REDCap Project

{"type":"doc","content":[{"type":"extension","attrs":{"layout":"default","extensionType":"com.atlassian.confluence.macro.core","extensionKey":"toc","parameters":{"macroParams":{},"macroMetadata":{"macroId":{"value":"33462c25-680c-4f96-9a23-c9872196cfd1"},"schemaVersion":{"value":"1"},"title":"Table of Contents"}},"localId":"e49c573a-4dd5-4834-a40d-16ddc53f1a7e"}},{"type":"heading","attrs":{"level":1},"content":[{"text":"Download","type":"text"}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"REDCap PHP plugin","type":"text","marks":[{"type":"strong"}]},{"text":": To download the REDCap_PHP file, please contact Krishagni.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"OpenSpecimen-REDCap Plugin","type":"text","marks":[{"type":"strong"}]},{"text":": To download the OpenSpecimen-REDCap plugin, please contact Krishagni.","type":"text"}]}]}]},{"type":"heading","attrs":{"level":1},"content":[{"text":"Installation","type":"text"}]},{"type":"paragraph","content":[{"text":"The installation of these plugins on the remote server helps in sharing data or information across datasets. There are two parts to this process:","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Installation of REDCap PHP Plugin","type":"text"}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Log in to the REDCap server and navigate to the REDCap install directory containing the file redcap_connect.php and database.php files.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"The following are example commands executed in our dev environment. ","type":"text"}]},{"type":"codeBlock","attrs":{"language":"none"},"content":[{"text":"$ cd /home/var-www/html/redcap/\n$ ls database.php redcap_connect.php\ndatabase.php redcap_connect.php","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Create a new 'plugins' directory if not present.","type":"text"}]},{"type":"codeBlock","content":[{"text":"$ mkdir -p plugins","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Copy the REDCap_PHP file to the plugin's directory.","type":"text"}]},{"type":"codeBlock","content":[{"text":"$ cp $RC_OS_PLUGIN/openspecimen_plugin.php plugins","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"To ensure that the plugins are correctly installed, you can invoke the following API using the HTTP client program of choice or run the commands as shown below.","type":"text"}]}]}]},{"type":"expand","attrs":{"title":"Click here to see the example"},"content":[{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Below is an example done using ","type":"text"},{"text":"Postman","type":"text","marks":[{"type":"link","attrs":{"href":"https://www.getpostman.com/apps"}}]}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Replace with hostname where REDCap server is deployed","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Replace with actual API token issued for accessing REDCap project using APIs","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"In response, you should see the REDCap audit log events nicely formatted using JSON.","type":"text"}]},{"type":"mediaSingle","attrs":{"layout":"center","width":85.0},"content":[{"type":"media","attrs":{"width":960,"id":"93d377e8-bba8-4a50-a8da-fa47b24d6614","collection":"contentId-2322661457","type":"file","height":540}}]},{"type":"paragraph"}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"The following commands should succeed with printing JSON string on the console. ","type":"text"}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"RC_HOST","type":"text","marks":[{"type":"code"}]},{"text":" - URL of the REDCap server. E.g. ","type":"text"},{"text":"https://redcap.openspecimen.org","type":"text","marks":[{"type":"link","attrs":{"href":"https://redcap.openspecimen.org"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"RC_DOCROOT","type":"text","marks":[{"type":"code"}]},{"text":" - Document root of the REDCap server. E.g. /, /r","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"OS_PLUGIN","type":"text","marks":[{"type":"code"}]},{"text":" - Relative path of the OpenSpecimen REDCap plugin w.r.t document root. E.g. /plugins/openspecimen_plugin.php","type":"text"}]}]}]}]}]},{"type":"paragraph","content":[{"text":"Test Project Details","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"$ curl -X POST -D \"token=\" -d \"content=project\" -d \"format=json\" -d \"returnFormat=json\" $RC_HOST/$RC_DOCROOT/api/\n\nExample command:\ncurl -X POST -d \"token=xxxx\" -d \"content=project\" -d \"format=json\" -d \"returnFormat=json\" https://redcap.openspecimen.org/r/api/\n// project details JSON\n\nOutput\n\n\n\n\nREDCap Project\n\n\n........