Answers.Body: <p>This is a tough one, because the only relevant lines from your GSEA debug log were these two:</p>
  
  <pre><code>DEBUG - http-outgoing-4 &lt;&lt; "Failed: empty String"
  DEBUG - http-outgoing-4 &lt;&lt; HTTP/1.1 500 Internal Server Error
  </code></pre>
  
  <p>My recommendations to you at the time would've been</p>
  
  <ol>
  <li>try closing all the programs, restarting them, possibly rebooting and restarting them, and even analyzing a completely different set of data to see if you get the same results, <strong>—or—</strong></li>
  <li>update to the latest Java 8, reinstall Cytoscape 3.7.whatever and the EnrichmentMap plugin from scratch, and re-download GSEA, <strong>—or—</strong></li>
  <li>lastly, try reinstalling everything on a completely different machine/OS and see if you get different results (<em>e.g.,</em> try on a Mac or Linux if you had problems with Windows originally, or vice-versa)</li>
  </ol>
  
  <p>I know that's lame, but sometimes that's how you solve weird computer errors, when the error message the application itself gives you is non-specific and unhelpful.</p>
  
  <p>If you had seen the error message</p>
  
  <pre><code>None of the gene sets have passed the filter. Try relaxing the gene set filter parameters.
  </code></pre>
  
  <p>in the GSEA application logs, then you would've had the problem described in EnrichmentMap's GitHub <a href="https://github.com/BaderLab/EnrichmentMapApp/issues/358" rel="nofollow noreferrer">issue #358</a>, and the solution would be to use less stringent p- and FDR Q-value cutoffs, as prescribed in the "<a href="https://enrichmentmap.readthedocs.io/en/latest/Parameters.html?highlight=filter#id1" rel="nofollow noreferrer">Tips on Parameter Choice</a>" section of the <a href="https://enrichmentmap.readthedocs.io/en/latest/index.html" rel="nofollow noreferrer">EnrichmentMap documentation</a>.</p>
  
  <p><em>My</em> problem was that GSEA's default cutoffs (p-value &lt; 0.005 and FDR Q-value &lt; 0.1) were entirely too stringent for my results set, and using the "Very permissive" settings of p-value &lt; 0.05 and FDR &lt; 0.25 from the documentation solved it for me. </p>
  
  <p>Hopefully this benefits someone who ends up here after googling for "Unable to create Enrichment Map:Internal Server ErrorResponseEntityProxy," which is just a stupendously unhelpful error message when "None of the gene sets have passed the filter" is <em>actually</em> what went wrong. Maybe go thumbs-up <a href="https://github.com/BaderLab/EnrichmentMapApp/issues/358#issuecomment-488370349" rel="nofollow noreferrer">this comment</a> in the EnrichmentMap issue tracker, if you think the maintainers need to work on that.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-01T19:42:38.677Z
Answers.LastActivityDate: 2019-05-01T19:48:06.460Z
Answers.LastEditDate: 2019-05-01T19:48:06.460Z
Answers.UserDisplayName: Kevin E
Body: <p>I am trying to visualize a GSEA analysis I conducted using the Broad Institute's GSEA Enrichment Map Visualization, however I get the following error and am not sure what the issue is: any help would be greatly appreciated. </p>
  
