Portal:CPTAC

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[[Category:Portals]]

Current revision

edit  

CPTAC Pathways

Welcome to the CPTAC Pathway Portal

This portal highlights pathway content relevant to the Clinical Proteomic Tumor Analysis Consortium (CPTAC).

The National Cancer Institute, part of the National Institutes of Health, announced the launch of a Clinical Proteomic Tumor Analysis Consortium in August 2011. CPTAC is a comprehensive and coordinated effort to accelerate the understanding of the molecular basis of cancer through the application of robust, quantitative, proteomic technologies and workflows. The overarching goal of CPTAC is to improve our ability to diagnose, treat and prevent cancer. To achieve this goal in a scientifically rigorous manner, the NCI launched CPTAC to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, and provide this data with accompanying assays and protocols to the public.

The pathways included in this portal have been organized into classic cancer hallmark categories, based on the different biological capabilities acquired during the multistep development of human tumors. To read more, see Hallmarks of cancer: the next generation, Hanahan and Weinberg, Cell 2011.

edit  

Cancer Hallmark Categories

Sustaining proliferative signaling

FBXL10 enhancement of MAP/ERK signaling in diffuse large B-cell lymphoma (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/4/41/WP4553_94637.svg:
Status:1
Message:Exception in thread "main" java.lang.NullPointerException at org.pathvisio.core.Engine.getPathwayImporters(Unknown Source) at org.pathvisio.core.Engine.importPathway(Unknown Source) at org.pathvisio.core.util.Converter.main(Unknown Source)


Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways" "/var/www/wikipathways/images/4/41/WP4553_94637.svg" 2>&1
' in /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php:1255 Stack trace:

  1. 0 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1227): Pathway::convertWithPathVisio(false, '/var/www/wikipa...')
  2. 1 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1137): Pathway->saveConvertedByPathVisioCache('svg')
  3. 2 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1153): Pathway->updateCache('svg')
  4. 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(129): Pathway->getImage()
  5. 4 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(53): makeThumbLinkObj(Object(Pathway), 'FBXL10 enhancem...', 'https://classic...', 'FBXL10 enhancem...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP4553', '300', 'center', 'FBXL10 enhancem...', 'pathway', 'FBXL10 enhancem...')
  7. 6 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
  8. 7 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  9. 8 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  10. 9 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  11. 10 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  12. 11 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{Template:Toda...')
  13. 12 /var/www/wikipathways/includes/parser/Parser.php(439): Parser->internalParse('{{Template:Toda...')
  14. 13 /var/www/wikipathways/wpi/extensions/PathwayOfTheDay/PathwayOfTheDay.php(60): Parser->recursiveTagParse('{{Template:Toda...')
  15. 14 [internal function]: getPathwayOfTheDay(Object(Parser), 'Friday 3 May 20...', 'Portal:CPTAC/Ha...')
  16. 15 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('getPathwayOfThe...', Array)
  17. 16 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  18. 17 /var/www/wikipathways/includes/parser/Parser.php(2981): PPFrame_DOM->expand(Object(PPNode_DOM))
  19. 18 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  20. 19 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1239): PPFrame_DOM->expand(Object(DOMElement), 4)
  21. 20 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1247): PPTemplateFrame_DOM->getNamedArgument('contents')
  22. 21 /var/www/wikipathways/includes/parser/Parser.php(3201): PPTemplateFrame_DOM->getArgument('contents')
  23. 22 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(934): Parser->argSubstitution(Array, Object(PPTemplateFrame_DOM))
  24. 23 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  25. 24 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  26. 25 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  27. 26 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  28. 27 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  29. 28 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{{{FULLPAGENAM...')
  30. 29 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{{{{FULLPAGENAM...')
  31. 30 /var/www/wikipathways/includes/OutputPage.php(405): Parser->parse('{{{{FULLPAGENAM...', Object(Title), Object(ParserOptions), true, true, 107410)
  32. 31 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('{{{{FULLPAGENAM...', Object(Title), true, true)
  33. 32 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('{{{{FULLPAGENAM...', Object(Title), true)
  34. 33 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('{{{{FULLPAGENAM...')
  35. 34 /var/www/wikipathways/includes/DifferenceEngine.php(271): DifferenceEngine->renderNewRevision()
  36. 35 /var/www/wikipathways/includes/Article.php(729): DifferenceEngine->showDiffPage(false)
  37. 36 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  38. 37 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  39. 38 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  40. 39 {main}
Evading growth suppressors

Cell cycle (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/2/2f/WP179_94637.svg:
Status:1
Message:Exception in thread "main" java.lang.NullPointerException at org.pathvisio.core.Engine.getPathwayImporters(Unknown Source) at org.pathvisio.core.Engine.importPathway(Unknown Source) at org.pathvisio.core.util.Converter.main(Unknown Source)


Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways" "/var/www/wikipathways/images/2/2f/WP179_94637.svg" 2>&1
' in /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php:1255 Stack trace:

