Reworked properties files.

pom.xml

@@ -50,7 +50,6 @@
             <artifactId>ccd-db</artifactId>
             <version>0.6.2</version>
         </dependency>
-
         <dependency>
             <groupId>edu.pitt.dbmi</groupId>
             <artifactId>ccd-commons</artifactId>
@@ -73,19 +72,16 @@
             <groupId>org.glassfish.jersey.media</groupId>
             <artifactId>jersey-media-multipart</artifactId>
             <version>2.23.1</version>
-            <!--            <type>jar</type>-->
         </dependency>
-                
+
         <!-- Auth0 JTW - https://github.com/auth0/java-jwt -->
         <dependency>
             <groupId>com.auth0</groupId>
             <artifactId>java-jwt</artifactId>
             <version>2.2.0</version>
         </dependency>
-
     </dependencies>
 
-    <!-- This makes the jar execuitable, don not use it with other dependencies, like ccd-db -->
     <build>
         <plugins>
             <plugin>

src/main/java/edu/pitt/dbmi/ccd/causal/rest/api/prop/CausalRestProperties.java

@@ -32,39 +32,39 @@
 @PropertySource("classpath:causal.properties")
 public class CausalRestProperties {
 
-    @Value("${ccd.dir.workspace}")
-    private String workspaceDir;
-
-    @Value("${ccd.folder.lib}")
-    private String libFolder;
-
     @Value("${ccd.jar.algorithm}")
     private String algorithmJar;
 
-    @Value("${ccd.folder.data}")
+    @Value("${ccd.algorithm.fgs:fgs}")
+    private String fgs;
+
+    @Value("${ccd.algorithm.fgs.discrete:fgsc}")
+    private String fgsDiscrete;
+
+    @Value("${ccd.algorithm.gfci:gfci}")
+    private String gfci;
+
+    @Value("${ccd.server.workspace:}")
+    private String workspaceDir;
+
+    @Value("${ccd.folder.data:data}")
     private String dataFolder;
 
-    @Value("${ccd.folder.tmp}")
+    @Value("${ccd.folder.lib:lib}")
+    private String libFolder;
+
+    @Value("${ccd.folder.tmp:tmp}")
     private String tmpFolder;
 
-    @Value("${ccd.folder.results}")
+    @Value("${ccd.folder.results:results}")
     private String resultsFolder;
 
-    @Value("${ccd.folder.results.algorithm}")
+    @Value("${ccd.folder.results.algorithm:algorithm}")
     private String algorithmFolder;
 
-    @Value("${ccd.folder.results.comparison}")
+    @Value("${ccd.folder.results.comparison:comparison}")
     private String comparisonFolder;
 
-    @Value("${ccd.algorithm.fgs}")
-    private String fgs;
-
-    @Value("${ccd.algorithm.fgs.discrete}")
-    private String fgsDiscrete;
-
-    @Value("${ccd.algorithm.gfci}")
-    private String gfci;
-
     @Value("${ccd.jwt.issuer}")
     private String jwtIssuer;
 
@@ -77,28 +77,44 @@ public class CausalRestProperties {
     public CausalRestProperties() {
     }
 
-    public String getWorkspaceDir() {
-        return workspaceDir;
+    public String getAlgorithmJar() {
+        return algorithmJar;
     }
 
-    public void setWorkspaceDir(String workspaceDir) {
-        this.workspaceDir = workspaceDir;
+    public void setAlgorithmJar(String algorithmJar) {
+        this.algorithmJar = algorithmJar;
     }
 
-    public String getLibFolder() {
-        return libFolder;
+    public String getFgs() {
+        return fgs;
     }
 
-    public void setLibFolder(String libFolder) {
-        this.libFolder = libFolder;
+    public void setFgs(String fgs) {
+        this.fgs = fgs;
     }
 
-    public String getAlgorithmJar() {
-        return algorithmJar;
+    public String getFgsDiscrete() {
+        return fgsDiscrete;
     }
 
