Merge pull request #890 from ohmage/ohmage-2.18

ohmage 2.18 release

.dockerignore

@@ -0,0 +1 @@
+.git/objects/pack

Dockerfile

@@ -0,0 +1,77 @@
+FROM debian:jessie
+MAINTAINER Steve Nolen <[email protected]>
+# Report issues here: https://github.com/ohmage/server
+
+RUN set -x \
+    && export DEBIAN_FRONTEND=noninteractive \
+    && apt-get update \
+    && apt-get install -y openjdk-7-jdk ant curl libtcnative-1 netcat git mysql-client\
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# download tomcat
+ENV CATALINA_HOME /usr/local/tomcat
+ENV PATH $CATALINA_HOME/bin:$PATH
+RUN mkdir -p "$CATALINA_HOME"
+WORKDIR $CATALINA_HOME
+
+# see https://www.apache.org/dist/tomcat/tomcat-8/KEYS
+RUN gpg --keyserver pool.sks-keyservers.net --recv-keys \
+  05AB33110949707C93A279E3D3EFE6B686867BA6 \
+  07E48665A34DCAFAE522E5E6266191C37C037D42 \
+  47309207D818FFD8DCD3F83F1931D684307A10A5 \
+  541FBE7D8F78B25E055DDEE13C370389288584E7 \
+  61B832AC2F1C5A90F0F9B00A1C506407564C17A3 \
+  713DA88BE50911535FE716F5208B0AB1D63011C7 \
+  79F7026C690BAA50B92CD8B66A3AD3F4F22C4FED \
+  9BA44C2621385CB966EBA586F72C284D731FABEE \
+  A27677289986DB50844682F8ACB77FC2E86E29AC \
+  A9C5DF4D22E99998D9875A5110C01C5A2F6059E7 \
+  DCFD35E0BF8CA7344752DE8B6FB21E8933C60243 \
+  F3A04C595DB5B6A5F1ECA43E3B7BBB100D811BBE \
+  F7DA48BB64BCB84ECBA7EE6935CD23C10D498E23
+
+ENV TOMCAT_MAJOR 7
+ENV TOMCAT_VERSION 7.0.67
+ENV TOMCAT_TGZ_URL https://www.apache.org/dist/tomcat/tomcat-$TOMCAT_MAJOR/v$TOMCAT_VERSION/bin/apache-tomcat-$TOMCAT_VERSION.tar.gz
+
+RUN set -x \
+  && curl -fSL "$TOMCAT_TGZ_URL" -o tomcat.tar.gz \
+  && curl -fSL "$TOMCAT_TGZ_URL.asc" -o tomcat.tar.gz.asc \
+  && gpg --verify tomcat.tar.gz.asc \
+  && tar -xvf tomcat.tar.gz --strip-components=1 \
+  && rm bin/*.bat \
+  && rm tomcat.tar.gz* \
+  && rm -rf /usr/local/tomcat/webapps/ROOT \
+  && rm -rf /usr/local/tomcat/webapps/docs \
+  && rm -rf /usr/local/tomcat/webapps/examples \
+  && rm -rf /usr/local/tomcat/webapps/manager \
+  && rm -rf /usr/local/tomcat/webapps/host-manager
+
+#### download flyway (ohmage doesn't do migrations) ####
+WORKDIR /flyway
+ENV FLYWAY_TGZ_URL http://repo1.maven.org/maven2/org/flywaydb/flyway-commandline/3.2.1/flyway-commandline-3.2.1.tar.gz
+RUN set -x \
+    && curl -fSL "$FLYWAY_TGZ_URL" -o flyway.tar.gz \
+    && tar -xvf flyway.tar.gz --strip-components=1 \
+    && rm flyway.tar.gz
+
+WORKDIR /app
+ADD . /app
+RUN cp db/migration/* /flyway/sql/ \
+  && ant clean dist \
+  && cp dist/webapp-ohmage* "$CATALINA_HOME"/webapps/app.war \
+  && cp docker_entrypoint.sh /run.sh \
+  && chmod +x /run.sh \
+  && rm -rf /app
+
+RUN mkdir -p /var/lib/ohmage && ln -s /var/lib/ohmage /ohmage
+RUN useradd -ms /bin/bash ohmage && \
+    chown -R ohmage.ohmage "$CATALINA_HOME" && \
+    chown -R ohmage.ohmage /var/lib/ohmage
+
+EXPOSE 8080
+
+VOLUME /ohmage
+
+CMD ["/run.sh"]

