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Merged
YvanOceanops merged 6 commits into from
Apr 28, 2026
Merged

V3.0.3 #52

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4729fcf
fix VERTICAL_SAMPLING_SCHEME check
Apr 23, 2026
c9b6a55
add basic e2e check for vertical sampling scheme
Apr 23, 2026
21abddc
add internal copy of specs during build process
Apr 27, 2026
64853b0
add clean resources/file_checker_spec before copying it from ../file_…
Apr 27, 2026
f47cb0b
add missing mapping in R27 table
Apr 28, 2026
e278853
update ressources folder
Apr 28, 2026
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54 changes: 53 additions & 1 deletion file_checker_exec/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>fr.ifremer</groupId>
<artifactId>file_checker_exec</artifactId>
<version>3.0.2</version>
<version>3.0.3</version>

<name>Argo NetCDF file format checker</name>

Expand Down Expand Up @@ -161,6 +161,58 @@
</testResource>
</testResources>
<plugins>
<!-- delete resources/file_checker_spec folder before copying it from source folder -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-clean-plugin</artifactId>
<version>3.4.0</version>
<executions>
<execution>
<id>delete-spec-folder</id>
<phase>initialize</phase>
<goals>
<goal>clean</goal>
</goals>
<configuration>
<excludeDefaultDirectories>true</excludeDefaultDirectories>
<filesets>
<fileset>
<directory>
${project.basedir}/src/main/resources/file_checker_spec
</directory>
</fileset>
</filesets>
</configuration>
</execution>
</executions>
</plugin>
<!-- Copy /file_checker_spec folder in resources -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>3.3.1</version>
<executions>
<execution>
<id>copy-external-folder</id>
<phase>generate-resources</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>
${project.basedir}/src/main/resources/file_checker_spec
</outputDirectory>
<overwrite>true</overwrite>
<resources>
<resource>
<directory>${project.basedir}/../file_checker_spec</directory>
<filtering>false</filtering>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
<!-- Enforce Java 8 API compatibility -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
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2 changes: 1 addition & 1 deletion file_checker_exec/src/main/java/fr/coriolis/checker/validators/ArgoProfileFileValidator.java
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Expand Up @@ -880,7 +880,7 @@ public boolean validateMetaData(int nProf, ArgoReferenceTable.DACS dac, boolean

} else {
// need to delete optionnal free text ([free text]) :
s = s.replaceAll("\\s*\\[[^\\]]*\\]\\s*", "").trim();
s = s.replaceAll("\\s*\\[.*\\]\\s*", "").trim();

tableEntry = ArgoNVSReferenceTable.VERTICAL_SAMPLING_SCHEME_TABLE.getConceptMembersByPrefLabelMap()
.get(s);
Expand Down
2 changes: 1 addition & 1 deletion file_checker_exec/src/main/resources/file_checker_spec/NVS/R01.jsonld
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Expand Up @@ -269,7 +269,7 @@
"dce:identifier": "SDN:R01::METAAUX",
"pav:version": "1",
"skos:notation": "SDN:R01::METAAUX",
"skos:altLabel": "",
"skos:altLabel": "METAAUX",
"dc:date": "2024-09-11 11:40:41.0",
"owl:versionInfo": "1",
"skos:prefLabel": {
Expand Down
22 changes: 16 additions & 6 deletions file_checker_exec/src/main/resources/file_checker_spec/NVS/R08.jsonld
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Expand Up @@ -684,9 +684,14 @@
"dc:date": "2023-10-05 14:39:49.0",
"skos:altLabel": "836",
"skos:notation": "SDN:R08::836",
"skos:broader": {
"@id": "http://vocab.nerc.ac.uk/collection/R23/current/PROVOR_III/"
},
"skos:broader": [
{
"@id": "http://vocab.nerc.ac.uk/collection/R23/current/PROVOR_III/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R23/current/PROVOR_III_JUMBO/"
}
],
"pav:version": "2",
"dce:identifier": "SDN:R08::836",
"pav:hasCurrentVersion": {
Expand All @@ -702,9 +707,14 @@
},
"dce:identifier": "SDN:R08::843",
"pav:version": "1",
"skos:broader": {
"@id": "http://vocab.nerc.ac.uk/collection/R23/current/POPS_PROVOR/"
},
"skos:broader": [
{
"@id": "http://vocab.nerc.ac.uk/collection/R23/current/POPS_PROVOR/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R23/current/POPS_NEMO/"
}
],
"skos:notation": "SDN:R08::843",
"skos:altLabel": "843",
"dc:date": "2020-05-03 20:28:54.0",
Expand Down
11 changes: 10 additions & 1 deletion file_checker_exec/src/main/resources/file_checker_spec/NVS/R23.jsonld
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Expand Up @@ -99,6 +99,9 @@
},
"skos:related": {
"@id": "http://vocab.nerc.ac.uk/collection/R24/current/OPTIMARE/"
},
"skos:narrower": {
"@id": "http://vocab.nerc.ac.uk/collection/R08/current/843/"
},
"@type": "skos:Concept"
},
Expand All @@ -111,7 +114,7 @@
"dce:identifier": "SDN:R23::PROVOR_III_JUMBO",
"pav:version": "1",
"skos:notation": "SDN:R23::PROVOR_III_JUMBO",
"skos:altLabel": "",
"skos:altLabel": "PROVOR_III_JUMBO",
"dc:date": "2024-09-11 11:40:41.0",
"owl:versionInfo": "1",
"skos:prefLabel": {
Expand All @@ -130,6 +133,12 @@
"skos:definition": {
"@language": "en",
"@value": "PROVOR float with additional battery pack. PLATFORM_ TYPE_ KEY = 108."
},
"skos:related": {
"@id": "http://vocab.nerc.ac.uk/collection/R24/current/NKE/"
},
"skos:narrower": {
"@id": "http://vocab.nerc.ac.uk/collection/R08/current/836/"
},
"@type": "skos:Concept"
},
Expand Down
6 changes: 5 additions & 1 deletion file_checker_exec/src/main/resources/file_checker_spec/NVS/R25.jsonld
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Expand Up @@ -83,7 +83,7 @@
},
"owl:versionInfo": "1",
"dc:date": "2023-11-24 09:35:13.0",
"skos:altLabel": ""
"skos:altLabel": "CTD_TEMP_CNDC"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R25/current/FLUOROMETER_CHLA/",
Expand Down Expand Up @@ -1059,7 +1059,11 @@
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/RAMSES_ACC/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/OCR504_ICSW/"
}

