Add `FileMap` options to `put_filemap()` Fix function. #266

blackwinter · 2022-10-20T16:08:43Z

WIP until a stable metafacture-core release artifact becomes available.

Resolves #265.

blackwinter · 2022-10-20T16:24:47Z

There seems to be an issue with the newly built metafacture-core artifacts (see metafacture/metafacture-core#473).

All integration tests are failing:

SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:~/.gradle/caches/modules-2/files-2.1/org.slf4j/slf4j-log4j12/1.7.21/7238b064d1aba20da2ac03217d700d91e02460fa/slf4j-log4j12-1.7.21.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:~/.gradle/caches/modules-2/files-2.1/org.slf4j/slf4j-simple/1.7.21/be4b3c560a37e69b6c58278116740db28832232c/slf4j-simple-1.7.21.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
Exception in thread "main" org.metafacture.commons.reflection.ReflectionException: class could not be instantiated: class org.metafacture.metafix.Metafix
        at org.metafacture.commons.reflection.ConfigurableClass.newInstance(ConfigurableClass.java:149)
        at org.metafacture.commons.reflection.ObjectFactory.newInstance(ObjectFactory.java:105)
        at org.metafacture.flux.parser.FluxProgramm.createElement(FluxProgramm.java:78)
        at org.metafacture.flux.parser.FluxProgramm.addElement(FluxProgramm.java:90)
        at org.metafacture.flux.parser.FlowBuilder.pipe(FlowBuilder.java:736)
        at org.metafacture.flux.parser.FlowBuilder.flowtail(FlowBuilder.java:514)
        at org.metafacture.flux.parser.FlowBuilder.flow(FlowBuilder.java:226)
        at org.metafacture.flux.parser.FlowBuilder.flux(FlowBuilder.java:122)
        at org.metafacture.flux.FluxCompiler.compileFlow(FluxCompiler.java:66)
        at org.metafacture.flux.FluxCompiler.compile(FluxCompiler.java:54)
        at org.metafacture.runner.Flux.main(Flux.java:85)
Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
        at org.metafacture.commons.reflection.ConfigurableClass.newInstance(ConfigurableClass.java:144)
        ... 10 more
Caused by: java.lang.NoSuchFieldError: EOF_TOKEN
        at org.eclipse.xtext.parser.antlr.Lexer.nextToken(Lexer.java:60)
        at org.antlr.runtime.BufferedTokenStream.fetch(BufferedTokenStream.java:143)
        at org.antlr.runtime.BufferedTokenStream.sync(BufferedTokenStream.java:137)
        at org.antlr.runtime.BufferedTokenStream.fill(BufferedTokenStream.java:286)
        at org.antlr.runtime.BufferedTokenStream.toString(BufferedTokenStream.java:251)
        at org.eclipse.xtext.parser.antlr.AbstractInternalAntlrParser.parse(AbstractInternalAntlrParser.java:586)
        at org.eclipse.xtext.parser.antlr.AbstractAntlrParser.doParse(AbstractAntlrParser.java:103)
        at org.eclipse.xtext.parser.antlr.AbstractAntlrParser.parse(AbstractAntlrParser.java:85)
        at org.eclipse.xtext.parser.antlr.AbstractAntlrParser.doParse(AbstractAntlrParser.java:63)
        at org.eclipse.xtext.parser.AbstractParser.parse(AbstractParser.java:34)
        at org.eclipse.xtext.resource.XtextResource.doLoad(XtextResource.java:178)
        at org.eclipse.xtext.linking.lazy.LazyLinkingResource.doLoad(LazyLinkingResource.java:115)
        at org.eclipse.emf.ecore.resource.impl.ResourceImpl.load(ResourceImpl.java:1563)
        at org.eclipse.emf.ecore.resource.impl.ResourceImpl.load(ResourceImpl.java:1342)
        at org.eclipse.xtext.resource.persistence.StorageAwareResource.load(StorageAwareResource.java:64)
        at org.eclipse.emf.ecore.resource.impl.ResourceSetImpl.demandLoad(ResourceSetImpl.java:259)
        at org.eclipse.emf.ecore.resource.impl.ResourceSetImpl.demandLoadHelper(ResourceSetImpl.java:274)
        at org.eclipse.xtext.resource.XtextResourceSet.getResource(XtextResourceSet.java:266)
        at org.eclipse.xtext.resource.SynchronizedXtextResourceSet.getResource(SynchronizedXtextResourceSet.java:33)
        at org.metafacture.metafix.validation.XtextValidator.getResource(XtextValidator.java:63)
        at org.metafacture.metafix.validation.XtextValidator.getValidatedResource(XtextValidator.java:67)
        at org.metafacture.metafix.FixStandaloneSetup.parseFix(FixStandaloneSetup.java:31)
        at org.metafacture.metafix.Metafix.lambda$getRecordTransformer$0(Metafix.java:162)
        at java.util.HashMap.computeIfAbsent(HashMap.java:1128)
        at org.metafacture.metafix.Metafix.getRecordTransformer(Metafix.java:162)
        at org.metafacture.metafix.Metafix.<init>(Metafix.java:111)
        ... 15 more

