Merge pull request #150 from pdowler/master

update caom2 TAP to use DALI-1.2 xtypes
opencadc · May 9, 2024 · 7ad37d1 · 7ad37d1
2 parents cfa7522 + d82847e
commit 7ad37d1
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Showing 10 changed files with 257 additions and 102 deletions.
diff --git a/caom2-tap-server/build.gradle b/caom2-tap-server/build.gradle
@@ -17,7 +17,7 @@ sourceCompatibility = 1.8
 
 group = 'org.opencadc'
 
-version = '1.2.11'
+version = '1.2.12'
 
 description = 'OpenCADC CAOM2 TAP server library'
 def git_url = 'https://github.com/opencadc/caom2service'
@@ -34,6 +34,7 @@ dependencies {
     compile 'org.opencadc:cadc-tap-server-pg:[1.1.0,)'
     compile 'org.opencadc:cadc-tap-schema:[1.1.6,)'
     compile 'org.opencadc:cadc-adql:[1.1.14,)'
+    compile 'org.opencadc:caom2:[2.4.8,)'
     compile 'org.opencadc:caom2-artifact-resolvers:[1.2.3,)'
 
     compile 'org.opencadc:cadc-gms:[1.0.0,)'

diff --git a/caom2-tap-server/src/main/java/ca/nrc/cadc/tap/caom2/PositionBoundsSamplesFormat.java b/caom2-tap-server/src/main/java/ca/nrc/cadc/tap/caom2/PositionBoundsSamplesFormat.java
@@ -68,21 +68,27 @@
 package ca.nrc.cadc.tap.caom2;
 
 
+import ca.nrc.cadc.caom2.types.SegmentType;
+import ca.nrc.cadc.dali.MultiPolygon;
+import ca.nrc.cadc.dali.Point;
+import ca.nrc.cadc.dali.Polygon;
+import ca.nrc.cadc.dali.util.MultiPolygonFormat;
 import ca.nrc.cadc.tap.writer.format.AbstractResultSetFormat;
 import ca.nrc.cadc.tap.writer.format.DoubleArrayFormat;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import org.apache.log4j.Logger;
 
 /**
- * Format position_bounds_samples as a xtype="caom2:multipolygon".
+ * Format position_bounds_samples as a xtype="multipolygon".
  * 
  * @author pdowler
  */
 public class PositionBoundsSamplesFormat extends AbstractResultSetFormat {
     private static final Logger log = Logger.getLogger(PositionBoundsSamplesFormat.class);
 
     private DoubleArrayFormat daf = new DoubleArrayFormat();
+    private MultiPolygonFormat mpf = new MultiPolygonFormat();
 
     public PositionBoundsSamplesFormat() { 
     }
@@ -94,6 +100,25 @@ public Object extract(ResultSet resultSet, int columnIndex) throws SQLException
 
