testing the visualization plugins

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testing the visualization plugins

Hans-Rudolf Hotz
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 to me.


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
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Re: testing the visualization plugins

Carl Eberhard
Hi, Hans,

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")

Trackster by default accepts all datatypes (all subclasses inheriting data.Data) and is the only visualization that ships with Galaxy that allows visualization on all datatypes. You can change that by editing the 

'Charts' and 'scatterplot' can work with any tabular datatype (or subclasses of). If a datatype isn't tabular, those visualizations won't appear as options in the menu.

Do the 'charts' and 'scatterplot' visualizations show up in the visualization icon popup menu when you check on an interval or bed datatype?


Thanks for the report and any info you can provide,
Carl



On Wed, Aug 27, 2014 at 4:03 AM, Hans-Rudolf Hotz <[hidden email]> 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 to me.


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:
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Re: testing the visualization plugins

Carl Eberhard
(oops, to continue the truncated sentence in the prev. email):
You can change that by editing the ...

config/trackster.xml 'datatype' as you did in your email to restrict what Trackster can run on.

(sorry about that)


On Wed, Aug 27, 2014 at 9:39 AM, Carl Eberhard <[hidden email]> wrote:
Hi, Hans,

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")

Trackster by default accepts all datatypes (all subclasses inheriting data.Data) and is the only visualization that ships with Galaxy that allows visualization on all datatypes. You can change that by editing the 

'Charts' and 'scatterplot' can work with any tabular datatype (or subclasses of). If a datatype isn't tabular, those visualizations won't appear as options in the menu.

Do the 'charts' and 'scatterplot' visualizations show up in the visualization icon popup menu when you check on an interval or bed datatype?


Thanks for the report and any info you can provide,
Carl



On Wed, Aug 27, 2014 at 4:03 AM, Hans-Rudolf Hotz <[hidden email]> 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 to me.


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/



___________________________________________________________
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/

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Re: testing the visualization plugins

Hans-Rudolf Hotz
In reply to this post by Carl Eberhard
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 <[hidden email]
> <mailto:[hidden email]>> 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 to me.
>
>
>     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/>
>
>
___________________________________________________________
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:
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Re: testing the visualization plugins

Carl Eberhard
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: 

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 <[hidden email]> 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 <[hidden email]
<mailto:[hidden email]>> 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 to me.


    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/>




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Re: testing the visualization plugins

Hans-Rudolf Hotz
Hi Carl

Thanks for your help  - unfortunately no success so far


> Let's try two things:
>
> *First*, let's clear the browser cache to rule out that annoyance:

This didn't change anything. I have also tried different computers and
different browsers

>
> *Second*, let's see what the server ends up sending the client for
> visualizations:

it just looks like this:

     "visible": true,
     "visualizations": [
         {
             "embeddable": false,
             "href":
"/visualization/trackster?dataset_id=b1c72d84f3501797&dbkey=%3F&hda_ldda=hda",

             "html": "Trackster",
             "target": "_top"
         }
     ]
}


Hans-Rudolf


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Re: testing the visualization plugins

Carl Eberhard
Ok. Very strange. I'm unable to reproduce this with galaxy-dist 57d1b77 (stable).

Can you apply the attached patch, load a history with a simple bed file (say: test-data/1.bed - or any bed file), and reply with what the logs say?

You can safely revert that change after we're done.


On Thu, Aug 28, 2014 at 9:29 AM, Hans-Rudolf Hotz <[hidden email]> wrote:
Hi Carl

Thanks for your help  - unfortunately no success so far


Let's try two things:

*First*, let's clear the browser cache to rule out that annoyance:

This didn't change anything. I have also tried different computers and different browsers


*Second*, let's see what the server ends up sending the client for
visualizations:

it just looks like this:

    "visible": true,
    "visualizations": [
        {
            "embeddable": false,
            "href": "/visualization/trackster?dataset_id=b1c72d84f3501797&dbkey=%3F&hda_ldda=hda",
            "html": "Trackster",
            "target": "_top"
        }
    ]
}


Hans-Rudolf




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Solved - Re: testing the visualization plugins

Hans-Rudolf Hotz
Hi all

First of all, a big Thanks to Carl who helped me fixing this problem.

So as a summary for all, the problem was caused by a datatype (an
extension to tabular), I manually added to "datatypes_conf.xml"

Removing the datatype fixed the problem. I couldn't identify a syntax
problem, neither in "datatypes_conf.xml" nor in
"~/lib/galaxy/datatypes/registry.py" and
"~/lib/galaxy/datatypes/tabular.py". However, renaming it (in all three
files) fixed it as well.

Regards, Hans-Rudolf
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