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seanfinan pushed a commit to branch main
in repository https://gitbox.apache.org/repos/asf/ctakes.git
The following commit(s) were added to refs/heads/main by this push:
new d998331 updated some pom files, moved example notes, still working
on getting web-rest and user-resources happy
d998331 is described below
commit d998331c1cfef48d792c78a8d3c1670498a8b925
Author: Sean Finan <[email protected]>
AuthorDate: Fri Dec 23 17:38:08 2022 -0500
updated some pom files, moved example notes, still working on getting
web-rest and user-resources happy
---
ctakes-dictionary-lookup-fast/pom.xml | 2 +-
ctakes-distribution/pom.xml | 4 +
ctakes-dockhand/pom.xml | 4 +-
.../notes/small/SampleInputRadiologyNotes.txt | 7 +
.../ctakes/examples/notes/small/claudication | 7 +
.../examples/notes/small/dr_nutritious_1.txt | 12 +
.../examples/notes/small/dr_nutritious_2.txt | 12 +
.../notes/small/edge_cases_plaintext_1.txt | 2 +
.../examples/notes/small/pain_no_swelling.txt | 4 +
.../examples/notes/small/right_knee_arthroscopy | 2 +
ctakes-user-resources/pom.xml | 257 ++++++++++++++++++++-
ctakes-web-rest/pom.xml | 138 +++++------
ctakes-ytex-uima/pom.xml | 4 +-
ctakes-ytex-web/pom.xml | 4 +-
ctakes-ytex/pom.xml | 2 +-
ctakes-ytex/scripts/data/build.xml | 24 +-
pom.xml | 18 --
17 files changed, 381 insertions(+), 122 deletions(-)
diff --git a/ctakes-dictionary-lookup-fast/pom.xml
b/ctakes-dictionary-lookup-fast/pom.xml
index b43f2e0..2995a51 100644
--- a/ctakes-dictionary-lookup-fast/pom.xml
+++ b/ctakes-dictionary-lookup-fast/pom.xml
@@ -56,7 +56,7 @@
<goal>unpack-dependencies</goal>
</goals>
<configuration>
- <!-- copy the hsql database to ${basedir}/resources to
work with IDE -->
+ <!-- copy the hsql database to
${project.basedir}/resources to work with IDE -->
<includeArtifactIds>ctakes-resources-sno_rx</includeArtifactIds>
<excludes>**/META-INF/**</excludes>
<outputDirectory>${project.basedir}/../resources</outputDirectory>
diff --git a/ctakes-distribution/pom.xml b/ctakes-distribution/pom.xml
index 9305838..53ca24a 100644
--- a/ctakes-distribution/pom.xml
+++ b/ctakes-distribution/pom.xml
@@ -154,6 +154,10 @@
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-tiny-rest</artifactId>
</dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-user-resources</artifactId>
+ </dependency>
</dependencies>
<profiles>
diff --git a/ctakes-dockhand/pom.xml b/ctakes-dockhand/pom.xml
index 69a720f..6097940 100644
--- a/ctakes-dockhand/pom.xml
+++ b/ctakes-dockhand/pom.xml
@@ -62,10 +62,10 @@
<goal>copy-resources</goal>
</goals>
<configuration>
-
<outputDirectory>${basedir}/target/classes/org/apache/ctakes/dockhand/goal/rest/webapp</outputDirectory>
+
<outputDirectory>${project.basedir}/target/classes/org/apache/ctakes/dockhand/goal/rest/webapp</outputDirectory>
<resources>
<resource>
-
<directory>${basedir}/../ctakes-tiny-rest/src/main/webapp</directory>
+
<directory>${project.basedir}/../ctakes-tiny-rest/src/main/webapp</directory>
<filtering>true</filtering>
</resource>
</resources>
diff --git
a/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/SampleInputRadiologyNotes.txt
b/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/SampleInputRadiologyNotes.txt
new file mode 100644
index 0000000..49faa73
--- /dev/null
+++
b/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/SampleInputRadiologyNotes.txt
@@ -0,0 +1,7 @@
+CLINIC`rimsdate`rimstime`resultno`subtype`accesion`lastname`birth_dt`gender`status`secure`testcode`testdesc`doctor`COMMENTS
+54321`02/20/1999`13:21:00`14`GENRAD`987654-3`SMITH`04/03/1916`F`F`N`70955-RRIMS`CT
ANGIO ABD W/WO CST ADD SECT`DAVIS, WILLIAM R`20Feb1999 1:21PM CT ABDOMEN w &
PELVIS w Indications: ct abd/pel - hernia ventral nos;USE IV CON ORIGINAL
REPORT - 10 Aug 2009 3:15PM ROMAYO CT abdomen and pelvis with IV contrast.
