Requirement #308 does not appear to be working for checking referential integrity from products to others in the bundle #432

jordanpadams · 2021-10-26T17:27:42Z

🐛 Describe the bug identified during I&T

Caught by @rchenatjpl here: #308 (comment)

Looks like #308 implementation was refactored out.

🥼 Related Test Case(s)

🔁 : Related issues

➕ Additional Details

📜 To Reproduce

See comment referenced above, in the attached test data below, validate does not catch browse product's reference to a LID in this bundle doesn't exist.

🕵️ Expected behavior

Validate should catch invalid reference.

📚 Version of Software Used

🩺 Test Data / Additional context

https://github.com/NASA-PDS/validate/files/7414791/val308b.zip

🏞Screenshots

🖥 System Info

OS: [e.g. iOS]
Browser [e.g. chrome, safari]
Version [e.g. 22]

🦄 Related requirements

🦄 #308

⚙️ Engineering Details

…n the bundle 1. Add test resources : src/test/resources/github432 2. Add debug statements : src/main/java/gov/nasa/pds/tools/util/ReferentialIntegrityUtil.java 3. Modify uppercase 'ERROR' to lowercase 'error' so as not to confuse the log file : src/main/java/gov/nasa/pds/tools/validate/rule/pds4/LabelValidationRule.java 4. Add debug statements and printing of warning message when the exceptions.get(location) call returns null : src/main/java/gov/nasa/pds/validate/ValidateLauncher.java 5. Add debug statements and checking for null-ness before calling toString() to avoid NullPointerException : src/main/java/gov/nasa/pds/validate/report/Report.java Refs: #432 Missing referential integrity checks from browse products to others in the bundle

jordanpadams · 2021-11-12T23:23:04Z

@qchaupds merging the PR #442 also merged #440, but that did not fix this issue.

jordanpadams · 2021-11-12T23:23:40Z

see comments here for more details: #440 (review)

mace-space · 2023-11-17T00:31:36Z

Here are bugs I've encountered.

I ran validate using --rule pds4.bundle but no referential checks were performed (even though with that rule option it should check references):

Referential Integrity Check Summary:
0 check(s) passed
0 check(s) failed
0 check(s) skipped

I also tried running it on the specific collection where I had spotted LID errors:

% validate --rule pds4.collection --report-file rav1ciun_validate_browse_collection.log --verbose 2 --target ./wenkert_pdart16_vgr_rav1ciun/browse

Here's an example browse label from that collection:

1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2
3 <?xml-model href="https://pds.nasa.gov/pds4/pds/v1/PDS4_PDS_1G00.sch"
4 schematypens="http://purl.oclc.org/dsdl/schematron"?>
5
6 <Product_Browse xmlns="http://pds.nasa.gov/pds4/pds/v1"
7 xmlns:pds="http://pds.nasa.gov/pds4/pds/v1"
8 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
9 xsi:schemaLocation="http://pds.nasa.gov/pds4/pds/v1 https://pds.nasa.gov/pds4/pds/v1/PDS4_PDS_1G00.xsd">
10 <Identification_Area>
11 <logical_identifier>urn:nasa:pds:wenkert_pdart16_vgr_rav1ciun:browse_qedr:vgr_1201-mamqtv-001010-data-001010.001.png</logical_identifier>
12 <version_id>1.0</version_id>
13 <title>RAV1CIUN DATA Browse Product - vgr_1201-mamqtv-001010-data-001010.001.png</title>
14 <information_model_version>1.16.0.0</information_model_version>
15 <product_class>Product_Browse</product_class>
16 </Identification_Area>
17 <Reference_List>
18 <Internal_Reference>
19 <lid_reference>urn:nasa:pds:wenkert_pdart16_vgr_rav1ciun:browse_qedr:vgr_1201-mamqtv-001010-data-001010.001</lid_reference>
20 <reference_type>browse_to_data</reference_type>
21 This is a reference to the full resolution data file corresponding to this browse image.
22 </Internal_Reference>
23 </Reference_List>
24 <File_Area_Browse>
25
26 <file_name>VGR_1201-MAMQTV-001010-DATA-001010.001.png</file_name>
27 <local_identifier>BROWSE_FILE</local_identifier>
28 <creation_date_time>2023-08-18</creation_date_time>
29
30 <Encoded_Image>
31 <local_identifier>BROWSE_IMAGE</local_identifier>
32 0
33 <encoding_standard_id>PNG</encoding_standard_id>
34 </Encoded_Image>
35 </File_Area_Browse>
36 </Product_Browse>

Line 19 points to an incorrect LID, but Validate does not report any of these:

183531 Referential Integrity Check Summary:
183532 30582 check(s) passed
183533 1 check(s) failed
183534 0 check(s) skipped

It passed all of the browse labels (the one fail refers to a .DS_Store file). So, unlike the -R pds4.bundle option, with the -R pds4.collection it does report referential integrity checks passing but it is not catching incorrect LIDs.

