Update Cadc libraries / Enable UWS init action / Switch to tomcat image

CHANGELOG.md

@@ -0,0 +1,25 @@
+# Change log
+
+lsst-tap-service is versioned with [semver](https://semver.org/). Dependencies are updated to the latest available version during each release. Those changes are not noted here explicitly.
+
+Find changes for the upcoming release in the project's [changelog.d](https://github.com/lsst-sqre/lsst-tap-service/tree/main/changelog.d/).
+
+<!-- scriv-insert-here -->
+
+# 2024-06-11
+
+## New features
+
+- Added UWSInitAction class to initialise a UWS database
+- Added scriv changelogs
+
+## Other Changes
+
+- Changed the build.gradle to use fixed version of the latest cadc libs
+- Changed Dockerfile for lsst-tap-service to use cadc-tomcat base image
+- Deprecated AuthenticatorImpl class
+
+## Bug Fixes
+
+- Fixed capabilities output (securityMethods)
+

build.gradle

@@ -40,16 +40,27 @@ configurations {
 }
 
 dependencies {
-    implementation 'log4j:log4j:[1.2,2.0)'
-    implementation 'org.opencadc:cadc-log:[1.0,)'
-    implementation 'org.opencadc:cadc-util:[1.2,)'
-    implementation 'org.opencadc:cadc-dali:[1.1,)'
-    implementation 'org.opencadc:cadc-uws:[1.0,)'
-    implementation 'org.opencadc:cadc-uws-server:[1.2,)'
-    implementation 'org.opencadc:cadc-tap-server:[1.1.5,)'
-    implementation 'org.opencadc:cadc-vosi:[1.4.1,)'
-    implementation 'org.opencadc:cadc-adql:[1.1.13,)'
-    implementation 'org.opencadc:cadc-tap-server-oracle:[1.0.0,)'
+    implementation 'log4j:log4j:1.2.+'
+    implementation 'org.opencadc:cadc-adql:1.1.13'
+    implementation 'org.opencadc:cadc-cdp:1.3.7'
+    implementation 'org.opencadc:cadc-dali:1.2.17'
+    implementation 'org.opencadc:cadc-dali-pg:0.3.1'
+    implementation 'org.opencadc:cadc-gms:1.0.12'
+    implementation 'org.opencadc:cadc-jsqlparser-compat:0.6.5'
+    implementation 'org.opencadc:cadc-log:1.2.1'
+    implementation 'org.opencadc:cadc-registry:1.7.6'
+    implementation 'org.opencadc:cadc-rest:1.3.18'
+    implementation 'org.opencadc:cadc-tap:1.1.16'
+    implementation 'org.opencadc:cadc-tap-schema:1.1.32'
+    implementation 'org.opencadc:cadc-tap-server:1.1.23'
+    implementation 'org.opencadc:cadc-tap-server-pg:1.0.5'
+    implementation 'org.opencadc:cadc-tap-server-oracle:1.2.11'
+    implementation 'org.opencadc:cadc-util:1.10.6'
+    implementation 'org.opencadc:cadc-uws:1.0.5'
+    implementation 'org.opencadc:cadc-uws-server:1.2.20'
+    implementation 'org.opencadc:cadc-tap-server:1.1.23'
+    implementation 'org.opencadc:cadc-vosi:1.4.4'
+    implementation 'org.opencadc:cadc-adql:1.1.13'
 
     // Switch out this to use any supported database instead of PostgreSQL.
     // ## START CUSTOM DATABASE ##

changelog.d/_template.md.jinja

@@ -0,0 +1,7 @@
+<!-- Delete the sections that don't apply -->
+{%- for cat in config.categories %}
+
+### {{ cat }}
+
+-
+{%- endfor %}

changelog.d/scriv.ini

@@ -0,0 +1,3 @@
+[scriv]
+format = md
+categories = Backwards-incompatible changes,New features,Bug fixes,Other changes

docker/Dockerfile.lsst-tap-service

@@ -1,10 +1,15 @@
-FROM tomcat:9.0
+FROM images.opencadc.org/library/cadc-tomcat:1
 
-RUN rm -rf webapps/*
+LABEL org.opencontainers.image.source = "https://github.com/lsst-sqre/lsst-tap-service"
 
-RUN apt-get update && apt-get install -y zip unzip
+RUN dnf update -y && dnf install -y zip unzip
 
+# Copy start into container and set permissions
 ADD docker/start.sh /usr/local/bin/
-ADD docker/*.war webapps/
+RUN chmod +x /usr/local/bin/start.sh
 
-CMD ["start.sh"]
+# Copy war into tomcat webapps
+ADD docker/*.war /usr/share/tomcat/webapps/
+
+# Run the start script to handle the datalink task
+RUN /usr/local/bin/start.sh

docker/start.sh

@@ -6,5 +6,3 @@ if [ -n "$DATALINK_PAYLOAD_URL" ]; then
     curl -L "$DATALINK_PAYLOAD_URL" -o /tmp/datalink_payload.zip
     unzip /tmp/datalink_payload.zip -d /tmp/datalink
 fi
-
-exec catalina.sh run

src/main/java/org/opencadc/tap/impl/AuthenticatorImpl.java

@@ -29,14 +29,12 @@
 import org.apache.log4j.Logger;
 
