argus: update build for a couple of critical CVEs

argus/VERSION

@@ -1,7 +1,7 @@
 ## deployable containers have a semantic and build tag
 # semantic version tag: major.minor
 # build version tag: timestamp
-VER=2.0-BETA-07
+VER=2.0-BETA-08
 TAGS="${VER} ${VER}-$(date -u +"%Y%m%dT%H%M%S")"
 unset VER
 

argus/build.gradle

@@ -51,6 +51,7 @@ dependencies {
     runtimeOnly 'org.opencadc:cadc-log:[1.1.0,2.0)'
 
     // force min versions for CVEs
+    runtimeOnly 'org.apache.commons:commons-configuration2:[2.15.0,)'
     runtimeOnly 'org.apache.commons:commons-lang3:[3.18.0,)'
     runtimeOnly 'com.nimbusds:nimbus-jose-jwt:[9.37.4,)'
     // this breaks CI build on gradle 6 because of library variants 
@@ -92,5 +93,6 @@ configurations {
   runtimeOnly.exclude group: 'org.eclipse.jetty'
   runtimeOnly.exclude group: 'org.eclipse.jetty'
   runtimeOnly.exclude group: 'io.netty'
+  runtimeOnly.exclude group: 'org.jline'
 }
 

argus/src/main/java/org/opencadc/argus/tap/InitCaomTapSchemaContent.java

@@ -87,7 +87,7 @@ public class InitCaomTapSchemaContent extends InitDatabase {
     private static final Logger log = Logger.getLogger(InitCaomTapSchemaContent.class);
 
     public static final String MODEL_NAME = "caom2-schema";
-    public static final String MODEL_VERSION = "2.5.0-P";
+    public static final String MODEL_VERSION = "2.5.0-beta-2";
 
     // the SQL is tightly coupled to cadc-tap-schema table names (for TAP-1.1)
     static String[] BASE_SQL = new String[] {
@@ -114,7 +114,9 @@ public class InitCaomTapSchemaContent extends InitDatabase {
     public InitCaomTapSchemaContent(DataSource dataSource, String database, String schema, boolean extras) {
         // use MODELVERSION/extras so changing extras will cause a recreate
         // eg 1.2.13/false <-> 1.2.13/true
-        super(dataSource, database, schema, MODEL_NAME, MODEL_VERSION + "/" + extras);
+        //super(dataSource, database, schema, MODEL_NAME, MODEL_VERSION + "/" + extras);
+        // TODO: currently no extras in 2.5 beta
+        super(dataSource, database, schema, MODEL_NAME, MODEL_VERSION);
         String[] src = BASE_SQL;
         if (extras) {
             src = BASE_EXTRA_SQL;

argus/src/main/resources/sql/ivoa.tap_schema_content11.sql

@@ -42,16 +42,16 @@ insert into tap_schema.tables11 (schema_name,table_name,table_type,description,t
 insert into tap_schema.columns11 
     (table_name,column_name,utype,description,ucd,unit,datatype,arraysize,xtype,principal,indexed,std,column_index,column_id) values
 ( 'ivoa.ObsCore', 'obs_publisher_did', 	'obscore:Curation.PublisherDID',
-    'publisher dataset identifier', 'meta.ref.uri;meta.curation', NULL, 'char', '256*','uri', 1,1,1,1, 'ivoaPublisherID');
+    'publisher dataset identifier', 'meta.ref.ivoid', NULL, 'char', '256*','uri', 1,1,1,1, 'ivoaPublisherID');
 