(The LID urn:nasa:pds:wenkert_pdart16_vgr_rav1ciun:browse_qedr:vgr_1201-mamqtv-001010-data-001010.001 does not exist (the browse LIDs have .png suffixes), although it shouldn't even be self-referencing the browse_qedr collection but rather the data_qedr collection).

al-niessner · 2023-11-17T17:38:24Z

@jordanpadams

The check being requested here was purposely turned off by another user request #368 and here is the code that got me there:

validate/src/main/java/gov/nasa/pds/tools/util/ReferentialIntegrityUtil.java

Lines 303 to 308 in 56491e7

    
           // https://github.com/NASA-PDS/validate/issues/368 Product referential integrity 
        
           // check throws invalid WARNINGs 
        
           // Per request of user, we will disable the reporting until further 
        
           // instructions. 
        
           // Set the reportFlag to true if desire to do the reporting of this warning. 
        
           boolean reportFlag = false;

How do you want to resolve conflicting user requests here?

al-niessner · 2023-11-17T18:05:34Z

@rchenatjpl @jordanpadams

Will someone who understand PDS well enough please tell me if there should be 1 or 2 warning messages for the tiny test data set attached to this ticket (see val308b.zip at the top of this issue). I found what look like 2 using grep exist but validate only reports one. The other does not look as though it should be part of the bundle and thus not reported here.

jordanpadams · 2023-11-17T20:21:31Z

@al-niessner you are correct. in an ideal world, we would have some AI algorithm say "these bundle LIDs look kind of a alike, but are different. did you want them to be the same?", but until openAI does out validation, we are stuck with explicit checks.

jordanpadams · 2023-11-17T21:07:18Z

@mace-space can you try out the latest SNAPSHOT with this fix in place to see if it catches the error?

https://github.com/NASA-PDS/validate/releases/tag/v3.4.0-SNAPSHOT

rchenatjpl · 2023-11-18T05:20:26Z

@al-niessner @jordanpadams: validate (Release Date: 2023-11-17 21:11:37) caught that browse-ion-moments/ION_MOM.xml incorrectly referenced
urn:nasa:pds:vg1-pls-sat:data-ion-moments-96sec:nonexistentxxx
but missed that data-ion-moments-96sec/ION_MOM.xml incorrectly referenced
urn:nasa:pds:mess-mag-kt17-model-residuals:document:xxxnoexistent

al-niessner · 2023-11-18T13:41:52Z

The current level of filtering ignored the second because it does not appear to be part of the bundle by name: mess-mag instead of vg1-pls. Non bundle items are deferred to validate-refs. @jordanpadams is this sufficient?

…

On Fri, Nov 17, 2023, 21:20 rchenatjpl ***@***.***> wrote: @al-niessner <https://github.com/al-niessner> @jordanpadams <https://github.com/jordanpadams>: validate (Release Date: 2023-11-17 21:11:37) caught that browse-ion-moments/ION_MOM.xml incorrectly referenced urn:nasa:pds:vg1-pls-sat:data-ion-moments-96sec:nonexistentxxx but missed that data-ion-moments-96sec/ION_MOM.xml incorrectly referenced urn:nasa:pds:mess-mag-kt17-model-residuals:document:xxxnoexistent — Reply to this email directly, view it on GitHub <#432 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAIUBIQ2MQW6PRJ2BD2AL53YFBASLAVCNFSM5GYLGUVKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOBRG4ZTQNRUHA3A> . You are receiving this because you were mentioned.Message ID: ***@***.***>

jordanpadams · 2023-11-18T18:27:36Z

@al-niessner looks like we have success. Thanks!

mace-space · 2023-11-19T00:30:14Z

Sorry for my delay in responding, in the middle of a move. I will look into this more early next week. Thanks for all your help.

