Santiago Florez (Sep 26 2023 at 14:28): Santiago Florez (Sep 26 2023 at 14:28):I have been asking in the Google Groups community about customizing the new metadata block (this is the "https://groups.google.com/g/dataverse-community/c/VFMoX9G-D60" thread). I want to create a selected element as "authorIdentifierScheme" in the citation block. I share with you my .tvs file and my .properties file. Furthermore, I got help from Julian, but what he told me to do didn't work.
Santiago Florez (Sep 26 2023 at 14:28):lineaInvProperties.png
lineaInvtvs.png
Santiago Florez (Sep 26 2023 at 14:29):This is like my two fields is showing in my dataverse installation.
dataverseLineaInv.png
Santiago Florez (Sep 26 2023 at 14:30):This is how I want it to look.
option.png
Santiago Florez (Sep 26 2023 at 14:31):Someone know how can I do it?, thanks
Philip Durbin 🚀 (Sep 26 2023 at 14:32):You say you shared the .tsv already? Can you please upload it here?
Santiago Florez (Sep 26 2023 at 14:35): Santiago Florez (Sep 26 2023 at 14:38):lineaInv.properties
this is the .properties file
Philip Durbin 🚀 (Sep 26 2023 at 14:38):Thanks!
Santiago Florez (Sep 26 2023 at 15:38):@Philip Durbin have you seen something wrong in my files ?
Philip Durbin 🚀 (Sep 26 2023 at 17:58):Are you able to load that file? I get an error:
dev_dataverse> java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 15
dev_dataverse> at java.base/java.util.Arrays$ArrayList.get(Unknown Source)
dev_dataverse> at edu.harvard.iq.dataverse.api.DatasetFieldServiceApi.getArrayIndexOutOfBoundMessage(DatasetFieldServiceApi.java:349)
dev_dataverse> at edu.harvard.iq.dataverse.api.DatasetFieldServiceApi.loadDatasetFields(DatasetFieldServiceApi.java:294)
I am doing on a regular dataverse install, not a developer install. So when I index solr I don't get any errors.
Philip Durbin 🚀 (Sep 26 2023 at 18:26):Sorry, I mean I get that error when I try to load it like this:
curl http://localhost:8080/api/admin/datasetfield/load -H "Content-type: text/tab-separated-values" -X POST --upload-file lineaInv.tvs
Santiago Florez (Sep 26 2023 at 18:31):I run the command while I have been viewing the logs and I get this error
[2023-09-26T13:29:26.968-0500] [Payara 5.2022.3] [SEVERE] [] [edu.harvard.iq.dataverse.api.errorhandlers.ThrowableHandler] [tid: _ThreadID=75 _ThreadName=http-thread-pool::http-listener-1(3)] [timeMillis: 1695752966968] [levelValue: 1000] [[
_status="ERROR";_code=500;_message="Internal server error. More details available at the server logs.";_incidentId="9720d5b8-7689-4954-a2e0-85626a0be975";_interalError="ArrayIndexOutOfBoundsException";_requestUrl="http://localhost:8080/api/v1/admin/datasetfield/load";_requestMethod="POST"|]]
[2023-09-26T13:29:26.968-0500] [Payara 5.2022.3] [SEVERE] [] [edu.harvard.iq.dataverse.api.errorhandlers.ThrowableHandler] [tid: _ThreadID=75 _ThreadName=http-thread-pool::http-listener-1(3)] [timeMillis: 1695752966968] [levelValue: 1000] [[
java.lang.ArrayIndexOutOfBoundsException
]]
[2023-09-26T13:29:26.968-0500] [Payara 5.2022.3] [SEVERE] [] [] [tid: _ThreadID=75 _ThreadName=http-thread-pool::http-listener-1(3)] [timeMillis: 1695752966968] [levelValue: 1000] [[
java.lang.ArrayIndexOutOfBoundsException
]]
Philip Durbin 🚀 (Sep 26 2023 at 18:32):Yes, exactly. :big_smile:
Philip Durbin 🚀 (Sep 26 2023 at 18:32):It's ok. We'll fix it. But I'm a little busy right now. :sweat_smile:
Santiago Florez (Sep 26 2023 at 18:33):Is there an error in the tvs file?
