Merge pull request #174 from NASA-PDS-Incubator/i173

Fix bug introduced from #149 fix
NASA-PDS · Jan 22, 2020 · 7cd9a67 · 7cd9a67
2 parents 3b79ba3 + 581af7f
commit 7cd9a67
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Showing 20 changed files with 1,976 additions and 5 deletions.
diff --git a/src/main/java/gov/nasa/pds/tools/validate/rule/pds4/CollectionReferentialIntegrityRule.java b/src/main/java/gov/nasa/pds/tools/validate/rule/pds4/CollectionReferentialIntegrityRule.java
@@ -59,8 +59,6 @@ public class CollectionReferentialIntegrityRule extends AbstractValidationRule {
 
   private String lid = null;
 
-  private int numOfCollections = 0;
-
   @Override
   public boolean isApplicable(String location) {
     if (Utility.isDir(location)) {
@@ -103,10 +101,13 @@ public void collectionReferentialIntegrityRule() {
 
   private void getCollectionMembers(URL collection) {
     try {
+      int numOfCollectionMembers = 0;
+      numOfCollectionMembers = 0;
+
       InventoryTableReader reader = new InventoryTableReader(collection);
       for (InventoryEntry entry = new InventoryEntry(); entry != null;) {
         if (!entry.isEmpty()) {
-          numOfCollections++;
+            numOfCollectionMembers++;
           String identifier = entry.getIdentifier();
           if (!identifier.equals("")) {
             //Check for a LID or LIDVID
@@ -190,10 +191,10 @@ private void getCollectionMembers(URL collection) {
         entry = reader.getNext();
       }
       int records = reader.getNumRecords();
-      if (this.numOfCollections>0 && records>0 && this.numOfCollections!=records) {
+      if (numOfCollectionMembers>0 && records>0 && numOfCollectionMembers!=records) {
     	  String message = "Number of records read is not equal "
                   + "to the defined number of records in the collection (expected "
-                  + records + ", got " + this.numOfCollections + ").";
+                  + records + ", got " + numOfCollectionMembers + ").";
     	  getListener().addProblem(new ValidationProblem(
                   new ProblemDefinition(ExceptionType.ERROR,
                       ProblemType.RECORDS_MISMATCH,

diff --git a/src/test/java/gov/nasa/pds/validate/ValidationIntegrationTests.java b/src/test/java/gov/nasa/pds/validate/ValidationIntegrationTests.java
@@ -705,6 +705,61 @@ void testGithub137() {
         }
     }
 
+    @Test
+    void testGithub173() {
+        try {
+            // Setup paths
+            String testPath = Utility.getAbsolutePath(TestConstants.TEST_DATA_DIR + "/github173");
+            String outFilePath = TestConstants.TEST_OUT_DIR;
+            File report = new File(outFilePath + File.separator + "report_github173_1.json");
+
+            String[] args = {
+                    "-r", report.getAbsolutePath(),
+                    "-s", "json",
+                    "-R", "pds4.bundle",
+                    "-t" , testPath + File.separator + "valid" + File.separator,
+                    "--skip-content-validation"
+
+                    };
+            this.launcher.processMain(args);
+
+            Gson gson = new Gson();
+            JsonObject reportJson = gson.fromJson(new FileReader(report), JsonObject.class);
+
+            reportJson = gson.fromJson(new FileReader(report), JsonObject.class);
+
+            int count = this.getMessageCount(reportJson, ProblemType.RECORDS_MISMATCH.getKey());
+
+            assertEquals(count, 0, ProblemType.RECORDS_MISMATCH.getKey() + " info/error messages expected.");
+
+            // Now test with added context products
+            report = new File(outFilePath + File.separator + "report_github173_2.json");
+            String[] args2 = {
+                    "-r", report.getAbsolutePath(),
+                    "-s", "json",
+                    "-R", "pds4.bundle",
+                    "-t" , testPath + File.separator + "invalid" + File.separator,
+                    "--skip-content-validation"
+                    };
+            this.launcher = new ValidateLauncher();
+            this.launcher.processMain(args2);
+
+            gson = new Gson();
+
+            reportJson = gson.fromJson(new FileReader(report), JsonObject.class);
+
+            count = this.getMessageCount(reportJson, ProblemType.RECORDS_MISMATCH.getKey());
+
+            assertEquals(count, 1, ProblemType.RECORDS_MISMATCH.getKey() + " info/error messages not expected.");
+
+        } catch (ExitException e) {
+            assertEquals(0, e.status, "Exit status");
+        } catch (Exception e) {
+            e.printStackTrace();
+            fail("Test Failed Due To Exception: " + e.getMessage());
+        }
+    }
+
     int getMessageCount(JsonObject reportJson, String messageTypeName) {
         int i = 0;
         JsonObject message = null;

