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From Stian Soiland-Reyes <st...@apache.org>
Subject Re: Problem on Taverna Plugin Installation
Date Wed, 10 Feb 2016 10:02:48 GMT
Looking at ~/.taverna-core-2.5.0/taverna-core-2.5.0.log I get

WARN  2016-02-10 09:40:48,187
(net.sf.taverna.raven.repository.impl.ArtifactImpl:85) - XML SAX error
for /home/stain/.taverna-core-2.5.0
/repository/gr/dianatools/diana.services-activity/1.0-SNAPSHOT/diana.services-activity-1.0-SNAPSHOT.pom
org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 50; White
spaces are required between publicId and systemId.
        at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
        at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)
        at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
        at net.sf.taverna.raven.repository.impl.ArtifactImpl.readAndParseXML(ArtifactImpl.java:560)
        at net.sf.taverna.raven.repository.impl.ArtifactImpl.readXML(ArtifactImpl.java:526)
        at net.sf.taverna.raven.repository.impl.ArtifactImpl.getPackageType(ArtifactImpl.java:280)
        at net.sf.taverna.raven.repository.impl.LocalRepository.act(LocalRepository.java:530)
        at net.sf.taverna.raven.repository.impl.LocalRepository.update(LocalRepository.java:510)
        at net.sf.taverna.raven.plugins.PluginManager.addPlugin(PluginManager.java:221)
        at net.sf.taverna.raven.plugins.ui.PluginSiteFrame$4.run(PluginSiteFrame.java:426)

and the same for diana-services-activity-ui.

If I inspect those downloaded POM files locally I see it's no wonder
the XML is not parsing, as I find HTML like:

<title>300 Multiple Choices</title>
</head><body>
<h1>Multiple Choices</h1>
The document name you requested
(<code>/~diana/DIANA_plugin_updated/test-plugins/gr/dianatools/diana.services-activity-ui/1.0-SNAPSHOT/diana.services-activity-ui-1.0-SNAPSHOT.pom</code>)
could not be found on this server.
However, we found documents with names similar to the one you
requested.<p>Available documents:
<ul>
<li><a href="/~diana/DIANA_plugin_updated/test-plugins/gr/dianatools/diana.services-activity-ui/1.0-SNAPSHOT/diana.services-activity-ui-1.0-20150430.174001-1.pom.md5">/~diana/DIANA_plugin_updated/test-plugins/gr/dianatools/diana.services-activity-ui/1.0-SNAPSHOT/diana.services-activity-ui-1.0-20150430.174001-1.pom.md5</a>
(common basename)
<li><a href="/~diana/DIANA_plugin_updated/test-plugins/gr/dianatools/diana.services-activity-ui/1.0-SNAPSHOT/diana.services-activity-ui-1.0-20150430.174001-1-test-sources.jar.md5">/~diana/DIANA_plugin_updated/test-plugins/gr/dianatools/diana.services-activity-ui/1.0-SNAPSHOT/diana.services-activity-ui-1.0-20150430.174001-1-test-sources.jar.md5</a>
(common basename)

So this seems to come from Taverna trying to first fetch these URLs:

http://192.185.115.65/~diana/DIANA_plugin_updated/test-plugins/gr/dianatools/diana.services-activity/1.0-SNAPSHOT/diana.services-activity-1.0-SNAPSHOT.pom
http://192.185.115.65/~diana/DIANA_plugin_updated/test-plugins/gr/dianatools/diana.services-activity-ui/1.0-SNAPSHOT/diana.services-activity-ui-1.0-SNAPSHOT.pom


I don't think Taverna 2's plugin system is handling that 300 response
correctly as it stores the 300 error HTML as if it was the successful
pom downloaded.  Taverna would normally try to get the specific
version directly, if a 404 Not Found, it will looking in
maven-metadata.xml to find the latest version

See https://github.com/taverna/taverna2-raven/blob/maintenance/raven/src/main/java/net/sf/taverna/raven/repository/impl/LocalRepository.java#L766


Are you able to reconfigure your Apache server to avoid this "similar
name matching" and return 404 for those non-matching URIs?

Something like

CheckSpelling Off

in .htaccess for /~diana/DIANA_plugin_updated/ should do.


Alternatively if you release your plugin in a non-SNAPSHOT version,
then it should also work well.

BTW - in your repository list at
http://192.185.115.65/~diana/DIANA_plugin_updated/test-plugins/diana.services-plugin-1.0-SNAPSHOT.xml
you should remove all repositories except:

<repository>http://www.mygrid.org.uk/maven/repository/</repository>
<repository>http://192.185.115.65/~diana/DIANA_plugin_updated/test-plugins/</repository>


http://192.185.115.65/~diana/DIANA_plugin_updated should also be
removed as it is one level too high (e.g.
http://192.185.115.65/~diana/DIANA_plugin_updated/gr/dianatools/diana.services-activity-ui
does not exist) - this adds lots of unnecessary requests.