FAILURE: Build failed with an exception.

blackwinter · 2022-10-20T16:39:00Z

Note that we've seen this error before in #90.

dr0i · 2022-10-21T08:19:30Z

Seems similar to hbz/lobid-resources#1462 - a conflict between different xtext libraries.

blackwinter · 2022-10-21T08:29:50Z

Seems similar to hbz/lobid-resources#1462 - a conflict between different xtext libraries.

How do you figure?

dr0i · 2022-10-21T10:12:20Z

Because of your error message (how did you get this , btw - I only see that it fails). It's said there "NoSuchFieldError" and that reminded me. Also, locally build and consumed mf-master works, and metafacture-flux (which uses ANTLR) has the same bytes on github-packages as the locally one. But this is only a "smell", no really proof, so this may be misleading.

blackwinter · 2022-10-21T10:21:58Z

It's said there "NoSuchFieldError" and that reminded me.

True, but it's a different field. EOF_TOKEN comes from ANTLR, not Xtext. As I said, it's the same error as in #90.

blackwinter · 2022-10-21T10:22:03Z

how did you get this , btw - I only see that it fails

Ran it locally. Maybe we should change the integration tests to print errors to the console in CI.

dr0i · 2022-10-21T10:34:35Z

Yeah but xtext uses ANTLR. I am unsure - is there no connection?

blackwinter · 2022-10-21T10:44:46Z

Yeah but xtext uses ANTLR. I am unsure - is there no connection?

I don't know. Since we weren't able to identify the actual root cause in hbz/lobid-resources#1462 or any cause in #90, I really can't say. It's clearly reminiscent of the former (works in one environment, but not the other), so it might make sense to investigate in that direction.

blackwinter · 2022-10-21T11:00:27Z

Maybe we should change the integration tests to print errors to the console in CI.

Done in 9ee2194.

This resolves "Caused by: java.lang.NoSuchFieldError: EOF_TOKEN at org.eclipse.xtext.parser.antlr.Lexer.nextToken(Lexer.java:60)" so that integration tests passes again.

dr0i · 2022-11-11T17:52:03Z

@blackwinter : updated to a "stable" 5.4.1-rc1 and force psuhed. Rebased. Fixed the integration test error. You may want take over?

metafacture/metafacture-core#425 metafacture/metafacture-core#455 metafacture/metafacture-core#471 metafacture/metafacture-core#472

This resolves "Caused by: java.lang.NoSuchFieldError: EOF_TOKEN at org.eclipse.xtext.parser.antlr.Lexer.nextToken(Lexer.java:60)" so that integration tests pass again.

blackwinter · 2022-11-14T10:04:56Z

Thanks @dr0i. I can't say I particularly like the version pinning, but let's just move on I guess...

Ready for review.

dr0i · 2022-11-14T13:46:06Z

Thx for correcting the commit.