  1. 0 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1227): Pathway::convertWithPathVisio(false, '/var/www/wikipa...')
  2. 1 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1137): Pathway->saveConvertedByPathVisioCache('svg')
  3. 2 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1153): Pathway->updateCache('svg')
  4. 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(129): Pathway->getImage()
  5. 4 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(53): makeThumbLinkObj(Object(Pathway), 'Cell cycle', 'https://classic...', 'Cell cycle', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP179', '300', 'center', 'Cell cycle', 'pathway', 'Cell cycle')
  7. 6 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
  8. 7 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  9. 8 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  10. 9 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  11. 10 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  12. 11 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{Template:Toda...')
  13. 12 /var/www/wikipathways/includes/parser/Parser.php(439): Parser->internalParse('{{Template:Toda...')
  14. 13 /var/www/wikipathways/wpi/extensions/PathwayOfTheDay/PathwayOfTheDay.php(60): Parser->recursiveTagParse('{{Template:Toda...')
  15. 14 [internal function]: getPathwayOfTheDay(Object(Parser), 'Friday 3 May 20...', 'Portal:CPTAC/Ha...')
  16. 15 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('getPathwayOfThe...', Array)
  17. 16 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  18. 17 /var/www/wikipathways/includes/parser/Parser.php(2981): PPFrame_DOM->expand(Object(PPNode_DOM))
  19. 18 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  20. 19 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1239): PPFrame_DOM->expand(Object(DOMElement), 4)
  21. 20 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1247): PPTemplateFrame_DOM->getNamedArgument('contents')
  22. 21 /var/www/wikipathways/includes/parser/Parser.php(3201): PPTemplateFrame_DOM->getArgument('contents')
  23. 22 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(934): Parser->argSubstitution(Array, Object(PPTemplateFrame_DOM))
  24. 23 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  25. 24 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  26. 25 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  27. 26 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  28. 27 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  29. 28 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{{{FULLPAGENAM...')
  30. 29 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{{{{FULLPAGENAM...')
  31. 30 /var/www/wikipathways/includes/OutputPage.php(405): Parser->parse('{{{{FULLPAGENAM...', Object(Title), Object(ParserOptions), true, true, 107410)
  32. 31 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('{{{{FULLPAGENAM...', Object(Title), true, true)
  33. 32 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('{{{{FULLPAGENAM...', Object(Title), true)
  34. 33 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('{{{{FULLPAGENAM...')
  35. 34 /var/www/wikipathways/includes/DifferenceEngine.php(271): DifferenceEngine->renderNewRevision()
  36. 35 /var/www/wikipathways/includes/Article.php(729): DifferenceEngine->showDiffPage(false)
  37. 36 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  38. 37 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  39. 38 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  40. 39 {main}
Activating invasion and metastasis

Focal adhesion: PI3K-Akt-mTOR-signaling pathway (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/8/88/WP3932_94637.svg:
Status:1
Message:Exception in thread "main" java.lang.NullPointerException at org.pathvisio.core.Engine.getPathwayImporters(Unknown Source) at org.pathvisio.core.Engine.importPathway(Unknown Source) at org.pathvisio.core.util.Converter.main(Unknown Source)


Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways" "/var/www/wikipathways/images/8/88/WP3932_94637.svg" 2>&1
' in /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php:1255 Stack trace:

  1. 0 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1227): Pathway::convertWithPathVisio(false, '/var/www/wikipa...')
  2. 1 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1137): Pathway->saveConvertedByPathVisioCache('svg')
  3. 2 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1153): Pathway->updateCache('svg')
  4. 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(129): Pathway->getImage()
  5. 4 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(53): makeThumbLinkObj(Object(Pathway), 'Focal adhesion:...', 'https://classic...', 'Focal adhesion:...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP3932', '300', 'center', 'Focal adhesion:...', 'pathway', 'Focal adhesion:...')
  7. 6 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
  8. 7 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  9. 8 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  10. 9 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  11. 10 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  12. 11 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{Template:Toda...')
  13. 12 /var/www/wikipathways/includes/parser/Parser.php(439): Parser->internalParse('{{Template:Toda...')
  14. 13 /var/www/wikipathways/wpi/extensions/PathwayOfTheDay/PathwayOfTheDay.php(60): Parser->recursiveTagParse('{{Template:Toda...')
  15. 14 [internal function]: getPathwayOfTheDay(Object(Parser), 'Friday 3 May 20...', 'Portal:CPTAC/Ha...')
  16. 15 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('getPathwayOfThe...', Array)
  17. 16 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  18. 17 /var/www/wikipathways/includes/parser/Parser.php(2981): PPFrame_DOM->expand(Object(PPNode_DOM))
  19. 18 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  20. 19 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1239): PPFrame_DOM->expand(Object(DOMElement), 4)
  21. 20 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1247): PPTemplateFrame_DOM->getNamedArgument('contents')
  22. 21 /var/www/wikipathways/includes/parser/Parser.php(3201): PPTemplateFrame_DOM->getArgument('contents')
  23. 22 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(934): Parser->argSubstitution(Array, Object(PPTemplateFrame_DOM))
  24. 23 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  25. 24 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  26. 25 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  27. 26 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  28. 27 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  29. 28 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{{{FULLPAGENAM...')
  30. 29 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{{{{FULLPAGENAM...')
  31. 30 /var/www/wikipathways/includes/OutputPage.php(405): Parser->parse('{{{{FULLPAGENAM...', Object(Title), Object(ParserOptions), true, true, 107410)
  32. 31 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('{{{{FULLPAGENAM...', Object(Title), true, true)
  33. 32 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('{{{{FULLPAGENAM...', Object(Title), true)
  34. 33 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('{{{{FULLPAGENAM...')
  35. 34 /var/www/wikipathways/includes/DifferenceEngine.php(271): DifferenceEngine->renderNewRevision()
  36. 35 /var/www/wikipathways/includes/Article.php(729): DifferenceEngine->showDiffPage(false)
  37. 36 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  38. 37 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  39. 38 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  40. 39 {main}
Enabling replicative immortality

