This guide serves as a reference for users of the Cancer Report Validator (CRV).
There are two ways to install CRV. The first is to build the project locally as described in the Source Build Guide. The second is to obtain the latest version of the WAR here.
The following optional system properties control logging:
Name | Value Type | Default Value | Description |
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crigtt.logging.console.tty | boolean | <availability of an interactive console to the JVM> |
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crigtt.logging.file.dir | string (directory path) | CLI: <executable directory>/../logs Webapp: <webapp container log directory> |
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crigtt.logging.file.name | string (file name) | CLI: crigtt-cli Webapp: crigtt-web |
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crigtt.logging.file.ext | string (file extension) | .log |
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crigtt.logging.file.size.max | string (file size) | 50MB |
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Install Tomcat 9.0
If the file ${TOMCAT9_INSTALLATION_PATH}/bin/setenv.sh does not exist, create it by running:
${TOMCAT9_INSTALLATION_PATH}/bin/setenv.sh |
Append the following lines to the file ${TOMCAT9_INSTALLATION_PATH}/bin/setenv.sh:
CATALINA_OPTS="$CATALINA_OPTS -Dcrigtt.data.db.dir=<path to database directory> -Dcrigtt.data.validate.vocab.dynamic.dir=<path to vocab file directory>" |
<path to database directory>: path to a directory where you want data to be persisted.
<path to vocab file directory>: path to a directory where you want to place the vocab files that will be persisted.
Install Java 8.0 and point JAVA_HOME environment variable to the install location of Java 8.0.
The code systems and value sets that are collected according to the Vocabulary Data Sets Source Documentation are available in the vocab.tar.gz file, unzipped and placed in a specific directory structure within the <path to vocab file directory>.
The code system files collected from the Code Systems tab ("File Name(s)" column) need to be placed in the following structure:
codes/ ICD-O-3/ ICD10CM/ ICD10PCS/ ICD9CM_DX/ LOINC/ RXNORM/ SNOMED-CT/ |
The value set files collected from the Value Sets tab ("File Name(s)" column) need to be placed in the following structure:
valueSets/ PHVS/ VSAC/ |
The files with the .txt extension should be placed in PHVS and the files with the .xls extension should be placed in VSAC.
Once the configuration has been complete, the WAR file should be deployed. There are several methods to deploy WAR files in Tomcat, as described in the Tomcat Configuration.
The first time the WAR is deployed, the data in the code system and value set files placed in the directory described in the Code System and Value Set Configuration section will be loaded into the OrientDB database, which can take up to an hour. The log can be monitored to determine when that process has been completed.
If any code system or value set files need to be updated, the contents of the <path to database directory> should be removed, the updated vocab.tar.gz should be unzipped to <path to vocab file directory>, and the webapp should be restarted. This will cause the vocabulary files to be loaded anew.
To build the tools from source, run:
mvn -pl="crigtt-parent,crigtt-core,crigtt-cli" |
The tools can be found in ~/crigtt/crigtt-cli/target/crigtt-cli/bin or extracted from ~/crigtt/crigtt-cli/target/crigtt-cli-<version>-cli.tar.gz
Within the crigtt-cli directory, a data directory should be added so that the directory structure looks like:
The vocabulary files need to be obtained as indicated in the Code System and Value Set Configuration section and the codes and valueSets directory should be placed under the vocab directory as indicated above. |
Usage: crigtt-cli [options]
Option(s) | Required (Y/N)? | Default Value | Description |
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-f, --format | N | true | Flag for whether to format the output. |
-h, --help | N | false | Display help. |
-i, --in-file | Y | Input file or "-" for standard input. | |
-n, --in-file-name | N | Input file name. | |
-d, --out-dir | N | ${crigtt.app.home}/out | Output directory. |
-o, --out-file | N | Output file or "-" for standard output. | |
-c, --testcase | N | testcase0 | Test case for running conformance against test data. Possible Values: [testcase0, testcase1a, testcase1b, testcase2, testcase3, testcase4] |
-t, --type | Y | Output render type. Possible Values: [HTML, JSON, XML] |
Name | Value Type | Default Value | Description |
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format | boolean | false |
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timeZone | string, time zone offset | <the local time zone of the JVM> |
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Name | Value Type | Description |
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X-Crigtt-Response-File-Name | string (file name) |
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