\n\n\n","type":"text"}]},{"type":"paragraph","content":[{"text":"Test Events list","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"$ curl -X POST -d \"token=\" -d \"content=event\" -d \"format=json\" -d \"returnFormat=json\" $RC_HOST/$RC_DOCROOT/$OS_PLUGIN\n// events list JSON\n\nExample command:\ncurl -X POST -d \"token=xxxx\" -d \"content=event\" -d \"format=json\" -d \"returnFormat=json\" https://redcap.openspecimen.org/r/plugins/openspecimen_plugin.php\n\nOutput\n>>[{\"event_id\":\"40\",\"day_offset\":\"1\",\"offset_min\":\"0\",\"offset_max\":\"0\",\"event_name\":\"Event 1\",\"arm_num\":\"1\",\"repeatable\":\"0\"}]","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Please contact your REDCap system admin for these steps. There might be slight differences based on the REDCap version, operating system, etc.","type":"text"}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Installation of OpenSpecimen plugin","type":"text"}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Exact the JAR file from your downloaded zip file.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Login to your OpenSpecimen server and navigate to the ","type":"text"},{"text":"$TOMCAT_HOME/bin","type":"text","marks":[{"type":"code"}]},{"text":" directory.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Stop the tomcat service using the command: ","type":"text"}]},{"type":"codeBlock","content":[{"text":"./shutdown.sh force","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Now, navigate to the ","type":"text"},{"text":"$plugins/paid","type":"text","marks":[{"type":"code"}]},{"text":"directory and remove an older copy of the REDCap-OpenSpecimen plugin (if any) and copy the current version.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Navigate back to the ","type":"text"},{"text":"$TOMCAT_HOME/bin","type":"text","marks":[{"type":"code"}]},{"text":" directory and restart the Tomcat service using the command: ","type":"text"}]},{"type":"codeBlock","content":[{"text":"./startup.sh","type":"text"}]}]}]},{"type":"heading","attrs":{"level":1},"content":[{"text":"Update REDCap PHP Plugin","type":"text"}]},{"type":"paragraph","content":[{"text":"To update the existing REDCap PHP plugin with a new one, please follow the steps below:","type":"text"}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Rename Old Plugin","type":"text"},{"type":"hardBreak"},{"text":"$ cp .php to .php.old","type":"text","marks":[{"type":"code"}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Copy the new plugin to the required folder.","type":"text"},{"type":"hardBreak"},{"text":"$ cp /data_log_events.php .php","type":"text","marks":[{"type":"code"}]}]}]}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":" is the name chosen by the REDCap admin during the first install and used in the OpenSpecimen configurations.","type":"text"}]}]},{"type":"heading","attrs":{"level":1},"content":[{"text":"How to check the plugin version?","type":"text"}]},{"type":"paragraph","content":[{"text":"Use the below command to check the version of the plugin installed on the REDCap server-side","type":"text"}]},{"type":"paragraph","content":[{"text":"PHP plugin version","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"$ curl -X POST -d \"token=\" -d \"content=version\" -d \"format=json\" -d \"returnFormat=json\" $RC_HOST/$RC_DOCROOT/$OS_PLUGIN\n\nExample command:\ncurl -X POST -d \"token=xxxx\" -d \"content=version\" -d \"format=json\" -d \"returnFormat=json\" https://redcap.openspecimen.org/r/plugins/openspecimen_plugin.php\n\nOutput\n\n>>{\"version\":\"2020-10-12T07:58:48.225Z\"} (Before OS v8.2)\n>>{\"version\":\"2021-10-11T09:30:00.000Z\"} (After OS v8.2)\n>>{\"version\":\"2024-03-25T02:24:38.307Z\"} (After RCv14 support)","type":"text"}]},{"type":"paragraph"},{"type":"paragraph"},{"type":"paragraph"}],"version":1}