ncRNAs involved in STAT3 signaling in hepatocellular carcinoma (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/f/f3/WP4337_94637.svg:
Status:1
Message:Exception in thread "main" java.lang.NullPointerException at org.pathvisio.core.Engine.getPathwayImporters(Unknown Source) at org.pathvisio.core.Engine.importPathway(Unknown Source) at org.pathvisio.core.util.Converter.main(Unknown Source)


Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways" "/var/www/wikipathways/images/f/f3/WP4337_94637.svg" 2>&1
' in /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php:1255 Stack trace:

  1. 0 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1227): Pathway::convertWithPathVisio(false, '/var/www/wikipa...')
  2. 1 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1137): Pathway->saveConvertedByPathVisioCache('svg')
  3. 2 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1153): Pathway->updateCache('svg')
  4. 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(129): Pathway->getImage()
  5. 4 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(53): makeThumbLinkObj(Object(Pathway), 'ncRNAs involved...', 'https://classic...', 'ncRNAs involved...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP4337', '300', 'center', 'ncRNAs involved...', 'pathway', 'ncRNAs involved...')
  7. 6 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
  8. 7 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  9. 8 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  10. 9 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  11. 10 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  12. 11 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{Template:Toda...')
  13. 12 /var/www/wikipathways/includes/parser/Parser.php(439): Parser->internalParse('{{Template:Toda...')
  14. 13 /var/www/wikipathways/wpi/extensions/PathwayOfTheDay/PathwayOfTheDay.php(60): Parser->recursiveTagParse('{{Template:Toda...')
  15. 14 [internal function]: getPathwayOfTheDay(Object(Parser), 'Friday 3 May 20...', 'Portal:CPTAC/Ha...')
  16. 15 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('getPathwayOfThe...', Array)
  17. 16 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  18. 17 /var/www/wikipathways/includes/parser/Parser.php(2981): PPFrame_DOM->expand(Object(PPNode_DOM))
  19. 18 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  20. 19 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1239): PPFrame_DOM->expand(Object(DOMElement), 4)
  21. 20 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1247): PPTemplateFrame_DOM->getNamedArgument('contents')
  22. 21 /var/www/wikipathways/includes/parser/Parser.php(3201): PPTemplateFrame_DOM->getArgument('contents')
  23. 22 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(934): Parser->argSubstitution(Array, Object(PPTemplateFrame_DOM))
  24. 23 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  25. 24 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  26. 25 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  27. 26 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  28. 27 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  29. 28 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{{{FULLPAGENAM...')
  30. 29 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{{{{FULLPAGENAM...')
  31. 30 /var/www/wikipathways/includes/OutputPage.php(405): Parser->parse('{{{{FULLPAGENAM...', Object(Title), Object(ParserOptions), true, true, 107410)
  32. 31 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('{{{{FULLPAGENAM...', Object(Title), true, true)
  33. 32 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('{{{{FULLPAGENAM...', Object(Title), true)
  34. 33 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('{{{{FULLPAGENAM...')
  35. 34 /var/www/wikipathways/includes/DifferenceEngine.php(271): DifferenceEngine->renderNewRevision()
  36. 35 /var/www/wikipathways/includes/Article.php(729): DifferenceEngine->showDiffPage(false)
  37. 36 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  38. 37 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  39. 38 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  40. 39 {main}
Inducing angiogenesis

Model for regulation of MSMP expression in cancer cells and its proangiogenic role in ovarian tumors (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/b/b9/WP4397_94637.svg:
Status:1
Message:Exception in thread "main" java.lang.NullPointerException at org.pathvisio.core.Engine.getPathwayImporters(Unknown Source) at org.pathvisio.core.Engine.importPathway(Unknown Source) at org.pathvisio.core.util.Converter.main(Unknown Source)


Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways" "/var/www/wikipathways/images/b/b9/WP4397_94637.svg" 2>&1
' in /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php:1255 Stack trace:

