I'm new to OpenRefine and just started having an issue after updating my OS to Sequoia 15.3.1. When I go to open a project it never loads, just the spinning wheel. It also won't let me import a new project and gives me this error message:
Failed to import project:
java.util.zip.ZipException: Not in GZIP format
at java.base/java.util.zip.GZIPInputStream.readHeader(Unknown Source)
at java.base/java.util.zip.GZIPInputStream.(Unknown Source)
at java.base/java.util.zip.GZIPInputStream.(Unknown Source)
at com.google.refine.io.FileProjectManager.importProject(FileProjectManager.java:165)
at com.google.refine.commands.project.ImportProjectCommand.internalImport(ImportProjectCommand.java:120)
at com.google.refine.commands.project.ImportProjectCommand.doPost(ImportProjectCommand.java:78)
at com.google.refine.RefineServlet.service(RefineServlet.java:187)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:750)
at org.eclipse.jetty.servlet.ServletHolder$NotAsync.service(ServletHolder.java:1410)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:764)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:529)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:131)
at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:578)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:122)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:223)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1570)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:131)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:122)
at org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:790)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:122)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:223)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1384)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:176)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:484)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1543)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:174)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1306)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:129)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:122)
at com.google.refine.ValidateHostHandler.handle(ValidateHostHandler.java:93)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:122)
at org.eclipse.jetty.server.Server.handle(Server.java:563)
at org.eclipse.jetty.server.HttpChannel$RequestDispatchable.dispatch(HttpChannel.java:1598)
at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:753)
at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:501)
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:282)
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:314)
at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:100)
at org.eclipse.jetty.io.SelectableChannelEndPoint$1.run(SelectableChannelEndPoint.java:53)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
I tried downloading OpenRefine again, same issue. I also updated Java to the newest version. Would really appreciate any help!
I just made a new project using clipboard and I'm able to open that one. How can I see if the project file is corrupted?
The new project I was trying to create was from an excel spreadsheet.
Thank you!
I just checked the files for my projects and I see that there are files that say corrupted but not the project that I'm trying to open (2253873716036). I also only have two projects so I'm not sure what the other files are.
I've tried a few more things and have been able to create new projects, but I can't import the files from the old project that refuses to open- it always comes up with an error even though it doesn't say that it's corrupted.
If it's the same error that "Not in GZIP format", then that leads me to assume you are:
- Trying to open an OpenRefine exported project that is saved in .tar.gz format?
- Opening a project from a file that you think is an OpenRefine project (in it's .tar.gz format) but is not an OpenRefine project but some kind of other file?
If one of your project files is not private, can you zip up and attach and share one of the files from the old project that refuses to open? Then we can try to reproduce on our end.
Here is the file that I find when I go to "browse workspace directory" (the forum won't let me upload a file so I've uploaded it to google 2253873716036.project copy.zip - Google Drive). If there is another place where OpenRefine files are stored I am not aware of it.
@antonin_d I tried to help recover their project, which shows in the project listing just fine now, so it's recovered, but then, but when I click on the link for their project name in our Project view "Pompeii Architectural Feature Database xlsx", it tries to read the data files and then I get the spinner and the following output:
01:32:50.740 [ project_utilities] Failed to load from data file E:\Downloads\workspaceTestA\1111111111111.project / data.zip (74ms)
com.fasterxml.jackson.databind.exc.ValueInstantiationException: Cannot construct instance of `com.google.refine.model.Cell`,
problem: No injectable id with value 'pool' found (for property '')
at [Source: REDACTED (`StreamReadFeature.INCLUDE_SOURCE_IN_LOCATION` disabled);
line: 1, column: 166] (through reference chain:
com.google.refine.history.HistoryEntry["operation"]->
com.google.refine.operations.row.RowAdditionOperation["rows"]->
java.util.ArrayList[0]->
com.google.refine.model.Row["cells"]->
java.util.ArrayList[0])
at com.fasterxml.jackson.databind.exc.ValueInstantiationException.from(ValueInstantiationException.java:47)
at com.fasterxml.jackson.databind.DeserializationContext.instantiationException(DeserializationContext.java:2015)
at com.fasterxml.jackson.databind.DeserializationContext.handleInstantiationProblem(DeserializationContext.java:1426)
at com.fasterxml.jackson.databind.deser.BeanDeserializerBase.wrapInstantiationProblem(BeanDeserializerBase.java:2010)
at com.fasterxml.jackson.databind.deser.BeanDeserializer._deserializeUsingPropertyBased(BeanDeserializer.java:543)
