csip-oms Displaying differences for changeset

Displaying differences for changeset

display as Allow wrapping

nbproject/ant-deploy.xml

 @@ -1,42 +1,23 @@
   <?xml version="1.0" encoding="UTF-8"?>
   <!--
--DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
--Copyright (c) 2006, 2016 Oracle and/or its affiliates. All rights reserved.
++    Licensed to the Apache Software Foundation (ASF) under one
++    or more contributor license agreements.  See the NOTICE file
++    distributed with this work for additional information
++    regarding copyright ownership.  The ASF licenses this file
++    to you under the Apache License, Version 2.0 (the
++    "License"); you may not use this file except in compliance
++    with the License.  You may obtain a copy of the License at
--Oracle and Java are registered trademarks of Oracle and/or its affiliates.
--Other names may be trademarks of their respective owners.
++      http://www.apache.org/licenses/LICENSE-2.0
--The contents of this file are subject to the terms of either the GNU
--General Public License Version 2 only ("GPL") or the Common
--Development and Distribution License("CDDL") (collectively, the
--"License"). You may not use this file except in compliance with the
--License. You can obtain a copy of the License at
--http://www.netbeans.org/cddl-gplv2.html
--or nbbuild/licenses/CDDL-GPL-2-CP. See the License for the
--specific language governing permissions and limitations under the
--License.  When distributing the software, include this License Header
--Notice in each file and include the License file at
--nbbuild/licenses/CDDL-GPL-2-CP.  Oracle designates this
--particular file as subject to the "Classpath" exception as provided
--by Oracle in the GPL Version 2 section of the License file that
--accompanied this code. If applicable, add the following below the
--License Header, with the fields enclosed by brackets [] replaced by
--your own identifying information:
--"Portions Copyrighted [year] [name of copyright owner]"
++    Unless required by applicable law or agreed to in writing,
++    software distributed under the License is distributed on an
++    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
++    KIND, either express or implied.  See the License for the
++    specific language governing permissions and limitations
++    under the License.
--If you wish your version of this file to be governed by only the CDDL
--or only the GPL Version 2, indicate your decision by adding
--"[Contributor] elects to include this software in this distribution
--under the [CDDL or GPL Version 2] license." If you do not indicate a
--single choice of license, a recipient has the option to distribute
--your version of this file under either the CDDL, the GPL Version 2 or
--to extend the choice of license to its licensees as provided above.
--However, if you add GPL Version 2 code and therefore, elected the GPL
--Version 2 license, then the option applies only if the new code is
--made subject to such option by the copyright holder.
--
--Contributor(s):
   -->
   <project default="-deploy-ant" basedir=".">
       <target name="-init" if="deploy.ant.enabled">

nbproject/build-impl.xml~

nbproject/project.properties

@@ -27,17 +27,19 @@

endorsed.classpath=\

${libs.javaee-endorsed-api-6.0.classpath}

excludes=

+file.reference.oms-3.5.jar=lib/oms-3.5.jar

includes=**

j2ee.compile.on.save=false

j2ee.copy.static.files.on.save=true

j2ee.deploy.on.save=false

j2ee.platform=1.6-web

-j2ee.platform.classpath=${j2ee.server.home}/lib/annotations-api.jar:${j2ee.server.home}/lib/catalina-ant.jar:${j2ee.server.home}/lib/catalina-ha.jar:${j2ee.server.home}/lib/catalina-storeconfig.jar:${j2ee.server.home}/lib/catalina-tribes.jar:${j2ee.server.home}/lib/catalina.jar:${j2ee.server.home}/lib/ecj-4.4.2.jar:${j2ee.server.home}/lib/el-api.jar:${j2ee.server.home}/lib/jasper-el.jar:${j2ee.server.home}/lib/jasper.jar:${j2ee.server.home}/lib/jsp-api.jar:${j2ee.server.home}/lib/servlet-api.jar:${j2ee.server.home}/lib/tomcat-api.jar:${j2ee.server.home}/lib/tomcat-coyote.jar:${j2ee.server.home}/lib/tomcat-dbcp.jar:${j2ee.server.home}/lib/tomcat-i18n-es.jar:${j2ee.server.home}/lib/tomcat-i18n-fr.jar:${j2ee.server.home}/lib/tomcat-i18n-ja.jar:${j2ee.server.home}/lib/tomcat-jdbc.jar:${j2ee.server.home}/lib/tomcat-jni.jar:${j2ee.server.home}/lib/tomcat-util-scan.jar:${j2ee.server.home}/lib/tomcat-util.jar:${j2ee.server.home}/lib/tomcat-websocket.jar:${j2ee.server.home}/lib/websocket-api.jar