 insert into tap_schema.columns11 
     (table_name,column_name,utype,description,ucd,unit,datatype,arraysize,xtype,principal,indexed,std, column_index) values
 ( 'ivoa.ObsCore', 'obs_collection', 	'obscore:DataID.Collection',
-    'short name for the data colection', 'meta.id', NULL, 'char','128*',NULL, 1,0,1,2),
+    'short name for the data colection', 'meta.id', NULL, 'char','128*',NULL, 1,1,1,2),
 ( 'ivoa.ObsCore', 'facility_name', 	'obscore:Provenance.ObsConfig.Facility.name',
-    'telescope name', 'meta.id;instr.tel', NULL, 'char','128*',NULL, 1,0,1,3),
+    'telescope name', 'meta.id;instr.tel', NULL, 'char','128*',NULL, 1,1,1,3),
 ( 'ivoa.ObsCore', 'instrument_name', 	'obscore:Provenance.ObsConfig.Instrument.name',
-    'instrument name', 'meta.id;instr', NULL, 'char','128*',NULL, 1,0,1,4),
+    'instrument name', 'meta.id;instr', NULL, 'char','128*',NULL, 1,1,1,4),
 ( 'ivoa.ObsCore', 'target_name', 'obscore:Target.Name',
     'name of intended target', 'meta.id;src', NULL, 'char', '32*',NULL, 1,0,1,5),
 ( 'ivoa.ObsCore', 'obs_id', 	'obscore:DataID.observationID',
@@ -88,9 +88,9 @@ insert into tap_schema.columns11
     'region bounded by observation', 'pos.outline;obs.field', NULL, 'char','*','shape', 1,1,1,44),
 ( 'ivoa.ObsCore', 's_resolution', 'obscore:Char.SpatialAxis.Resolution.refval.value',
     'typical spatial resolution', 'pos.angResolution', 'arcsec', 'double',NULL,NULL, 1,0,1,45),
-( 'ivoa.ObsCore', 's_resolution_min', '???',
+( 'ivoa.ObsCore', 's_resolution_min', 'obscore:Char.SpatialAxis.Resolution.Bounds.Limits.LoLimit',
     'smallest spatial resolution', 'pos.angResolution;stat.min', 'arcsec', 'double',NULL,NULL, 1,0,1,46),
-( 'ivoa.ObsCore', 's_resolution_max', '???',
+( 'ivoa.ObsCore', 's_resolution_max', 'obscore:Char.SpatialAxis.Resolution.Bounds.Limits.HiLimit',
     'largest spatial resolution', 'pos.angResolution;stat.max', 'arcsec', 'double',NULL,NULL, 1,0,1,47),
 ( 'ivoa.ObsCore', 's_xel1', 'obscore:Char.SpatialAxis.numBins1', 
     'dimensions (number of pixels) along one spatial axis', 'meta.number', NULL, 'long',NULL,NULL, 1,0,1,48),
@@ -100,13 +100,13 @@ insert into tap_schema.columns11
 insert into tap_schema.columns11 
     (table_name,column_name,utype,description,ucd,unit,datatype,arraysize,xtype,principal,indexed,std, column_index) values
 ( 'ivoa.ObsCore', 'em_min', 'obscore:Char.SpectralAxis.Coverage.Bounds.Limits.LoLimit',
-    'start spectral coordinate value', 'em.wl;stat.min', 'm', 'double',NULL,NULL, 1,1,1,50),
+    'start spectral coordinate value', 'em.wl;stat.min', 'm', 'double',NULL,NULL, 1,0,1,50),
 ( 'ivoa.ObsCore', 'em_max', 'obscore:Char.SpectralAxis.Coverage.Bounds.Limits.HiLimit',
-    'stop spectral coordinate value', 'em.wl;stat.max', 'm', 'double',NULL,NULL, 1,1,1,51),