  <pre><code>INFO - successfully connected to cytoscape rest
  INFO - successfully connected to cytoscape rest
  INFO - Found enrichment map command
  INFO - Get URL:http://localhost:1234/v1/commands/enrichmentmap/gseabuild?edbdir=C%3A%5CUsers%5CHatim%5Cgsea_home%5Coutput%5Cmar15%5Cmy_analysis.Gsea.1552686798457%5Cedb&amp;pvalue=0.005&amp;qvalue=0.1&amp;overlap=0.5&amp;similaritymetric=OVERLAP&amp;combinedconstant=0.5&amp;expressionfile=C%3A%5CUsers%5CHatim%5CDesktop%5CJunior%5Csem+2%5CKarras+Lab%5CGSEA%5CKarrasEXP.gct.txt
  DEBUG - CookieSpec selected: default
  DEBUG - Auth cache not set in the context
  DEBUG - Connection request: [route: {}-&gt;http://localhost:1234][total kept alive: 0; route allocated: 0 of 2; total allocated: 0 of 20]
  DEBUG - Connection leased: [id: 4][route: {}-&gt;http://localhost:1234][total kept alive: 0; route allocated: 1 of 2; total allocated: 1 of 20]
  DEBUG - Opening connection {}-&gt;http://localhost:1234
  DEBUG - Connecting to localhost/127.0.0.1:1234
  DEBUG - Connection established 127.0.0.1:51968&lt;-&gt;127.0.0.1:1234
  DEBUG - Executing request GET /v1/commands/enrichmentmap/gseabuild?edbdir=C%3A%5CUsers%5CHatim%5Cgsea_home%5Coutput%5Cmar15%5Cmy_analysis.Gsea.1552686798457%5Cedb&amp;pvalue=0.005&amp;qvalue=0.1&amp;overlap=0.5&amp;similaritymetric=OVERLAP&amp;combinedconstant=0.5&amp;expressionfile=C%3A%5CUsers%5CHatim%5CDesktop%5CJunior%5Csem+2%5CKarras+Lab%5CGSEA%5CKarrasEXP.gct.txt HTTP/1.1
  DEBUG - Target auth state: UNCHALLENGED
  DEBUG - Proxy auth state: UNCHALLENGED
  DEBUG - http-outgoing-4 &gt;&gt; GET /v1/commands/enrichmentmap/gseabuild?edbdir=C%3A%5CUsers%5CHatim%5Cgsea_home%5Coutput%5Cmar15%5Cmy_analysis.Gsea.1552686798457%5Cedb&amp;pvalue=0.005&amp;qvalue=0.1&amp;overlap=0.5&amp;similaritymetric=OVERLAP&amp;combinedconstant=0.5&amp;expressionfile=C%3A%5CUsers%5CHatim%5CDesktop%5CJunior%5Csem+2%5CKarras+Lab%5CGSEA%5CKarrasEXP.gct.txt HTTP/1.1
  DEBUG - http-outgoing-4 &gt;&gt; Host: localhost:1234
  DEBUG - http-outgoing-4 &gt;&gt; Connection: Keep-Alive
  DEBUG - http-outgoing-4 &gt;&gt; User-Agent: Apache-HttpClient/4.5.2 (Java/1.8.0_201)
  DEBUG - http-outgoing-4 &gt;&gt; Accept-Encoding: gzip,deflate
  DEBUG - http-outgoing-4 &gt;&gt; "GET /v1/commands/enrichmentmap/gseabuild?edbdir=C%3A%5CUsers%5CHatim%5Cgsea_home%5Coutput%5Cmar15%5Cmy_analysis.Gsea.1552686798457%5Cedb&amp;pvalue=0.005&amp;qvalue=0.1&amp;overlap=0.5&amp;similaritymetric=OVERLAP&amp;combinedconstant=0.5&amp;expressionfile=C%3A%5CUsers%5CHatim%5CDesktop%5CJunior%5Csem+2%5CKarras+Lab%5CGSEA%5CKarrasEXP.gct.txt HTTP/1.1[\r][\n]"
  DEBUG - http-outgoing-4 &gt;&gt; "Host: localhost:1234[\r][\n]"
  DEBUG - http-outgoing-4 &gt;&gt; "Connection: Keep-Alive[\r][\n]"
  DEBUG - http-outgoing-4 &gt;&gt; "User-Agent: Apache-HttpClient/4.5.2 (Java/1.8.0_201)[\r][\n]"
  DEBUG - http-outgoing-4 &gt;&gt; "Accept-Encoding: gzip,deflate[\r][\n]"