You should delete all of ~/.taverna-core-2.5.0/repository (or
equivalent) to force re-download, and delete
~/.taverna-core-2.5.0/plugins to install the plugin from fresh.

On 10 February 2016 at 09:16, Alan Williams <alaninmcr@googlemail.com> wrote:
>
>
>
> -------- Forwarded Message --------
> Subject: Re: Problem on Taverna Plugin Installation
> Date: Tue, 09 Feb 2016 21:46:13 +0200
> From: PARASKEVOPOULOU MARIA <mparaskevopoulou@uth.gr>
> To: alaninmcr <alaninmcr@googlemail.com>
>
> Hi Ian,
>
> For Taverna v2.5. in order to install the plugin, the following plugin
> site should be added :
> http://192.185.115.65/~diana/DIANA_plugin_updated/test-plugins/. You
> can also see the relevant information on our site
> http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=site/help&topic=taverna.
>
> Thank you in advance for your support.
>
> Best regards,
> Maria
>
> Quoting alaninmcr <alaninmcr@googlemail.com>:
>
>
>> -------- Forwarded Message --------
>> Subject: Re: Problem on Taverna Plugin Installation
>> Date: Tue, 9 Feb 2016 13:57:08 +0000
>> From: Ian Dunlop <ian.dunlop@manchester.ac.uk>
>> Reply-To: dev@taverna.incubator.apache.org
>> To: dev@taverna.incubator.apache.org
>>
>> Hello,
>>
>> What does the plugins.xml say eg
>> /home/johndoe/.taverna-core-2.5.0/plugins.xml. Maybe taverna can't find
>> your server for some reason.
>>
>> Where is your plugin deployed ie the info you put in when adding a new
>> plugin site? We could then try and install it and see if we get the same
>> result.
>>
>> Cheers,
>>
>> Ian
>>
>> On 08/02/2016 18:52, PARASKEVOPOULOU MARIA wrote:
>>>
>>> Dear Taverna team,
>>>
>>> We have implemented a Taverna plugin incorporating services and
>>> algorithms implemented in the DIANA LAB (www.microrna.gr).
>>> The plugin initially worked for Taverna 2.3, while several months ago we
>>> have updated the plugin and had it functional for both Taverna 2.3 and
>>> 2.5 versions.
>>>
>>> However, the last month DIANA users complain that they cannot add the
>>> DIANA Taverna plugin in their Taverna workbench.
>>>
>>> The installation has been performed several times in the past with
>>> success.
>>> We uninstalled the plugin from our server and also observed a failure in
>>> the reinstallation.
>>> We redeployed the plugin but the error remains.
>>>
>>> The logs produced in Taverna, report a failure in fetching a Pom file.
>>>
>>>
>>> "WARN  2015-07-22 19:34:34,036
>>> (net.sf.taverna.raven.repository.impl.LocalRepository:85) - Could not
>>> read com.example:DIANA_Services-activity-ui:1.2-SNAPSHOT from
>>> http://www.mygrid.org.uk/maven/biomoby/biomoby.org/m2repo/
>>> java.io.IOException: Server returned HTTP response code: 409 for URL:
>>>
>>> http://repository.mygrid.org.uk/artifactory/biomoby/com/example/DIANA_Services-activity-ui/1.2-SNAPSHOT/DIANA_Services-activity-ui-1.2-SNAPSHOT.pom
>>>
>>> "
>>> We assume that this failure is due to the fact that Taverna is not
>>> trying to install/download the DIANA plugin from our server,defined in
>>> the plugin's project pom.xml, but from http://repository.mygrid.org.uk.
>>>
>>> Did something change concerning the format of the project pom.xml that
>>> is utilized for the plugin deployment?
>>> Will the error be fixed, if we change the pom.xml? For the the pom.xml
>>> design we followed a similar format as in the following pom file
>>> https://github.com/taverna/taverna-prov/blob/master/pom.xml.
>>>
>>> It would be grateful if we could have your feedback on how to
>>> troubleshoot the issue.
>>>
>>> Thank you in advance,
>>>
>>> DIANA Team
>>>
>>
>> --
>> Ian Dunlop, eScience Lab
>> School of Computer Science
>> The University of Manchester
>> http://orcid.org/0000-0001-7066-3350
>
>
>
>
>
>



-- 
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718

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