+    'stop spectral coordinate value', 'em.wl;stat.max', 'm', 'double',NULL,NULL, 1,0,1,51),
 ( 'ivoa.ObsCore', 'em_res_power', 'obscore:Char.SpectralAxis.Resolution.ResolPower.refval',
     'typical spectral resolution', 'spect.resolution', NULL, 'double',NULL,NULL, 1,0,1,52),
-( 'ivoa.ObsCore', 'em_resolution', '???',
-    'typical spectral resolution', 'spect.resolution', NULL, 'double',NULL,NULL, 1,0,1,53),
+( 'ivoa.ObsCore', 'em_resolution', 'obscore:Char.SpectralAxis.Resolution.refval.value',
+    'typical spectral resolution', 'spect.resolution;stat.mean', 'm', 'double',NULL,NULL, 1,0,1,53),
 ( 'ivoa.ObsCore', 'em_resolution_min', '???',
     'minimum spectral resolution', 'spect.resolution;stat.min', NULL, 'double',NULL,NULL, 1,0,1,54),
 ( 'ivoa.ObsCore', 'em_resolution_max', '???',
@@ -119,9 +119,9 @@ insert into tap_schema.columns11
 insert into tap_schema.columns11 
     (table_name,column_name,utype,description,ucd,unit,datatype,arraysize,xtype,principal,indexed,std, column_index) values
 ( 'ivoa.ObsCore', 't_min', 'obscore:Char.TimeAxis.Coverage.Bounds.Limits.StartTime',
-    'start time of observation (MJD)', 'time.start;obs.exposure', 'd', 'double',NULL,NULL, 1,1,1,60),
+    'start time of observation (MJD)', 'time.start;obs.exposure', 'd', 'double',NULL,NULL, 1,0,1,60),
 ( 'ivoa.ObsCore', 't_max', 'obscore:Char.TimeAxis.Coverage.Bounds.Limits.StopTime',
-    'end time of observation (MJD)', 'time.end;obs.exposure', 'd', 'double',NULL,NULL, 1,1,1,61),
+    'end time of observation (MJD)', 'time.end;obs.exposure', 'd', 'double',NULL,NULL, 1,0,1,61),
 ( 'ivoa.ObsCore', 't_exptime', 'obscore:Char.TimeAxis.Coverage.Support.Extent',
     'typical exposure time', 'time.duration;obs.exposure', 's', 'double',NULL,NULL, 1,1,1,62),
 ( 'ivoa.ObsCore', 't_exptime_min', '???',
@@ -136,7 +136,7 @@ insert into tap_schema.columns11
 insert into tap_schema.columns11 
     (table_name,column_name,utype,description,ucd,unit,datatype,arraysize,xtype,principal,indexed,std, column_index) values
 ( 'ivoa.ObsCore', 'pol_states', 'obscore:Char.PolarizationAxis.stateList',
-    'polarization states present in the data', 'meta.code;phys.polarization', NULL, 'char','32*',NULL, 1,0,1,70),
+    'polarization states present in the data', 'meta.code;phys.polarization', NULL, 'char','32*',NULL, 1,1,1,70),
 ( 'ivoa.ObsCore', 'pol_xel', 'obscore:Char.PolarizationAxis.numBins', 
     'dimensions (number of pixels) along the polarization axis', 'meta.number', NULL, 'long',NULL,NULL, 1,0,1,71),
 ( 'ivoa.ObsCore', 'o_ucd', 'obscore:Char.ObservableAxis.ucd',
@@ -163,7 +163,7 @@ insert into tap_schema.keys11 (key_id,from_table,target_table,description) value
 ('ivoa-core-radio', 'ivoa.ObsCore_radio', 'ivoa.ObsCore','standard way to join ivoa.ObsCore and ivoa.ObsCore_radio');
 