  DEBUG - http-outgoing-4 &gt;&gt; "[\r][\n]"
  DEBUG - http-outgoing-4 &lt;&lt; "HTTP/1.1 500 Internal Server Error[\r][\n]"
  DEBUG - http-outgoing-4 &lt;&lt; "Date: Sun, 17 Mar 2019 06:55:04 GMT[\r][\n]"
  DEBUG - http-outgoing-4 &lt;&lt; "Content-Type: text/plain[\r][\n]"
  DEBUG - http-outgoing-4 &lt;&lt; "Access-Control-Allow-Origin: *[\r][\n]"
  DEBUG - http-outgoing-4 &lt;&lt; "Access-Control-Allow-Headers: origin, content-type, accept, authorization[\r][\n]"
  DEBUG - http-outgoing-4 &lt;&lt; "Access-Control-Allow-Credentials: true[\r][\n]"
  DEBUG - http-outgoing-4 &lt;&lt; "Access-Control-Allow-Methods: GET, POST, PUT, DELETE, OPTIONS, HEAD[\r][\n]"
  DEBUG - http-outgoing-4 &lt;&lt; "Content-Length: 20[\r][\n]"
  DEBUG - http-outgoing-4 &lt;&lt; "Server: Jetty(9.4.10.v20180503)[\r][\n]"
  DEBUG - http-outgoing-4 &lt;&lt; "[\r][\n]"
  DEBUG - http-outgoing-4 &lt;&lt; "Failed: empty String"
  DEBUG - http-outgoing-4 &lt;&lt; HTTP/1.1 500 Internal Server Error
  DEBUG - http-outgoing-4 &lt;&lt; Date: Sun, 17 Mar 2019 06:55:04 GMT
  DEBUG - http-outgoing-4 &lt;&lt; Content-Type: text/plain
  DEBUG - http-outgoing-4 &lt;&lt; Access-Control-Allow-Origin: *
  DEBUG - http-outgoing-4 &lt;&lt; Access-Control-Allow-Headers: origin, content-type, accept, authorization
  DEBUG - http-outgoing-4 &lt;&lt; Access-Control-Allow-Credentials: true
  DEBUG - http-outgoing-4 &lt;&lt; Access-Control-Allow-Methods: GET, POST, PUT, DELETE, OPTIONS, HEAD
  DEBUG - http-outgoing-4 &lt;&lt; Content-Length: 20
  DEBUG - http-outgoing-4 &lt;&lt; Server: Jetty(9.4.10.v20180503)
  DEBUG - Connection can be kept alive indefinitely
  INFO - status:Internal Server Error
  INFO - Unable to create Enrichment Map:Internal Server ErrorResponseEntityProxy{[Content-Type: text/plain,Content-Length: 20,Chunked: false]}
  DEBUG - Connection manager is shutting down
  DEBUG - http-outgoing-4: Close connection
  DEBUG - Connection manager shut down
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-03-18T08:22:52.447Z
Comments.Text: Could you please explain the steps to reproduce this error? What data did you load, the settings and steps to connect to Cytoscape... and what do you expect from us. To me it seems like we should debug the GSEA software in order to solve this problem...
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-08T08:56:35.763Z
Comments.Text: @ham123 Could you kindly review the answer below? I believe this should be definitely be upvoted and "accepted". The site member is knowledgeable in this specific problem.
Comments.UserDisplayName: M__
Tags: <errors><gsea>
Title: I get the following error when using the GSEA software 'Enrichment Map Visualization' tool using the Cytoscape 3.7.1 application
ThreadText: # I get the following error when using the GSEA software 'Enrichment Map Visualization' tool using the Cytoscape 3.7.1 application
  