Philip Durbin 🚀 (Sep 26 2023 at 18:33):Yes, there must be.
Philip Durbin 🚀 (Sep 26 2023 at 18:33):We don't have a validator for tsv files. We should.
Philip Durbin 🚀 (Sep 26 2023 at 18:39):I forget, are you comfortable adding some logger.log lines to DatasetFieldServiceApi and recompiling the code? Because that's what we'll probably need to do to debug the tsv file.
Santiago Florez (Sep 26 2023 at 18:40):yes, I'm comfortable
Santiago Florez (Sep 26 2023 at 18:40):How can I do it?
Philip Durbin 🚀 (Sep 26 2023 at 18:43):Can you please try adding this?
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApi.java b/src/main/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApi.java
index 00b7dfa6e3..f3421fb626 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApi.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApi.java
@@ -243,8 +243,10 @@ public class DatasetFieldServiceApi extends AbstractApiBean {
try {
br = new BufferedReader(new FileReader("/" + file));
while ((line = br.readLine()) != null) {
+ logger.log(Level.INFO, "line: " + line);
lineNumber++;
values = line.split(splitBy);
+ logger.log(Level.INFO, "values: " + values);
if (values[0].startsWith("#")) { // Header row
switch (values[0]) {
case "#metadataBlock":
ok
Santiago Florez (Sep 26 2023 at 18:47):
Philip Durbin 🚀 (Sep 26 2023 at 18:49):Oh, sorry, I'm just showing you the output of git diff.
Philip Durbin 🚀 (Sep 26 2023 at 18:49):I'm hoping you can add those two logger.log lines to the code, recompile, redeploy, reload the tsv, and look at server.log.
Santiago Florez (Sep 26 2023 at 18:50):Yes, I was confused.
Philip Durbin ha dicho:
Oh, sorry, I'm just showing you the output of
git diff.
Santiago Florez (Sep 26 2023 at 18:52):Philip Durbin ha dicho:
I'm hoping you can add those two
logger.loglines to the code, recompile, redeploy, reload the tsv, and look at server.log.
what I need to add?
Philip Durbin 🚀 (Sep 26 2023 at 18:54):Do you see those two logger.log lines? With the +?
Santiago Florez (Sep 26 2023 at 18:58):ok ok hahahaha
Santiago Florez (Sep 26 2023 at 18:59):I'm so tired my brain doesn't work at all hahaha.
Philip Durbin 🚀 (Sep 26 2023 at 18:59):me too :sweat_smile:
Santiago Florez (Sep 26 2023 at 19:10):I am recompiling with "mvn clean package"
Santiago Florez (Sep 26 2023 at 19:18):image.png
I got this error
Philip Durbin 🚀 (Sep 26 2023 at 19:40):You'll need to make a change like this:
diff --git a/pom.xml b/pom.xml
index 7ba22d2a07..353682353f 100644
--- a/pom.xml
+++ b/pom.xml
@@ -305,7 +305,7 @@
<dependency>
<groupId>org.dataverse</groupId>
<artifactId>unf</artifactId>
- <version>6.0</version>
+ <version>6.0.1</version>
</dependency>
<!-- Rosuda Rengine and Rserve, packaged by org.nuiton.thirdparty -->
<!-- TODO: see if there's another, better maintained maven repository for Rosuda libraries? - L.A. -->
More background on that UNF problem: https://groups.google.com/g/dataverse-community/c/YQgMEpSX360/m/GUqvuJDzAQAJ
Oliver Bertuch (Sep 26 2023 at 19:53):Philip Durbin said:
We don't have a validator for tsv files. We should.
Once upon a time I started working on gdcc/mdbtool exactly because of this.
