Changes between Version 2 and Version 3 of CaTissue HowTo Build & Deploying CaTissue from the source code?


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Timestamp:
11/23/11 17:44:07 (13 years ago)
Author:
somaraja.surampudi
Comment:

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  • CaTissue HowTo Build & Deploying CaTissue from the source code?

    v2 v3  
    111) Download caTissue suite from caTissue site (https://gforge.nci.nih.gov/frs/?group_id=689) named with caTissue v1.2 installable[[BR]]
    2 2) Once you have downloaded the caTISSUE_SUITE_v12_Installable_Pack.zip, extract the contents of the file to any directory.
    3 This folder contains two additional compressed files; caTissue_Suite_v1.2_Installable and caTissue_Suite_API_Client_v1.2_Installable
    4 3) Unzip the caTissue_Suite_v1.2_Installable.zip, extract the contents of the file to any directory.
    5 4) Unzip the caTissue_Suite_API_Client_v1.2_Installable.zip, extract the contents of the file to any directory.
    6 5) In the installation folder caTissueInstall.properties is the Property file in which all the application configuration parameters are listed, we need to change it according to our local environment
    7 6) In the installation folder build.xml is ANT script used to deploy the application on a JBoss server. This also creates the database schema for Oracle or MySQL.
    8 7) In the installation folder SQL folder containing SQL scripts required for deployment
    9 8) In the installation folder modules folder containing various caTissue modules
    10 9) JBoss version should be 4.2.3 GA and Mysql version should be 5.0.45
    11 10) In order to prevent lower case problem in ubuntu mysql you have to set set lower_case_table_names=1 in your /etc/mysql/my.cnf file.
    12 11) Once above step is done shutdown the mysql server and restart it.
    13 12) Before starting deployment make sure that jboss shouldn't be running.
    14 13) Create the database first (eg: catissuecore) in mysql before starting of the building the application, as shown below,
     22) Once you have downloaded the caTISSUE_SUITE_v12_Installable_Pack.zip, extract the contents of the file to any directory.[[BR]]
     3This folder contains two additional compressed files; caTissue_Suite_v1.2_Installable and caTissue_Suite_API_Client_v1.2_Installable[[BR]]
     43) Unzip the caTissue_Suite_v1.2_Installable.zip, extract the contents of the file to any directory. [[BR]]
     54) Unzip the caTissue_Suite_API_Client_v1.2_Installable.zip, extract the contents of the file to any directory.[[BR]]
     65) In the installation folder caTissueInstall.properties is the Property file in which all the application configuration parameters are listed, we need to change it according to our local environment[[BR]]
     76) In the installation folder build.xml is ANT script used to deploy the application on a JBoss server. This also creates the database schema for Oracle or MySQL.[[BR]]
     87) In the installation folder SQL folder containing SQL scripts required for deployment[[BR]]
     98) In the installation folder modules folder containing various caTissue modules[[BR]]
     109) JBoss version should be 4.2.3 GA and Mysql version should be 5.0.45[[BR]]
     1110) In order to prevent lower case problem in ubuntu mysql you have to set set lower_case_table_names=1 in your /etc/mysql/my.cnf file. [[BR]]
     1211) Once above step is done shutdown the mysql server and restart it.[[BR]]
     1312) Before starting deployment make sure that jboss shouldn't be running.[[BR]]
     1413) Create the database first (eg: catissuecore) in mysql before starting of the building the application, as shown below,[[BR]]
    1515
    16 Drop DATABASE if exists catissuecore;
     16Drop DATABASE if exists catissuecore;[[BR]]
     17[[BR]]
     18CREATE DATABASE catissuecore;[[BR]]
    1719
    18 CREATE DATABASE catissuecore;
    19 
    20 GRANT ALL PRIVILEGES ON catissuecore.* TO 'root'@'localhost' IDENTIFIED BY 'root' WITH GRANT OPTION;
    21 
    22 GRANT ALL PRIVILEGES ON catissuecore.* TO 'root'@'%' IDENTIFIED BY 'root' WITH GRANT OPTION;
    23 
    24 USE mysql;
    25 
    26 UPDATE  User SET File_priv = 'Y' where User='root';
    27 
    28 FLUSH PRIVILEGES;
    29 
    30 14) Start deploying the catissue application using build.xml with the argument deploy_all, if you see any error while in deployment because of upgrade_metadata_cnstrProp.sql then uncomment ALTER TABLE DYEXTN_COLUMN_PROPERTIES TYPE = INNODB; and ALTER TABLE DYEXTN_CONSTRAINTKEY_PROP TYPE = INNODB; in the same file. Start redeploying the application.