  (Asked by: username_0 on 2019-03-17)
  
  I am trying to visualize a GSEA analysis I conducted using the Broad Institute's GSEA Enrichment Map Visualization, however I get the following error and am not sure what the issue is: any help would be greatly appreciated.
  
  ```
  INFO - successfully connected to cytoscape rest
  INFO - successfully connected to cytoscape rest
  INFO - Found enrichment map command
  INFO - Get URL:http://localhost:1234/v1/commands/enrichmentmap/gseabuild?edbdir=C%3A%5CUsers%5CHatim%5Cgsea_home%5Coutput%5Cmar15%5Cmy_analysis.Gsea.1552686798457%5Cedb&pvalue=0.005&qvalue=0.1&overlap=0.5&similaritymetric=OVERLAP&combinedconstant=0.5&expressionfile=C%3A%5CUsers%5CHatim%5CDesktop%5CJunior%5Csem+2%5CKarras+Lab%5CGSEA%5CKarrasEXP.gct.txt
  DEBUG - CookieSpec selected: default
  DEBUG - Auth cache not set in the context
  DEBUG - Connection request: [route: {}->http://localhost:1234][total kept alive: 0; route allocated: 0 of 2; total allocated: 0 of 20]
  DEBUG - Connection leased: [id: 4][route: {}->http://localhost:1234][total kept alive: 0; route allocated: 1 of 2; total allocated: 1 of 20]
  DEBUG - Opening connection {}->http://localhost:1234
  DEBUG - Connecting to localhost/127.0.0.1:1234
  DEBUG - Connection established 127.0.0.1:51968<->127.0.0.1:1234
  DEBUG - Executing request GET /v1/commands/enrichmentmap/gseabuild?edbdir=C%3A%5CUsers%5CHatim%5Cgsea_home%5Coutput%5Cmar15%5Cmy_analysis.Gsea.1552686798457%5Cedb&pvalue=0.005&qvalue=0.1&overlap=0.5&similaritymetric=OVERLAP&combinedconstant=0.5&expressionfile=C%3A%5CUsers%5CHatim%5CDesktop%5CJunior%5Csem+2%5CKarras+Lab%5CGSEA%5CKarrasEXP.gct.txt HTTP/1.1
  DEBUG - Target auth state: UNCHALLENGED
  DEBUG - Proxy auth state: UNCHALLENGED
  DEBUG - http-outgoing-4 >> GET /v1/commands/enrichmentmap/gseabuild?edbdir=C%3A%5CUsers%5CHatim%5Cgsea_home%5Coutput%5Cmar15%5Cmy_analysis.Gsea.1552686798457%5Cedb&pvalue=0.005&qvalue=0.1&overlap=0.5&similaritymetric=OVERLAP&combinedconstant=0.5&expressionfile=C%3A%5CUsers%5CHatim%5CDesktop%5CJunior%5Csem+2%5CKarras+Lab%5CGSEA%5CKarrasEXP.gct.txt HTTP/1.1
  DEBUG - http-outgoing-4 >> Host: localhost:1234
  DEBUG - http-outgoing-4 >> Connection: Keep-Alive
  DEBUG - http-outgoing-4 >> User-Agent: Apache-HttpClient/4.5.2 (Java/1.8.0_201)
  DEBUG - http-outgoing-4 >> Accept-Encoding: gzip,deflate
  DEBUG - http-outgoing-4 >> "GET /v1/commands/enrichmentmap/gseabuild?edbdir=C%3A%5CUsers%5CHatim%5Cgsea_home%5Coutput%5Cmar15%5Cmy_analysis.Gsea.1552686798457%5Cedb&pvalue=0.005&qvalue=0.1&overlap=0.5&similaritymetric=OVERLAP&combinedconstant=0.5&expressionfile=C%3A%5CUsers%5CHatim%5CDesktop%5CJunior%5Csem+2%5CKarras+Lab%5CGSEA%5CKarrasEXP.gct.txt HTTP/1.1[\r][\n]"
  DEBUG - http-outgoing-4 >> "Host: localhost:1234[\r][\n]"
  DEBUG - http-outgoing-4 >> "Connection: Keep-Alive[\r][\n]"
  DEBUG - http-outgoing-4 >> "User-Agent: Apache-HttpClient/4.5.2 (Java/1.8.0_201)[\r][\n]"
  DEBUG - http-outgoing-4 >> "Accept-Encoding: gzip,deflate[\r][\n]"
  DEBUG - http-outgoing-4 >> "[\r][\n]"
  DEBUG - http-outgoing-4 << "HTTP/1.1 500 Internal Server Error[\r][\n]"
  DEBUG - http-outgoing-4 << "Date: Sun, 17 Mar 2019 06:55:04 GMT[\r][\n]"
  DEBUG - http-outgoing-4 << "Content-Type: text/plain[\r][\n]"
  DEBUG - http-outgoing-4 << "Access-Control-Allow-Origin: *[\r][\n]"
  DEBUG - http-outgoing-4 << "Access-Control-Allow-Headers: origin, content-type, accept, authorization[\r][\n]"
  DEBUG - http-outgoing-4 << "Access-Control-Allow-Credentials: true[\r][\n]"
  DEBUG - http-outgoing-4 << "Access-Control-Allow-Methods: GET, POST, PUT, DELETE, OPTIONS, HEAD[\r][\n]"
  DEBUG - http-outgoing-4 << "Content-Length: 20[\r][\n]"
  DEBUG - http-outgoing-4 << "Server: Jetty(9.4.10.v20180503)[\r][\n]"
  DEBUG - http-outgoing-4 << "[\r][\n]"
  DEBUG - http-outgoing-4 << "Failed: empty String"
  DEBUG - http-outgoing-4 << HTTP/1.1 500 Internal Server Error
  DEBUG - http-outgoing-4 << Date: Sun, 17 Mar 2019 06:55:04 GMT
  DEBUG - http-outgoing-4 << Content-Type: text/plain
  DEBUG - http-outgoing-4 << Access-Control-Allow-Origin: *
  DEBUG - http-outgoing-4 << Access-Control-Allow-Headers: origin, content-type, accept, authorization
  DEBUG - http-outgoing-4 << Access-Control-Allow-Credentials: true
  DEBUG - http-outgoing-4 << Access-Control-Allow-Methods: GET, POST, PUT, DELETE, OPTIONS, HEAD
  DEBUG - http-outgoing-4 << Content-Length: 20
  DEBUG - http-outgoing-4 << Server: Jetty(9.4.10.v20180503)
  DEBUG - Connection can be kept alive indefinitely
  INFO - status:Internal Server Error
  INFO - Unable to create Enrichment Map:Internal Server ErrorResponseEntityProxy{[Content-Type: text/plain,Content-Length: 20,Chunked: false]}
  DEBUG - Connection manager is shutting down
  DEBUG - http-outgoing-4: Close connection
  DEBUG - Connection manager shut down
  
  ```
  
