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XML parsing fails when running built version #625

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tarheel opened this issue Feb 5, 2023 · 4 comments · Fixed by #626
Closed

XML parsing fails when running built version #625

tarheel opened this issue Feb 5, 2023 · 4 comments · Fixed by #626
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@HEdingfield
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@tarheel
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tarheel commented Feb 5, 2023

If you try to tabulate an XML file, you get this:

javax.xml.stream.FactoryConfigurationError: Provider for javax.xml.stream.XMLInputFactory cannot be found

This doesn't happen if you run directly from IntelliJ.
@tarheel tarheel added the bug label Feb 5, 2023
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tarheel commented Feb 5, 2023

Btw, when I open Project Structure, the Problems section has a ton of issues listed:


Library Gradle: com.fasterxml.jackson.core:jackson-annotations:2.13.3 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/com.fasterxml.jackson.core/jackson-annotations/2.13.3/ba85620155c9143d2f9e731008c94cf778ffe91e/jackson-annotations-2.13.3-sources.jar [Fix]
Library Gradle: com.fasterxml.jackson.core:jackson-core:2.13.3 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/com.fasterxml.jackson.core/jackson-core/2.13.3/f86da50dc26b8f89ed97197be1e106589b6aa19d/jackson-core-2.13.3-sources.jar [Fix]
Library Gradle: com.fasterxml.jackson.core:jackson-databind:2.13.3 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/com.fasterxml.jackson.core/jackson-databind/2.13.3/87fe580a4141d26b6036234fb0c240aa1d4592db/jackson-databind-2.13.3-sources.jar [Fix]
Library Gradle: com.fasterxml.jackson.dataformat:jackson-dataformat-xml:2.13.3 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/com.fasterxml.jackson.dataformat/jackson-dataformat-xml/2.13.3/d58bebe4785dd2efd90e418416f7e40173d25c99/jackson-dataformat-xml-2.13.3-sources.jar [Fix]
Library Gradle: com.fasterxml.woodstox:woodstox-core:6.2.7 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/com.fasterxml.woodstox/woodstox-core/6.2.7/2b5a0c908f0c485908bbc4f4d413126aa3dd9796/woodstox-core-6.2.7-sources.jar [Fix]
Library Gradle: com.github.virtuald:curvesapi:1.07 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/com.github.virtuald/curvesapi/1.07/6c71d0b9162233d7651d9abead7210ea4f9e62b7/curvesapi-1.07-sources.jar [Fix]
Library Gradle: com.zaxxer:SparseBitSet:1.2 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/com.zaxxer/SparseBitSet/1.2/ee5e8ac60eb99a373a4d3e0a35d1feccfabddc33/SparseBitSet-1.2-sources.jar [Fix]
Library Gradle: commons-codec:commons-codec:1.15 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/commons-codec/commons-codec/1.15/843bc57fd042051e994846da8167bb7ca677a6d/commons-codec-1.15-sources.jar [Fix]
Library Gradle: commons-io:commons-io:2.11.0 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/commons-io/commons-io/2.11.0/2ef0187124bbfc7aed3038d4ffdd2241e8992937/commons-io-2.11.0-sources.jar [Fix]
Library Gradle: org.apache.commons:commons-collections4:4.4 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.apache.commons/commons-collections4/4.4/6260e416ff273ee938b31b0a8e512a367b1ee500/commons-collections4-4.4-sources.jar [Fix]
Library Gradle: org.apache.commons:commons-compress:1.21 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.apache.commons/commons-compress/1.21/b3e0a269baa0d05b02f9b4447be463d25da8c097/commons-compress-1.21-sources.jar [Fix]
Library Gradle: org.apache.commons:commons-csv:1.9.0 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.apache.commons/commons-csv/1.9.0/64f8c96463796f2e62c5e91fbb617ce28207b4bc/commons-csv-1.9.0-sources.jar [Fix]
Library Gradle: org.apache.commons:commons-math3:3.6.1 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.apache.commons/commons-math3/3.6.1/8fab23986ea8886af34818daf32a718e81dc98ba/commons-math3-3.6.1-sources.jar [Fix]
Library Gradle: org.apache.logging.log4j:log4j-api:2.17.2 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.apache.logging.log4j/log4j-api/2.17.2/91a89f75de4f567c38dc7ec9f83f2a1afd2c2915/log4j-api-2.17.2-sources.jar [Fix]
Library Gradle: org.apache.poi:poi-ooxml-lite:5.2.2 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.apache.poi/poi-ooxml-lite/5.2.2/b496a5d21143cd1e30c41af7b38562362a19812/poi-ooxml-lite-5.2.2-sources.jar [Fix]
Library Gradle: org.apache.poi:poi-ooxml:5.2.2 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.apache.poi/poi-ooxml/5.2.2/3f1de93dec45fa263ec2691ad8be11b479d36e8b/poi-ooxml-5.2.2-sources.jar [Fix]
Library Gradle: org.apache.poi:poi:5.2.2 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.apache.poi/poi/5.2.2/1f1fc5784b86c5527c6d101eab3b77e4bdc588a1/poi-5.2.2-sources.jar [Fix]
