Commit 20b9f1cb authored by jcorvi's avatar jcorvi
Browse files

README, LICENSE, CI CD structure

parent 6b31b7d5
variables:
DOCKER_USER: javicorvi
DOCKER_BUILD: $DOCKER_USER/$CI_PROJECT_NAME:$CI_COMMIT_REF_NAME
stages:
- build
build_docker_image:
stage: build
only:
- tags
script:
- docker login -u javicorvi -p $DOCKER_PASS
- docker build -t $DOCKER_BUILD .
- docker push $DOCKER_BUILD
tags:
- build
\ No newline at end of file
# Change Log
## Version 1.0, 2020-03-03
First version of the component.
This diff is collapsed.
......@@ -6,12 +6,11 @@ This component export the treatment-related findings annotated in XML GATE forma
This component is only used inside the treatment-related findings pipeline because is tired up to that specific domain.
## For clone this component
git clone --depth 1 https://github.com/inab/docker-textmining-tools.git ades-export-to-json
cd ades-export-to-json
git filter-branch --prune-empty --subdirectory-filter ades-export-to-json HEAD
## Actual Version: 1.0, 2020-03-04
## [Changelog](https://gitlab.bsc.es/inb/etransafe/ades-export-to-json/blob/master/CHANGELOG)
## Docker
javicorvi/own-ades-terminology-annotation
## Build and Run the Docker
# To build the docker, just go into the ades-export-to-json folder and execute
......
......@@ -20,7 +20,7 @@
<dependency>
<groupId>uk.ac.gate</groupId>
<artifactId>gate-core</artifactId>
<version>8.5.1</version>
<version>8.6.1</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
......
......@@ -189,7 +189,7 @@ public class App {
document.addProperty("id", System.currentTimeMillis());
JsonObject section = new JsonObject();
section.addProperty("name", "document");
Set<String> types = Stream.of("FINDING","SEX","SPECIMEN","GROUP","DOSE","DOSE_DURATION","DOSE_QUANTITY","DOSE_FREQUENCY","MANIFESTATION_FINDING","RISK_LEVEL","NO_TREATMENT_RELATED_TRIGGER",
Set<String> types = Stream.of("FINDING","SEX","SPECIMEN","GROUP","DOSE","MANIFESTATION_FINDING","RISK_LEVEL","NO_TREATMENT_RELATED_TRIGGER",
"TREATMENT_RELATED_TRIGGER","STUDY_DOMAIN","STUDY_DAY_FINDING","STUDY_TESTCD", "ROUTE_OF_ADMINISTRATION","MODE_OF_ACTION","STATISTICAL_SIGNIFICANCE","CYPS").collect(Collectors.toCollection(HashSet::new));
JsonObject entities = new JsonObject();
AnnotationSet as = doc.getAnnotations(annotationSet).get(types);
......
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