  **Tags:** errors, gsea
  
  > **Comments:**
  > **username_1**: Could you please explain the steps to reproduce this error? What data did you load, the settings and steps to connect to Cytoscape... and what do you expect from us. To me it seems like we should debug the GSEA software in order to solve this problem...  
  > **username_2**: @username_0 Could you kindly review the answer below? I believe this should be definitely be upvoted and "accepted". The site member is knowledgeable in this specific problem.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2019-05-01. Score: 1
  
  This is a tough one, because the only relevant lines from your GSEA debug log were these two:
  
  ```
  DEBUG - http-outgoing-4 << "Failed: empty String"
  DEBUG - http-outgoing-4 << HTTP/1.1 500 Internal Server Error
  
  ```
  
  My recommendations to you at the time would've been
  
  1. try closing all the programs, restarting them, possibly rebooting and restarting them, and even analyzing a completely different set of data to see if you get the same results, **—or—**
  2. update to the latest Java 8, reinstall Cytoscape 3.7.whatever and the EnrichmentMap plugin from scratch, and re-download GSEA, **—or—**
  3. lastly, try reinstalling everything on a completely different machine/OS and see if you get different results (*e.g.,* try on a Mac or Linux if you had problems with Windows originally, or vice-versa)
  
  I know that's lame, but sometimes that's how you solve weird computer errors, when the error message the application itself gives you is non-specific and unhelpful.
  
  If you had seen the error message
  
  ```
  None of the gene sets have passed the filter. Try relaxing the gene set filter parameters.
  
  ```
  
  in the GSEA application logs, then you would've had the problem described in EnrichmentMap's GitHub [issue #358](https://github.com/BaderLab/EnrichmentMapApp/issues/358), and the solution would be to use less stringent p- and FDR Q-value cutoffs, as prescribed in the "[Tips on Parameter Choice](https://enrichmentmap.readthedocs.io/en/latest/Parameters.html?highlight=filter#id1)" section of the [EnrichmentMap documentation](https://enrichmentmap.readthedocs.io/en/latest/index.html).
  
  *My* problem was that GSEA's default cutoffs (p-value < 0.005 and FDR Q-value < 0.1) were entirely too stringent for my results set, and using the "Very permissive" settings of p-value < 0.05 and FDR < 0.25 from the documentation solved it for me.
  
  Hopefully this benefits someone who ends up here after googling for "Unable to create Enrichment Map:Internal Server ErrorResponseEntityProxy," which is just a stupendously unhelpful error message when "None of the gene sets have passed the filter" is *actually* what went wrong. Maybe go thumbs-up [this comment](https://github.com/BaderLab/EnrichmentMapApp/issues/358#issuecomment-488370349) in the EnrichmentMap issue tracker, if you think the maintainers need to work on that.
  
  
  ---
  
  