Dockerfile.wildfly

@@ -0,0 +1,37 @@
+FROM jboss/wildfly
+MAINTAINER Steve Nolen <[email protected]>
+# Report issues here: https://github.com/ohmage/server
+
+USER root
+
+RUN yum install -y ant ant-junit curl nc git mysql
+
+#### download flyway (ohmage doesn't do migrations) ####
+WORKDIR /flyway
+ENV FLYWAY_TGZ_URL http://repo1.maven.org/maven2/org/flywaydb/flyway-commandline/3.2.1/flyway-commandline-3.2.1.tar.gz
+RUN set -x \
+    && curl -fSL "$FLYWAY_TGZ_URL" -o flyway.tar.gz \
+    && tar -xvf flyway.tar.gz --strip-components=1 \
+    && rm flyway.tar.gz
+
+WORKDIR /app
+ADD . /app
+RUN cp db/migration/* /flyway/sql/ \
+  && ant clean dist \
+  && cp dist/webapp-ohmage* /opt/jboss/wildfly/standalone/deployments/app.war \
+  && cp docker_entrypoint.sh /run.sh \
+  # modify run.sh to run wildfly instead of tomcat!
+  && sed -i 's|^exec.*$|exec /opt/jboss/wildfly/bin/standalone.sh -b 0.0.0.0|g' /run.sh \
+  && chmod +x /run.sh \
+  && rm -rf /app
+
+RUN mkdir -p /var/lib/ohmage && ln -s /var/lib/ohmage /ohmage
+RUN useradd -ms /bin/bash ohmage && \
+    chown -R ohmage.ohmage /opt/jboss/wildfly/ && \
+    chown -R ohmage.ohmage /var/lib/ohmage
+
+EXPOSE 8080
+
+VOLUME /ohmage
+
+CMD ["/run.sh"]

build.xml

@@ -3,7 +3,7 @@
   <property file="build.properties"/>
   <property name="library" location="lib"/>
   <property name="app_name" value="ohmage"/>
-  <property name="app_version" value="2.17.3"/>
+  <property name="app_version" value="2.18.0"/>
   <property name="src" location="src"/>
   <property name="test" location="test"/>
   <property name="view" location="view"/>
@@ -41,6 +41,7 @@
     <include name="js.jar"/>
     <include name="catalina-2012-09-10.jar"/>
     <include name="RunKeeperOmhLayer.jar"/>
+    <include name="jose4j-0.4.4.jar"/>
   </fileset>
 
   <fileset id="run-dependencies" dir="${library}">
@@ -76,6 +77,8 @@
     <include name="slf4j-log4j12-1.7.5.jar"/>
     <include name="tomcat-dbcp-7.0.42.jar" />
     <include name="tomcat-jdbc-7.0.42.jar" />
+    <include name="tomcat-juli.jar" />
+    <include name="jose4j-0.4.4.jar"/>
   </fileset>
 