mace-space · 2023-11-21T00:01:32Z

@jordanpadams I'm seeing exceptions of the following kind when I run validate-3.4.0-SNAPSHOT:

java.lang.reflect.InvocationTargetException
	at jdk.internal.reflect.GeneratedMethodAccessor19.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at gov.nasa.pds.tools.validate.rule.AbstractValidationRule.execute(AbstractValidationRule.java:64)
	at org.apache.commons.chain.impl.ChainBase.execute(ChainBase.java:191)
	at gov.nasa.pds.tools.validate.rule.pds4.LabelInFolderRule$1.run(LabelInFolderRule.java:149)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
	at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: java.lang.NullPointerException
	at gov.nasa.pds.tools.validate.TargetExaminer.isTargetBundleType(TargetExaminer.java:59)
	at gov.nasa.pds.tools.util.Utility.getTargetType(Utility.java:301)
	at gov.nasa.pds.tools.validate.ValidationTarget.<init>(ValidationTarget.java:47)
	at gov.nasa.pds.tools.validate.ValidationTarget.<init>(ValidationTarget.java:41)
	at gov.nasa.pds.tools.util.Utility.getValidationTarget(Utility.java:88)
	at gov.nasa.pds.tools.validate.ValidationProblem.<init>(ValidationProblem.java:69)
	at gov.nasa.pds.tools.label.CachedLSResourceResolver.resolveResource(CachedLSResourceResolver.java:207)
	at gov.nasa.pds.tools.label.XMLCatalogResolver.resolveResource(XMLCatalogResolver.java:381)
	at gov.nasa.pds.tools.validate.rule.pds4.LabelValidationRule.loadSingleSchemaIntoSources(LabelValidationRule.java:397)
	at gov.nasa.pds.tools.validate.rule.pds4.LabelValidationRule.validateLabelSchemas(LabelValidationRule.java:572)
	at gov.nasa.pds.tools.validate.rule.pds4.LabelValidationRule.validateLabel(LabelValidationRule.java:250)
	... 11 more
...etc

Does this indicate I need to update java?

% java -version
openjdk version "11.0.15" 2022-04-19
OpenJDK Runtime Environment Temurin-11.0.15+10 (build 11.0.15+10)
OpenJDK 64-Bit Server VM Temurin-11.0.15+10 (build 11.0.15+10, mixed mode)

jordanpadams · 2023-11-21T00:12:48Z

@mace-space hmmm. not sure what is going on here. let me check some things out.

jordanpadams · 2023-11-21T00:17:55Z

@mace-space how are you executing validate? I can't seem to replicate on our test data sets.

mace-space · 2023-11-21T00:28:40Z

I'm running:
% validate-3.4.0-SNAPSHOT/bin/validate --rule pds4.bundle --report-file ./log/rav1ciun_validate_snapshot3.4.0.log --verbose 2 --target ./wenkert_pdart16_vgr_rav1ciun

mace-space · 2023-12-16T17:23:38Z

Hi @jordanpadams

I've validating Voyager Jupiter raw radio science bundles and encountered a related error to do with referential integrity checking, so thought I would add details to this issue. (But if you would like me to open another issue, I'm happy to do so).

In the bundle XMLs, it states:

<Target_Identification>
...
        <reference_type>collection_to_target</reference_type>  
    </Internal_Reference>
</Target_Identification>

This should be bundle_to_target but Validate (v3.1.1) did not flag any warnings or errors.
Unlike my comment last month, I have since been able to run the snapshot you provided (v3.4.0) successfully, however it did not flag any errors/warnings either.

jordanpadams · 2023-12-16T19:24:57Z

@mace-space thanks for the inputs. we actually have never validated reference_types, so this would be a new requirement. In the end, the most important thing is the lid(vid)_reference, but agreed, this is not correct.

Per the IM Spec, it looks like bundle_to_target is not being checked by the schematron in Target_Identification. Only in Reference_List.

jordanpadams · 2023-12-16T19:28:37Z

Created new SCR: https://github.com/NASA-PDS/PDS4-CCB/issues/7

mace-space · 2023-12-19T17:08:46Z

Thanks very much. Is NASA-PDS/PDS4-CCB a private repo? I can't access your link

jordanpadams · 2023-12-19T17:28:50Z

@mace-space yes. I can add you to the DDWG Team.

matthewtiscareno · 2023-12-19T18:24:18Z

@mace-space yes. I can add you to the DDWG Team.