Comparison with prior MR angiography dated 4-2-04. Again seen is a large
ventral hernia containing multiple nonobstructed loops of small bowel and
ascending colon. No evidence of vasc [...]
+54321`02/20/1999`11:20:00`13`GENRAD`987654-4`SMITH`04/03/1916`F`F`N`07552-RRIMS`US
Lower Extrem Art-Graft Cmpl`DAVIS, WILLIAM R`20Feb1999 11:20AM US Lower Extrem
Art-Graft Cmpl ASO. Patent left femoral-popliteal bypass. Diffuse tibial
artery disease with posterior tibial occlusion. The anterior tibial is patent
into the dorsalis pedis and the peroneal artery contributes to the plantar arch
via a patent calcaneal branch. Right hypogastric artery stenosis. W. R. Davis
MD 5-4321
+54321`02/20/2000`17:15:00`12`CT`876543-2`SMITH`04/03/1916`F`F`N`73200-RRIMS`CT
EXT UPPER wo`DAVIS, WILLIAM R`20Feb2000 5:15PM Exam: CT RECONSTRUCTION
20Feb2000 3:17PM Exam: L CT EXT LOWER w Indications: le - L femur pain,
r/o^osteomyelitis vs tumor ORIGINAL REPORT - 17 Apr 2006 2:31PM SMH CT left
femur with IV contrast. No comparison exam. Along the mid left femoral
diaphysis there is an aggressive, malignant appearing process involving the
lateral cortex. Adjacent cortical scalloping is [...]
+12345`02/20/1999`13:21:00`14`GENRAD`987654-3`SMITH`04/03/1916`F`F`N`07075-RRIMS`Tibia
Fibula 2vw AP/Lat`DAVIS, WILLIAM R`20Feb1999 1:21PM Exam: R Tibia Fibula 2vw
AP/Lat Indications: Exposed tibia;R/O osteo;S/p BKA ORIGINAL REPORT - 02 Feb
1999 1:21PM ROMAYO Amputation through the proximal shafts of the right tibia
and fibula. Ulceration of soft tissues distally. No radiographic evidence of
osteomyelitis. The right popliteal artery is largely obscured by metallic
artifact from a right TK [...]
+12345`02/20/1999`11:20:00`13`GENRAD`987654-4`SMITH`04/03/1916`F`F`N`07552-RRIMS`US
Lower Extrem Art-Graft Cmpl`DAVIS, WILLIAM R`20Feb1999 11:20AM Exam: Both
popliteal arteries are patent with normal flow. W. R. Davis MD 5-4321
+12345`02/20/2000`17:15:00`12`CT`876543-2`SMITH`04/03/1916`F`F`N`73200-RRIMS`CT
EXT UPPER wo`DAVIS, WILLIAM R`20Feb2000 5:15PM Exam: CT RECONSTRUCTION
20Feb2000 3:17PM Exam: CT EXT UPPER W/O CONTRAST Indications: Indications: Left
shoulder fracture 02/20/2001 3:55PM SMH (2B-3495) CT of the left shoulder
including oblique sagittal and oblique coronal reformats demonstrates a
slightly comminuted fracture of the surgical neck of the proximal left humerus
with anterior and proximal displaceme [...]
\ No newline at end of file
diff --git
a/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/claudication
b/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/claudication
new file mode 100644
index 0000000..23558e0
--- /dev/null
+++
b/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/claudication
@@ -0,0 +1,7 @@
+IMPRESSION/REPORT/PLAN
+The patient has very typical history for claudication. Yet the patient does
not have any significant bruit at the pelvic area, abdominal area.
+
+Aspirin 200-mg once-a-day.
+Ibuprofen increased from 200 mg to 300 mg p.o. twice a day.
+Aspirin 80 mg.
+acetaminophen discontinued.
diff --git
a/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/dr_nutritious_1.txt
b/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/dr_nutritious_1.txt
new file mode 100644
index 0000000..8b28745
--- /dev/null
+++
b/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/dr_nutritious_1.txt
@@ -0,0 +1,12 @@
+
+Dr. Nutritious
+
+Medical Nutrition Therapy for Hyperlipidemia
+
+Referral from: Julie Tester, RD, LD, CNSD
+Phone contact: (555) 555-1212
+Height: 144 cm Current Weight: 45 kg Date of current weight: 02-29-2001
Admit Weight: 53 kg BMI: 18 kg/m2
+Diet: General
+Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity.
+Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
+Pt has been on a 3-day calorie count and has had an average intake of 1100
calories. She was instructed to drink 2-3 cans of liquid supplement to help
promote weight gain. She agrees with the plan and has my number for further
assessment. May want a Resting Metabolic Rate as well. She takes an aspirin a
day for knee pain.
diff --git
a/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/dr_nutritious_2.txt
b/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/dr_nutritious_2.txt
new file mode 100644
index 0000000..51b19f6
--- /dev/null
+++
b/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/dr_nutritious_2.txt
@@ -0,0 +1,12 @@
+
+Dr. Nutritious
+
+Medical Nutrition Therapy for Hyperlipidemia
+
+Significant for her father, who died at 50 years from colon cancer.
+Phone contact: (555) 555-1212
+Height: 144 cm Current Weight: 45 kg
+Diet: General
+Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity.
+Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
+Colonoscopy. No pain or discomfort reported.
diff --git
a/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/edge_cases_plaintext_1.txt
b/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/edge_cases_plaintext_1.txt
new file mode 100644
index 0000000..8f7ef7e
--- /dev/null
+++
b/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/edge_cases_plaintext_1.txt
@@ -0,0 +1,2 @@
+patient complained that the n'tion didn't make sense. This is a test of an
edge case in contraction in the tokezier.
+aspirin decreased from 2:00 PM. This used to cause the drug ner to go into an
infinte loop.
\ No newline at end of file
diff --git
a/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/pain_no_swelling.txt
b/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/pain_no_swelling.txt
new file mode 100644
index 0000000..27e5c03
--- /dev/null
+++
b/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/pain_no_swelling.txt
@@ -0,0 +1,4 @@
+
+The patient reported pain in her upper arm.
+No swelling.
+Aspirin 325 mg.
diff --git
a/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/right_knee_arthroscopy
b/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/right_knee_arthroscopy
new file mode 100644
index 0000000..a97d8f0
--- /dev/null
+++
b/ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/small/right_knee_arthroscopy
@@ -0,0 +1,2 @@
+S/P right knee arthroscopy.
+Knee x-ray. Patient denies knee pain.
diff --git a/ctakes-user-resources/pom.xml b/ctakes-user-resources/pom.xml
index 1c5da23..b69bf15 100644
--- a/ctakes-user-resources/pom.xml
+++ b/ctakes-user-resources/pom.xml
@@ -34,10 +34,265 @@
<!-- 4. Given #2 and #3 above, we do not want multiple copies of user
resources in jars and resources/ dirs. -->
<!-- 5. There are external projects that depend upon user resources, so
they must be available for 'getting'. -->
<!-- Note: External projects include Apache cTAKES projects such as
ctakes-web-rest. -->
-
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
<version>5.0.0-SNAPSHOT</version>
</parent>
+ <packaging>jar</packaging>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-type-system</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-core</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-utils</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-template-filler</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-context-tokenizer</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-dictionary-lookup</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-dictionary-lookup-fast</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-examples</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-preprocessor</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-lvg</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-chunker</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-ne-contexts</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-pos-tagger</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-assertion</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-assertion-zoner</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-dependency-parser</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-clinical-pipeline</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-constituency-parser</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-coreference</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-drug-ner</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-relation-extractor</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-side-effect</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-smoking-status</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-temporal</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-ytex</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-ytex-uima</artifactId>
+ </dependency>
+ <!-- <dependency>-->
+ <!-- <groupId>org.apache.ctakes</groupId>-->
+ <!--
<artifactId>ctakes-ytex-web</artifactId>-->
+ <!-- <version>${project.version}</version>-->
+ <!-- <classifier>classes</classifier>-->
+ <!-- </dependency>-->
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-gui</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-fhir</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-tiny-rest</artifactId>
+ </dependency>
+ </dependencies>
+
+ <build>
+ <plugins>
+
+ <plugin>
+ <artifactId>maven-resources-plugin</artifactId>
+ <version>3.0.2</version>
+ <executions>
+ <execution>
+ <id>copy-user-resources</id>
+ <phase>prepare-package</phase>
+ <goals>
+
<goal>copy-resources</goal>
+ </goals>
+ <configuration>
+ <resources>
+ <resource>
+