     @Override
     public String format(Object o) {
-        return daf.format(o);
+        if (o == null) {
+            return "";
+        }
+        double[] arr = daf.unwrap(o);
+        MultiPolygon mp = new MultiPolygon();
+        // caom2 MP has longitude,latitide,segmentType
+        Polygon poly = new Polygon();
+        for (int i = 0; i < arr.length; i += 3) {
+            double cv1 = arr[i];
+            double cv2 = arr[i + 1];
+            SegmentType st = SegmentType.toValue((int) arr[i + 2]);
+            if (SegmentType.CLOSE.equals(st)) {
+                mp.getPolygons().add(poly);
+                poly = new Polygon();
+            } else {
+                poly.getVertices().add(new Point(cv1, cv2));
+            }
+        }
+
+        return mpf.format(mp);
     }
 }
diff --git a/...2-tap-server/src/main/java/ca/nrc/cadc/tap/caom2/PositionBoundsSamplesInternalFormat.java b/...2-tap-server/src/main/java/ca/nrc/cadc/tap/caom2/PositionBoundsSamplesInternalFormat.java
@@ -0,0 +1,99 @@
+/*
+************************************************************************
+*******************  CANADIAN ASTRONOMY DATA CENTRE  *******************
+**************  CENTRE CANADIEN DE DONNÉES ASTRONOMIQUES  **************
+*
+*  (c) 2019.                            (c) 2019.
+*  Government of Canada                 Gouvernement du Canada
+*  National Research Council            Conseil national de recherches
+*  Ottawa, Canada, K1A 0R6              Ottawa, Canada, K1A 0R6
+*  All rights reserved                  Tous droits réservés
+*
+*  NRC disclaims any warranties,        Le CNRC dénie toute garantie
+*  expressed, implied, or               énoncée, implicite ou légale,
+*  statutory, of any kind with          de quelque nature que ce
+*  respect to the software,             soit, concernant le logiciel,
+*  including without limitation         y compris sans restriction
+*  any warranty of merchantability      toute garantie de valeur
+*  or fitness for a particular          marchande ou de pertinence
+*  purpose. NRC shall not be            pour un usage particulier.
+*  liable in any event for any          Le CNRC ne pourra en aucun cas
+*  damages, whether direct or           être tenu responsable de tout
+*  indirect, special or general,        dommage, direct ou indirect,
+*  consequential or incidental,         particulier ou général,
+*  arising from the use of the          accessoire ou fortuit, résultant
+*  software.  Neither the name          de l'utilisation du logiciel. Ni
+*  of the National Research             le nom du Conseil National de
+*  Council of Canada nor the            Recherches du Canada ni les noms
+*  names of its contributors may        de ses  participants ne peuvent
+*  be used to endorse or promote        être utilisés pour approuver ou
+*  products derived from this           promouvoir les produits dérivés
+*  software without specific prior      de ce logiciel sans autorisation
+*  written permission.                  préalable et particulière
+*                                       par écrit.
+*
+*  This file is part of the             Ce fichier fait partie du projet
+*  OpenCADC project.                    OpenCADC.
+*
+*  OpenCADC is free software:           OpenCADC est un logiciel libre ;
+*  you can redistribute it and/or       vous pouvez le redistribuer ou le
+*  modify it under the terms of         modifier suivant les termes de
+*  the GNU Affero General Public        la “GNU Affero General Public
+*  License as published by the          License” telle que publiée
+*  Free Software Foundation,            par la Free Software Foundation
+*  either version 3 of the              : soit la version 3 de cette
+*  License, or (at your option)         licence, soit (à votre gré)
+*  any later version.                   toute version ultérieure.
+*
+*  OpenCADC is distributed in the       OpenCADC est distribué
+*  hope that it will be useful,         dans l’espoir qu’il vous
+*  but WITHOUT ANY WARRANTY;            sera utile, mais SANS AUCUNE
+*  without even the implied             GARANTIE : sans même la garantie
+*  warranty of MERCHANTABILITY          implicite de COMMERCIALISABILITÉ
+*  or FITNESS FOR A PARTICULAR          ni d’ADÉQUATION À UN OBJECTIF
+*  PURPOSE.  See the GNU Affero         PARTICULIER. Consultez la Licence
+*  General Public License for           Générale Publique GNU Affero
+*  more details.                        pour plus de détails.
+*
+*  You should have received             Vous devriez avoir reçu une
+*  a copy of the GNU Affero             copie de la Licence Générale
+*  General Public License along         Publique GNU Affero avec
+*  with OpenCADC.  If not, see          OpenCADC ; si ce n’est
+*  <http://www.gnu.org/licenses/>.      pas le cas, consultez :
+*                                       <http://www.gnu.org/licenses/>.
+*
+************************************************************************
+*/
+
+package ca.nrc.cadc.tap.caom2;
+
+
+import ca.nrc.cadc.tap.writer.format.AbstractResultSetFormat;
+import ca.nrc.cadc.tap.writer.format.DoubleArrayFormat;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import org.apache.log4j.Logger;
+
+/**
+ * Format position_bounds_samples as a xtype="caom2:multipolygon".
+ * 
+ * @author pdowler
+ */
+public class PositionBoundsSamplesInternalFormat extends AbstractResultSetFormat {
+    private static final Logger log = Logger.getLogger(PositionBoundsSamplesFormat.class);
+
+    private DoubleArrayFormat daf = new DoubleArrayFormat();
+
+    public PositionBoundsSamplesInternalFormat() { 
+    }
+
+    @Override
+    public Object extract(ResultSet resultSet, int columnIndex) throws SQLException {
+        return daf.extract(resultSet, columnIndex);
+    }
+
+    @Override
+    public String format(Object o) {
+        return daf.format(o);
+    }
+}
diff --git a/caom2-tap-server/src/main/java/ca/nrc/cadc/tap/caom2/PositionBoundsShapeFormat.java b/caom2-tap-server/src/main/java/ca/nrc/cadc/tap/caom2/PositionBoundsShapeFormat.java
@@ -104,19 +104,21 @@ public Object extract(ResultSet resultSet, int columnIndex)
 