  1. 0 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1227): Pathway::convertWithPathVisio(false, '/var/www/wikipa...')
  2. 1 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1137): Pathway->saveConvertedByPathVisioCache('svg')
  3. 2 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1153): Pathway->updateCache('svg')
  4. 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(129): Pathway->getImage()
  5. 4 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(53): makeThumbLinkObj(Object(Pathway), 'Model for regul...', 'https://classic...', 'Model for regul...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP4397', '300', 'center', 'Model for regul...', 'pathway', 'Model for regul...')
  7. 6 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
  8. 7 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  9. 8 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  10. 9 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  11. 10 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  12. 11 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{Template:Toda...')
  13. 12 /var/www/wikipathways/includes/parser/Parser.php(439): Parser->internalParse('{{Template:Toda...')
  14. 13 /var/www/wikipathways/wpi/extensions/PathwayOfTheDay/PathwayOfTheDay.php(60): Parser->recursiveTagParse('{{Template:Toda...')
  15. 14 [internal function]: getPathwayOfTheDay(Object(Parser), 'Friday 3 May 20...', 'Portal:CPTAC/Ha...')
  16. 15 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('getPathwayOfThe...', Array)
  17. 16 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  18. 17 /var/www/wikipathways/includes/parser/Parser.php(2981): PPFrame_DOM->expand(Object(PPNode_DOM))
  19. 18 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  20. 19 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1239): PPFrame_DOM->expand(Object(DOMElement), 4)
  21. 20 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1247): PPTemplateFrame_DOM->getNamedArgument('contents')
  22. 21 /var/www/wikipathways/includes/parser/Parser.php(3201): PPTemplateFrame_DOM->getArgument('contents')
  23. 22 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(934): Parser->argSubstitution(Array, Object(PPTemplateFrame_DOM))
  24. 23 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  25. 24 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  26. 25 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  27. 26 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  28. 27 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  29. 28 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{{{FULLPAGENAM...')
  30. 29 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{{{{FULLPAGENAM...')
  31. 30 /var/www/wikipathways/includes/OutputPage.php(405): Parser->parse('{{{{FULLPAGENAM...', Object(Title), Object(ParserOptions), true, true, 107410)
  32. 31 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('{{{{FULLPAGENAM...', Object(Title), true, true)
  33. 32 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('{{{{FULLPAGENAM...', Object(Title), true)
  34. 33 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('{{{{FULLPAGENAM...')
  35. 34 /var/www/wikipathways/includes/DifferenceEngine.php(271): DifferenceEngine->renderNewRevision()
  36. 35 /var/www/wikipathways/includes/Article.php(729): DifferenceEngine->showDiffPage(false)
  37. 36 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  38. 37 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  39. 38 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  40. 39 {main}
Resisting cell death

PI3K-AKT-mTOR signaling pathway and therapeutic opportunities in prostate cancer (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/0/06/WP3844_94637.svg:
Status:1
Message:Exception in thread "main" java.lang.NullPointerException at org.pathvisio.core.Engine.getPathwayImporters(Unknown Source) at org.pathvisio.core.Engine.importPathway(Unknown Source) at org.pathvisio.core.util.Converter.main(Unknown Source)


Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways" "/var/www/wikipathways/images/0/06/WP3844_94637.svg" 2>&1
' in /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php:1255 Stack trace:

  1. 0 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1227): Pathway::convertWithPathVisio(false, '/var/www/wikipa...')
  2. 1 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1137): Pathway->saveConvertedByPathVisioCache('svg')
  3. 2 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1153): Pathway->updateCache('svg')
  4. 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(129): Pathway->getImage()
  5. 4 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(53): makeThumbLinkObj(Object(Pathway), 'PI3K-AKT-mTOR s...', 'https://classic...', 'PI3K-AKT-mTOR s...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP3844', '300', 'center', 'PI3K-AKT-mTOR s...', 'pathway', 'PI3K-AKT-mTOR s...')
  7. 6 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
  8. 7 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  9. 8 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  10. 9 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  11. 10 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  12. 11 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{Template:Toda...')
  13. 12 /var/www/wikipathways/includes/parser/Parser.php(439): Parser->internalParse('{{Template:Toda...')
  14. 13 /var/www/wikipathways/wpi/extensions/PathwayOfTheDay/PathwayOfTheDay.php(60): Parser->recursiveTagParse('{{Template:Toda...')
  15. 14 [internal function]: getPathwayOfTheDay(Object(Parser), 'Friday 3 May 20...', 'Portal:CPTAC/Ha...')
  16. 15 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('getPathwayOfThe...', Array)
  17. 16 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  18. 17 /var/www/wikipathways/includes/parser/Parser.php(2981): PPFrame_DOM->expand(Object(PPNode_DOM))
  19. 18 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  20. 19 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1239): PPFrame_DOM->expand(Object(DOMElement), 4)
  21. 20 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1247): PPTemplateFrame_DOM->getNamedArgument('contents')
  22. 21 /var/www/wikipathways/includes/parser/Parser.php(3201): PPTemplateFrame_DOM->getArgument('contents')
  23. 22 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(934): Parser->argSubstitution(Array, Object(PPTemplateFrame_DOM))
  24. 23 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  25. 24 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  26. 25 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  27. 26 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  28. 27 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  29. 28 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{{{FULLPAGENAM...')
  30. 29 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{{{{FULLPAGENAM...')
  31. 30 /var/www/wikipathways/includes/OutputPage.php(405): Parser->parse('{{{{FULLPAGENAM...', Object(Title), Object(ParserOptions), true, true, 107410)
  32. 31 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('{{{{FULLPAGENAM...', Object(Title), true, true)
  33. 32 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('{{{{FULLPAGENAM...', Object(Title), true)
  34. 33 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('{{{{FULLPAGENAM...')
  35. 34 /var/www/wikipathways/includes/DifferenceEngine.php(271): DifferenceEngine->renderNewRevision()
  36. 35 /var/www/wikipathways/includes/Article.php(729): DifferenceEngine->showDiffPage(false)
  37. 36 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  38. 37 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  39. 38 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  40. 39 {main}
Deregulating cellular energetics

