Get Data from Cloud

The get API allows a user to copy data from a cloud-based storage (e.g., Amazon S3, and Microsoft Azure BLOB) to a specified Galaxy history.

You may use the following steps to use this API:

  1. Login to Galaxy using your Google account (read how);
  2. Define a cloud authzorization configuration (read how);
  3. Get a Galaxy API key by going to User -> Manage API key On Galaxy's webpage and clicking on the Create a new key button;
  4. Make the API call as it follows:

    4.1. Open Postman;

    4.2. Choose POST and enter the following in the fields highlighted in the following figure:

     http://127.0.0.1:8080/api/cloud/storage/get?key=1234567890

    Replace http://127.0.0.1:8080 with the IP address of the Galaxy instance you're using, and replace 1234567890 with the your API key.

    image

    4.3. Get the ID of Galaxy history to which you want to copy data, by going to the following address on your browser:

     http://127.0.0.1:8080/api/histories

    This will display a JSON object similar to the following, note the value of id field:

     [
        {
           "name":"Unnamed history",
           "tags":[
           ],
           "deleted": false,
           "purged": false,
           "annotation": null,
           "url": "/api/histories/df7a1f0c02a5b08e",
           "published": false,
           "model_class": "History",
           "id": "df7a1f0c02a5b08e"
        }
     ]

    4.4. Get the ID of authorization defined in step #2, which you want to use to read the cloud-based storage, by going to following address:

     http://127.0.0.1:8080/api/cloud/authz

    This will display a JSON object similar to the following, note the value of id field:

     [
        {
           "authn_id": "f2db41e1fa331b3e",
           "user_id": "f2db41e1fa331b3e",
           "last_update": "2018-12-07 17:53:55.714802",
           "last_activity": "2018-12-07 17:53:55.714818",
           "provider": "aws",
           "model_class": "CloudAuthz",
           "config": "{u'role_arn': u'arn:aws:iam:: ...'}",
           "id": "f2db41e1fa331b3e"
        }
     ]

    4.5. On Postman, goto Body tab as shown in the following figure and enter the following API payload:

    image

     {
         "history_id": "df7a1f0c02a5b08e",
         "authz_id": "f2db41e1fa331b3e",
         "bucket": "vahid-objectstore",
         "objects": [
             "rep1.bed",
             "rep2.bed"
         ]
     }

    Replace vahid-objectstore with a bucket name from which you want to get data, and replace ["rep1.bed", "rep2.bed"] with the list of objects you want to copy to Galaxy from the bucket.

    4.6. Click on the Send button; Postman will submit a request to Galaxy to get data and will shows a result as the following.

     [
         {
             "update_time": "2018-12-07T22:41:39.844046",
             "uuid": "7d1a6d7d-6651-4cfe-8792-beb13a79949d",
             "deleted": false,
             "purged": false,
             "purgable": true,
             "total_size": 0,
             "state": "queued",
             "create_time": "2018-12-07T22:41:39.790590",
             "file_size": 0,
             "id": "5969b1f7201f12ae"
         },
         {
             "update_time": "2018-12-07T22:41:40.058628",
             "uuid": "195e1cee-326c-4f88-bbf5-63a51bdc51bf",
             "deleted": false,
             "purged": false,
             "purgable": true,
             "total_size": 0,
             "state": "queued",
             "create_time": "2018-12-07T22:41:40.005482",
             "file_size": 0,
             "id": "df7a1f0c02a5b08e"
         }
     ]  

    This JSON object shows two Galaxy datasets created for rep1.bed and rep2.bed.