I would think that all CCB reps (including @mace-space) should be added to that repo.

tbarnes4 · 2024-06-21T10:48:22Z

@jordanpadams Does the referencial checking for all lid(vid)_reference found in a label, cross checking at least within the realm (-R or --rule) validate is running on? I have an instance where the SB dictionary reference is not being flagged as an error when I'm running validate on a bundle to contains two collections, where processed products are referencing the raw products they were processed from. The LIDVID below does not exist.

                <sb:Raw_Data_Product>
                    <Internal_Reference>
                        <lidvid_reference>urn:nasa:pds:nh_alice:kem1_raw:ali_0408629333_0x4b5_eng::1.0</lidvid_reference>
                        <reference_type>processed_data_to_raw_data</reference_type>
                    </Internal_Reference>
                </sb:Raw_Data_Product>

jordanpadams · 2024-06-21T16:49:40Z

it should... would you mind creating a ticket for this with the example you are referring to?

jordanpadams · 2024-06-21T16:49:48Z

@tbarnes4 ☝️

mace-space · 2024-07-08T18:04:15Z

It looks like the issue I described above is still happening. @jordanpadams shall I open a new issue?

jordanpadams · 2024-07-08T18:47:22Z

@mace-space yes please. If you wouldn't mind providing a specific data set example, that would be really helpful. thanks!

jordanpadams · 2024-07-08T18:47:22Z

@mace-space yes please. If you wouldn't mind providing a specific data set example, that would be really helpful. thanks!

jordanpadams added bug Something isn't working I&T needs:triage labels Oct 26, 2021

jordanpadams self-assigned this Oct 26, 2021

jordanpadams added B12.1 s.medium B12.0 and removed needs:triage labels Oct 26, 2021

jordanpadams added this to the 16.Tyson.Gay milestone Oct 26, 2021

jordanpadams assigned qchaupds and unassigned jordanpadams Oct 26, 2021

jordanpadams mentioned this issue Oct 26, 2021

As a user, I want to check that all Internal References are valid references to other PDS4 products within the current validating bundle #308

Closed

jordanpadams added proj.validate sprint-backlog labels Oct 29, 2021

qchaupds mentioned this issue Nov 9, 2021

Missing referential integrity checks from browse products to others i… #440

Merged

jordanpadams closed this as completed in #440 Nov 12, 2021

jordanpadams reopened this Nov 12, 2021

tloubrieu-jpl modified the milestones: 16.Tyson.Gay, 17.Usain.Bolt Nov 18, 2021

tloubrieu-jpl added the d.running-late label Nov 18, 2021

jordanpadams removed the B12.0 label Nov 19, 2021

tloubrieu-jpl modified the milestones: 17.Usain.Bolt, 18.Jackie.Joyner-Kersee Dec 9, 2021

tloubrieu-jpl added d.getting-later and removed d.running-late labels Dec 9, 2021

jordanpadams assigned jordanpadams and unassigned qchaupds Dec 13, 2021

al-niessner mentioned this issue Nov 17, 2023

Re-enable internal reference checking within a bundle on the file system #762

Merged

jordanpadams closed this as completed in #762 Nov 17, 2023

miguelp1986 added the i&t.done label Jan 10, 2024

mace-space mentioned this issue Jul 11, 2024

Validate appears to not perform integrity checks for bundles/pass incorrect <Internal_Reference>s for collections #959

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jordanpadams removed the sprint-backlog label Aug 6, 2024

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Requirement #308 does not appear to be working for checking referential integrity from products to others in the bundle #432

Requirement #308 does not appear to be working for checking referential integrity from products to others in the bundle #432

jordanpadams commented Oct 26, 2021 •

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jordanpadams commented Jul 8, 2024

Requirement #308 does not appear to be working for checking referential integrity from products to others in the bundle #432

Requirement #308 does not appear to be working for checking referential integrity from products to others in the bundle #432

Comments

jordanpadams commented Oct 26, 2021 • edited Loading

🐛 Describe the bug identified during I&T

🥼 Related Test Case(s)

🔁 : Related issues

➕ Additional Details

📜 To Reproduce

🕵️ Expected behavior

📚 Version of Software Used

🩺 Test Data / Additional context

🏞Screenshots

🖥 System Info

🦄 Related requirements

⚙️ Engineering Details

jordanpadams commented Nov 12, 2021 • edited Loading

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al-niessner commented Nov 18, 2023 via email

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