Hello,<div><br></div><div>I have been working on running a workflow programmatically on my local galaxy instance using library datasets.</div><div>It took me a few hours to figure out the problem I was having so I thought I would document it here in case it helps anyone. Also, I have a question regarding &#39;ldda&#39; IDs (see below).</div>


<div>After looking at this post: <a href="http://gmod.827538.n3.nabble.com/Running-a-workflow-programatically-td2572556.html" target="_blank">http://gmod.827538.n3.nabble.com/Running-a-workflow-programatically-td2572556.html</a> and the comments in workflow_execute.py I was trying to run a workflow in the following way:</div>


<div><br></div><div>1) get the dataset ID&#39;s from the library</div><div><br></div><div><div>./display.py &lt;api_key&gt; <a href="http://localhost:8080/api/libraries/ebfb8f50c6abde6d/contents" target="_blank">http://localhost:8080/api/libraries/ebfb8f50c6abde6d/contents</a></div>


<div>Collection Members</div><div>------------------</div><div>#1: /api/libraries/ebfb8f50c6abde6d/contents/c6ca0ddb55be603a016bf252082cbf1f</div><div>  name: /</div><div>  type: folder</div><div>  id: c6ca0ddb55be603a016bf252082cbf1f</div>


<div>#2: /api/libraries/ebfb8f50c6abde6d/contents/a0e1686ccf7a028a</div><div>  name: /<a href="http://smane.vbi.vt.edu/SRR014335.fastq" target="_blank">http://smane.vbi.vt.edu/SRR014335.fastq</a></div><div>  type: file</div>

<div>  id: a0e1686ccf7a028a</div>
<div>#3: /api/libraries/ebfb8f50c6abde6d/contents/98a64dc1a6526c8e</div><div>  name: /<a href="http://smane.vbi.vt.edu/SRR014339.fastq" target="_blank">http://smane.vbi.vt.edu/SRR014339.fastq</a></div><div>  type: file</div>

<div>  id: 98a64dc1a6526c8e</div>
<div>#4: /api/libraries/ebfb8f50c6abde6d/contents/2764e29c8c7b7454</div><div>  name: /<a href="http://smane.vbi.vt.edu/Yeast.gtf" target="_blank">http://smane.vbi.vt.edu/Yeast.gtf</a></div><div>  type: file</div><div>  id: 2764e29c8c7b7454</div>


</div><div><br></div><div>2) get input IDs for the workflow</div><div><div>./display.py &lt;api_key&gt; <a href="http://localhost:8080/api/workflows/f2db41e1fa331b3e" target="_blank">http://localhost:8080/api/workflows/f2db41e1fa331b3e</a></div>


<div>Member Information</div><div>------------------</div><div>url: /api/workflows/f2db41e1fa331b3e</div><div>inputs: {&#39;102&#39;: {&#39;value&#39;: &#39;&#39;, &#39;label&#39;: &#39;Illumina2&#39;}, &#39;104&#39;: {&#39;value&#39;: &#39;&#39;, &#39;label&#39;: &#39;ReferenceAnnotation&#39;}, &#39;96&#39;: {&#39;value&#39;: &#39;&#39;, &#39;label&#39;: &#39;Illumina1&#39;}}</div>


<div>id: f2db41e1fa331b3e</div></div><div><br></div><div>Then I ran:</div><div>python /opt/galaxy_server/galaxy-dist/scripts/api/workflow_execute.py &lt;api_key&gt; <a href="http://localhost:8080/api/workflows" target="_blank">http://localhost:8080/api/workflows</a> f2db41e1fa331b3e &#39;Test API&#39; &#39;102=ldda=a0e1686ccf7a028a&#39; &#39;104=ldda=2764e29c8c7b7454&#39; &#39;96=ldda=98a64dc1a6526c8e&#39;</div>


<div><br>This gives the following error at the end of the stack trace for HTTP Error 500: <span style="color:rgb(51, 51, 51);font-family:Verdana, Arial, sans-serif;font-size:18px;line-height:24px"><b>ValueError: invalid literal for int() with base 10: &#39;file.37&#39;</b></span></div>


<div><span style="color:rgb(51, 51, 51);font-family:Verdana, Arial, sans-serif;font-size:18px;line-height:24px"><b><br></b></span></div>After looking through the code for a while I saw that when the &quot;src id type&quot; is given as &quot;ld&quot; then the decoded name is split and the number is used to retrieve the ldda or &quot;<span style="color:rgb(51, 51, 51);font-family:monospace;font-size:18px;line-height:24px;white-space:pre-wrap">library_dataset_dataset_association&quot;</span><div>


<font color="#333333" face="monospace"><span style="line-height:24px;white-space:pre-wrap"><br></span></font></div>So instead I ran the above command with: &#39;102=ld=a0e1686ccf7a028a&#39; &#39;104=ld=2764e29c8c7b7454&#39; &#39;96=ld=98a64dc1a6526c8e&#39;<div>


And everything worked, woo!</div><div><br></div><div>This brings me to my question: Where can I find ldda ID&#39;s ? I imagine I could find them in my database and there looks like some functions in <span style="color:rgb(51, 51, 51);font-family:Verdana, Arial, sans-serif;font-size:18px;line-height:24px">lib/galaxy/web/api/workflows.py </span>for handling them but I am having trouble locating them via an API script or on the library management interface.</div>


<div><br></div><div>Note: I am assuming that the ID&#39;s returned by display.py are in fact &quot;ld&quot; ID&#39;s since this is the ID type I used to avoid the error listed above.</div><div><br>Thanks,</div><div>Andrew</div>


<div><br></div><div><br></div>