| 33 | | == Notes from watching Nitesh upgrade our dev version |
| 34 | | |
| 35 | | 1. Our customisations are in the file {{{/local/os_v20/app/plugin-dir/os-le-1.0.0.jar}}}. This file can be copied between installations. |
| 36 | | 2. He copied the build zip file (linked in the page above) into the directory {{{/local/os_v20/installable}}} and unzipped it. |
| 37 | | 3. `cd` into the newly unzipped folder. |
| 38 | | 3. `chmod 744 install.sh |
| 39 | | 6. Run: |
| 40 | | |
| 41 | | {{{ |
| 42 | | nohup ./install.sh -dhost localhost -dport 3306 -dname {db name} -duser {db user name} -dpass {db password name} -dtype mysql -ahome /local/{Open Specimen Directory}/app -ahost localhost -aport 8280 -adtype fresh -adatadir /local/{Open Specimen Directory}/app/os-data -aplugindir /local/{Open Specimen Directory}/app/plugin-dir & |
| 43 | | }}} |
| 44 | | |
| 45 | | 7. Run `cp /local/{Open Specimen Directory}/installable/os-le-1.0.0.jar /local/{Open Specimen Directory}/app/plugin-dir` |
| 46 | | |
| 47 | | 7. Create the script `run_open_specimen.sh`: |
| 48 | | |
| 49 | | {{{ |
| 50 | | #!/bin/bash |
| 51 | | |
| 52 | | unset JAVA_TOOL_OPTIONS |
| 53 | | export JAVA_ROOT=/usr/lib64/jvm/java |
| 54 | | export JDK_HOME=/usr/lib64/jvm/java |
| 55 | | export SDK_HOME=/usr/lib64/jvm/java |
| 56 | | export JAVA_BINDIR=/usr/lib64/jvm/java/bin |
| 57 | | export JRE_HOME=/usr/lib64/jvm/java/jre |
| 58 | | JAVA_HOME=/opt/java |
| 59 | | JRE_HOME=/opt/java/jre |
| 60 | | OPEN_SPECIMEN_DIR=/local/{Open Specimen Directory}/app |
| 61 | | |
| 62 | | export JAVA_TOOL_OPTIONS=-XX:CompressedClassSpaceSize=10m |
| 63 | | export JAVA_OPTS="-Xmx2G -XX:-UseCompressedClassPointers" |
| 64 | | |
| 65 | | $OPEN_SPECIMEN_DIR/bin/catalina.sh start >$OPEN_SPECIMEN_DIR/logs/tomcat-start.log 2>$OPEN_SPECIMEN_DIR/logs/tomcat-start.err & |
| 66 | | }}} |
| 67 | | |
| 68 | | 8. Create the script `stop_open_specimen.sh`: |
| 69 | | |
| 70 | | {{{ |
| 71 | | #!/bin/bash |
| 72 | | |
| 73 | | unset JAVA_TOOL_OPTIONS |
| 74 | | export JAVA_ROOT=/usr/lib64/jvm/java |
| 75 | | export JDK_HOME=/usr/lib64/jvm/java |
| 76 | | export SDK_HOME=/usr/lib64/jvm/java |
| 77 | | export JAVA_BINDIR=/usr/lib64/jvm/java/bin |
| 78 | | export JRE_HOME=/usr/lib64/jvm/java/jre |
| 79 | | JAVA_HOME=/opt/java |
| 80 | | JRE_HOME=/opt/java/jre |
| 81 | | OPEN_SPECIMEN_DIR=/local/openSpecimen_v2_4/app |
| 82 | | |
| 83 | | export JAVA_TOOL_OPTIONS=-XX:CompressedClassSpaceSize=10m |
| 84 | | export JAVA_OPTS="-Xmx2G -XX:-UseCompressedClassPointers" |
| 85 | | |
| 86 | | $OPEN_SPECIMEN_DIR/bin/catalina.sh stop |
| 87 | | }}} |
| 88 | | |
| 89 | | 9. Give `www-run` account permission to run the scripts: |
| 90 | | |
| 91 | | {{{ |
| 92 | | setfacl -m u:wwwrun:rx /local/{Open Specimen Directory}/run_open_specimen.sh |
| 93 | | setfacl -m u:wwwrun:rx /local/{Open Specimen Directory}/stop_open_specimen.sh |
| 94 | | }}} |
| 95 | | |
| 96 | | 10. Give `www-run` permission to write to the logs and work directories: |
| 97 | | |
| 98 | | {{{ |
| 99 | | setfacl -R -m u:wwwrun:rwx /local/{Open Specimen Directory}/app/logs/ |
| 100 | | setfacl -R -m u:wwwrun:rwx /local/{Open Specimen Directory}/app/work/ |
| 101 | | }}} |
| 102 | | |
| 103 | | 11. Give `www-run` and yourself (go on, treat yourself) permission to run Tomcat: |
| 104 | | {{{ |
| 105 | | chmod 774 /local/{Open Specimen Directory}/app/bin/catalina.sh |
| 106 | | setfacl -m u:wwwrun:rx /local/{Open Specimen Directory}/app/bin/catalina.sh |
| 107 | | }}} |
| 108 | | |
| 109 | | 12. Then `run_open_specimen.sh` as yourself. You need to do this to be able to unpack the WAR file. The site will not come up successfully because there is a bug or somesuch in the database upgrade scripts. |
| 110 | | |
| 111 | | 13. Nitesh changed one of the change sets because it fails if you don't. Hurray. |
| 112 | | 1. The file is `/local/{Open Specimen Directory}/app/webapps/openspecimen/WEB-INF/classes/db/2.0/schema.xml` |
| 113 | | 2. Change `<changeSet author="vlonushte" id="FK on domain name of users table">` to `<changeSet author="vlonushte" id="FK on domain name of users table" failOnError="false">` |
| 114 | | |
| 115 | | == UPDATE WORKFLOW table to correct format |
| 116 | | |
| 117 | | Run the command: |
| 118 | | |
| 119 | | {{{ |
| 120 | | update os_cp_workflows set workflows = '[{"name":"registerParticipant","view":"plugin-ui-resources/le/collect-specimens.html","ctrl":"leRegAndCollectSpecimensCtrl","data":{"boxOpts":{"dimension":{"rows":8,"columns":12},"compact":false}}}]'; |
| 121 | | }}} |
| 122 | | |
| 123 | | == New Process |
| | 33 | == Process |