 /**
- * Implementes the Authenticator for processing Gafaelfawr auth,
- * and using it to authenticate against the TAP service.
- *
- * The token in the authorization header is used to make a call
- * to Gafaelfawr to retrieve details such as the uid and uidNumber.
- *
+ * @deprecated This class is deprecated and will be removed in future releases.
+ * The TAP Service now uses IdentityManager for authentication, available in the opencadc library
+ * 
  * @author cbanek
  */
+@Deprecated
 public class AuthenticatorImpl implements Authenticator
 {
     private static final Logger log = Logger.getLogger(AuthenticatorImpl.class);

src/main/java/org/opencadc/tap/impl/UWSInitAction.java

@@ -0,0 +1,156 @@
+/*
+************************************************************************
+*******************  CANADIAN ASTRONOMY DATA CENTRE  *******************
+**************  CENTRE CANADIEN DE DONNÉES ASTRONOMIQUES  **************
+*
+*  (c) 2022.                            (c) 2022.
+*  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 org.opencadc.tap.impl;
+
+import ca.nrc.cadc.db.DBUtil;
+import ca.nrc.cadc.rest.InitAction;
+import ca.nrc.cadc.uws.server.impl.InitDatabaseUWS;
+import javax.sql.DataSource;
+import org.apache.log4j.Logger;
+
+import java.sql.Connection;
+import java.sql.DatabaseMetaData;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+
+/**
+ *
+ * @author pdowler
+ */
+public class UWSInitAction extends InitAction {
+    private static final Logger log = Logger.getLogger(UWSInitAction.class);
+
+    public UWSInitAction() {
+    }
+
+    @Override
+    public void doInit() {
+        DataSource uws = null;
+         try {
+            uws = DBUtil.findJNDIDataSource("jdbc/uws");
+            if (!schemaExists(uws, "uws")) {
+                log.info("uws schema does not exist, creating...");
+                createSchema(uws, "uws");
+                log.info("uws schema created");
+                // Continue with initialization only if the schema was just created
+                InitDatabaseUWS uwsi = new InitDatabaseUWS(uws, null, "uws");
+                uwsi.doInit();
+                log.info("init uws: OK");
+            } else {
+                log.info("uws schema already exists");
+                return; // Exit the method early if the schema already exists
+            }
+        } catch (Exception ex) {
+            throw new RuntimeException("INIT FAIL", ex);
+        } 
+    }
+
+    private boolean schemaExists(DataSource uws, String schemaName) throws SQLException {
+        Connection conn = null;
+        try {
+            conn = uws.getConnection();
+            DatabaseMetaData dbMetaData = conn.getMetaData();
+            ResultSet rs = dbMetaData.getSchemas();
+            while (rs.next()) {
+                if (schemaName.equalsIgnoreCase(rs.getString("TABLE_SCHEM").trim())) {
+                    return true;
+                }
+            }
+        } catch (Exception ex) {
+              throw new RuntimeException("Failed to check if schema exists", ex);
+        } finally {
+            if (conn != null) {
+                try {
+                    conn.close();
+                } catch (SQLException e) {
+                    log.error("Failed to close connection", e);
+                }
+            }
+        }
+        return false;
+    }
+
+    private void createSchema(DataSource uws, String schemaName) throws SQLException {
+        Connection conn = null;
+        try {
+            conn = uws.getConnection();
+            java.sql.Statement stmt = conn.createStatement();
+            stmt.execute("CREATE SCHEMA " + schemaName);
+        } catch (Exception ex) {
+            throw new RuntimeException("Create Schema failed", ex);
+        } finally {
+            if (conn != null) {
+                try {
+                    conn.close();
+                } catch (SQLException e) {
+                    log.error("Failed to close connection", e);
+                }
+            }
+        }
+    }
+}

src/main/webapp/META-INF/context.xml

@@ -41,14 +41,14 @@
               type="javax.sql.DataSource"
               factory="org.apache.tomcat.jdbc.pool.DataSourceFactory"
               minEvictableIdleTimeMillis="30000"
-              maxActive="1" maxIdle="1" maxWait="20000" initialSize="1" minIdle="1"
+              maxActive="${uws.maxActive}" maxIdle="1" maxWait="20000" initialSize="5" minIdle="1"
               username="${uws.username}" password="${uws.password}"
               driverClassName="${uws.driverClassName}"
               url="${uws.url}"
               removeAbandoned="false"
               removeAbandonedTimeout="600"
               logAbandoned="true"
               testOnBorrow="true"
-              validationQuery="SELECT 1 FROM JobAvailability"
+              validationQuery="SELECT 1"
     />
 </Context>

src/main/webapp/WEB-INF/web.xml

@@ -59,6 +59,10 @@
         <load-on-startup>2</load-on-startup>
         <servlet-name>SyncServlet</servlet-name>
         <servlet-class>ca.nrc.cadc.uws.server.JobServlet</servlet-class>
+        <init-param>
+            <param-name>init</param-name>
+            <param-value>org.opencadc.tap.impl.UWSInitAction</param-value>
+        </init-param>
         <init-param>
             <param-name>get</param-name>
             <param-value>ca.nrc.cadc.uws.web.SyncGetAction</param-value>
@@ -67,7 +71,6 @@
             <param-name>post</param-name>
             <param-value>ca.nrc.cadc.uws.web.SyncPostAction</param-value>
         </init-param>
-
         <init-param>
             <param-name>ca.nrc.cadc.uws.server.JobManager</param-name>
             <param-value>org.opencadc.tap.ws.QueryJobManager</param-value>