     @Override
     public String format(Object o) {
-        if (o == null)
+        if (o == null) {
             return "";
-
+        }
+
         double[] dd = daf.unwrap(o);
         StringBuilder sb = new StringBuilder();
 
-        if (dd.length == 3)
+        if (dd.length == 3) {
             sb.append("circle ");
-        else if (dd.length >= 6)
+        } else if (dd.length >= 6) {
             sb.append("polygon ");
-        else
+        } else {
             throw new RuntimeException("CONTENT: unexpected position_bounds length: " + dd.length); 
-
+        }
+
         sb.append(daf.format(dd));
 
         return sb.toString();

diff --git a/caom2-tap-server/src/main/java/ca/nrc/cadc/tap/impl/CaomFormatFactory.java b/caom2-tap-server/src/main/java/ca/nrc/cadc/tap/impl/CaomFormatFactory.java
@@ -105,6 +105,7 @@ protected Format<Object> getShapeFormat(TapSelectItem columnDesc) {
                     || columnDesc.utype.equals("obscore:Char.SpatialAxis.Coverage.Support.Area"))) {
             return new PositionBoundsShapeFormat();
         }
+        // default to pgsphere formatters
         return super.getShapeFormat(columnDesc);
     }
 

diff --git a/caom2-tap-server/src/main/java/ca/nrc/cadc/tap/impl/InitCaomTapSchemaContent.java b/caom2-tap-server/src/main/java/ca/nrc/cadc/tap/impl/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 = "caom-schema";
-    public static final String MODEL_VERSION = "1.2.8";
+    public static final String MODEL_VERSION = "1.2.12";
 
     // the SQL is tightly coupled to cadc-tap-schema table names (for TAP-1.1)
     static String[] CREATE_SQL = new String[] {

diff --git a/caom2-tap-server/src/main/resources/sql/caom2.tap_schema_content11.sql b/caom2-tap-server/src/main/resources/sql/caom2.tap_schema_content11.sql
@@ -148,8 +148,8 @@ insert into tap_schema.columns11 (table_name,column_name,description,utype,ucd,u
 ( 'caom2.Plane', 'observable_ucd', 'UCD (Universal Content Descriptor) for the observed/measure quantity', 'caom2:Plane.observable.ucd', NULL, NULL, 'char', '64*', NULL, 0,0,0 , 40),
 ( 'caom2.Plane', 'quality_flag', 'flag describing the data quality (possible values: junk)', 'caom2:Plane.quality.flag', NULL, NULL, 'char', '16*', NULL, 0,0,0 , 41),
 
