Why i can't install ChEMBL nodes on KNIME

#1

I have some workflows (for example, the workflows developed by 3D-e-Chem) that use this nodes and now i can’t use this because in the installation files are not included.

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#2

Hi @ocasanova,
are you having trouble installing these extensions, you probably do not have the Experimental community extensions update site enabled. Take a look at the community extensions documentation page, it explains how to enable that update site, then your extensions should work again.

https://docs.knime.com/2019-06/analytics_platform_extensions_and_integrations/index.html#community-extensions

best,
Gabriel

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#3

Hi, thanks for the answer.
Are you referring to Nightly Builds???
because in another case I have enabled the Community Contributions (Experimental) and when I install the extensions I mark all of them.

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#4

I see you are using downloaded jar files instead of the online update sites, maybe they are not up to date?
Can you try using the online update site?
best,
Gabriel

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#5

Thanks again for the answer.
I use the last .zip available and the version 4.0.2. The problem now is that when I put the trunk file or Nightly Builds (.zip) and execute the installation, after restart, KNIME open and all views are white and don’t work any view and report several problems.

I can’t use the direct url because my university use a proxy server and I can’t use the online form.

Best
Omar

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#6

That is disconcerting, can you please send us your knime.log files?

Did you try entering the proxy information in the KNIME AP preferences? Then you should be able to use the online instal.

best,
Gabriel

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#7

Hi, gab1one
Thanks for your answer again
Here there is a picture showing how it look like.


And the log file is here
knime.log (2.6 MB)

About the internet connection when i start KNIME, ask for authentication and in this point I ask Is sufficient with that or not?

Best
Omar

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#8

Did you try starting KNIME AP with the -clean option?

Are you installing all available extensions from the nightly update site, or just the ChEMBL ones? If the former is true, try only installing the ChEMBL extension, confirm that it works and then add additional extensions as needed.

best,
Gabriel

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#9

Thanks for your answer

Using -clean options don´t solve the problem. I solve installing KNIME 4.0.1 and installing the nodes from the Community of the 4.0.0 version (Community Contributions and Trusted Community Contributions). Nightly builds continue without work properly.

But when I try to connect directly to the site through the proxy I have this errors
Some sites could not be found. See the error log for more detail.
Unable to read repository at http://update.knime.com/community-contributions/4.0/content.xml.
Connect to update.knime.com:80 timed out
Unable to read repository at http://update.knime.com/community-contributions/trusted/4.0/content.xml.
Connect to update.knime.com:80 timed out

The log file say

2019-10-30 13:49:09,589 : WARN : KNIME-Worker-1 : : TipsAndNewsInjector : : : Could not modify intro page: connect timed out
java.net.SocketTimeoutException: connect timed out
at java.net.DualStackPlainSocketImpl.waitForConnect(Native Method)
at java.net.DualStackPlainSocketImpl.socketConnect(DualStackPlainSocketImpl.java:85)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:666)
at sun.net.NetworkClient.doConnect(NetworkClient.java:175)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:463)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:558)
at sun.net.www.protocol.https.HttpsClient.(HttpsClient.java:264)
at sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:367)
at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:191)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1156)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1050)
at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:177)
at sun.net.www.protocol.https.HttpsURLConnectionImpl.connect(HttpsURLConnectionImpl.java:162)
at org.knime.product.rcp.intro.TipsAndNewsInjector.prepareData(TipsAndNewsInjector.java:220)
at org.knime.product.rcp.intro.AbstractInjector.run(AbstractInjector.java:145)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:246)
2019-10-30 13:49:09,964 : WARN : KNIME-Worker-0 : : TileUpdateMessageInjector : : : Could not modify intro page: connect timed out
java.net.SocketTimeoutException: connect timed out
at java.net.DualStackPlainSocketImpl.waitForConnect(Native Method)
at java.net.DualStackPlainSocketImpl.socketConnect(DualStackPlainSocketImpl.java:85)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at sun.net.NetworkClient.doConnect(NetworkClient.java:175)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:463)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:558)
at sun.net.www.http.HttpClient.(HttpClient.java:242)
at sun.net.www.http.HttpClient.New(HttpClient.java:339)
at sun.net.www.http.HttpClient.New(HttpClient.java:357)
at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1220)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1156)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1050)
at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:984)
at org.knime.core.eclipseUtil.UpdateChecker.checkForNewRelease(UpdateChecker.java:181)
at org.knime.product.rcp.intro.UpdateDetector.checkForNewRelease(UpdateDetector.java:85)
at org.knime.product.rcp.intro.TileUpdateMessageInjector.prepareData(TileUpdateMessageInjector.java:89)
at org.knime.product.rcp.intro.AbstractInjector.run(AbstractInjector.java:145)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:246)
2019-10-30 14:11:56,714 : ERROR : Clear OSGi configuration : : InvokeInstallSiteAction : : : Could not clean OSGi configuration area: C:\Program Files\KNIME\configuration\org.eclipse.osgi\193\0.cp\os\win32\x86_64\localfile_1_0_0.dll
2019-10-30 14:29:46,933 : ERROR : Clear OSGi configuration : : InvokeInstallSiteAction : : : Could not clean OSGi configuration area: C:\Program Files\KNIME\configuration\org.eclipse.osgi\1137\0.cp\org\xerial\snappy\native\Windows\x86_64\snappyjava.dll
2019-10-30 14:46:59,627 : ERROR : Clear OSGi configuration : : InvokeInstallSiteAction : : : Could not clean OSGi configuration area: C:\Program Files\KNIME\configuration\org.eclipse.osgi\1270\0.cp\org\xerial\snappy\native\Windows\x86_64\snappyjava.dll
2019-10-30 14:54:49,852 : ERROR : Clear OSGi configuration : : InvokeInstallSiteAction : : : Could not clean OSGi configuration area: C:\Program Files\KNIME\configuration\org.eclipse.osgi\1270\0.cp\org\xerial\snappy\native\Windows\x86_64\snappyjava.dll

I transform in Edit/Preferences/General/Network Connections to connect and say that errors.

strong text
Best
Omar

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#10

Hi @ocasanova,

I investigated the ChEMBL extension and it is not available for KNIME 4.0, as the authors did not update them for 4.0.
You can however take a look at the following components:

You see how to access ChEMBL without this extension.

Regarding the proxy, it seems like the configuration is not correct, I know from personal experience that the proxy setup is prone to mistakes.

best,
Gabriel

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#11

Hi @gab1one

Thanks for the reply
Thanks for the answer and I am going to fix the proxy configuration
Thanks for all your effort

Best

Omar

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closed #12

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