I can't say I particularly like the version pinning

Why?The underlying problem seems to be a conflicting dependency , i.e. the erratic choosing of an one of the two antrl libraries in the classpath. Pinning the correct version in metafix-runner makes this a stable solution, no? Resp. is there a better solution?

blackwinter · 2022-11-14T14:16:49Z

Because it's non-obvious (to me, at least). No dependencies have changed between 5.4.0 and 5.4.1-rc1, only the publishing process. I don't see anything erratic about it either, it's consistently selecting the wrong version - but only in the runner (integration tests), not in the library (unit tests). I don't understand it, pure and simple.

dr0i · 2022-11-15T09:21:52Z

From https://stackoverflow.com/questions/24962607/multiple-versions-of-the-same-dependency-in-maven :

Note that if two dependency versions are at the same depth in the dependency tree, the first declaration wins.

My understanding (may be wrong - but "explains" the phenomenon):
What has changed is the packaging (done as GitHub packages). Assumption: The build of these packages changes
the order of the dependency tree (why and how I also don't understand, admittedly). Thus, consuming the GitHub packages results in picking versionA while in local builds versionB is choosen.

blackwinter · 2022-11-15T09:30:28Z

Thus, consuming the GitHub packages results in picking versionA while in local builds versionB is choosen.

Both metafix (unit tests) and metafix-runner (integration tests) consume the same package do they not? And integration tests fail(ed) both locally and in CI.

dr0i · 2022-11-15T09:55:58Z

Oh, yes, you are correct.
So, let's compare the dependency-tree:

git reset --hard 4976755d3a2182d71059c38ea34fdab5347bc4ec # where everything was fine
./gradlew metafix-runner:dependencies > before266_allfine.txt
git reset --hard 6d82e08df665ffd5b90a8aba86dc5aa446267c63 # where things broke
./gradlew metafix-runner:dependencies > 255_broken.txt
diff 255_broken.txt before266_allfine.txt

in 255_broken.txt there is:

[...]
runtimeClasspath - Runtime classpath of source set 'main'.
+--- org.eclipse.xtext:xtext-dev-bom:2.26.0
[...]
| +--- org.antlr:antlr-runtime:3.2 -> 3.5.2 (c)
[...]

while in before266_allfine.txt there is:

| +--- org.antlr:antlr-runtime:3.2 (c)

So: why is there "3.5.2 (c)" using GithubPackages?

dr0i · 2022-11-15T13:16:45Z

@blackwinter can we merge this and resolve #265 ?
We could further investigate the version problem here or open another issue, if you want.

blackwinter · 2022-11-15T13:19:50Z

can we merge this and resolve #265 ?

@TobiasNx hasn't finished his functional review.

blackwinter · 2022-11-15T13:51:12Z

We could further investigate the version problem here or open another issue, if you want.

Yes. We should probably do it in a dedicated issue, but I'm not sure what the right angle would be (I so desperately want Metafacture's Gradle build cleaned up, and also updated to a current Gradle version). And seeing as we already started here, let me just post another observation:

The new publishing process (via maven-publish plugin, e.g. publishToMavenLocal; or to only generate the Maven POM files: generatePomFileForMavenArtifactsPublication) includes metafacture-flux's antlr dependency (via antlr plugin), while the old process (via maven plugin, e.g. uploadArchives) did not.

--- metafacture-flux-uploadArchives-pom.xml 2022-11-15 14:39:31.375148909 +0100
+++ metafacture-flux-publishToMavenLocal-pom.xml  2022-11-15 14:39:15.143648173 +0100
@@ -63,6 +68,12 @@
     <url>https://github.com/metafacture/metafacture-core/actions</url>
   </ciManagement>
   <dependencies>
+    <dependency>
+      <groupId>org.antlr</groupId>
+      <artifactId>antlr</artifactId>
+      <version>3.5.2</version>
+      <scope>compile</scope>
+    </dependency>
     <dependency>
       <groupId>org.metafacture</groupId>
       <artifactId>metafacture-framework</artifactId>
@@ -81,17 +92,5 @@
       <version>master-SNAPSHOT</version>
       <scope>runtime</scope>
     </dependency>
-    <dependency>
-      <groupId>junit</groupId>
-      <artifactId>junit</artifactId>
-      <version>4.12</version>
-      <scope>test</scope>
-    </dependency>
-    <dependency>
-      <groupId>org.metafacture</groupId>
-      <artifactId>metafacture-plumbing</artifactId>
-      <version>master-SNAPSHOT</version>
-      <scope>test</scope>
-    </dependency>
   </dependencies>
 </project>