   <path id="compile-classpath">

db/migration/V10__2.18_editable_campaign.sql

@@ -0,0 +1,4 @@
+-- Adds a bit column in campaign table to determine if campaign is editable or not.
+-- defaults to false since the "participatory sensing"-ness of it is a bit lacking.
+ALTER TABLE campaign
+    ADD COLUMN `editable` bit NOT NULL DEFAULT FALSE;

db/migration/V5__2.17_cleanup_user_role_campaign.sql

@@ -38,5 +38,5 @@ WHERE id IN (
     GROUP BY u.id, cp.id, ur.id
     HAVING count(cc.class_id) - SUM(IF(uc.class_id IS NULL, 1, 0)) = 0
   ) t1
-) 
+);
 

db/migration/V6__2.18_access_request.sql

@@ -0,0 +1,27 @@
+-- ----------------------------------------------------------------------
+-- The table to store the user access request 
+-------------------------------------------------------------------------
+-- use status:varchar for simplicity. possible values: pending/approved/rejected
+CREATE TABLE IF NOT EXISTS access_request (
+  id int unsigned NOT NULL auto_increment,
+  uuid CHAR(36) NOT NULL UNIQUE,
+  user_id int unsigned NOT NULL,
+  email_address varchar(320) NOT NULL,
+  type varchar(25) NOT NULL,  
+  status varchar(25) NOT NULL,  
+  content mediumtext NOT NULL,
+  creation_timestamp datetime NOT NULL, 
+  last_modified_timestamp timestamp DEFAULT now() ON UPDATE now(),
+  PRIMARY KEY (id),
+  UNIQUE (uuid),
+  INDEX (uuid),
+  INDEX (user_id),
+  CONSTRAINT FOREIGN KEY (user_id) REFERENCES user (id) ON DELETE CASCADE ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+INSERT INTO preference (p_key, p_value) VALUES 
+ 	('mail_admin_address', 'root@localhost'),
+    ('mail_access_request_notify_admin', 'false'),
+    ('mail_access_request_sender_address', '[email protected]'),
+    ('mail_access_request_subject', 'ohmage: Access Request Status')
+    ON DUPLICATE KEY UPDATE p_value=VALUES(p_value);

db/migration/V7__2.18_add_app_name_to_preferences.sql

@@ -0,0 +1,8 @@
+-- ----------------------------------------------------------------------
+-- Inserts a default preference key so as not to be statefully reliant on
+-- the compiled war file.
+-------------------------------------------------------------------------
+
+INSERT INTO preference (p_key, p_value) VALUES 
+  ('application_name', 'ohmage')
+    ON DUPLICATE KEY UPDATE p_value=VALUES(p_value);

db/migration/V8__2.18_add_keycloak_integration.sql

@@ -0,0 +1,13 @@
+-- Inserts a default preference key to determine keycloak enabledness
+INSERT INTO preference (p_key, p_value) VALUES 
+  ('keycloak_auth_enabled', 'false')
+    ON DUPLICATE KEY UPDATE p_value=VALUES(p_value);
+
+-- Inserts a default preference key to determine local auth enabledness
+INSERT INTO preference (p_key, p_value) VALUES 
+  ('local_auth_enabled', 'true')
+    ON DUPLICATE KEY UPDATE p_value=VALUES(p_value);
+
+-- Adds a bit column in user table to determine if user is local or external
+ALTER TABLE user
+    ADD COLUMN `external` bit NOT NULL DEFAULT FALSE;

db/migration/V9__2.18_bugfix_887.sql

@@ -0,0 +1,30 @@
+-- get public class id
+SET @public_class_id =
+  (SELECT id
+   FROM class
+   WHERE urn IN
+       (SELECT p_value
+        FROM preference
+        WHERE p_key="public_class_id"));
+
+-- perhaps the analyst role isn't id=3 ?
+SET @analyst_role_id = 
+  (SELECT id
+    FROM user_role
+    WHERE role = "analyst");
+
+-- add users who are currently *only* "participants" in public campaigns
+-- as "analysts" as well. so they can see shared data.
+INSERT INTO user_role_campaign (user_id, campaign_id, user_role_id)
+SELECT user_id,
+       campaign_id,
+       @analyst_role_id
+FROM user_role_campaign
+WHERE campaign_id IN
+    (SELECT campaign.id
+     FROM campaign
+     JOIN campaign_class ON campaign.id = campaign_class.campaign_id
+     WHERE campaign_class.class_id = @public_class_id)
+GROUP BY user_id,
+         campaign_id 
+HAVING sum(user_role_id) = 1;

