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INB
eTRANSAFE
pretox-sr-domain-identification
Commits
20b9f1cb
Commit
20b9f1cb
authored
Mar 10, 2020
by
jcorvi
Browse files
README, LICENSE, CI CD structure
parent
6b31b7d5
Changes
6
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.gitlab-ci.yml
0 → 100644
View file @
20b9f1cb
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
CHANGELOG
0 → 100644
View file @
20b9f1cb
# Change Log
## Version 1.0, 2020-03-03
First version of the component.
LICENSE.txt
0 → 100644
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20b9f1cb
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Click to expand it.
README.md
View file @
20b9f1cb
...
...
@@ -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
...
...
pom.xml
View file @
20b9f1cb
...
...
@@ -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>
...
...
src/main/java/es/bsc/inb/ades/export/json/main/App.java
View file @
20b9f1cb
...
...
@@ -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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