+j2ee.platform.classpath=${j2ee.server.home}/lib/annotations-api.jar:${j2ee.server.home}/lib/catalina-ant.jar:${j2ee.server.home}/lib/catalina-ha.jar:${j2ee.server.home}/lib/catalina-storeconfig.jar:${j2ee.server.home}/lib/catalina-tribes.jar:${j2ee.server.home}/lib/catalina.jar:${j2ee.server.home}/lib/ecj-4.6.3.jar:${j2ee.server.home}/lib/el-api.jar:${j2ee.server.home}/lib/jasper-el.jar:${j2ee.server.home}/lib/jasper.jar:${j2ee.server.home}/lib/jaspic-api.jar:${j2ee.server.home}/lib/jsp-api.jar:${j2ee.server.home}/lib/servlet-api.jar:${j2ee.server.home}/lib/tomcat-api.jar:${j2ee.server.home}/lib/tomcat-coyote.jar:${j2ee.server.home}/lib/tomcat-dbcp.jar:${j2ee.server.home}/lib/tomcat-i18n-de.jar:${j2ee.server.home}/lib/tomcat-i18n-es.jar:${j2ee.server.home}/lib/tomcat-i18n-fr.jar:${j2ee.server.home}/lib/tomcat-i18n-ja.jar:${j2ee.server.home}/lib/tomcat-i18n-ko.jar:${j2ee.server.home}/lib/tomcat-i18n-ru.jar:${j2ee.server.home}/lib/tomcat-i18n-zh-CN.jar:${j2ee.server.home}/lib/tomcat-jdbc.jar:${j2ee.server.home}/lib/tomcat-jni.jar:${j2ee.server.home}/lib/tomcat-util-scan.jar:${j2ee.server.home}/lib/tomcat-util.jar:${j2ee.server.home}/lib/tomcat-websocket.jar:${j2ee.server.home}/lib/websocket-api.jar

j2ee.server.type=Tomcat

jar.compress=false

javac.classpath=\

${reference.csip-core.jar}:\

- ${libs.CSIP-Jersey-2.16.classpath}

+ ${libs.CSIP-Jersey-2.16.classpath}:\

+ ${file.reference.oms-3.5.jar}

# Space-separated list of extra javac options

javac.compilerargs=

javac.debug=true

nbproject/project.xml

 @@ -19,6 +19,10 @@
                       <file>${libs.CSIP-Jersey-2.16.classpath}</file>
                       <path-in-war>WEB-INF/lib</path-in-war>
                   </library>
++                <library dirs="200">
++                    <file>${file.reference.oms-3.5.jar}</file>
++                    <path-in-war>WEB-INF/lib</path-in-war>
++                </library>
               </web-module-libraries>
               <web-module-additional-libraries/>
               <source-roots>

src/java/m/oms/ApplicationConfig.java

@@ -5,7 +5,7 @@

package m.oms;

import csip.Config;

-import csip.ContextConfig;

import java.util.Set;

import javax.servlet.ServletContext;

import javax.ws.rs.core.Application;

@@ -25,8 +25,8 @@

public Set<Class<?>> getClasses() {

Set<Class<?>> resources = new java.util.HashSet<>();

addRestResourceClasses(resources);

- ContextConfig.filterServices(context, resources);

- Config.register(resources);

+ Config.register(resources, context);

return resources;

}

src/java/m/oms/ages/V1_0.java

@@ -5,7 +5,7 @@

package m.oms.ages;

import csip.ModelDataService;

-import csip.ServiceException;

+import csip.api.server.ServiceException;

import csip.annotations.*;

import static csip.annotations.ResourceType.*;

import java.io.File;

@@ -308,7 +308,7 @@

Utils.passOptQuotedParam(agesParam, parameter(), flags);

// create parameter include file

- Utils.createParamInclude(agesParam, getWorkspaceFile(RUN_INC));

+ Utils.createParamInclude(agesParam, workspace().getFile(RUN_INC));

String start = parameter().getString(PAR_STARTTIME);

String end = parameter().getString(PAR_ENDTIME);

@@ -319,13 +319,13 @@

File d = new File(dsl);

if (!(d.isAbsolute() && d.exists())) {

- d = getWorkspaceFile(dsl);

+ d = workspace().getFile(dsl);

}

- getWorkspaceFile("output").mkdirs();

- getWorkspaceFile("logs").mkdirs();

+ workspace().getFile("output").mkdirs();

+ workspace().getFile("logs").mkdirs();

- Utils.runAges(d, getWorkspaceDir(), parameter(), resources(), LOG);

+ Utils.runAges(d, workspace().getDir(), parameter(), resources(), LOG);

for (String namee : parameter().getNames()) {

for (String ofNameM : getRequestedObjfunc(OF.keySet())) {

@@ -354,10 +354,10 @@

String new_string = "/tmp/csip/bin/ages/data/" + data_folder;

obsData = Utils.getData(obs, new File(new_string), start, end);

} else {

- obsData = Utils.getData(obs, getWorkspaceDir(), start, end);

+ obsData = Utils.getData(obs, workspace().getDir(), start, end);

}

// e.g. output/csip_run/out/Outlet.csv/output/catchmentSimRunoff

- double[] simData = Utils.getData(sim, getWorkspaceDir(), start, end);

+ double[] simData = Utils.getData(sim, workspace().getDir(), start, end);

double result = of.calculate(obsData, simData, parameter().getDouble("missing", -9999d));

return checkForNaN(result);

}

src/java/m/oms/dsl/V1_0.java

@@ -4,9 +4,9 @@

package m.oms.dsl;

-import csip.Executable;

+import csip.api.server.Executable;

import csip.ModelDataService;

-import csip.ServiceException;

+import csip.api.server.ServiceException;

import csip.annotations.*;

import csip.utils.Binaries;

//import csip.utils.ZipFiles;

@@ -17,7 +17,7 @@

import java.util.Map;

import javax.ws.rs.Path;

import org.apache.commons.io.FileUtils;

-import org.apache.commons.lang.ArrayUtils;

+import org.apache.commons.lang3.ArrayUtils;

/**

* OMS service.