Metabolic reprogramming in colon cancer (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/2/2c/WP4290_94637.svg:
Status:1
Message:Exception in thread "main" java.lang.NullPointerException at org.pathvisio.core.Engine.getPathwayImporters(Unknown Source) at org.pathvisio.core.Engine.importPathway(Unknown Source) at org.pathvisio.core.util.Converter.main(Unknown Source)


Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways" "/var/www/wikipathways/images/2/2c/WP4290_94637.svg" 2>&1
' in /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php:1255 Stack trace:

  1. 0 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1227): Pathway::convertWithPathVisio(false, '/var/www/wikipa...')
  2. 1 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1137): Pathway->saveConvertedByPathVisioCache('svg')
  3. 2 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1153): Pathway->updateCache('svg')
  4. 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(129): Pathway->getImage()
  5. 4 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(53): makeThumbLinkObj(Object(Pathway), 'Metabolic repro...', 'https://classic...', 'Metabolic repro...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP4290', '300', 'center', 'Metabolic repro...', 'pathway', 'Metabolic repro...')
  7. 6 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
  8. 7 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  9. 8 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  10. 9 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  11. 10 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  12. 11 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{Template:Toda...')
  13. 12 /var/www/wikipathways/includes/parser/Parser.php(439): Parser->internalParse('{{Template:Toda...')
  14. 13 /var/www/wikipathways/wpi/extensions/PathwayOfTheDay/PathwayOfTheDay.php(60): Parser->recursiveTagParse('{{Template:Toda...')
  15. 14 [internal function]: getPathwayOfTheDay(Object(Parser), 'Friday 3 May 20...', 'Portal:CPTAC/Ha...')
  16. 15 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('getPathwayOfThe...', Array)
  17. 16 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  18. 17 /var/www/wikipathways/includes/parser/Parser.php(2981): PPFrame_DOM->expand(Object(PPNode_DOM))
  19. 18 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  20. 19 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1239): PPFrame_DOM->expand(Object(DOMElement), 4)
  21. 20 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1247): PPTemplateFrame_DOM->getNamedArgument('contents')
  22. 21 /var/www/wikipathways/includes/parser/Parser.php(3201): PPTemplateFrame_DOM->getArgument('contents')
  23. 22 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(934): Parser->argSubstitution(Array, Object(PPTemplateFrame_DOM))
  24. 23 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  25. 24 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  26. 25 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  27. 26 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  28. 27 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  29. 28 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{{{FULLPAGENAM...')
  30. 29 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{{{{FULLPAGENAM...')
  31. 30 /var/www/wikipathways/includes/OutputPage.php(405): Parser->parse('{{{{FULLPAGENAM...', Object(Title), Object(ParserOptions), true, true, 107410)
  32. 31 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('{{{{FULLPAGENAM...', Object(Title), true, true)
  33. 32 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('{{{{FULLPAGENAM...', Object(Title), true)
  34. 33 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('{{{{FULLPAGENAM...')
  35. 34 /var/www/wikipathways/includes/DifferenceEngine.php(271): DifferenceEngine->renderNewRevision()
  36. 35 /var/www/wikipathways/includes/Article.php(729): DifferenceEngine->showDiffPage(false)
  37. 36 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  38. 37 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  39. 38 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  40. 39 {main}
Genome instability and mutation

ATM signaling in development and disease (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/7/72/WP3878_94637.svg:
Status:1
Message:Exception in thread "main" java.lang.NullPointerException at org.pathvisio.core.Engine.getPathwayImporters(Unknown Source) at org.pathvisio.core.Engine.importPathway(Unknown Source) at org.pathvisio.core.util.Converter.main(Unknown Source)


Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways" "/var/www/wikipathways/images/7/72/WP3878_94637.svg" 2>&1
' in /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php:1255 Stack trace:

  1. 0 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1227): Pathway::convertWithPathVisio(false, '/var/www/wikipa...')
  2. 1 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1137): Pathway->saveConvertedByPathVisioCache('svg')
  3. 2 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1153): Pathway->updateCache('svg')
  4. 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(129): Pathway->getImage()
  5. 4 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(53): makeThumbLinkObj(Object(Pathway), 'ATM signaling i...', 'https://classic...', 'ATM signaling i...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP3878', '300', 'center', 'ATM signaling i...', 'pathway', 'ATM signaling i...')
  7. 6 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
  8. 7 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  9. 8 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  10. 9 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  11. 10 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  12. 11 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{Template:Toda...')
  13. 12 /var/www/wikipathways/includes/parser/Parser.php(439): Parser->internalParse('{{Template:Toda...')
  14. 13 /var/www/wikipathways/wpi/extensions/PathwayOfTheDay/PathwayOfTheDay.php(60): Parser->recursiveTagParse('{{Template:Toda...')
  15. 14 [internal function]: getPathwayOfTheDay(Object(Parser), 'Friday 3 May 20...', 'Portal:CPTAC/Ha...')
  16. 15 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('getPathwayOfThe...', Array)
  17. 16 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  18. 17 /var/www/wikipathways/includes/parser/Parser.php(2981): PPFrame_DOM->expand(Object(PPNode_DOM))
  19. 18 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  20. 19 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1239): PPFrame_DOM->expand(Object(DOMElement), 4)
  21. 20 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1247): PPTemplateFrame_DOM->getNamedArgument('contents')
  22. 21 /var/www/wikipathways/includes/parser/Parser.php(3201): PPTemplateFrame_DOM->getArgument('contents')
  23. 22 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(934): Parser->argSubstitution(Array, Object(PPTemplateFrame_DOM))
  24. 23 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  25. 24 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  26. 25 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  27. 26 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  28. 27 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  29. 28 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{{{FULLPAGENAM...')
  30. 29 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{{{{FULLPAGENAM...')
  31. 30 /var/www/wikipathways/includes/OutputPage.php(405): Parser->parse('{{{{FULLPAGENAM...', Object(Title), Object(ParserOptions), true, true, 107410)
  32. 31 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('{{{{FULLPAGENAM...', Object(Title), true, true)
  33. 32 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('{{{{FULLPAGENAM...', Object(Title), true)
  34. 33 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('{{{{FULLPAGENAM...')
  35. 34 /var/www/wikipathways/includes/DifferenceEngine.php(271): DifferenceEngine->renderNewRevision()
  36. 35 /var/www/wikipathways/includes/Article.php(729): DifferenceEngine->showDiffPage(false)
  37. 36 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  38. 37 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  39. 38 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  40. 39 {main}
Tumor promoting inflammation