db/sql/base/ohmage-ddl.sql

@@ -805,3 +805,25 @@ CREATE TABLE IF NOT EXISTS `observer_stream_data_invalid` (
       ON DELETE CASCADE
       ON UPDATE CASCADE
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+-- ----------------------------------------------------------------------
+-- The table to store the user access request 
+-------------------------------------------------------------------------
+-- use status:varchar for simplicity. possible values: pending/approved/rejected
+CREATE TABLE IF NOT EXISTS access_request (
+  id int unsigned NOT NULL auto_increment,
+  uuid CHAR(36) NOT NULL UNIQUE,
+  user_id int unsigned NOT NULL,
+  email_address varchar(320) NOT NULL,
+  type varchar(25) NOT NULL,  
+  status varchar(25) NOT NULL DEFAULT "pending",  
+  content mediumtext NOT NULL,
+  creation_timestamp datetime NOT NULL, 
+  last_modified_timestamp timestamp DEFAULT now() ON UPDATE now(),
+  PRIMARY KEY (id),
+  UNIQUE (uuid),
+  INDEX (uuid),
+  INDEX (user_id),
+  CONSTRAINT FOREIGN KEY (user_id) REFERENCES user (id) ON DELETE CASCADE ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+

db/sql/update/2.16-2.17.sql

@@ -581,7 +581,7 @@ WHERE id IN (
       AND cc.id IS NULL
     GROUP BY u.id, cp.id, ur.id
   ) t1
-)
+);
 
 -- delete the relationship between user and campaigns where the campaigns are in
 -- classes that users are not members of. Delete all roles except "author". 
@@ -600,6 +600,6 @@ WHERE id IN (
     GROUP BY u.id, cp.id, ur.id
     HAVING count(cc.class_id) - SUM(IF(uc.class_id IS NULL, 1, 0)) = 0
   ) t1
-) 
+); 
 
 

