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Ontology download failed #775

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zhibor opened this issue Jun 17, 2022 · 0 comments
Open

Ontology download failed #775

zhibor opened this issue Jun 17, 2022 · 0 comments
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Status: Needs Triage Should be the default status for issues that have been acknowledged, but not yet processed. Type: Bug Indicates that WebProtege is not working as expected

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@zhibor
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zhibor commented Jun 17, 2022

Describe the bug
Download project errors

To Reproduce
Steps to reproduce the behavior:

  1. Go to the project list at https://webprotege.stanford.edu/#projects/list
  2. Click the menu button for the project of interest
  3. Select Download from the popup menu
  4. See the error below
WebProtege Initialization Error
An error occurred during the initialization of WebProtege which prevented WebProtege from starting.

Error Message
java.nio.file.NoSuchFileException: /srv/protege/webprotege-data/data-store/project-data/0b6dcf4c-0ed4-4b80-9955-3117cd6333a2/change-data/change-data.binary
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:92)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:219)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:371)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:422)
	at java.base/java.nio.file.spi.FileSystemProvider.newInputStream(FileSystemProvider.java:420)
	at java.base/java.nio.file.Files.newInputStream(Files.java:156)
	at edu.stanford.bmir.protege.web.server.revision.HeadRevisionNumberFinder.getHeadRevisionNumber(HeadRevisionNumberFinder.java:50)
	at edu.stanford.bmir.protege.web.server.download.ProjectDownloadService.getHeadRevisionNumber(ProjectDownloadService.java:214)
	at edu.stanford.bmir.protege.web.server.download.ProjectDownloadService.downloadProject(ProjectDownloadService.java:84)
	at edu.stanford.bmir.protege.web.server.download.ProjectDownloadServlet.startProjectDownload(ProjectDownloadServlet.java:91)
	at edu.stanford.bmir.protege.web.server.download.ProjectDownloadServlet.doGet(ProjectDownloadServlet.java:81)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
	at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
	at edu.stanford.bmir.protege.web.server.filter.WebProtegeWebAppFilter.doFilter(WebProtegeWebAppFilter.java:75)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:218)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
	at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:498)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
	at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:962)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445)
	at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1091)
	at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637)
	at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2549)
	at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2538)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
	at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
	at java.base/java.lang.Thread.run(Thread.java:829)

Expected behavior
Expect to export/download an ontology

Desktop (please complete the following information):

  • OS: macOS
  • Browser: Chrome, Safari
  • Version: most recent

Additional context
None

@zhibor zhibor added Status: Needs Triage Should be the default status for issues that have been acknowledged, but not yet processed. Type: Bug Indicates that WebProtege is not working as expected labels Jun 17, 2022
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Labels
Status: Needs Triage Should be the default status for issues that have been acknowledged, but not yet processed. Type: Bug Indicates that WebProtege is not working as expected
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