    31 15) If you see any errors in building the application, once you resolved the issues freshly build the application with the arguments clean_server and delete_files (delete the previously created dependencies). Once this is done then you build the application with deploy_all.
    32 16) Once build is successful war file will be automatically deployed into your jboss, start the jboss server.
     20GRANT ALL PRIVILEGES ON catissuecore.* TO 'root'@'localhost' IDENTIFIED BY 'root' WITH GRANT OPTION;[[BR]]
     21[[BR]]
     22GRANT ALL PRIVILEGES ON catissuecore.* TO 'root'@'%' IDENTIFIED BY 'root' WITH GRANT OPTION;[[BR]]
     23[[BR]]
     24USE mysql;[[BR]]
     25[[BR]]
     26UPDATE  User SET File_priv = 'Y' where User='root';[[BR]]
     27[[BR]]
     28FLUSH PRIVILEGES;[[BR]]
     29[[BR]]
     3014) Start deploying the catissue application using build.xml with the argument deploy_all, if you see any error while in deployment because of upgrade_metadata_cnstrProp.sql then uncomment ALTER TABLE DYEXTN_COLUMN_PROPERTIES TYPE = INNODB; and ALTER TABLE DYEXTN_CONSTRAINTKEY_PROP TYPE = INNODB; in the same file. Start redeploying the application.[[BR]]
     3115) If you see any errors in building the application, once you resolved the issues freshly build the application with the arguments clean_server and delete_files (delete the previously created dependencies). Once this is done then you build the application with deploy_all.[[BR]]
     3216) Once build is successful war file will be automatically deployed into your jboss, start the jboss server.[[BR]]
    333317) Once the JBoss server is started, you can access the application using a web browser. The following is the URL pattern used for the application:
    34 http://machine_name:port_number/catissuecore.
     34http://machine_name:port_number/catissuecore.[[BR]]
    353518) When the browser displays the home page of caTissue Suite, you can log on to the application by specifying the values which were configured in
    36 first.admin.emailAddress and first.admin.password of caTissueInstall.properties before deployment.
     36first.admin.emailAddress and first.admin.password of caTissueInstall.properties before deployment.[[BR]]
    3737
    3838
    3939
    4040
    41 Following is the sample caTissueInstall.properties file
    42 -------------------------------------------------------
    43 
    44 #Enter absolute path of the installed directory of JBoss server {JBOSS_HOME}.
    45 #Please note that the path must be separated by Unix style path separator "/".
    46 jboss.home.dir=/home/localadmin1/jboss-4.2.3.GA
    47 
    48 #Please specify the server configuration name of jboss where you want to deploy.
    49 #By default it is set to 'default' configuration. This is useful if someone wants
    50 #to run multiple instances of suite application on same jboss.
    51 jboss.server.name=default
    52 
    53 #Enter server port on which JBoss is listing the client request
    54 # Please do not specify the port number in case of an Apache Front ended server
    55 #Default port is 8080
    56 jboss.server.port=8080
    57 
    58 #Hostname or IP address of the machine on which the JBoss server is running.
    59 #CAUTION: This parameter should not be set to localhost. Set the actual hostname or IP address
    60 jboss.server.host=localhost
    61 
    62 #Enter yes/no to specify Secure HTTP connection
    63 jboss.container.secure=
    64 
    65 #database type permissible values: oracle or mysql
    66 database.type=mysql
    67 
    68 #Hostname or IP address of the machine on which the database server is running.
    69 database.host=localhost
    70 
    71 #Port number to connect with the database server
    72 #Default port for MySQL : 3306
    73 #Default Port for Oracle: 1521
    74 database.port=3306
    75 
    76 #Oracle TNS name, applicable only when database.type=oracle
    77 oracle.tns.name=
    78 
    79 database.name=catissuecore
    80 database.username=root
    81 database.password=root
    82 
    83 #If CAS authentication server needs to be deployed on the
    84 #same server as caTissue (specified by jboss.home.dir), then set this property to "true"
    85 deploy.cas.on.catissue.jboss=true
    86 
    87 #If cas.deploy is "false", then fill the following CAS related properties:
    88 #Hostname or IP address of the machine on which the CAS server is running.
    89 #CAUTION: This parameter should not be set to localhost. Set the actual hostname or IP address
    90 cas.jboss.server.host=
    91 cas.jboss.port=
    92 #Enter yes/no to specify Secure HTTP connection for CAS
    93 cas.jboss.container.secure=
    94 #CAS is deployed on HTTPS server then Specify the .keystore file path of CAS server.