Library Gradle: org.apache.xmlbeans:xmlbeans:5.0.3 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.apache.xmlbeans/xmlbeans/5.0.3/109aef31c516b0485c92e3554b39ed18cebae523/xmlbeans-5.0.3-sources.jar [Fix]
Library Gradle: org.apiguardian:apiguardian-api:1.1.2 has broken classes paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.apiguardian/apiguardian-api/1.1.2/a231e0d844d2721b0fa1b238006d15c6ded6842a/apiguardian-api-1.1.2.jar [Fix]
Library Gradle: org.apiguardian:apiguardian-api:1.1.2 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.apiguardian/apiguardian-api/1.1.2/e0787a997746ac32639e0bf3cb27af8dce8a3428/apiguardian-api-1.1.2-sources.jar [Fix]
Library Gradle: org.codehaus.woodstox:stax2-api:4.2.1 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.codehaus.woodstox/stax2-api/4.2.1/8d0d447792449c247f739781838cd620687074b/stax2-api-4.2.1-sources.jar [Fix]
Library Gradle: org.junit.jupiter:junit-jupiter-api:5.9.0 has broken classes paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.junit.jupiter/junit-jupiter-api/5.9.0/a44f7eba3ea214f6ec87ad9fccd3b2ac4681a4/junit-jupiter-api-5.9.0.jar [Fix]
Library Gradle: org.junit.jupiter:junit-jupiter-api:5.9.0 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.junit.jupiter/junit-jupiter-api/5.9.0/e23e68771c361cdc17004c5ec30095d609df980/junit-jupiter-api-5.9.0-sources.jar [Fix]
Library Gradle: org.junit.jupiter:junit-jupiter-engine:5.9.0 has broken classes paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.junit.jupiter/junit-jupiter-engine/5.9.0/cc1cb5efae97493dcffb687253a0964ad2e7b99/junit-jupiter-engine-5.9.0.jar [Fix]
Library Gradle: org.junit.jupiter:junit-jupiter-engine:5.9.0 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.junit.jupiter/junit-jupiter-engine/5.9.0/1342cdbc880788707e133ec3a8dc9cbf84b041df/junit-jupiter-engine-5.9.0-sources.jar [Fix]
Library Gradle: org.junit.platform:junit-platform-commons:1.9.0 has broken classes paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.junit.platform/junit-platform-commons/1.9.0/b727889107fc28c7460b21d1083212f8ce7602c6/junit-platform-commons-1.9.0.jar [Fix]
Library Gradle: org.junit.platform:junit-platform-commons:1.9.0 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.junit.platform/junit-platform-commons/1.9.0/18dd59a6622942632cfc7a38c2feae4a3066fc7c/junit-platform-commons-1.9.0-sources.jar [Fix]
Library Gradle: org.junit.platform:junit-platform-engine:1.9.0 has broken classes paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.junit.platform/junit-platform-engine/1.9.0/bd46891f01817b5ffdd368cb0482a34746610acb/junit-platform-engine-1.9.0.jar [Fix]
Library Gradle: org.junit.platform:junit-platform-engine:1.9.0 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.junit.platform/junit-platform-engine/1.9.0/bda902e43fe1f62674224452defd31f4c251e29d/junit-platform-engine-1.9.0-sources.jar [Fix]
Library Gradle: org.openjfx:javafx-base:18 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.openjfx/javafx-base/18/cac820d6d96488cc3047b5c842cf5a2f77fe891d/javafx-base-18-sources.jar [Fix]
Library Gradle: org.openjfx:javafx-base:mac:18 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.openjfx/javafx-base/18/cac820d6d96488cc3047b5c842cf5a2f77fe891d/javafx-base-18-sources.jar [Fix]
Library Gradle: org.openjfx:javafx-controls:18 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.openjfx/javafx-controls/18/8c859ce09ccb70be69a4cdb7f004f53f48e9483/javafx-controls-18-sources.jar [Fix]
Library Gradle: org.openjfx:javafx-controls:mac:18 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.openjfx/javafx-controls/18/8c859ce09ccb70be69a4cdb7f004f53f48e9483/javafx-controls-18-sources.jar [Fix]
Library Gradle: org.openjfx:javafx-fxml:mac:18 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.openjfx/javafx-fxml/18/36422fa188977034132e8131f3f654cc472005e8/javafx-fxml-18-sources.jar [Fix]
Library Gradle: org.openjfx:javafx-graphics:18 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.openjfx/javafx-graphics/18/3423a2d8be374a635e77f04bcf06da4d66251007/javafx-graphics-18-sources.jar [Fix]
Library Gradle: org.openjfx:javafx-graphics:mac:18 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.openjfx/javafx-graphics/18/3423a2d8be374a635e77f04bcf06da4d66251007/javafx-graphics-18-sources.jar [Fix]
Library Gradle: org.opentest4j:opentest4j:1.2.0 has broken classes paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.opentest4j/opentest4j/1.2.0/28c11eb91f9b6d8e200631d46e20a7f407f2a046/opentest4j-1.2.0.jar [Fix]
Library Gradle: org.opentest4j:opentest4j:1.2.0 has broken sources paths:   /Users/tarheel/.gradle/caches/modules-2/files-2.1/org.opentest4j/opentest4j/1.2.0/41d55b3c2254de9837b4ec8923cbd371b8a7eab5/opentest4j-1.2.0-sources.jar [Fix]

