch'''
<pre>
<pre>
curl http://genomevolution.org/api/v1/genomes/16911
curl https://genomevolution.org/coge/api/v1/genomes/16911
{
{
   "id": 16911
   "id": 16911
Line 59: Line 72:
   "experiments": [31,32,33, ...],
   "experiments": [31,32,33, ...],
   "metadata": [],
   "metadata": [],
  ...
}
}
</pre>
</pre>
'''Genome Sequence Download'''
Full Genome:
<pre>curl https://genomevolution.org//coge/api/v1/genomes/16911/sequence</pre>
Partial Genome:
<pre>https://genomevolution.org/coge/coge/api/v1/genomes/16911/sequence/<chr>?start=<x>&stop=<y></pre>
More examples to be added soon!

Latest revision as of 22:53, 23 March 2017

Our web services let you incorporate CoGe's database of organisms, genomes, and other data sets into your web site or pipeline. You can also run any type of analysis on CoGe.

Documentation

Examples

Organism Search 

curl https://genomevolution.org/coge/api/v1/organisms/search/col-0
{
   "organisms":
      [
         {
            "id": "1",
            "name": "Arabidopsis thaliana Col-0 (thale cress)",    
            "description": "Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis"
         }
      ]
}

Genome Search 

curl https://genomevolution.org/coge/api/v1/genomes/search/col-0
[
    {
        "name": "",
        "chromosome_count": 7,
        "sequence_type": {
            "id": "1",
            "description": "unmasked sequence data",
            "name": "unmasked"
        },
        "info": "Arabidopsis thaliana Col-0 (thale cress) (v10.02, id16911): unmasked",
        "description": "",
        "organism": {
            "id": 1,
            "description": "Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis",
            "name": "Arabidopsis thaliana Col-0 (thale cress)"
        },
        "restricted": false,
        "organism_id": 1,
        "version": "10.02",
        "id": 16911,
        "link": ""
    },
    ...
]

Genome Fetch 

curl https://genomevolution.org/coge/api/v1/genomes/16911
{
   "id": 16911
   "name": "",
   "description": "",
   "version": "10.02",
   "link": "",
   "restricted": false,
   "sequence_type": {
      "name": "unmasked",
      "description": "unmasked sequence data"
   },
   "experiments": [31,32,33, ...],
   "metadata": [],
   ...
}

Genome Sequence Download

Full Genome: 

curl https://genomevolution.org//coge/api/v1/genomes/16911/sequence

Partial Genome: 

https://genomevolution.org/coge/coge/api/v1/genomes/16911/sequence/<chr>?start=<x>&stop=<y>


More examples to be added soon!

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