    95 cas.server.keystore.path=
    96 
    97 email.administrative.emailAddress=
    98 email.sendEmailFrom.emailAddress=
    99 email.mailServer=
    100 
    101 # Option to use the common package's email handler on server exception. Values = [true|false]
    102 # Default = [false]
    103 use.email.commonpackage.config=false
    104 # Send the exception email to e-addresses. Can have comma seperated values.
    105 email.sendEmailTo.emailAddress=
    106 # Admin Email address. This would be included in case above entry is empty or invalid.
    107 email.admin.support.emailAddress=
    108 # Email-From Name.
    109 email.sendEmailFrom.name=
    110 # The subject line of the email.
    111 email.exception.subject=System Exception Occured.
    112 
    113 #Application login timeout interval in minutes.
    114 #Default value is 30 minutes
    115 session.timeout=30
    116 #sets the addition info on home page
    117 app.additional.info=
    118 
    119 #Information related to first administrator account
    120 first.admin.department=d
    121 first.admin.institution=i
    122 first.admin.cancerresearchgroup=c
    123 first.admin.emailAddress=admin@admin.com
    124 first.admin.password=Login123
    125 
    126 #Enter path for the MMTx home directory
    127 caties.mmtx.home=
    128 
    129 #Values for DE API
    130 caCORE.jBoss.home.dir=
    131 caCORE.project.name=
    132 
    133 #Choose below option to associate dynamic extensions default clinical and pathology forms to the Collection Protocols.
    134 #Choose false to show all clinical and pathology default annotations for data entry
    135 #Choose true and edit the Show_Hide_Forms.xml present in the installable folder to associate selective forms to Collection Protocol for data entry
    136 show.hide.forms.based.on.CPs=false
    137 
    138 #URL needed for category creation.
    139 Application.url=
    140 
    141 #Set the location where caCore is generated
    142 cacore.deployable.location=./cacore_deployable
    143 
    144 #Comma separated Entity Groups which are to be excluded.
    145 exclude.entitygroup=
    146 
    147 #Comma separated Entity Groups which are only to be included.
    148 include.entitygroup=
    149 
    150 #Set the owner for the old saved queries prior to v1.2. Enter the login name of the user whom
    151 #you want to make the owner.
    152 saved.query.owner=
    153 
    154 #CSM DATABASE CREDENTIALS
    155 csm.database.type=
    156 csm.database.host=
    157 csm.database.port=
    158 csm.database.name=
    159 csm.database.username=
    160 csm.database.password=
     41Following is the sample caTissueInstall.properties file[[BR]]
     42-------------------------------------------------------[[BR]]
     43[[BR]]
     44#Enter absolute path of the installed directory of JBoss server {JBOSS_HOME}.[[BR]]
     45#Please note that the path must be separated by Unix style path separator "/".[[BR]]
     46jboss.home.dir=/home/localadmin1/jboss-4.2.3.GA[[BR]]
     47[[BR]]
     48#Please specify the server configuration name of jboss where you want to deploy.[[BR]]
     49#By default it is set to 'default' configuration. This is useful if someone wants[[BR]]
     50#to run multiple instances of suite application on same jboss.[[BR]]
     51jboss.server.name=default[[BR]]
     52[[BR]]
     53#Enter server port on which JBoss is listing the client request[[BR]]
     54# Please do not specify the port number in case of an Apache Front ended server[[BR]]
     55#Default port is 8080[[BR]]
     56jboss.server.port=8080[[BR]]
     57[[BR]]
     58#Hostname or IP address of the machine on which the JBoss server is running.[[BR]]
     59#CAUTION: This parameter should not be set to localhost. Set the actual hostname or IP address[[BR]]
     60jboss.server.host=localhost[[BR]]
     61[[BR]]
     62#Enter yes/no to specify Secure HTTP connection[[BR]]
     63jboss.container.secure=[[BR]]
     64[[BR]]
     65#database type permissible values: oracle or mysql[[BR]]
     66database.type=mysql[[BR]]
     67[[BR]]
     68#Hostname or IP address of the machine on which the database server is running.[[BR]]
     69database.host=localhost[[BR]]
     70[[BR]]