],
"skos:definition": {
"@language": "en",
Expand Down
15 changes: 15 additions & 0 deletions file_checker_exec/src/main/resources/file_checker_spec/NVS/R26.jsonld
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Expand Up @@ -863,6 +863,9 @@
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/RBR_PRES/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/RBR_CTD/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/RBR_ARGO/"
Expand Down Expand Up @@ -1098,6 +1101,9 @@
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/SBE41N_V5.3.4/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/SBE41N_V5.3.5/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/SBE41CP_V1.2/"
Expand Down Expand Up @@ -1164,6 +1170,9 @@
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/SBE63_OPTODE/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/SBE83_OPTODE/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/SBE41CP_V1/"
Expand Down Expand Up @@ -1272,6 +1281,9 @@
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/SATLANTIC_OCR504_ICSW/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/OCR504_ICSW/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/SBE41CP_V1.9/"
Expand Down Expand Up @@ -1299,6 +1311,9 @@
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/SATLANTIC_OCR504_R10W/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/OCR504_R10W/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/C_ROVER/"
Expand Down
79 changes: 79 additions & 0 deletions file_checker_exec/src/main/resources/file_checker_spec/NVS/R27.jsonld
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Expand Up @@ -95,6 +95,9 @@
"dc:date": "2025-11-18 12:09:41.0",
"skos:altLabel": "SBE83_OPTODE",
"skos:notation": "SDN:R27::SBE83_OPTODE",
"skos:broader": {
"@id": "http://vocab.nerc.ac.uk/collection/R26/current/SBE/"
},
"pav:version": "2",
"dce:identifier": "SDN:R27::SBE83_OPTODE",
"pav:hasCurrentVersion": {
Expand Down Expand Up @@ -124,6 +127,9 @@
"@id": "http://vocab.nerc.ac.uk/collection/R25/current/CTD_TEMP_CNDC/"
}
],
"skos:broader": {
"@id": "http://vocab.nerc.ac.uk/collection/R26/current/RBR/"
},
"skos:definition": {
"@language": "en",
"@value": "A system comprising temperature, conductivity and pressure sensors, manufactured by RBR for moored applications. This cell was not optimized for use on profiling floats, and this was used in only one test deployment. The system supports both spot and continuous sampling modes, with sampling speeds configurable to up to 12 Hz. The depth rating for a standard profile is 2000 dbar, with energy consumption of approximately 700 J."
Expand Down Expand Up @@ -168,6 +174,14 @@
{
"@id": "http://vocab.nerc.ac.uk/collection/R25/current/RADIOMETER_UP_RAD412/"
}
],
"skos:broader": [
{
"@id": "http://vocab.nerc.ac.uk/collection/R26/current/SATLANTIC/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R26/current/SBE/"
}
],
"skos:definition": {
"@language": "en",
Expand Down Expand Up @@ -216,6 +230,17 @@
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R25/current/RADIOMETER_DOWN_IRR490/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R25/current/RADIOMETER_PAR/"
}
],
"skos:broader": [
{
"@id": "http://vocab.nerc.ac.uk/collection/R26/current/SATLANTIC/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R26/current/SBE/"
}
],
"skos:definition": {
Expand Down Expand Up @@ -2669,6 +2694,57 @@
"skos:broader": {
"@id": "http://vocab.nerc.ac.uk/collection/R26/current/SBE/"
}
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/SBE41N_V5.3.5/",
