API Questions

[bbarrick]

Hi, sorry if this isn't the right place. I'm working on a project that needs to integrate with the Ion Torrent S5 API.

I'm having trouble figuring out how to get bed files using the API. If you don't mind could you point me in the right direction?

Thank you

[sukumar-ranganathan]

Hi,
Here is the cook book for Ion Torrent : https://ion-torrent-sdk.readthedocs.io/en/v5.12/index.html
Refer below pages for:

• API Reference : https://ion-torrent-sdk.readthedocs.io/en/v5.12/api/getting_started.html

• Plugin development : https://ion-torrent-sdk.readthedocs.io/en/v5.12/plugin/getting_started.html

Please let me know if you have any questions.

Thank you!
-Sukumar

[bbarrick]

HI @sukumar-ranganathan, thank you , I have been looking through the API and have built some integration that lets me get a list of the runs and individual run data. However, I didn't quite see anything about getting the bam files specifically.

[sukumar-ranganathan]

Hi @bbarrick,
Check out this API https://ion-torrent-sdk.readthedocs.io/en/v5.12/api/references_auto_generated/results.html?highlight=results
Resource URL http://mytorrentserver/rundb/api/v1/results
"bamLink": "/output/Home/CA_Combined_demo_001_007/download_links/NONE_ReportOnly_NONE_CA_Combined_demo_001.bam",

[bbarrick]

Hi @bbarrick,
Check out this API https://ion-torrent-sdk.readthedocs.io/en/v5.12/api/references_auto_generated/results.html?highlight=results
Resource URL http://mytorrentserver/rundb/api/v1/results
"bamLink": "/output/Home/CA_Combined_demo_001_007/download_links/NONE_ReportOnly_NONE_CA_Combined_demo_001.bam",

Thanks @sukumar-ranganathan,

I've tried several bam endpoints and all I get is a 404 error. Any suggestions?

/rundb/api/v1/output/Home/Auto_user_S5XL-0079-5-170424_OT2_LymphoTrack_95_tn_013/download_links/R_2017_04_26_15_33_36_user_S5XL-0079-5-170424_OT2_LymphoTrack_Auto_user_S5XL-0079-5-170424_OT2_LymphoTrack_95_tn.bam?username=ionadmin&api_key=3f2cdec72f8b1783dfc1222cb4f4164c79de53a7): failed to open stream: HTTP request failed! HTTP/1.1 404 NOT FOUND

[bbarrick]

        $file_url = BASE_URL . $endpoint . '?username=' . USERNAME . '&api_key=' . APIKEY;
        $destination_path = "/file_downloads";
        $fp = fopen($destination_path, 'wb+');

        $ch = curl_init($file_url);
        curl_setopt($ch, CURLOPT_FILE, $fp);
        curl_exec($ch);
        $st_code = curl_getinfo($ch, CURLINFO_HTTP_CODE);
        curl_close($ch);
        fclose($fp);

        return $st_code;

[bbarrick]

@sukumar-ranganathan I think I may have figured it out - the result endpoint by default is returning data from 2017, it's not being sorted so the files may not even be there anymore.

[sukumar-ranganathan]

Hi, did you try order by id? Ex: http://mytorrentsever/rundb/api/v1/results/?order_by=-id

[bbarrick]

Hi, did you try order by id? Ex: http://mytorrentsever/rundb/api/v1/results/?order_by=-id

I did, I was able to order it by the timeStamp field. I'm getting a 200 response now but no file - slowly but surely getting there though. Thank you for the help.

[bbarrick]

Hi, did you try order by id? Ex: http://mytorrentsever/rundb/api/v1/results/?order_by=-id

@sukumar-ranganathan So I'm looking at the response from the bamLink endpoint and this is a screenshot of the data that it returned, can you tell me what I'm looking at here?

[sukumar-ranganathan]

@bbarrick , hope your issue is resolved.

[bbarrick]

@sukumar-ranganathan thank you, I gave up on using the API to retrieve the file. Working on just automating a transfer of the file via ssh in my project.