Question: Using a JSON object for visualization plugin
0
asmariyaz23 • 10 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
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" } ]}Looks like this was solved. I moved the comment to an answer.