-( 'caom2.Plane', 'position_bounds', 'positional coverage of the data', 'caom2:Plane.position.bounds', NULL, 'deg', 'char', '*', 'caom2:shape', 0,0,0 , 50),
-( 'caom2.Plane', 'position_bounds_samples', 'positional coverage of the data', 'caom2:Plane.position.bounds.samples', NULL, 'deg', 'double', '*', 'caom2:multipolygon', 0,0,0 , 50),
+( 'caom2.Plane', 'position_bounds', 'positional coverage of the data', 'caom2:Plane.position.bounds', NULL, 'deg', 'char', '*', 'shape', 0,0,0 , 50),
+( 'caom2.Plane', 'position_bounds_samples', 'positional coverage of the data', 'caom2:Plane.position.bounds.samples', NULL, 'deg', 'double', '*', 'multipolygon', 0,0,0 , 50),
 ( 'caom2.Plane', 'position_bounds_size', 'size of the polygon bounds (diameter of minimum spanning circle)', 'caom2:Plane.position.bounds.size', NULL, 'deg', 'double', NULL, NULL, 0,0,0 , 51),
 ( 'caom2.Plane', 'position_resolution', 'median spatial resolution (FWHM)', 'caom2:Plane.position.resolution', NULL, 'arcsec', 'double', NULL, NULL, 0,0,0 , 52),
 ( 'caom2.Plane', 'position_resolutionBounds', 'range of spatial resolution (FWHM) [new in 2.4]', 'caom2:Plane.position.resolutionBounds', NULL, 'arcsec', 'double', '2', 'interval', 0,0,0 , 52),
@@ -159,7 +159,7 @@ insert into tap_schema.columns11 (table_name,column_name,description,utype,ucd,u
 ( 'caom2.Plane', 'position_timeDependent', 'flag indicating that the position is time-dependent (0=false, 1=true)', 'caom2:Plane.position.timeDependent', NULL, NULL, 'int', NULL, NULL, 0,0,0 , 56),
 
 ( 'caom2.Plane', 'energy_bounds', 'energy coverage (barycentric wavelength)', 'caom2:Plane.energy.bounds', NULL, 'm', 'double', '2','interval', 0,1,0 , 61),
-( 'caom2.Plane', 'energy_bounds_samples', 'detailed energy coverage (barycentric wavelength)', 'caom2:Plane.energy.bounds.samples', NULL, 'm', 'double', '*', 'caom2:multiinterval', 0,0,0 , 61),
+( 'caom2.Plane', 'energy_bounds_samples', 'detailed energy coverage (barycentric wavelength)', 'caom2:Plane.energy.bounds.samples', NULL, 'm', 'double', '2x*', 'interval', 0,0,0 , 61),
 ( 'caom2.Plane', 'energy_bounds_lower', 'lower bound on energy axis (barycentric wavelength)', 'caom2:Plane.energy.bounds.lower', NULL, 'm', 'double', NULL, NULL, 0,1,0 , 62),
 ( 'caom2.Plane', 'energy_bounds_upper', 'upper bound on energy axis (barycentric wavelength)', 'caom2:Plane.energy.bounds.upper', NULL, 'm', 'double', NULL, NULL, 0,1,0 , 63),
 ( 'caom2.Plane', 'energy_bounds_width', 'width of the energy bounds', 'caom2:Plane.energy.bounds.width', NULL, 'm', 'double', NULL, NULL, 0,0,0 , 64),
@@ -179,7 +179,7 @@ insert into tap_schema.columns11 (table_name,column_name,description,utype,ucd,u
 ( 'caom2.Plane', 'energy_restwav', 'rest wavelength of target spectral feature (barycentric)', 'caom2:Plane.energy.restwav', NULL, 'm', 'double', NULL, NULL, 0,1,0 , 75),
 