     71#Port number to connect with the database server[[BR]]
     72#Default port for MySQL : 3306[[BR]]
     73#Default Port for Oracle: 1521[[BR]]
     74database.port=3306[[BR]]
     75[[BR]]
     76#Oracle TNS name, applicable only when database.type=oracle[[BR]]
     77oracle.tns.name=[[BR]]
     78[[BR]]
     79database.name=catissuecore[[BR]]
     80database.username=root[[BR]]
     81database.password=root[[BR]]
     82[[BR]]
     83#If CAS authentication server needs to be deployed on the[[BR]]
     84#same server as caTissue (specified by jboss.home.dir), then set this property to "true"[[BR]]
     85deploy.cas.on.catissue.jboss=true[[BR]]
     86[[BR]]
     87#If cas.deploy is "false", then fill the following CAS related properties:[[BR]]
     88#Hostname or IP address of the machine on which the CAS server is running.[[BR]]
     89#CAUTION: This parameter should not be set to localhost. Set the actual hostname or IP address[[BR]]
     90cas.jboss.server.host=[[BR]]
     91cas.jboss.port=[[BR]]
     92#Enter yes/no to specify Secure HTTP connection for CAS[[BR]]
     93cas.jboss.container.secure=[[BR]]
     94#CAS is deployed on HTTPS server then Specify the .keystore file path of CAS server.[[BR]]
     95cas.server.keystore.path=[[BR]]
     96[[BR]]
     97email.administrative.emailAddress=[[BR]]
     98email.sendEmailFrom.emailAddress=[[BR]]
     99email.mailServer=[[BR]]
     100[[BR]]
     101# Option to use the common package's email handler on server exception. Values = [true|false][[BR]]
     102# Default = [false][[BR]]
     103use.email.commonpackage.config=false[[BR]]
     104# Send the exception email to e-addresses. Can have comma seperated values.[[BR]]
     105email.sendEmailTo.emailAddress=[[BR]]
     106# Admin Email address. This would be included in case above entry is empty or invalid.[[BR]]
     107email.admin.support.emailAddress=[[BR]]
     108# Email-From Name.[[BR]]
     109email.sendEmailFrom.name=[[BR]]
     110# The subject line of the email.[[BR]]
     111email.exception.subject=System Exception Occured.[[BR]]
     112[[BR]]
     113#Application login timeout interval in minutes.[[BR]]
     114#Default value is 30 minutes[[BR]]
     115session.timeout=30[[BR]]
     116#sets the addition info on home page[[BR]]
     117app.additional.info=[[BR]]
     118[[BR]]
     119#Information related to first administrator account[[BR]]
     120first.admin.department=d[[BR]]
     121first.admin.institution=i[[BR]]
     122first.admin.cancerresearchgroup=c[[BR]]
     123first.admin.emailAddress=admin@admin.com[[BR]]
     124first.admin.password=Login123[[BR]]
     125[[BR]]
     126#Enter path for the MMTx home directory[[BR]]
     127caties.mmtx.home=[[BR]]
     128[[BR]]
     129#Values for DE API[[BR]]
     130caCORE.jBoss.home.dir=[[BR]]
     131caCORE.project.name=[[BR]]
     132[[BR]]
     133#Choose below option to associate dynamic extensions default clinical and pathology forms to the Collection Protocols.[[BR]]
     134#Choose false to show all clinical and pathology default annotations for data entry[[BR]]
     135#Choose true and edit the Show_Hide_Forms.xml present in the installable folder to associate selective forms to Collection Protocol for data entry[[BR]]
     136show.hide.forms.based.on.CPs=false[[BR]]
     137[[BR]]
     138#URL needed for category creation.[[BR]]
     139Application.url=[[BR]]
     140[[BR]]
     141#Set the location where caCore is generated[[BR]]
     142cacore.deployable.location=./cacore_deployable[[BR]]
     143[[BR]]
     144#Comma separated Entity Groups which are to be excluded.[[BR]]
     145exclude.entitygroup=[[BR]]
     146[[BR]]
     147#Comma separated Entity Groups which are only to be included.[[BR]]
     148include.entitygroup=[[BR]]
     149[[BR]]
     150#Set the owner for the old saved queries prior to v1.2. Enter the login name of the user whom[[BR]]
     151#you want to make the owner.[[BR]]
     152saved.query.owner=[[BR]]
     153[[BR]]
     154#CSM DATABASE CREDENTIALS[[BR]]
     155csm.database.type=[[BR]]
     156csm.database.host=[[BR]]
     157csm.database.port=[[BR]]
     158csm.database.name=[[BR]]
     159csm.database.username=[[BR]]
     160csm.database.password=[[BR]]