NOTE: I added the Maven project description to the new POM in order to reduce noise; but we should probably do it anyway if we want to preserve this information. [Done in metafacture/metafacture-core@d9a47e4.]

dr0i · 2022-11-15T14:16:54Z

Ah, that explains it!

blackwinter · 2022-11-15T14:28:57Z

Ah, that explains it!

Well, not exactly. We still don't know why... (need to look into the antlr plugin next; maybe some dependency mapping issue: maven vs. maven-publish).

...afacture/metafix/integration/lookup/fromJson/toJson/lookupSimpleWithMultiColumnFile/test.fix

TobiasNx · 2022-11-18T07:22:54Z

There are options that are unknown to me. I could add a documentation, if somebody explains their function to me.

compression
decompress_concatenated
encoding
ignore_pattern

blackwinter · 2022-11-18T08:18:17Z

All options are documented in the source (Javadoc; ignore_pattern hasn't been released yet, though).

blackwinter · 2022-11-18T08:27:36Z

Please note that I already added some lookup() documentation in #269.

TobiasNx · 2022-11-18T09:15:01Z

I added some documentation. Reused some of the existing documentation and ignored ignore_pattern.

TobiasNx · 2022-11-18T09:15:25Z

Otherwise +1 from me concerning functional review.

README.md

blackwinter · 2022-11-18T09:25:15Z

I added some documentation. [...] Otherwise +1 from me concerning functional review.

Thanks! Can you approve then?

blackwinter requested review from dr0i and TobiasNx October 20, 2022 16:08

blackwinter assigned dr0i and TobiasNx Oct 20, 2022

blackwinter mentioned this pull request Oct 20, 2022

Add options for multi column lookup to put_filemap() #265

Closed

blackwinter force-pushed the 265-filemapOptions branch from 6b4f4b8 to 24647b6 Compare October 21, 2022 11:00

dr0i added a commit that referenced this pull request Nov 11, 2022

Pin antlr-runtime dependency to 3.2 (#266)

5edf835

This resolves "Caused by: java.lang.NoSuchFieldError: EOF_TOKEN at org.eclipse.xtext.parser.antlr.Lexer.nextToken(Lexer.java:60)" so that integration tests passes again.

dr0i force-pushed the 265-filemapOptions branch from 24647b6 to 5edf835 Compare November 11, 2022 17:29

dr0i assigned blackwinter and unassigned dr0i Nov 11, 2022

blackwinter and others added 3 commits November 14, 2022 10:26

Switch to metafacture-core pre-release.

71da106

Add FileMap options to put_filemap() Fix function.

6d82e08

metafacture/metafacture-core#425 metafacture/metafacture-core#455 metafacture/metafacture-core#471 metafacture/metafacture-core#472

Pin antlr-runtime dependency to 3.2 (#266)

08d992e

This resolves "Caused by: java.lang.NoSuchFieldError: EOF_TOKEN at org.eclipse.xtext.parser.antlr.Lexer.nextToken(Lexer.java:60)" so that integration tests pass again.

blackwinter force-pushed the 265-filemapOptions branch from 5edf835 to 08d992e Compare November 14, 2022 09:49

blackwinter marked this pull request as ready for review November 14, 2022 10:04

blackwinter assigned dr0i and unassigned blackwinter and TobiasNx Nov 14, 2022

blackwinter removed the request for review from TobiasNx November 14, 2022 12:49

dr0i approved these changes Nov 14, 2022

View reviewed changes

dr0i assigned blackwinter and unassigned dr0i Nov 14, 2022

blackwinter commented Nov 17, 2022

View reviewed changes

...afacture/metafix/integration/lookup/fromJson/toJson/lookupSimpleWithMultiColumnFile/test.fix Outdated Show resolved Hide resolved