at com.fasterxml.jackson.databind.deser.BeanDeserializerBase.deserializeFromObjectUsingNonDefault(BeanDeserializerBase.java:1497)
at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserializeFromObject(BeanDeserializer.java:348)
at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:185)
at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer._deserializeFromArray(CollectionDeserializer.java:361)
at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:246)
at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:30)
at com.fasterxml.jackson.databind.deser.SettableBeanProperty.deserialize(SettableBeanProperty.java:543)
at com.fasterxml.jackson.databind.deser.BeanDeserializer._deserializeWithErrorWrapping(BeanDeserializer.java:585)
at com.fasterxml.jackson.databind.deser.BeanDeserializer._deserializeUsingPropertyBased(BeanDeserializer.java:447)
at com.fasterxml.jackson.databind.deser.BeanDeserializerBase.deserializeFromObjectUsingNonDefault(BeanDeserializerBase.java:1497)
at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserializeFromObject(BeanDeserializer.java:348)
at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:185)
at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer._deserializeFromArray(CollectionDeserializer.java:361)
at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:246)
at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:30)
at com.fasterxml.jackson.databind.deser.SettableBeanProperty.deserialize(SettableBeanProperty.java:543)
at com.fasterxml.jackson.databind.deser.BeanDeserializer._deserializeWithErrorWrapping(BeanDeserializer.java:585)
at com.fasterxml.jackson.databind.deser.BeanDeserializer._deserializeUsingPropertyBased(BeanDeserializer.java:447)
at com.fasterxml.jackson.databind.deser.BeanDeserializerBase.deserializeFromObjectUsingNonDefault(BeanDeserializerBase.java:1497)
at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserializeFromObject(BeanDeserializer.java:348)
at com.fasterxml.jackson.databind.deser.BeanDeserializer._deserializeOther(BeanDeserializer.java:220)
at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:187)
at com.fasterxml.jackson.databind.jsontype.impl.AsPropertyTypeDeserializer._deserializeTypedForId(AsPropertyTypeDeserializer.java:170)
at com.fasterxml.jackson.databind.jsontype.impl.AsPropertyTypeDeserializer.deserializeTypedFromObject(AsPropertyTypeDeserializer.java:136)
at com.fasterxml.jackson.databind.deser.AbstractDeserializer.deserializeWithType(AbstractDeserializer.java:263)
at com.fasterxml.jackson.databind.deser.SettableBeanProperty.deserialize(SettableBeanProperty.java:540)
at com.fasterxml.jackson.databind.deser.BeanDeserializer._deserializeWithErrorWrapping(BeanDeserializer.java:585)
at com.fasterxml.jackson.databind.deser.BeanDeserializer._deserializeUsingPropertyBased(BeanDeserializer.java:447)
at com.fasterxml.jackson.databind.deser.BeanDeserializerBase.deserializeFromObjectUsingNonDefault(BeanDeserializerBase.java:1497)
at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserializeFromObject(BeanDeserializer.java:348)
at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:185)
at com.fasterxml.jackson.databind.deser.DefaultDeserializationContext.readRootValue(DefaultDeserializationContext.java:342)
at com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:4917)
at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:3860)
at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:3828)
at com.google.refine.history.HistoryEntry.load(HistoryEntry.java:184)
at com.google.refine.history.History.load(History.java:305)
at com.google.refine.model.Project.loadFromReader(Project.java:229)
at com.google.refine.model.Project.loadFromInputStream(Project.java:196)
at com.google.refine.io.ProjectUtilities.loadFromFile(ProjectUtilities.java:142)
at com.google.refine.io.ProjectUtilities.load(ProjectUtilities.java:121)
at com.google.refine.io.FileProjectManager.loadProject(FileProjectManager.java:269)
at com.google.refine.ProjectManager.getProject(ProjectManager.java:559)
at com.google.refine.commands.Command.getProject(Command.java:203)
at com.google.refine.commands.project.GetModelsCommand.internalRespond(GetModelsCommand.java:117)
at com.google.refine.commands.project.GetModelsCommand.doGet(GetModelsCommand.java:72)
at com.google.refine.RefineServlet.service(RefineServlet.java:180)
Thank you for looking into this- do you have any sense of if it is possible to recover the project completely? Otherwise I will need to start over working on this data.
I have the original excel sheet that I was cleaning but I'm unable to use the JSON file to apply the same operations as before. I get this error: Invalid JSON format: com.fasterxml.jackson.databind.exc.InvalidTypeIdException: Could not resolve subtype of [simple type, class com.google.refine.model.AbstractOperation]: missing type id property 'op' at [Source: REDACTED (StreamReadFeature.INCLUDE_SOURCE_IN_LOCATION disabled); line: 1, column: 1187] (through reference chain: java.util.ArrayList[0])
@cessatrix It would be ideal if we could get a copy of that JSON file and try to reproduce and see where we might have a bug.
I don't think that we can recover your project completely. The data folder contains data.txt and you'll see a starting line called history= that follows with the historical changes you did, which you might extract and apply and reuse.
I don't know enough of the entire inner workings of our Change operations, so I wouldn't be the person to help you further with this. I'm sorry.
@cessatrix For your current error with the original Excel sheet. Please open a new issue on our GitHub and attach or link the Excel file so that we can reproduce. Thanks!
@thadguidry thank you for your help on this, I ended up starting over and figuring out the changes I had done myself. I'm happy to share additional files or information if you're interested in trying to figure out what the issue was but for my own work it was more trouble to keep trying to fix the problem rather than just spending a few hours recreating the work.
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