diff --git a/src/test/resources/github173/invalid/bundle_kaguya_derived.xml b/src/test/resources/github173/invalid/bundle_kaguya_derived.xml
@@ -0,0 +1,130 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?xml-model href="https://pds.nasa.gov/pds4/pds/v1/PDS4_PDS_1B00.sch" schematypens="http://purl.oclc.org/dsdl/schematron"?>
+
+<Product_Bundle xmlns="http://pds.nasa.gov/pds4/pds/v1"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:schemaLocation="http://pds.nasa.gov/pds4/pds/v1 https://pds.nasa.gov/pds4/pds/v1/PDS4_PDS_1B00.xsd">
+    <Identification_Area>
+        <logical_identifier>urn:nasa:pds:kaguya_grs_spectra</logical_identifier>
+        <version_id>1.1</version_id>
+        <title>Kaguya Gamma-Ray Spectrometer Corrected Spectra Bundle</title>
+        <information_model_version>1.11.0.0</information_model_version>
+        <product_class>Product_Bundle</product_class>
+        <Citation_Information>
+            <publication_year>2019</publication_year>
+            <description>
+          This archive contains Kaguya Gamma-Ray Spectrometer (KGRS) corrected and calibrated time-series 
+          spectra and ephemerides, pointing, and geometry (EPG) data for the nominal and extended observation 
+          periods of JAXA's SELENE (Kaguya) mission.
+
+          The SELENE mission was the Japanese mission to the Moon with a main orbiter “Kaguya” and
+          two daughter relay satellites launched on Sep. 14, 2007. KGRS was mounted on the deck of the
+          main orbiter. It employed a high-purity Ge (HPGe) crystal as a main detector, and surrounding
+          BGO and plastic scintillators as anti-coincidence detectors to reduce backgrounds. The
+          Ge crystal was cooled by a Sterling refrigerator. It made close-proximity observations of the
+          Moon from Dec. 14, 2007 to Dec. 11, 2008 at the high circular orbital altitude of 100 km, and
+          from Feb. 10 to May 28 in 2009 at the low elliptical orbital altitude of ~30 x 50 km.
+
+          KGRS recorded energy spectra of gamma rays in two gain modes simultaneously; high gain (0.1
+          to 3 MeV) and low gain (0.1 to 13 MeV), each of which was analyzed by the 13-bit (8192 ch)
+          analog-to-digital converter (ADC). While the former has a higher spectral resolution over the
+          energy range of radioactive elements, the latter has better statistics and covers the whole energy
+          range of major rock-forming elements, including the Fe neutron capture line at 7.6 MeV. The
+          accumulation time of each spectrum was 17 s. Both modes of spectra are included in this archive.
+
+          The observation epochs of KGRS consists of three regular measurement periods (Period 1 to 3),
+          background measurements, and the annealing of the Ge crystal. The HPGe detector was annealed
+          from 16 to 25, December 2008, which improved energy resolution by a factor of two.
+          Period 1 and 2 lasted two and five months, respectively, with limited spatial or spectral
+          resolutions. Period 3 lasted ~3.5 months (including dead time) with the best spatial and spectral
+          resolutions. In addition, spectra from the background measurement when the satellite was flipped
+          and the detector faced deep space can be analyzed to estimate the background gamma-ray intensity
+          from the satellite due to the exposure to galactic cosmic rays.
+
+          This archive consists of three spectrum files (each corresponding to one KGRS epoch) and one unified
+          EPG file. The spectrum files contain a time series of corrected and calibrated pulse height spectra
+          acquired by KGRS's HPGe detector in the lunar orbit. In the spectrum files, each row contains the 
+          spacecraft clock (sclk) ticks and UTC time corresponding to the end of the accumulation interval 
+          (17 s), with the two sets of the 8192-channel HPGe spectra accumulated. In the EPG file, each row
+          starts with sclk recorded at the end of the accumulation interval to match spacecraft positions, 
