Ok - thanks! That is strange: the server seems to be configured properly for all the new plugins but the client side believes only trackster is available.
Let's try two things:
*First*, let's clear the browser cache to rule out that annoyance:
- In Chrome, I've had good luck with these instructions: http://superuser.com/questions/89809/how-to-force-refresh-without-cache-in-g...
- In Firefox, you can try: http://superuser.com/questions/173210/how-can-i-clear-a-single-site-from-the...
Does the full menu of visualization options appear after you've done that for the development server?
*Second*, let's see what the server ends up sending the client for visualizations:
1. When you're logged into the dev server, open a new tab/window and enter '<your dev server domain>/api/histories' - this will return the summary JSON data for your histories. 2. Look for the history you've been trying and add the 'id' value for it (a hex string) and the word 'contents' to the url in your address bar like this: '<your domain>/api/histories/<id>/contents' - this will be the JSON summaries of the datasets in that history 3. Finally, find a the JSON for a dataset in the summaries that should work with charts - a bed file or a tabular file should work - and add the 'id' value for that dataset to the url in the address bar: '<domain>/api/histories/<history id>/contents/<dataset id>' - this will be JSON details for that dataset.
The detailed JSON dataset data should have a key/value pair for 'visualizations'. Since the plugin registry *should* be enabled, the server should be returning an array of JSON objects for this key. Something like this:
"visualizations": [ { "embeddable": false, "href": "/visualization/show/charts?dataset_id=f597429621d6eb2b", "html": "Charts", "target": "galaxy_main" }, { "embeddable": false, "href": "/visualization/show/scatterplot?dataset_id=f597429621d6eb2b", "html": "Scatterplot", "target": "galaxy_main" }, { "embeddable": false, "href": "/visualization/trackster?dataset_id=f597429621d6eb2b&dbkey=%3F&hda_ldda=hda", "html": "Trackster", "target": "_top" } ]
If, for some reason, the registry is disabled (which strangely *should* have shown in the logs), you'll instead see an array of plain strings: [ 'trackster', ... ].
Does the array you see match the first structure? Are the JSON for charts and scatterplot included?
Tedious work, I know, and I appreciate the help in diagnosing this bug.
On Thu, Aug 28, 2014 at 5:24 AM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Hi Carl
What was the datatype (listed as 'format') of the dataset you tested
with here?:
However, if I hoover over the bar-plot icon, "Visualize in Trackster" pops up (instead of just "Visualize")any data type, eg wig, tabular, bed, etc
I currently have: 'result_type="datatype">data.Data'
in ~/config/plugins/visualizations/trackster/config/trackster.xml
If I change that to 'result_type="datatype">interval.Interval' (and do a restart), I lose the bar-plot icon for wig and tabular. It is still there for the bed file in the history.
Do the 'charts' and 'scatterplot' visualizations show up in the visualization icon popup menu when you check on an interval or bed datatype?
They never show up, I don't get the menu when I click on the bar-plot icon (for bed and/or interval data typ). It goes straight to the Trackster page, where, I am asked to define the Browser name and the Reference genome.
Hans-Rudolf
Thanks for the report and any info you can provide, Carl
On Wed, Aug 27, 2014 at 4:03 AM, Hans-Rudolf Hotz <hrh@fmi.ch mailto:hrh@fmi.ch> wrote:
Hi As part of my upgrade/testing work, I am looking at the visualization plugins. In a new galaxy installation ("latest_2014.08.11"), they (ie 'Charts', 'Scatterplot', and 'Trackster') seem to work fine. All I have done was: - I defined the visualization_plugins___directory in the universe_wsgi.ini file If I comment-out this line, I only get trackster, when I click on the icon which looks like a bar-plot Next, I have tried it on our development server (after I have upgraded from "release_2014.04.14" to "latest_2014.08.11"). I changed the universe_wsgi.ini file. I the logs I get: galaxy.web.base.__pluginframework INFO 2014-08-27 09:43:45,639 VisualizationsRegistry, loaded plugin: charts galaxy.web.base.__pluginframework WARNING 2014-08-27 09:43:45,641 VisualizationsRegistry, plugin load failed or disabled: ./config/plugins/__visualizations/circster. Skipping... galaxy.web.base.__pluginframework INFO 2014-08-27 09:43:45,655 VisualizationsRegistry, loaded plugin: graphview galaxy.web.base.__pluginframework INFO 2014-08-27 09:43:45,657 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.__pluginframework INFO 2014-08-27 09:43:45,675 VisualizationsRegistry, loaded plugin: scatterplot galaxy.web.base.__pluginframework WARNING 2014-08-27 09:43:45,677 VisualizationsRegistry, plugin load failed or disabled: ./config/plugins/__visualizations/sweepster. Skipping... galaxy.web.base.__pluginframework INFO 2014-08-27 09:43:45,679 VisualizationsRegistry, loaded plugin: trackster wrt to 'Charts', 'Scatterplot', and 'Trackster', this looks fine tome.
However, if I hoover over the bar-plot icon, "Visualize in Trackster" pops up (instead of just "Visualize"), and when I click on it I get straight to the Trackster page, where, I am asked to define the Browser name and the Reference genome. No links for 'Charts' and 'Scatterplot'. On the other hand, the plug in infrastructure seems to work: If I change ~/config/plugins/__visualizations/trackster/__config/trackster.xml I see the effects, ie if I change result_type="datatype">data.__Data< to result_type="datatype">__interval.Interval I can restrict the visualization to only the interval data. Somehow, I am running a mixture of the 'old' and the 'new' visualization set-up ? Has anyone seen similar problems when testing the new plug in infrastructure on an old/upgraded Galaxy installation Thank you very much for any hints and help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland _____________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/__search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>