@tarheel
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tarheel commented Feb 5, 2023

I think the problems in the Project Structure are unrelated. I reran the Gradle build and it resolved all of those. But the compiled version produced by jlinkZip is still failing.

@tarheel
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tarheel commented Feb 5, 2023

This looks relevant: https://stackoverflow.com/questions/73997099/jlink-xml-dependency-issue

HEdingfield added a commit that referenced this issue Feb 6, 2023
@HEdingfield
Fixes XML parsing failure due to missing transitive dependency (issue #…
abee871 
…625).
@HEdingfield HEdingfield mentioned this issue Feb 6, 2023
Merged
@HEdingfield
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Thanks for the research! Confirming this happens on 1.3.0 in Windows. Implemented a fix per the comment added to the answer in your SO link (#626).

@HEdingfield HEdingfield self-assigned this Feb 6, 2023
HEdingfield added a commit that referenced this issue Feb 7, 2023
@HEdingfield
Fixes XML parsing failure due to missing transitive dependency (issue #…
88808bc 
…625). (#626)
@tarheel tarheel mentioned this issue Feb 7, 2023
Closed
@tarheel tarheel mentioned this issue Feb 7, 2023
Closed
artoonie pushed a commit that referenced this issue Apr 16, 2023
@HEdingfield @artoonie
Fixes XML parsing failure due to missing transitive dependency (issue #…
9b0cf11 
…625). (#626)
artoonie pushed a commit that referenced this issue Apr 16, 2023
@HEdingfield @artoonie
Fixes XML parsing failure due to missing transitive dependency (issue #…
d86e1a6 
…625). (#626)
HEdingfield pushed a commit that referenced this issue Apr 16, 2023
@artoonie
Hotfix 1.3.1 merge into develop (#654)
8f19f56 
* Fixes XML parsing failure due to missing transitive dependency (issue #625). (#626)
* increment version to 1.3.1
artoonie added a commit that referenced this issue Apr 20, 2023
@artoonie
Hotfix 1.3.1 merge into develop (#654)
9c93ef2 
* Fixes XML parsing failure due to missing transitive dependency (issue #625). (#626)
* increment version to 1.3.1
HEdingfield pushed a commit that referenced this issue Apr 21, 2023
@artoonie
Hotfix 1.3.1 merge into master (#653)
2a43b4b 
* Fixes XML parsing failure due to missing transitive dependency (issue #625).
* increment version to 1.3.1
@HEdingfield HEdingfield mentioned this issue Apr 27, 2023
Merged
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Fixes XML parsing failure due to missing transitive dependency BrightSpots/rcv
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@tarheel @HEdingfield @yezr