-    public void setAlgorithmJar(String algorithmJar) {
-        this.algorithmJar = algorithmJar;
+    public void setFgsDiscrete(String fgsDiscrete) {
+        this.fgsDiscrete = fgsDiscrete;
+    }
+
+    public String getGfci() {
+        return gfci;
+    }
+
+    public void setGfci(String gfci) {
+        this.gfci = gfci;
+    }
+
+    public String getWorkspaceDir() {
+        return workspaceDir;
+    }
+
+    public void setWorkspaceDir(String workspaceDir) {
+        this.workspaceDir = workspaceDir;
     }
 
     public String getDataFolder() {
@@ -109,6 +125,14 @@ public void setDataFolder(String dataFolder) {
         this.dataFolder = dataFolder;
     }
 
+    public String getLibFolder() {
+        return libFolder;
+    }
+
+    public void setLibFolder(String libFolder) {
+        this.libFolder = libFolder;
+    }
+
     public String getTmpFolder() {
         return tmpFolder;
     }
@@ -141,30 +165,6 @@ public void setComparisonFolder(String comparisonFolder) {
         this.comparisonFolder = comparisonFolder;
     }
 
-    public String getFgs() {
-        return fgs;
-    }
-
-    public void setFgs(String fgs) {
-        this.fgs = fgs;
-    }
-
-    public String getFgsDiscrete() {
-        return fgsDiscrete;
-    }
-
-    public void setFgsDiscrete(String fgsDiscrete) {
-        this.fgsDiscrete = fgsDiscrete;
-    }
-
-    public String getGfci() {
-        return gfci;
-    }
-
-    public void setGfci(String gfci) {
-        this.gfci = gfci;
-    }
-
     public String getJwtIssuer() {
         return jwtIssuer;
     }

src/main/resources/application-hsqldb.properties

@@ -15,9 +15,9 @@
 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 # MA 02110-1301  USA
 
-# DATASOURCE (DataSourceAutoConfiguration & DataSourceProperties)
+# DATASOURCE (DataSourceProperties)
 spring.datasource.driver-class-name=org.hsqldb.jdbc.JDBCDriver
 spring.datasource.url=jdbc:hsqldb:mem:ccd;ifexists=false;shutdown=true
 
-# JPA (JpaBaseConfiguration, HibernateJpaAutoConfiguration)
-spring.jpa.properties.hibernate.dialect = org.hibernate.dialect.HSQLDialect
+# JPA (JpaBaseConfiguration)
+spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.HSQLDialect

src/main/resources/application-mysql.properties

@@ -15,14 +15,13 @@
 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 # MA 02110-1301  USA
 
-# DATASOURCE (DataSourceAutoConfiguration & DataSourceProperties)
+# DATASOURCE (DataSourceProperties)
 spring.datasource.driver-class-name=com.mysql.jdbc.Driver
 spring.datasource.url=jdbc:mysql://localhost:3306/ccd?zeroDateTimeBehavior=convertToNull
-# Remember to leave the username and password fields blank when pushing to github
-spring.datasource.username=root
-spring.datasource.password=123
+spring.datasource.username=
+spring.datasource.password=
 spring.datasource.validation-query=SELECT 1
 spring.datasource.test-on-borrow=true
 
-# JPA (JpaBaseConfiguration, HibernateJpaAutoConfiguration)
-spring.jpa.properties.hibernate.dialect = org.hibernate.dialect.MySQLDialect
+# JPA (JpaBaseConfiguration)
+spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.MySQLDialect

src/main/resources/application.properties

@@ -21,7 +21,7 @@ spring.main.banner-mode=off
 # PROFILES
 # scheduler, slurm
 # hsqldb, mysql
-spring.profiles.active=scheduler,mysql
+spring.profiles.active=scheduler,hsqldb
 
 # LOGGING
 logging.file=causal_rest_api.log
@@ -32,12 +32,11 @@ logging.level.org.hibernate=ERROR
 # EMBEDDED SERVER CONFIGURATION (ServerProperties)
 server.port=9000
 server.session-timeout=-1
-server.context-path=/causal/api/v1/
+server.context-path=/ccd-api/
 
 # JPA (JpaBaseConfiguration, HibernateJpaAutoConfiguration)
-# Hibernate ddl auto (create, create-drop, update)
+# Hibernate ddl auto (create,create-drop,update)
 spring.jpa.hibernate.ddl-auto=update
-spring.jpa.properties.hibernate.globally_quoted_identifiers=true
 spring.jpa.show-sql=false
 
 # MULTIPART (MultipartProperties)

src/main/resources/causal.properties

@@ -15,38 +15,25 @@
 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 # MA 02110-1301  USA
 
