Question: Visualisation Plugin - Icon is not visible
0
gravatar for sureshhewabi
2.4 years ago by
sureshhewabi20
sureshhewabi20 wrote:

 

Hi,

I am new to galaxy and trying to develop a visualisation plugin. I have downloaded a local galaxy.

1) I have config galaxy.ini file:

admin_users = myemail@gmail.com

visualization_plugins_directory = config/plugins/visualizations

2) changed datatypes_conf.xml.sample to datatypes_conf.xml

3) Created folder structure under config/plugins/visualizations

     folder name (protviewer), xml name (protviewer.xml) and mako(protviewer.mako) names are same

4) created config file protviewer.xml

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="ProtViewer">
    <data_sources>
        <data_source>
            <model_class>HistoryDatasetAssociation</model_class>
            <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test>
            <to_param param_attr="id">dataset_id</to_param>
        </data_source>
    </data_sources>
    <params>
        <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
    </params>
    <entry_point entry_point_type="mako">protviewer.mako</entry_point>
</visualization>

5) Created protviewer.mako file (for testing purpose I have only basic HTML)

<!DOCTYPE html>
<html>
<head>
<title>Page Title</title>
</head>
<body>

<h1>This is a Heading</h1>
<p>This is a paragraph.</p>
<h2>${hda.dataset.datatype} | ${hda.name}</h2>

</body>
</html>

Output of console

galaxy.web.base.pluginframework INFO 2016-03-02 08:09:22,836 VisualizationsRegistry, loaded plugin: charts

galaxy.visualization.plugins.config_parser INFO 2016-03-02 08:09:22,838 Visualizations plugin disabled: Circster. Skipping...

galaxy.visualization.plugins.config_parser INFO 2016-03-02 08:09:22,845 template syntax is deprecated: use entry_point instead

galaxy.web.base.pluginframework INFO 2016-03-02 08:09:22,845 VisualizationsRegistry, loaded plugin: csg

galaxy.web.base.pluginframework INFO 2016-03-02 08:09:22,848 VisualizationsRegistry, loaded plugin: graphview

galaxy.visualization.plugins.config_parser INFO 2016-03-02 08:09:22,850 template syntax is deprecated: use entry_point instead

galaxy.web.base.pluginframework INFO 2016-03-02 08:09:22,850 VisualizationsRegistry, loaded plugin: graphviz

galaxy.web.base.pluginframework INFO 2016-03-02 08:09:22,853 VisualizationsRegistry, loaded plugin: phyloviz

galaxy.web.base.pluginframework INFO 2016-03-02 08:09:22,854 VisualizationsRegistry, loaded plugin: protviewer

galaxy.web.base.pluginframework INFO 2016-03-02 08:09:22,856 VisualizationsRegistry, loaded plugin: scatterplot

galaxy.visualization.plugins.config_parser INFO 2016-03-02 08:09:22,858 Visualizations plugin disabled: Sweepster. Skipping...

galaxy.web.base.pluginframework INFO 2016-03-02 08:09:22,862 VisualizationsRegistry, loaded plugin: trackster

But still I do not see visualisation icon for tabular format file. Not only my visualisation, other visualisation also not working. Do you have any idea why?

Thanks

 

galaxy • 630 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by sureshhewabi20
1
gravatar for Hotz, Hans-Rudolf
2.4 years ago by
Switzerland
Hotz, Hans-Rudolf1.8k wrote:

Hi

Just double checking, before the visualization expert jump in and answer your question: Are you logged-in? The visualization icon will only show up if you are logged-in.

 

Regards, Hans-Rudolf

ADD COMMENTlink written 2.4 years ago by Hotz, Hans-Rudolf1.8k

Hi,

No, I am not logged-in. I am testing in localhost:8080. how can i incorporate login? do i need to connect a database or is there a easy way to test this? Thank you

 

ADD REPLYlink written 2.4 years ago by sureshhewabi20
1

In the top (black) bar, there is the tab 'User'. Click on "Register" and create your local account. And then you can log in via the same tab

 

Hans-Rudolf

 

ADD REPLYlink written 2.4 years ago by Hotz, Hans-Rudolf1.8k

Thank you! It works. Sorry I did not know there is a local database connected. Problem Solved!

ADD REPLYlink written 2.4 years ago by sureshhewabi20
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