 insert into tap_schema.key_columns11 (key_id,from_column,target_column) values
-('ivoa-core-radio', 'obs_publisher_id', 'obs_publisher_id');
+('ivoa-core-radio', 'obs_publisher_did', 'obs_publisher_did');
 
 -- backwards compatible: fill "size" column with values from arraysize set above
 -- where arraysize is a possibly variable-length 1-dimensional value

argus/src/main/webapp/capabilities.xml

@@ -30,6 +30,12 @@
     </interface>
   </capability>
 
+  <capability standardID="ivo://ivoa.net/std/DALI#examples">
+    <interface xsi:type="vs:ParamHTTP" role="std">
+      <accessURL use="base">https://replace.me.com/argus/examples</accessURL>
+    </interface>
+  </capability>
+
   <!-- TAP-1.1 -->
   <capability standardID="ivo://ivoa.net/std/TAP" 
         xmlns:tr="http://www.ivoa.net/xml/TAPRegExt/v1.0" xsi:type="tr:TableAccess">

argus/src/main/webapp/examples/index.html

@@ -0,0 +1,102 @@
+<!DOCTYPE html>
+<html>
+    <head>
+        <title>CAOM Query Examples</title>
+    </head>
+    <body>
+        <div vocab="http://www.ivoa.net/rdf/examples#">
+            <div id="caom-spatial-query" resource="#caom-spatial-query" typeof="example">
+                <h2 property="name">Standard CAOM Discovery Query with Spatial Constraint</h2>
+                <p>
+                    standardID: <span property="capability">ivo://ivoa.net/std/TAP</span>
+                </p>
+                <!-- Table target configuration -->
+                <p>
+                    tables: 
+                    <span property="table">caom2.Observation</span>
+                    JOIN
+                    <span property="table">caom2.Plane</span>
+                </p>
+
+                <p>parameters:</p>
+                <div property="generic-parameter" typeof="keyval">
+                    <span property="key">LANG</span> = <span property="value">ADQL</span>
+                </div>
+
+                <div property="generic-parameter" typeof="keyval">
+                    <span property="key">MAXREC</span> = <span property="value">100</span>
+                </div>
+
+                <div property="generic-parameter" typeof="keyval">
+                    <span property="key">QUERY</span> =
+                    <pre property="value">
+                    SELECT p.publisherID, o.telescope_name, o.instrument_name, 
+                        p.calibrationLevel, p.dataProductType, 
+                        p.position_bounds, p.energy_bounds, p.time_bounds, p.polarization_states
+                    FROM caom2.Observation AS o JOIN caom2.Plane AS p ON o.obsID = p.obsID
+                    WHERE o.intent = 'science' AND INTERSECTS(p.position_bounds, CIRCLE('ICRS', 180.0, 0.0, 0.5)) = 1
+                    </pre>
+                </div>
+                <p>
+                    The Plane.publisherID column is the identifier that is needed to call the CAOM DataLink service and initiate
+                    data access; when this column is selected, the service will include a <em>service descriptor</em>
+                    with the necessary information.
+                </p>
+            </div>
+
+            <div id="caom-artifact-join" resource="#caom-artifact-join" typeof="example">
+                <h2 property="name">Standard CAOM Query with Primary Artifact</h2>
+                <p>
+                    standardID: <span property="capability">ivo://ivoa.net/std/TAP</span>
+                </p>
+
+                <!-- Table target configuration -->
+                <p>
+                    tables:
+                    <span property="table">caom2.Observation</span>
+                    JOIN
+                    <span property="table">caom2.Plane</span>
+                    JOIN
+                    <span property="table">caom2.Artifact</span>
+                </p>
+
+                <p>parameters:</p>
+                <div property="generic-parameter" typeof="keyval">
+                    <span property="key">LANG</span> = <span property="value">ADQL</span>
+                </div>
+
+                <div property="generic-parameter" typeof="keyval">
+                    <span property="key">MAXREC</span> = <span property="value">100</span>
+                </div>
+
+                <div property="generic-parameter" typeof="keyval">
+                    <span property="key">QUERY</span> = 
+                    <pre property="value">
+                    SELECT p.publisherID, o.telescope_name, o.instrument_name, 
+                        p.calibrationLevel, p.dataProductType, 
+                        p.position_bounds, p.energy_bounds, p.time_bounds, p.polarization_states,
+                        a.uri
+                    FROM caom2.Observation AS o
+                    JOIN caom2.Plane AS p ON o.obsID = p.obsID
+                    JOIN caom2.Artifact AS a ON p.planeID = a.planeID
+                    WHERE o.intent = 'science'
+                      AND a.productType IN ('science', 'this')
+                      AND INTERSECTS(p.position_bounds, CIRCLE('ICRS', 180.0, 0.0, 0.5)) = 1
+                    </pre>
+                </div>
+
+                <p>
+                    The Plane.publisherID column is the identifier that is needed to call the CAOM DataLink service 
+                    and initiate data access; when this column is selected, the service will include a 
+                    <em>service descriptor</em> with the necessary information.
+                </p>
+                <p>
+                    Coming soon: The Artifact.uri column is the identifier that is needed to directly access 
+                    the file in the CADC Archive Storage system; when this column is selected, the service will 
+                    include a <em>service descriptor</em> with the necessary information.
+                </p>
+            </div>
+
+        </div>
+    </body>
+</html>

caom2-db/src/intTest/java/org/opencadc/caom2/db/version/InitDatabaseTest.java

@@ -90,8 +90,8 @@ public class InitDatabaseTest {
     static String schema = "caom2";
 
     static {
-        Log4jInit.setLevel("ca.nrc.cadc.caom2.version", Level.INFO);
-        Log4jInit.setLevel("ca.nrc.cadc.db.version", Level.INFO);
+        Log4jInit.setLevel("org.opencadc.caom2", Level.INFO);
+        Log4jInit.setLevel("ca.nrc.cadc.db", Level.INFO);
     }
 
     private DataSource dataSource;

caom2-db/src/main/java/org/opencadc/caom2/db/AbstractDAO.java

@@ -180,7 +180,7 @@ public void setConfig(Map<String, Object> config) {
         }
         try {
             this.dataSource = DBUtil.findJNDIDataSource(jndiDataSourceName);
-            log.warn("found: " + jndiDataSourceName);
+            log.debug("found: " + jndiDataSourceName);
         } catch (NamingException ex) {
             throw new IllegalArgumentException("cannot find JNDI DataSource: " + jndiDataSourceName);
         }

caom2-db/src/main/java/org/opencadc/caom2/db/DeletedObservationEventIteratorQuery.java