TobiasNx force-pushed the 265-filemapOptions branch from 83d1152 to 4a5e20f Compare November 18, 2022 07:01

Add integration test for #265

4a2b9ff

TobiasNx force-pushed the 265-filemapOptions branch from 4a5e20f to 4a2b9ff Compare November 18, 2022 07:10

Add documentation for filemap options #265

7388238

blackwinter commented Nov 18, 2022

View reviewed changes

README.md Outdated Show resolved Hide resolved

README.md Outdated Show resolved Hide resolved

README.md Outdated Show resolved Hide resolved

Format options documentation #265

4a674ef

blackwinter merged commit d223a4e into master Nov 18, 2022

blackwinter deleted the 265-filemapOptions branch November 18, 2022 11:09

dr0i mentioned this pull request Nov 24, 2022

Build fails with NoSuchFieldError: EOF_TOKEN hbz/rpb#24

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Add `FileMap` options to `put_filemap()` Fix function. #266

Add `FileMap` options to `put_filemap()` Fix function. #266

blackwinter commented Oct 20, 2022

blackwinter commented Oct 20, 2022 •

edited

blackwinter commented Oct 20, 2022

dr0i commented Oct 21, 2022

blackwinter commented Oct 21, 2022

dr0i commented Oct 21, 2022

blackwinter commented Oct 21, 2022

blackwinter commented Oct 21, 2022

dr0i commented Oct 21, 2022

blackwinter commented Oct 21, 2022

blackwinter commented Oct 21, 2022

dr0i commented Nov 11, 2022

blackwinter commented Nov 14, 2022

dr0i commented Nov 14, 2022

blackwinter commented Nov 14, 2022

dr0i commented Nov 15, 2022

blackwinter commented Nov 15, 2022

dr0i commented Nov 15, 2022

dr0i commented Nov 15, 2022

blackwinter commented Nov 15, 2022

blackwinter commented Nov 15, 2022 •

edited

dr0i commented Nov 15, 2022

blackwinter commented Nov 15, 2022

TobiasNx commented Nov 18, 2022

blackwinter commented Nov 18, 2022

blackwinter commented Nov 18, 2022 •

edited

TobiasNx commented Nov 18, 2022

TobiasNx commented Nov 18, 2022

blackwinter commented Nov 18, 2022

Add FileMap options to put_filemap() Fix function. #266

Add FileMap options to put_filemap() Fix function. #266

Conversation

blackwinter commented Oct 20, 2022

blackwinter commented Oct 20, 2022 • edited

blackwinter commented Oct 20, 2022

dr0i commented Oct 21, 2022

blackwinter commented Oct 21, 2022

dr0i commented Oct 21, 2022

blackwinter commented Oct 21, 2022

blackwinter commented Oct 21, 2022

dr0i commented Oct 21, 2022

blackwinter commented Oct 21, 2022

blackwinter commented Oct 21, 2022

dr0i commented Nov 11, 2022

blackwinter commented Nov 14, 2022

dr0i commented Nov 14, 2022

blackwinter commented Nov 14, 2022

dr0i commented Nov 15, 2022

blackwinter commented Nov 15, 2022

dr0i commented Nov 15, 2022

dr0i commented Nov 15, 2022

blackwinter commented Nov 15, 2022

blackwinter commented Nov 15, 2022 • edited

dr0i commented Nov 15, 2022

blackwinter commented Nov 15, 2022

TobiasNx commented Nov 18, 2022

blackwinter commented Nov 18, 2022

blackwinter commented Nov 18, 2022 • edited

TobiasNx commented Nov 18, 2022

TobiasNx commented Nov 18, 2022

blackwinter commented Nov 18, 2022

Add `FileMap` options to `put_filemap()` Fix function. #266

Add `FileMap` options to `put_filemap()` Fix function. #266

blackwinter commented Oct 20, 2022 •

edited

blackwinter commented Nov 15, 2022 •

edited

blackwinter commented Nov 18, 2022 •

edited