Qualifying Filters

Topics on this page:

• Select all experiments with a common expName field
• A more restrictive example
• Select experiments with a given date field

Select all experiments with a common expName field

Filter values can be qualified so the value does not need to be an exact match to select an element.

(!) The full set of filter qualifiers is listed in the Filter Qualifiers section of the Torrent Suite™ Software API User Guide.

Use the following syntax to specify a filter qualifier, where two underscore characters (__) separate the filter name from the filter qualifier name:

<filterName>__<filterQualifierName>=<value>

For some qualifiers, the behavior is similar to using a wildcard. The names of most qualifiers is self-explanatory, describing how it matches on a value.

In the following example, the startswith qualifier is used so any element whose field value “starts with” the specified value is returned, for the specified field.

General form of a URI request with a filter qualifier

http://myhost/rundb/api/v1/experiment?format=json&expName__startswith=R_2013

Python implementation of a filter qualifier

import json
import requests

base_url = 'http://myhost/rundb/api/v1'
resp = requests.get('%s/experiment?format=json&expName__startswith=R_2013'%base_url, auth=('myusername', 'mypassword'))
resp_json = resp.json()

The example returns two elements whose experiment name, expName, starts with R_2013.

{
        "meta": {
                "limit": 20,
                "next": null,
                "offset": 0,
                "previous": null,
                "total_count": 2
        },
        "objects": [
                {
                        "autoAnalyze": true,
                        "barcodeId": "",
                        "baselineRun": false,
                        "chipBarcode": "AA0000000",
                        "chipType": "\"314R\"",
                        "cycles": 27,
                        "date": "2013-03-07T17:48:53",
                        "expCompInfo": "",
                        "expDir": "/results/PGM_test/sample",
                        "expName": "R_2013_11_08_22_30_04_user_B15-45",
                                .
                                .
                                .
                        "unique": "/results/PGM_test/sample",
                        "usePreBeadfind": true
                },
                {
                        "autoAnalyze": true,
                        "barcodeId": "",
                        "baselineRun": false,
                        "chipBarcode": "AA0011641",
                        "chipType": "\"314R\"",
                        "cycles": 55,
                        "date": "2013-11-05T18:32:00",
                        "expCompInfo": "",
                        "expDir": "/results/B6/R_2013_11_05_18_32_00_user_B6--237",
                        "expName": "R_2013_11_05_18_32_00_user_B6--237",
                                .
                                .
                                .
                        "unique": "/results/B6/R_2013_11_05_18_32_00_user_B6--237",
                        "usePreBeadfind": true
                }
        ]
}

A more restrictive example

This example is the same as the previous example, except that the stricter criteria are applied by specifying that the experiment name must start with R_2013_11_05. From the results of the previous example, you can see that only one element is expected to meet this qualification.

General form of a more restrictive filter qualifier

http://myhost/rundb/api/v1/experiment?format=json&expName__startswith=R_2013_11_05

Python implementation of a stricter filter qualifier

import json
import requests
import requests

base_url = 'http://myhost/rundb/api/v1'
resp = requests.get('%s/experiment?format=json&expName__startswith=R_2013_11_05'%base_url, auth=('myusername', 'mypassword'))
resp_json = resp.json()

The response shows that only one element matches the expName filter:

{
        "meta": {
                "limit": 20,
                "next": null,
                "offset": 0,
                "previous": null,
                "total_count": 1
        },
        "objects": [
                {
                        "autoAnalyze": true,
                        "barcodeId": "",
                        "baselineRun": false,
                        "chipBarcode": "AA0011641",
                        "chipType": "\"314R\"",
                        "cycles": 55,
                        "date": "2013-11-05T18:32:00",
                        "expCompInfo": "",
                        "expDir": "/results/B6/R_2013_11_05_18_32_00_user_B6--237",
                        "expName": "R_2013_11_05_18_32_00_user_B6--237",
                                .
                                .
                                .
                        "unique": "/results/B6/R_2013_11_05_18_32_00_user_B6--237",
                        "usePreBeadfind": true
                }
        ]
}

Select experiments with a given date field

The filter qualifier shown in this example works, as most qualifiers do, similar to the previous examples. Here, instead of searching for an element that “starts with” a particular value, you are searching for elements that “contain” a particular value. This example looks for elements whose date field contains the string value 2013-03.

General form of a URI with a filter qualifier on the date field

http://myhost/rundb/api/v1/experiment?format=json&date__icontains=2013-03

Python implementation of applying a filter qualifier on the date field

import json
import requests

base_url = 'http://myhost/rundb/api/v1'
resp = requests.get('%s/experiment?format=json&date__icontains=2013-03'%base_url,
        auth=('myusername', 'mypassword'))

One experiment is returned whose date field contains the string 2013-03. Notice that the startswith filter qualifier could also have been used. Considerable flexibility is available to you in choosing a qualifier and the best choice depends on the application and the data set.

{
"meta": {
        "limit": 20,
        "next": null,
        "offset": 0,
        "previous": null,
        "total_count": 1
},
"objects": [
        {
                "autoAnalyze": true,
                "barcodeId": "",
                "baselineRun": false,
                "chipBarcode": "AA0000000",
                "chipType": "\"314R\"",
                "cycles": 27,
                "date": "2011-03-07T17:48:53",
                "expCompInfo": "",
                "expDir": "/results/PGM_test/sample",
                "expName": "R_2010_11_08_22_30_04_user_B15-45",
                        .
                        .
                        .
                "unique": "/results/PGM_test/sample",
                "usePreBeadfind": true
        }]
}

Sort Response Output demonstrates how to sort the returned experiment data by date.