@@ -138,7 +138,7 @@ public ResourceIterator<DeletedObservationEvent> query(DataSource ds) {
         }
 
         String sql = sb.toString();
-        log.warn("SQL: " + sb.toString());
+        log.debug("SQL: " + sb.toString());
 
         Calendar utc = Calendar.getInstance(DateUtil.UTC);
         try {

caom2-db/src/main/java/org/opencadc/caom2/db/ObservationStateIteratorQuery.java

@@ -90,6 +90,7 @@ public class ObservationStateIteratorQuery  {
     private static final Logger log = Logger.getLogger(ObservationStateIteratorQuery.class);
 
     private final SQLGenerator gen;
+    private final SQLDialect dbDialect;
 
     private final String collection;
     private final String namespace;
@@ -103,6 +104,7 @@ public ObservationStateIteratorQuery(SQLGenerator gen, String collection, String
         this.gen = gen;
         this.collection = collection;
         this.namespace = namespace;
+        this.dbDialect = gen.getDbDialect();
     }
 
     public void setUriBucket(String uriBucket) {
@@ -156,7 +158,7 @@ public ResourceIterator<ObservationState> query(DataSource ds) {
         }
 
         String sql = sb.toString();
-        log.warn("SQL: " + sb.toString());
+        log.debug("SQL: " + sb.toString());
 
         Calendar utc = Calendar.getInstance(DateUtil.UTC);
         try {
@@ -200,7 +202,7 @@ private class ObservationStateIterator implements ResourceIterator<ObservationSt
         private boolean hasRow;
         private int rowNum = 0;
 
-        private ObservationStateMapper mapper = new ObservationStateMapper();
+        private ObservationStateMapper mapper = new ObservationStateMapper(dbDialect);
 
         public ObservationStateIterator(Connection con, ResultSet rs) {
             this.con = con;

caom2-db/src/main/java/org/opencadc/caom2/db/SQLGenerator.java

@@ -428,9 +428,14 @@
         return schema;
     }
 
+    public SQLDialect getDbDialect() {
+        return dbDialect;
+    }
+
+
     /**
      * The default implementation uses the SQL standard CURRENT_TIMESTAMP symbol.
      * @return 
      */
 
     public String getCurrentTimeSQL() {
@@ -766,7 +771,7 @@
         }
 
         public ObservationState execute(JdbcTemplate jdbc) {
-            return jdbc.query(this, new ObservationStateExtractor());
+            return jdbc.query(this, new ObservationStateExtractor(gen.getDbDialect()));
         }
 
         @Override
@@ -2524,11 +2529,11 @@
     }
 
     public RowMapper getObservationStateMapper() {
-        return new ObservationStateMapper();
+        return new ObservationStateMapper(dbDialect);
     }
 
     public ResultSetExtractor<ObservationState> getObservationStateExtractor() {
-        return new ObservationStateExtractor();
+        return new ObservationStateExtractor(dbDialect);
     }
 
     public ResultSetExtractor getSkeletonExtractor(Class<? extends Skeleton> c) {

caom2-db/src/main/java/org/opencadc/caom2/db/mappers/ObservationStateExtractor.java

@@ -69,6 +69,7 @@
 
 import java.sql.ResultSet;
 import java.sql.SQLException;
+import org.opencadc.caom2.db.SQLDialect;
 import org.opencadc.caom2.util.ObservationState;
 import org.springframework.dao.DataAccessException;
 import org.springframework.jdbc.core.ResultSetExtractor;
@@ -79,14 +80,16 @@
  */
 public class ObservationStateExtractor implements ResultSetExtractor<ObservationState> {
 
-    public ObservationStateExtractor() {
+    private ObservationStateMapper mapper;
+
+    public ObservationStateExtractor(SQLDialect dbDialect) {
+        this.mapper = new ObservationStateMapper(dbDialect);
     }
 
     @Override
     public ObservationState extractData(ResultSet rs) throws SQLException, DataAccessException {
         if (rs.next()) {
-            ObservationStateMapper m = new ObservationStateMapper();
-            return m.mapRow(rs, 1);
+            return mapper.mapRow(rs, 1);
         }
         return null;
     }