Chemokine signaling pathway (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/a/a1/WP3929_94637.svg:
Status:1
Message:Exception in thread "main" java.lang.NullPointerException at org.pathvisio.core.Engine.getPathwayImporters(Unknown Source) at org.pathvisio.core.Engine.importPathway(Unknown Source) at org.pathvisio.core.util.Converter.main(Unknown Source)


Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways" "/var/www/wikipathways/images/a/a1/WP3929_94637.svg" 2>&1
' in /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php:1255 Stack trace:

  1. 0 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1227): Pathway::convertWithPathVisio(false, '/var/www/wikipa...')
  2. 1 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1137): Pathway->saveConvertedByPathVisioCache('svg')
  3. 2 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1153): Pathway->updateCache('svg')
  4. 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(129): Pathway->getImage()
  5. 4 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(53): makeThumbLinkObj(Object(Pathway), 'Chemokine signa...', 'https://classic...', 'Chemokine signa...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP3929', '300', 'center', 'Chemokine signa...', 'pathway', 'Chemokine signa...')
  7. 6 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
  8. 7 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  9. 8 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  10. 9 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  11. 10 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  12. 11 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{Template:Toda...')
  13. 12 /var/www/wikipathways/includes/parser/Parser.php(439): Parser->internalParse('{{Template:Toda...')
  14. 13 /var/www/wikipathways/wpi/extensions/PathwayOfTheDay/PathwayOfTheDay.php(60): Parser->recursiveTagParse('{{Template:Toda...')
  15. 14 [internal function]: getPathwayOfTheDay(Object(Parser), 'Friday 3 May 20...', 'Portal:CPTAC/Ha...')
  16. 15 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('getPathwayOfThe...', Array)
  17. 16 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  18. 17 /var/www/wikipathways/includes/parser/Parser.php(2981): PPFrame_DOM->expand(Object(PPNode_DOM))
  19. 18 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  20. 19 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1239): PPFrame_DOM->expand(Object(DOMElement), 4)
  21. 20 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1247): PPTemplateFrame_DOM->getNamedArgument('contents')
  22. 21 /var/www/wikipathways/includes/parser/Parser.php(3201): PPTemplateFrame_DOM->getArgument('contents')
  23. 22 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(934): Parser->argSubstitution(Array, Object(PPTemplateFrame_DOM))
  24. 23 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  25. 24 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  26. 25 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  27. 26 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  28. 27 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  29. 28 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{{{FULLPAGENAM...')
  30. 29 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{{{{FULLPAGENAM...')
  31. 30 /var/www/wikipathways/includes/OutputPage.php(405): Parser->parse('{{{{FULLPAGENAM...', Object(Title), Object(ParserOptions), true, true, 107410)
  32. 31 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('{{{{FULLPAGENAM...', Object(Title), true, true)
  33. 32 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('{{{{FULLPAGENAM...', Object(Title), true)
  34. 33 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('{{{{FULLPAGENAM...')
  35. 34 /var/www/wikipathways/includes/DifferenceEngine.php(271): DifferenceEngine->renderNewRevision()
  36. 35 /var/www/wikipathways/includes/Article.php(729): DifferenceEngine->showDiffPage(false)
  37. 36 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  38. 37 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  39. 38 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  40. 39 {main}
Avoiding immune destruction

Type II interferon signaling (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/7/73/WP619_94637.svg:
Status:1
Message:Exception in thread "main" java.lang.NullPointerException at org.pathvisio.core.Engine.getPathwayImporters(Unknown Source) at org.pathvisio.core.Engine.importPathway(Unknown Source) at org.pathvisio.core.util.Converter.main(Unknown Source)


Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways" "/var/www/wikipathways/images/7/73/WP619_94637.svg" 2>&1
' in /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php:1255 Stack trace:

  1. 0 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1227): Pathway::convertWithPathVisio(false, '/var/www/wikipa...')
  2. 1 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1137): Pathway->saveConvertedByPathVisioCache('svg')
  3. 2 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1153): Pathway->updateCache('svg')
  4. 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(129): Pathway->getImage()
  5. 4 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(53): makeThumbLinkObj(Object(Pathway), 'Type II interfe...', 'https://classic...', 'Type II interfe...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP619', '300', 'center', 'Type II interfe...', 'pathway', 'Type II interfe...')
  7. 6 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
  8. 7 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  9. 8 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  10. 9 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  11. 10 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  12. 11 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{Template:Toda...')
  13. 12 /var/www/wikipathways/includes/parser/Parser.php(439): Parser->internalParse('{{Template:Toda...')
  14. 13 /var/www/wikipathways/wpi/extensions/PathwayOfTheDay/PathwayOfTheDay.php(60): Parser->recursiveTagParse('{{Template:Toda...')
  15. 14 [internal function]: getPathwayOfTheDay(Object(Parser), 'Friday 3 May 20...', 'Portal:CPTAC/Ha...')
  16. 15 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('getPathwayOfThe...', Array)
  17. 16 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  18. 17 /var/www/wikipathways/includes/parser/Parser.php(2981): PPFrame_DOM->expand(Object(PPNode_DOM))
  19. 18 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  20. 19 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1239): PPFrame_DOM->expand(Object(DOMElement), 4)
  21. 20 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1247): PPTemplateFrame_DOM->getNamedArgument('contents')
  22. 21 /var/www/wikipathways/includes/parser/Parser.php(3201): PPTemplateFrame_DOM->getArgument('contents')
  23. 22 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(934): Parser->argSubstitution(Array, Object(PPTemplateFrame_DOM))
  24. 23 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  25. 24 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  26. 25 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  27. 26 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  28. 27 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  29. 28 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{{{FULLPAGENAM...')
  30. 29 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{{{{FULLPAGENAM...')
  31. 30 /var/www/wikipathways/includes/OutputPage.php(405): Parser->parse('{{{{FULLPAGENAM...', Object(Title), Object(ParserOptions), true, true, 107410)
  32. 31 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('{{{{FULLPAGENAM...', Object(Title), true, true)
  33. 32 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('{{{{FULLPAGENAM...', Object(Title), true)
  34. 33 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('{{{{FULLPAGENAM...')
  35. 34 /var/www/wikipathways/includes/DifferenceEngine.php(271): DifferenceEngine->renderNewRevision()
  36. 35 /var/www/wikipathways/includes/Article.php(729): DifferenceEngine->showDiffPage(false)
  37. 36 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  38. 37 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  39. 38 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  40. 39 {main}
Therapeutics

Cancer immunotherapy by PD-1 blockade (Homo sapiens)
invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/9/90/WP4585_94637.svg:
Status:1
Message:Exception in thread "main" java.lang.NullPointerException at org.pathvisio.core.Engine.getPathwayImporters(Unknown Source) at org.pathvisio.core.Engine.importPathway(Unknown Source) at org.pathvisio.core.util.Converter.main(Unknown Source)


Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways" "/var/www/wikipathways/images/9/90/WP4585_94637.svg" 2>&1
' in /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php:1255 Stack trace:

  1. 0 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1227): Pathway::convertWithPathVisio(false, '/var/www/wikipa...')
  2. 1 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1137): Pathway->saveConvertedByPathVisioCache('svg')
  3. 2 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1153): Pathway->updateCache('svg')
  4. 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(129): Pathway->getImage()
  5. 4 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(53): makeThumbLinkObj(Object(Pathway), 'Cancer immunoth...', 'https://classic...', 'Cancer immunoth...', 'center', 'pwthumb', '300')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP4585', '300', 'center', 'Cancer immunoth...', 'pathway', 'Cancer immunoth...')
  7. 6 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
  8. 7 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  9. 8 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  10. 9 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  11. 10 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  12. 11 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{Template:Toda...')
  13. 12 /var/www/wikipathways/includes/parser/Parser.php(439): Parser->internalParse('{{Template:Toda...')
  14. 13 /var/www/wikipathways/wpi/extensions/PathwayOfTheDay/PathwayOfTheDay.php(60): Parser->recursiveTagParse('{{Template:Toda...')
  15. 14 [internal function]: getPathwayOfTheDay(Object(Parser), 'Friday 3 May 20...', 'Portal:CPTAC/Ha...')
  16. 15 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('getPathwayOfThe...', Array)
  17. 16 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  18. 17 /var/www/wikipathways/includes/parser/Parser.php(2981): PPFrame_DOM->expand(Object(PPNode_DOM))
  19. 18 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  20. 19 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1239): PPFrame_DOM->expand(Object(DOMElement), 4)
  21. 20 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1247): PPTemplateFrame_DOM->getNamedArgument('contents')
  22. 21 /var/www/wikipathways/includes/parser/Parser.php(3201): PPTemplateFrame_DOM->getArgument('contents')
  23. 22 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(934): Parser->argSubstitution(Array, Object(PPTemplateFrame_DOM))
  24. 23 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  25. 24 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  26. 25 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  27. 26 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  28. 27 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  29. 28 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{{{FULLPAGENAM...')
  30. 29 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{{{{FULLPAGENAM...')
  31. 30 /var/www/wikipathways/includes/OutputPage.php(405): Parser->parse('{{{{FULLPAGENAM...', Object(Title), Object(ParserOptions), true, true, 107410)
  32. 31 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('{{{{FULLPAGENAM...', Object(Title), true, true)
  33. 32 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('{{{{FULLPAGENAM...', Object(Title), true)
  34. 33 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('{{{{FULLPAGENAM...')
  35. 34 /var/www/wikipathways/includes/DifferenceEngine.php(271): DifferenceEngine->renderNewRevision()
  36. 35 /var/www/wikipathways/includes/Article.php(729): DifferenceEngine->showDiffPage(false)
  37. 36 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  38. 37 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  39. 38 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  40. 39 {main}

edit  

Featured Pathways

invalid pathway title: exception 'Exception' with message 'Unable to convert to /var/www/wikipathways/images/9/9c/WP3972_94637.svg:


Status:1
Message:Exception in thread "main" java.lang.NullPointerException at org.pathvisio.core.Engine.getPathwayImporters(Unknown Source) at org.pathvisio.core.Engine.importPathway(Unknown Source) at org.pathvisio.core.util.Converter.main(Unknown Source)


Command:java -Xmx1024M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways" "/var/www/wikipathways/images/9/9c/WP3972_94637.svg" 2>&1
' in /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php:1255 Stack trace:

  1. 0 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1227): Pathway::convertWithPathVisio(false, '/var/www/wikipa...')
  2. 1 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1137): Pathway->saveConvertedByPathVisioCache('svg')
  3. 2 /var/www/wikipathways/wpi/extensions/Pathways/Pathway.php(1153): Pathway->updateCache('svg')
  4. 3 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(129): Pathway->getImage()
  5. 4 /var/www/wikipathways/wpi/extensions/pathwayThumb.php(53): makeThumbLinkObj(Object(Pathway), 'PDGFR-beta path...', 'https://classic...', , , 'pwthumb', '250px')
  6. 5 [internal function]: renderPathwayImage(Object(Parser), 'Pathway:WP3972', '250px', , 'PDGFR-beta path...')
  7. 6 /var/www/wikipathways/includes/parser/Parser.php(2860): call_user_func_array('renderPathwayIm...', Array)
  8. 7 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  9. 8 /var/www/wikipathways/includes/parser/Parser.php(2981): PPFrame_DOM->expand(Object(PPNode_DOM))
  10. 9 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  11. 10 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1239): PPFrame_DOM->expand(Object(DOMElement), 4)
  12. 11 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(1247): PPTemplateFrame_DOM->getNamedArgument('contents')
  13. 12 /var/www/wikipathways/includes/parser/Parser.php(3201): PPTemplateFrame_DOM->getArgument('contents')
  14. 13 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(934): Parser->argSubstitution(Array, Object(PPTemplateFrame_DOM))
  15. 14 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  16. 15 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPTemplateFrame_DOM))
  17. 16 /var/www/wikipathways/includes/parser/Parser.php(2986): PPFrame_DOM->expand(Object(PPNode_DOM))
  18. 17 /var/www/wikipathways/includes/parser/Preprocessor_DOM.php(915): Parser->braceSubstitution(Array, Object(PPFrame_DOM))
  19. 18 /var/www/wikipathways/includes/parser/Parser.php(2678): PPFrame_DOM->expand(Object(PPNode_DOM), 0)
  20. 19 /var/www/wikipathways/includes/parser/Parser.php(966): Parser->replaceVariables('{{{{FULLPAGENAM...')
  21. 20 /var/www/wikipathways/includes/parser/Parser.php(321): Parser->internalParse('{{{{FULLPAGENAM...')
  22. 21 /var/www/wikipathways/includes/OutputPage.php(405): Parser->parse('{{{{FULLPAGENAM...', Object(Title), Object(ParserOptions), true, true, 107410)
  23. 22 /var/www/wikipathways/includes/OutputPage.php(391): OutputPage->addWikiTextTitle('{{{{FULLPAGENAM...', Object(Title), true, true)
  24. 23 /var/www/wikipathways/includes/OutputPage.php(500): OutputPage->addWikiTextTitleTidy('{{{{FULLPAGENAM...', Object(Title), true)
  25. 24 /var/www/wikipathways/includes/DifferenceEngine.php(313): OutputPage->addWikiTextTidy('{{{{FULLPAGENAM...')
  26. 25 /var/www/wikipathways/includes/DifferenceEngine.php(271): DifferenceEngine->renderNewRevision()
  27. 26 /var/www/wikipathways/includes/Article.php(729): DifferenceEngine->showDiffPage(false)
  28. 27 /var/www/wikipathways/includes/Wiki.php(437): Article->view()
  29. 28 /var/www/wikipathways/includes/Wiki.php(59): MediaWiki->performAction(Object(OutputPage), Object(Article), Object(Title), Object(User), Object(WebRequest))
  30. 29 /var/www/wikipathways/index.php(93): MediaWiki->initialize(Object(Title), Object(Article), Object(OutputPage), Object(User), Object(WebRequest))
  31. 30 {main}

Zhang, et al. Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

View featured pathways
List of all pathways for this portal

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Assay Portal

CPTAC also includes an Assay Portal to widely disseminate highly characterized proteomic assays to the global research community, with access to SOPs, reagents, and assay characterization/validation data

Resources

Learn how they incorpated WikiPathways images with custom links on their site.

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Pathway Curation

On this page you see rotating displays of hallmark and featured pathways. Where did these pathways come from? They came from people like you! The CPTAC set of pathways can be edited, fixed and added to using the pathway drawing and annotation tools here at WikiPathways.

Getting Started

Resources

Curation projects

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Useful Links

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