+          pointing, and correction factors with the corrected spectra. Note that the UTC time and ephemeris time
+          included in the EPG file correspond to the midpoint of the accumulation interval.
+
+          The Kaguya Gamma-Ray Spectrometer Corrected Spectra bundle was created by Naoyuki Yamashita at Planetary
+          Science Institute, AZ, USA, with the permission of JAXA and the KGRS instrument PI Prof. Nobuyuki Hasebe.
+          This work was supported by the NASA under Grant No. NNX16AG54G issued through the Planetary Data Archiving,
+          Restoration, and Tools Program (PDART), Research Opportunities in Space and Earth Sciences (ROSES) 2015.
+	    </description>
+        </Citation_Information>
+        <Modification_History>
+            <Modification_Detail>
+                <modification_date>2019-09-30</modification_date>
+                <version_id>1.0</version_id>
+                <description>Peer reviewed version of Kaguya Gamma-Ray Spectrometer Corrected Spectra PDS4</description>
+            </Modification_Detail>
+        </Modification_History>
+    </Identification_Area>
+    <Context_Area>
+        <Time_Coordinates>
+           <start_date_time>2007-12-14T04:15:35Z</start_date_time>
+			<stop_date_time>2009-05-28T07:43:22Z</stop_date_time>
+        </Time_Coordinates>
+        <Primary_Result_Summary>
+            <purpose>Science</purpose>
+            <processing_level>Derived</processing_level>
+        </Primary_Result_Summary>
+        <Investigation_Area>
+          <name>Kaguya</name>
+          <type>Mission</type>
+          <Internal_Reference>
+            <lid_reference>urn:nasa:pds:context:investigation:mission.kaguya</lid_reference>
+            <reference_type>bundle_to_investigation</reference_type>
+          </Internal_Reference>
+        </Investigation_Area>
+        <Observing_System>
+          <name>Kaguya</name>
+          <Observing_System_Component>
+            <name>Kaguya</name>
+            <type>Spacecraft</type>
+            <Internal_Reference>
+              <lid_reference>urn:nasa:pds:context:instrument_host:spacecraft.kaguya</lid_reference>
+              <reference_type>is_instrument_host</reference_type>
+            </Internal_Reference>
+          </Observing_System_Component>
+          <Observing_System_Component>
+            <name>GRS</name>
+            <type>Instrument</type>
+            <Internal_Reference>
+              <lid_reference>urn:nasa:pds:context:instrument:kaguya.grs</lid_reference>
+              <reference_type>is_instrument</reference_type>
+            </Internal_Reference>
+          </Observing_System_Component>            
+        </Observing_System>
+        <Target_Identification>
+          <name>Moon</name>
+          <type>Satellite</type>
+          <Internal_Reference>
+            <lid_reference>urn:nasa:pds:context:target:satellite.earth.moon</lid_reference>
+            <reference_type>collection_to_target</reference_type>
+          </Internal_Reference>
+        </Target_Identification>
+    </Context_Area>
+    <Reference_List>
+		<Internal_Reference>
+			<lid_reference>urn:nasa:pds:kaguya_grs_spectra:document:kgrs_calibrated_spectra</lid_reference>
+			<reference_type>bundle_to_document</reference_type>
+		</Internal_Reference>
+		<Internal_Reference>
+			<lid_reference>urn:nasa:pds:kaguya_grs_spectra:document:kgrs_ephemerides_doc</lid_reference>
+			<reference_type>bundle_to_document</reference_type>
+		</Internal_Reference>
+    </Reference_List>
+    <Bundle>
+        <bundle_type>Archive</bundle_type>
+    </Bundle>
+    <Bundle_Member_Entry>
+        <lid_reference>urn:nasa:pds:kaguya_grs_spectra:data_spectra</lid_reference>
+        <member_status>Primary</member_status>
+        <reference_type>bundle_has_data_collection</reference_type>
+    </Bundle_Member_Entry>
+</Product_Bundle>
diff --git a/src/test/resources/github173/invalid/data_spectra/kgrs_calibrated_spectra_per1.csv b/src/test/resources/github173/invalid/data_spectra/kgrs_calibrated_spectra_per1.csv