 ( 'caom2.Plane', 'time_bounds', 'time coverage (Modified Julian Day)', 'caom2:Plane.time.bounds', NULL, 'd', 'double', '2', 'interval', 0,1,0 , 80),
-( 'caom2.Plane', 'time_bounds_samples', 'detailed time coverage (Modified Julian Day)', 'caom2:Plane.time.bounds.samples', NULL, 'd', 'double', '*', 'caom2:multiinterval', 0,0,0 , 81),
+( 'caom2.Plane', 'time_bounds_samples', 'detailed time coverage (Modified Julian Day)', 'caom2:Plane.time.bounds.samples', NULL, 'd', 'double', '2x*', 'interval', 0,0,0 , 81),
 ( 'caom2.Plane', 'time_bounds_lower', 'lower bound on time axis (Modified Julian Day)', 'caom2:Plane.time.bounds.lower', NULL, 'd', 'double', NULL, NULL, 0,1,0 , 81),
 ( 'caom2.Plane', 'time_bounds_upper', 'upper bound on time axis (Modified Julian Day)', 'caom2:Plane.time.bounds.upper', NULL, 'd', 'double', NULL, NULL, 0,1,0 , 82),
 ( 'caom2.Plane', 'time_bounds_width', 'width of the time bounds', 'caom2:Plane.time.bounds.width', NULL, 'd', 'double', NULL, NULL, 0,1,0 , 83),
@@ -194,7 +194,7 @@ insert into tap_schema.columns11 (table_name,column_name,description,utype,ucd,u
 
 ( 'caom2.Plane', 'custom_ctype', 'coordinate type for custom axis [new in 2.4]', 'caom2:Plane.custom.ctype', NULL, NULL, 'char', '32*', NULL, 0,0,0 , 100),
 ( 'caom2.Plane', 'custom_bounds', 'custom axis coverage [new in 2.4]', 'caom2:Plane.custom.bounds', NULL, NULL, 'double', '2', 'interval', 0,0,0 , 101),
-( 'caom2.Plane', 'custom_bounds_samples', 'detailed custom axis coverage [new in 2.4]', 'caom2:Plane.custom.bounds.samples', NULL, NULL, 'double', '*', 'caom2:multiinterval', 0,0,0 , 102),
+( 'caom2.Plane', 'custom_bounds_samples', 'detailed custom axis coverage [new in 2.4]', 'caom2:Plane.custom.bounds.samples', NULL, NULL, 'double', '2x*', 'interval', 0,0,0 , 102),
 ( 'caom2.Plane', 'custom_bounds_lower', 'lower bound on custom axis [new in 2.4]', 'caom2:Plane.custom.bounds.lower', NULL, NULL, 'double', NULL, NULL, 0,0,0 , 103),
 ( 'caom2.Plane', 'custom_bounds_upper', 'upper bound on custom axis [new in 2.4]', 'caom2:Plane.custom.bounds.upper', NULL, NULL, 'double', NULL, NULL, 0,0,0 , 104),
 ( 'caom2.Plane', 'custom_bounds_width', 'width of the custom bounds [new in 2.4]', 'caom2:Plane.custom.bounds.width', NULL, NULL, 'double', NULL, NULL, 0,0,0 , 105),

diff --git a/caom2-tap-server/src/main/resources/sql/ivoa.tap_schema_content11.sql b/caom2-tap-server/src/main/resources/sql/ivoa.tap_schema_content11.sql
@@ -40,7 +40,7 @@ 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,id) values
 ( 'ivoa.ObsCore', 'obs_publisher_did', 	'obscore:Curation.PublisherDID',
-    'publisher dataset identifier', 'meta.ref.ivoid', NULL, 'char', '256*',NULL, 1,1,1,1, 'caomPublisherID')
+    'publisher dataset identifier', 'meta.ref.ivoid', NULL, 'char', '256*','uri', 1,1,1,1, 'caomPublisherID')
 ;
 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',

diff --git a/caom2-tap/build.gradle b/caom2-tap/build.gradle
@@ -16,7 +16,7 @@ sourceCompatibility = 1.8
 
 group = 'org.opencadc'
 
-version = '1.8.0'
+version = '1.8.1'
 
 description = 'OpenCADC CAOM2 TAP client library'
 def git_url = 'https://github.com/opencadc/caom2service'