-# DIRECTORIES
-ccd.dir.workspace=/home/zhy19/ccd/workspace
-
-# Lib folder
-ccd.folder.lib=lib
-
-# causal-cmd JAR
+# JAR LIBRARIES
 ccd.jar.algorithm=causal-cmd-6.0.0.jar
 
-# WORKSPACE FOLDERS
-# User data folder
-ccd.folder.data=data
+# ALGORITHMS
+ccd.algorithm.fgs=fgsc
+ccd.algorithm.fgs.discrete=fgsd
+ccd.algorithm.gfci=gfcic
 
-# Tmp folder for running algorithm
+# DIRECTORIES
+ccd.server.workspace=
+ccd.folder.data=data
+ccd.folder.lib=lib
 ccd.folder.tmp=tmp
-
-# Results folder 
 ccd.folder.results=results
-
-# Algorithm Results folder inside ccd.folder.results
 ccd.folder.results.algorithm=algorithm
-
-# Algorithm Results comparison folder 
 ccd.folder.results.comparison=comparison
 
-# ALGORITHMS
-ccd.algorithm.fgs=fgsc
-ccd.algorithm.fgs.discrete=fgsd
-ccd.algorithm.gfci=gfcic
-
 # JWT settings for API Authentication
-ccd.jwt.issuer=https://cloud.ccd.pitt.edu/
+ccd.jwt.issuer=http://localhost/
 ccd.jwt.secret=causal
 # The token will expire after 3600 seconds
-ccd.jwt.lifetime=3600
+ccd.jwt.lifetime=3600

src/test/java/edu/pitt/dbmi/ccd/causal/rest/api/CausalRestApiApplicationTest.java

@@ -21,7 +21,6 @@
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.boot.test.context.SpringBootTest.WebEnvironment;
 import org.springframework.test.context.junit4.SpringRunner;
 
 /**
@@ -31,7 +30,7 @@
  * @author Kevin V. Bui ([email protected])
  */
 @RunWith(SpringRunner.class)
-@SpringBootTest(webEnvironment = WebEnvironment.RANDOM_PORT)
+@SpringBootTest
 public class CausalRestApiApplicationTest {
 
     @Test

src/test/resources/application-hsqldb.properties

@@ -0,0 +1,23 @@
+# Copyright (C) 2016 University of Pittsburgh.
+#
+# This library is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License as published by the Free Software Foundation; either
+# version 2.1 of the License, or (at your option) any later version.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this library; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+# MA 02110-1301  USA
+
+# DATASOURCE (DataSourceProperties)
+spring.datasource.driver-class-name=org.hsqldb.jdbc.JDBCDriver
+spring.datasource.url=jdbc:hsqldb:mem:ccd;ifexists=false;shutdown=true
+
+# JPA (JpaBaseConfiguration)
+spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.HSQLDialect

src/test/resources/application-mysql.properties

@@ -0,0 +1,27 @@
+# Copyright (C) 2016 University of Pittsburgh.
+#
+# This library is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License as published by the Free Software Foundation; either
+# version 2.1 of the License, or (at your option) any later version.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this library; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+# MA 02110-1301  USA
+
+# DATASOURCE (DataSourceProperties)
+spring.datasource.driver-class-name=com.mysql.jdbc.Driver
+spring.datasource.url=jdbc:mysql://localhost:3306/ccd?zeroDateTimeBehavior=convertToNull
+spring.datasource.username=
+spring.datasource.password=
+spring.datasource.validation-query=SELECT 1
+spring.datasource.test-on-borrow=true
+
+# JPA (JpaBaseConfiguration)
+spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.MySQLDialect

src/test/resources/application-slurm.properties

@@ -0,0 +1,27 @@
+# Copyright (C) 2015 University of Pittsburgh.
+#
+# This library is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License as published by the Free Software Foundation; either
+# version 2.1 of the License, or (at your option) any later version.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this library; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+# MA 02110-1301  USA
+
+# SLURM TEMPLATE
+ccd.template.checkuserdir=causalUserWorkspace.vm
+ccd.template.causaljob=slurmCausalJob.vm
+
+# DIRECTORIES
+ccd.remote.server.dataspace=
+ccd.remote.server.workspace=
+ccd.folder.job_templates=job_templates
+ccd.script.checkuserdir=checkUserDir
+ccd.script.runslurmjob=runSlurmJob