@@ -53,25 +53,25 @@

@Override

protected void postProcess() throws Exception {

-// ZipFiles.zip(getWorkspaceFile("output"));

-// results().put(new File(getWorkspaceDir(), "output"));

- results().put(getWorkspaceFile("output"));

+// ZipFiles.zip(workspace().getFile("output"));

+// results().put(new File(workspace().getDir(), "output"));

+ results().put(workspace().getFile("output"));

}

private void runSim(String dsl, String loglevel, String options) throws Exception {

Map sysprops = new HashMap();

- sysprops.put("oms3.work", getWorkspaceDir().toString());

+ sysprops.put("oms3.work", workspace().getDir().toString());

sysprops.put("oms.csip.server", "true");

- getWorkspaceFile("output").mkdirs();

+ workspace().getFile("output").mkdirs();

// Create a Process.

Executable p = createProcess(loglevel, dsl, sysprops, options);

int result = p.exec();

if (result != 0) {

- File err = getWorkspaceFile("java-stderr.txt");

+ File err = workspace().getFile("java-stderr.txt");

if (err.exists()) {

throw new ServiceException(FileUtils.readFileToString(err));

}

@@ -82,15 +82,15 @@

private Executable createProcess(String loglevel, String dsl,

Map<String, String> sysprops, String options) throws Exception {

- File ws = getWorkspaceDir();

+ File ws = workspace().getDir();

List<File> jars = new ArrayList<>();

jars.add(resources().getFile("oms_jar"));

jars.add(resources().getFile("jfreechart_jar"));

jars.add(resources().getFile("groovy_jar"));

jars.add(resources().getFile("jcommon_jar"));

- jars.addAll(Binaries.getJars(getWorkspaceFile("dist")));

- jars.addAll(Binaries.getJars(getWorkspaceFile("lib")));

+ jars.addAll(Binaries.getJars(workspace().getFile("dist")));

+ jars.addAll(Binaries.getJars(workspace().getFile("lib")));

jars.addAll(Binaries.getJars(ws));

String[] sp = Binaries.asSysProps(sysprops);

@@ -98,6 +98,6 @@

String[] opt = options.split("\\s+");

sp = (String[]) ArrayUtils.addAll(sp, opt);

}

- return Binaries.getResourceOMSDSL(getWorkspaceFile(dsl), sp, ws, jars, loglevel, LOG);

+ return Binaries.getResourceOMSDSL(workspace().getFile(dsl), sp, ws, jars, loglevel, LOG);

}

src/java/oms/utils/Utils.java

@@ -5,10 +5,10 @@

package oms.utils;

-import csip.Executable;

-import csip.PayloadParameter;

-import csip.ServiceException;

-import csip.ServiceResources;

+import csip.api.server.Executable;

+import csip.api.server.PayloadParameter;

+import csip.api.server.ServiceException;

+import csip.api.server.ServiceResources;

import csip.SessionLogger;

import csip.utils.Binaries;

import java.io.File;

@@ -22,7 +22,7 @@

import oms3.io.CSTable;

import oms3.io.DataIO;

import org.apache.commons.io.FileUtils;

-import org.apache.commons.lang.ArrayUtils;

+import org.apache.commons.lang3.ArrayUtils;

/**

@@ -231,7 +231,7 @@

* @param p

* @param param

* @param names

- * @throws csip.ServiceException

+ * @throws csip.api.server.ServiceException

public static void passReqQuotedParam(Map<String, String> p,

PayloadParameter param, String... names) throws ServiceException {

@@ -246,7 +246,7 @@

* @param p

* @param param

* @param names

- * @throws csip.ServiceException

+ * @throws csip.api.server.ServiceException

public static void passOptParam(Map<String, String> p,

PayloadParameter param, String... names) throws ServiceException {

web/WEB-INF/csip-defaults.json

@@ -1,5 +1,5 @@

{

- "csip.context.version": "$version: 0.1.40 6fa494a6e98e 2020-04-02 od, built at 2020-04-02 10:17 by od$",

+ "csip.context.version": "$version: 0.1.88 default 102 da3bb6d88964 2021-09-17 Holm Kipka <holm.kipka@colostate.edu>, built at 2021-12-28 12:34 by od$",

"oms.java.home": "/opt/jdk1.8.0_51",

"csip.keepworkspace": false,

"csip.session.ttl": "PT10S",