Question: Using a JSON object for visualization plugin
0
gravatar for asmariyaz23
3.3 years ago by
asmariyaz2310
United States
asmariyaz2310 wrote:

I need a JSON file to be recognized by a visualization plugin named - 'igv'. By following the VisualizationsRegistry galaxy wiki page I made the following directory structure under: $GALAXY_HOME_DIR/config/plugins/visualizations/igv

-config

    igv.xml

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="igv">
          <data_sources>
               <data_source>
                      <model_class>HistoryDatasetAssociation</model_class>
                       <test type="isinstance" test_attr="datatype" result_type="datatype">text.Json</test>
                       <to_param param_attr="id">dataset_id</to_param>
                </data_source>
           </data_sources>
           <params>
                     <param type="json" var_name_in_template="hda" required="true">dataset_id</param>
           </params>          <template>[path to plugin directory]/igv.mako</template>
</visualization>

-templates

    igv.mako 

-static

    MutationsWeb.js

    Spinner.css

My concern being this:

I cannot see the icon for visualization even though the file I upload is being recognized as JSON. Log displays the following:

galaxy.web.base.pluginframework INFO 2015-06-18 12:32:15,987 VisualizationsRegistry, loaded plugin: igv

which means that it is being registered BUT the dataset is not being recognized (i think). Can someone help me find any errors I may have made in igv.xml w.r.t to defining JSON as a datatype?

Thank you,

Asma 

 

 

 

visualization galaxy json • 1.1k views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by asmariyaz2310

Two things that may help future people who encounter this problem:

1) (as of June 2015) you need to be logged in to use visualizations. If you're not logged in, you won't see the visualizations button in your dataset in the history.

2) Developers can check for visualization links for a particular dataset using this API call:

/api/histories/{history_id}/contents/{hda_id}?keys=visualizations

(replacing with the appropriate {ids}). You should see a link to your visualization if Galaxy is considering that dataset applicable for the visualization:

{ "visualizations": [
    {
      "embeddable": false, 
      "href": "/visualization/show/charts?dataset_id=bbd44e69cb8906b5fda02c4ec7401d11", 
      "html": "Charts", 
      "target": "galaxy_main"
    }
]} 
ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by carlfeberhard390

Looks like this was solved. I moved the comment to an answer.

 

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by carlfeberhard390
0
gravatar for asmariyaz23
3.3 years ago by
asmariyaz2310
United States
asmariyaz2310 wrote:

Solved it! My post is edited to reflect the change..

ADD COMMENTlink written 3.3 years ago by asmariyaz2310
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