Philip Durbin 🚀 (Sep 26 2023 at 19:54):Yes. #containers > hacking on metadata blocks
Sherry Lake (Sep 26 2023 at 20:41):Hi, I replied in the Google group. Looks like the metadataBlock "name" is the same as one of the dataset field "name" in the block. All "names" need to be unique. Julian confirmed that with this: https://guides.dataverse.org/en/latest/admin/metadatacustomization.html#metadatablock-properties
Here's where the names are the same - linea_investigacion
Screenshot-2023-09-26-at-4.39.54-PM.png
Philip Durbin 🚀 (Sep 26 2023 at 20:44):Oh ho! Thanks, @Sherry Lake! I obviously missed that reply of yours!
Santiago Florez (Sep 26 2023 at 20:46):Sherry Lake ha dicho:
Hi, I replied in the Google group. Looks like the metadataBlock "name" is the same as one of the dataset field "name" in the block. All "names" need to be unique. Julian confirmed that with this: https://guides.dataverse.org/en/latest/admin/metadatacustomization.html#metadatablock-properties
Here's where the names are the same - linea_investigacion
Screenshot-2023-09-26-at-4.39.54-PM.png
Yeah, Sherry thanks, I change it, and it's the same don't show like a dropdown
Philip Durbin 🚀 (Sep 26 2023 at 20:48):Is the problem the extra line breaks in the middle?
Santiago Florez (Sep 26 2023 at 20:53):@Philip Durbin I have reinstalled dataverse with the changes you said to add, what is the next step?
Philip Durbin 🚀 (Sep 26 2023 at 20:53):I'm trying too.
Santiago Florez (Sep 26 2023 at 20:53):upload the tvs file and see the logs?
Philip Durbin 🚀 (Sep 26 2023 at 20:54):Generally, yes.
Philip Durbin 🚀 (Sep 26 2023 at 20:54):But I don't like that the tsv file gets into the database when there are errors. :rage:
Sherry Lake (Sep 26 2023 at 20:54):Does the file have to be ".tsv", not ".tvs"?
Does the dropdown box display? If so, is there nothing in the box?
Another thing to try. Remove the properties file (or at least rename it if you don't want to remove it. If the properties file does not exist (matching the metadata block) then the text from the database will be what is displayed.
One more thing - to try - remove the contents of the "Identifier" field in the controlled vocab section.
Here is what I used to create a new metadata block with controlled vocabulary:
Screenshot-2023-09-26-at-4.52.34-PM.png
Philip Durbin 🚀 (Sep 26 2023 at 20:59):If there's anything wrong with the tsv file I would like Dataverse to reject it. However, at least part of the tsv file is getting into the database. This is a bug. :lady_beetle:
Oliver Bertuch (Sep 26 2023 at 21:00):We did talk about this some place else and how a commit/rollback would help... Not sure where that was...
Oliver Bertuch (Sep 26 2023 at 21:02):And didn't someone want to open an issue?
Philip Durbin 🚀 (Sep 26 2023 at 21:03):In gray are the blank lines I'm wondering about. I don't know if they cause a problem or not:
Screen-Shot-2023-09-26-at-5.02.54-PM.png
Santiago Florez (Sep 26 2023 at 21:09):Philip Durbin ha dicho:
In gray are the blank lines I'm wondering about. I don't know if they cause a problem or not:
yes @Philip Durbin that was the trouble
Santiago Florez (Sep 26 2023 at 21:11):I have finished indexing solr with the tvs file uploaded and that fixes the error.
Santiago Florez (Sep 26 2023 at 21:12):
Santiago Florez (Sep 26 2023 at 21:13):Thank you very much @Philip Durbin @Oliver Bertuch @Sherry Lake
Philip Durbin 🚀 (Sep 26 2023 at 21:13)::tada:
Philip Durbin 🚀 (Sep 26 2023 at 21:14):Never give up! :grinning:
Philip Durbin 🚀 (Sep 26 2023 at 21:14):Great job, @Santiago Florez !
Notification Bot (Sep 28 2023 at 20:19):Philip Durbin has marked this topic as resolved.
Notification Bot (Sep 28 2023 at 20:20):This topic was moved here from #community > ✔ Custom metadata block by Philip Durbin.
Last updated: Oct 30 2025 at 06:21 UTC