docker_entrypoint.sh

@@ -0,0 +1,74 @@
+#!/usr/bin/env bash
+
+set -e
+
+# use passed env variable or defaults
+DB_HOST=$MYSQL_PORT_3306_TCP_ADDR
+DB_PORT=$MYSQL_PORT_3306_TCP_PORT
+DB_NAME=${DB_NAME:-ohmage}
+DB_USER=${DB_USER:-ohmage}
+DB_PASS=${DB_PASS:-ohmage}
+FQDN=${FQDN:-$HOSTNAME}
+LOG_LEVEL=${LOG_LEVEL:-WARN}
+ESCAPED_PW=${DB_PASS/\&/\\&}
+
+# cat out ohmage.conf
+echo "#
+# DATABASE
+#
+db.driver=com.mysql.jdbc.Driver
+db.jdbcurl=jdbc:mysql://$DB_HOST:$DB_PORT/$DB_NAME?characterEncoding=utf8
+db.username=$DB_USER
+db.password=$ESCAPED_PW
+#
+# LOGGING
+#
+# The root logger 
+log4j.rootLogger=$LOG_LEVEL, stdout
+
+log4j.appender.stdout = org.apache.log4j.ConsoleAppender
+log4j.appender.stdout.Threshold = $LOG_LEVEL
+log4j.appender.stdout.Target   = System.out
+log4j.appender.stdout.layout = org.apache.log4j.PatternLayout
+log4j.appender.stdout.layout.ConversionPattern = %-5p %d [%t][%F:%L] : %m%n
+ 
+log4j.logger.org.ohmage=$LOG_LEVEL
+log4j.logger.org.springframework=$LOG_LEVEL
+log4j.logger.org.ohmage.util.JsonUtils=$LOG_LEVEL
+log4j.logger.org.ohmage.cache.UserBin=$LOG_LEVEL" > /etc/ohmage.conf
+
+if [ -n "$KEYCLOAK_JSON" ]; then
+  echo "keycloak.config=$KEYCLOAK_JSON" >> /etc/ohmage.conf
+fi
+
+# cat out flyway.conf
+# note that the placeholders wont be updated at each boot.
+echo "flyway.url=jdbc:mysql://$DB_HOST:$DB_PORT/$DB_NAME
+flyway.user=$DB_USER
+flyway.password=$DB_PASS
+flyway.placeholders.fqdn=$FQDN
+flyway.placeholders.base_dir=/var/lib/ohmage" > /flyway/conf/flyway.conf
+
+# create database stuffz. different depending on linked mysql container.
+echo -n "waiting for mysql to start..."
+while ! nc -w 1 $DB_HOST $DB_PORT &> /dev/null
+do
+  echo -n .
+  sleep 1
+done
+echo 'mysql available.'
+mysql -uroot -p$MYSQL_ENV_MYSQL_ROOT_PASSWORD -h$DB_HOST -P$DB_PORT mysql -e "CREATE DATABASE IF NOT EXISTS $DB_NAME; grant all on $DB_NAME.* to \"$DB_USER\"@\"%\" IDENTIFIED BY \"$DB_PASS\"; FLUSH PRIVILEGES;"
+
+# execute migrations
+/flyway/flyway migrate
+
+# ensure ohmage directory structure exists
+mkdir -p /var/lib/ohmage/audio
+mkdir -p /var/lib/ohmage/audits
+mkdir -p /var/lib/ohmage/documents
+mkdir -p /var/lib/ohmage/images
+mkdir -p /var/lib/ohmage/videos
+chown -R ohmage.ohmage /var/lib/ohmage
+
+# start tomcat in foreground
+exec /usr/local/tomcat/bin/catalina.sh run

src/org/ohmage/annotator/Annotator.java

@@ -113,6 +113,7 @@ public static enum ErrorCode {
 		SURVEY_INVALID_PROMPT_RESPONSE_SEARCH ("0629"),
 		SURVEY_INVALID_SURVEY_PROMPT_MAP ("0630"),
 		SURVEY_DUPLICATE_MEDIA_UUIDS ("0631"), // when media or document uuids are duplicate
+		SURVEY_UPLOAD_INVALID_ARGUMENTS ("0632"),
 
 		CAMPAIGN_INVALID_ID ("0700"),
 		CAMPAIGN_INVALID_NAME ("0701"),
@@ -128,6 +129,7 @@ public static enum ErrorCode {
 		CAMPAIGN_INVALID_AUTHORED_BY_VALUE ("0711"),
 		CAMPAIGN_INVALID_SURVEY_ID ("O712"),
 		CAMPAIGN_INVALID_PROMPT_ID ("0713"),
+		CAMPAIGN_INVALID_EDITABLE ("0714"),
 
 		IMAGE_INVALID_ID ("0800"),
 		IMAGE_INVALID_SIZE ("0801"),
@@ -162,8 +164,11 @@ public static enum ErrorCode {
 		USER_INVALID_DELETE_PERSONAL_INFO ("1015"),
 		USER_INVALID_CLASS_CREATION_PRIVILEGE ("1016"),
 		USER_INVALID_USER_SETUP_PRIVILEGE ("1017"),
-		// user-setup
+		// user setup
 		USER_INVALID_USERNAME_PROPERTY ("1018"), 
+		// access request
+		USER_ACCESS_REQUEST_INVALID_PRAMETER ("1019"),
+		USER_ACCESS_REQUEST_EXECUTION_ERROR ("1020"),
 
 		DOCUMENT_INVALID_ID ("1100"),
 		DOCUMENT_INVALID_NAME ("1101"),