Skip to content

Commit

Permalink
Merge pull request #101 from lsst-sqre/tickets/DM-44607
Browse files Browse the repository at this point in the history
Update Cadc libraries / Enable UWS init action / Switch to tomcat image
  • Loading branch information
stvoutsin authored Jun 13, 2024
2 parents 511548e + 38f75b5 commit 913fdb5
Show file tree
Hide file tree
Showing 11 changed files with 289 additions and 140 deletions.
25 changes: 25 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -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)

31 changes: 21 additions & 10 deletions build.gradle
Original file line number Diff line number Diff line change
Expand Up @@ -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 ##
Expand Down
7 changes: 7 additions & 0 deletions changelog.d/_template.md.jinja
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
<!-- Delete the sections that don't apply -->
{%- for cat in config.categories %}

### {{ cat }}

-
{%- endfor %}
3 changes: 3 additions & 0 deletions changelog.d/scriv.ini
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
[scriv]
format = md
categories = Backwards-incompatible changes,New features,Bug fixes,Other changes
15 changes: 10 additions & 5 deletions docker/Dockerfile.lsst-tap-service
Original file line number Diff line number Diff line change
@@ -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
2 changes: 0 additions & 2 deletions docker/start.sh
Original file line number Diff line number Diff line change
Expand Up @@ -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
10 changes: 4 additions & 6 deletions src/main/java/org/opencadc/tap/impl/AuthenticatorImpl.java
Original file line number Diff line number Diff line change
Expand Up @@ -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);
Expand Down
156 changes: 156 additions & 0 deletions src/main/java/org/opencadc/tap/impl/UWSInitAction.java
Original file line number Diff line number Diff line change
@@ -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);
}
}
}
}
}
4 changes: 2 additions & 2 deletions src/main/webapp/META-INF/context.xml
Original file line number Diff line number Diff line change
Expand Up @@ -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>
5 changes: 4 additions & 1 deletion src/main/webapp/WEB-INF/web.xml
Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand All @@ -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>
Expand Down
Loading

0 comments on commit 913fdb5

Please sign in to comment.