"pav:hasVersion": {
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/SBE41N_V5.3.5/1/"
},
"pav:authoredOn": "2025-04-03 11:54:30.0",
"pav:hasCurrentVersion": {
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/SBE41N_V5.3.5/2/"
},
"dce:identifier": "SDN:R27::SBE41N_V5.3.5",
"pav:version": "2",
"@type": "skos:Concept",
"skos:related": [
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/SBE41N/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R25/current/CTD_PRES/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R25/current/CTD_TEMP/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R25/current/CTD_CNDC/"
}
],
"skos:definition": {
"@language": "en",
"@value": "A system comprising temperature, conductivity and pressure sensors with pump-controlled, T-C ducted flow, manufactured by Sea-Bir Scientific. The unit is designed for deployment on profiling floats hosting multiple biogeochemical (BGC) sensors. This CTD operates in continuous profiling (CP) mode, thus sampling at 1 Hz during float ascent. Data from all the float's sensors, including the optional bolt-on ones, are integrated in the data stream and transmitted to the float controller when the float reaches the surface. This SBE41N model has firmware version 5.3.5."
},
"void:inDataset": {
"@id": "http://vocab.nerc.ac.uk/.well-known/void"
},
"owl:deprecated": "true",
"skos:note": {
"@language": "en",
"@value": "deprecated"
},
"dc:identifier": "SDN:R27::SBE41N_V5.3.5",
"skos:prefLabel": {
"@language": "en",
"@value": "Sea-Bird Scientific SBE 41N CTD V5.3.5"
},
"owl:versionInfo": "2",
"dc:date": "2025-04-03 11:54:30.0",
"skos:altLabel": "SBE41N_V5.3.5",
"skos:notation": "SDN:R27::SBE41N_V5.3.5",
"skos:broader": {
"@id": "http://vocab.nerc.ac.uk/collection/R26/current/SBE/"
}
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/SBE41N/",
Expand Down Expand Up @@ -6684,6 +6760,9 @@
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/SBE41N_V5.3.4/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/SBE41N_V5.3.5/"
},
{
"@id": "http://vocab.nerc.ac.uk/collection/R27/current/SBE41CP_V1.2/"
Expand Down
3 changes: 2 additions & 1 deletion file_checker_exec/src/main/resources/file_checker_spec/NVS/dateOfUpdate.txt
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@@ -1 +1,2 @@
2026-04-21T09:24:48.256314
2026-04-21T09:24:48.256314
manual fixes done on R01, R08, R23, R25, R27
29 changes: 29 additions & 0 deletions ...cker_exec/src/test/java/fr/coriolis/checker/e2etests/validateVerticalSampingSchemeIT.java
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@@ -0,0 +1,29 @@
package fr.coriolis.checker.e2etests;

import java.io.IOException;

import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Tag;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.CsvSource;

class validateVerticalSampingSchemeIT {

private final String TEST_DIR_NAME = "TEST_PROFILE_0006";

@BeforeAll
public static void init() {
TestsUtils.init(validateVerticalSampingSchemeIT.class);
}

@Tag(TEST_DIR_NAME)
@ParameterizedTest(name = "{0} from dac {1} should have status {2} at phase {3}")
@CsvSource({ "BR6990526_136_imbricatedBrackets.nc,coriolis" })
void fileChecker_shouldNotRaiseWarning_WhenImbricatedBracketsInOptText(String fileName, String dac)
throws IOException, InterruptedException {

TestsUtils.e2eTestWarningAbsence(fileName, dac, TEST_DIR_NAME);

}

}
Binary file added ...ker_exec/src/test/netcdf-test-files/TEST_PROFILE_0006/BR6990526_136_imbricatedBrackets.nc
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