Hi, Asma

If you're looking through datasets via the mako part of your visualization, you can use:
users_current_history = trans.history
dataset_ids = [ trans.security.encode_id( d.id ) for d in users_current_history.datasets ]
(or similar) to build the ids needed for the urls.

If you want to get the info via javascript, you can use something like the python above and template into a js var:
var url = "/datasets/${ dna_dataset_id }/display?to_ext=bam"

...or encode and template the history id and use ajax and the api after the page is served:
var historyId = "${ trans.security.encode_id( trans.history.id ) }";
jQuery.ajax( galaxy_config.root + 'api/histories/' + historyId + '/contents' )
    .done( function( response ){ /* will contain summary json for each dataset including encoded ids for each */ })

Let me know if that's not what you were looking for or if you find any problems with it.

On Wed, Aug 19, 2015 at 11:01 AM, Asma Riyaz <asmariyaz23@gmail.com> wrote:
Hello Galaxy-dev,

I thank you so much for all the help you have given me. 

I have a question about data set ids in galaxy. As a background, I am running my own galaxy instance on a server. A pipeline implemented in the lab produces the following files in the history:

1) 2 BAM files
2) A JSON file

My goal is to use this JSON file to pass the path/URL of bam files into a custom JS we wrote for visualization purpose.

This JSON file contains among many other details the paths/URLs to the above bam files. I am using JSON filetypes to send data to the JS visualization within Galaxy. To do this, I have my own JS which loads a BAM file from URL provided into an IGV.js track. IGV.js, which is responsible for making the tracks, expects a valid URL which is updated in the JSON file in this manner:

1) Extract the API_key and history id from a loaded BAM file
2) Edit the JSON file to reflect the BAM file's dataset id to be something like this:

{
  "CLL-HL_pilot.r1.fastq": {
    "DNA": "/datasets/36ddb788a0f14eb3/display?to_ext=bam",
    ...
This works fine if I know the API Key for bam files. When a pipeline executes dataset ids are generated for each output. I want to access and include these ids in the JSON file and load the updated JSON file into the history with the bams. Is there a way to get the ids from the history in this manner?

Thank you,

Asma


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