<directory>${project.basedir}/../ctakes-assertion/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-assertion-zoner/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-chunker/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-clinical-pipeline/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-constituency-parser/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-context-tokenizer/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-core/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-coreference/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-dependency-parser/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-dictionary-lookup/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-dictionary-lookup-fast/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-drug-ner/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-fhir/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-lvg/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-ne-contexts/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-pos-tagger/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-preprocessor/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-relation-extractor/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-side-effect/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-smoking-status/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-template-filler/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-temporal/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-type-system/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-utils/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-ytex/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-ytex-uima/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
+ </resources>
+
<outputDirectory>${project.build.outputDirectory}</outputDirectory>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+
+ </plugins>
+ </build>
+
</project>
diff --git a/ctakes-web-rest/pom.xml b/ctakes-web-rest/pom.xml
index 44c0cde..5661519 100644
--- a/ctakes-web-rest/pom.xml
+++ b/ctakes-web-rest/pom.xml
@@ -38,11 +38,11 @@
<artifactId>ctakes-core</artifactId>
<version>${ctakes.version}</version>
</dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-core-models</artifactId>
- <version>${ctakes.version}</version>
- </dependency>
+<!-- <dependency>-->
+<!-- <groupId>org.apache.ctakes</groupId>-->
+<!-- <artifactId>ctakes-core-models</artifactId>-->
+<!-- <version>${ctakes.version}</version>-->
+<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup</artifactId>
@@ -63,21 +63,21 @@
<artifactId>ctakes-pos-tagger</artifactId>
<version>${ctakes.version}</version>
</dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-pos-tagger-models</artifactId>
- <version>${ctakes.version}</version>
- </dependency>
+<!-- <dependency>-->
+<!-- <groupId>org.apache.ctakes</groupId>-->
+<!-- <artifactId>ctakes-pos-tagger-models</artifactId>-->
+<!-- <version>${ctakes.version}</version>-->
+<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-chunker</artifactId>
<version>${ctakes.version}</version>
</dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-chunker-models</artifactId>
- <version>${ctakes.version}</version>
- </dependency>
+<!-- <dependency>-->
+<!-- <groupId>org.apache.ctakes</groupId>-->
+<!-- <artifactId>ctakes-chunker-models</artifactId>-->
+<!-- <version>${ctakes.version}</version>-->
+<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-lvg</artifactId>
@@ -103,11 +103,11 @@
<artifactId>ctakes-assertion</artifactId>
<version>${ctakes.version}</version>
</dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-assertion-models</artifactId>
- <version>${ctakes.version}</version>
- </dependency>
+<!-- <dependency>-->
+<!-- <groupId>org.apache.ctakes</groupId>-->
+<!-- <artifactId>ctakes-assertion-models</artifactId>-->
+<!-- <version>${ctakes.version}</version>-->
+<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-assertion-zoner</artifactId>
@@ -118,21 +118,21 @@
<artifactId>ctakes-constituency-parser</artifactId>
<version>${ctakes.version}</version>
</dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-constituency-parser-models</artifactId>
- <version>${ctakes.version}</version>
- </dependency>
+<!-- <dependency>-->
+<!-- <groupId>org.apache.ctakes</groupId>-->
+<!-- <artifactId>ctakes-constituency-parser-models</artifactId>-->
+<!-- <version>${ctakes.version}</version>-->
+<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-coreference</artifactId>
<version>${ctakes.version}</version>
</dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-coreference-models</artifactId>
- <version>${ctakes.version}</version>
- </dependency>
+<!-- <dependency>-->
+<!-- <groupId>org.apache.ctakes</groupId>-->
+<!-- <artifactId>ctakes-coreference-models</artifactId>-->
+<!-- <version>${ctakes.version}</version>-->
+<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-drug-ner</artifactId>
@@ -143,51 +143,51 @@
<artifactId>ctakes-side-effect</artifactId>
<version>${ctakes.version}</version>
</dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-side-effect-models</artifactId>
- <version>${ctakes.version}</version>
- </dependency>
+<!-- <dependency>-->
+<!-- <groupId>org.apache.ctakes</groupId>-->
+<!-- <artifactId>ctakes-side-effect-models</artifactId>-->
+<!-- <version>${ctakes.version}</version>-->
+<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-smoking-status</artifactId>
<version>${ctakes.version}</version>
</dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-smoking-status-models</artifactId>
- <version>${ctakes.version}</version>
- </dependency>
+<!-- <dependency>-->
+<!-- <groupId>org.apache.ctakes</groupId>-->
+<!-- <artifactId>ctakes-smoking-status-models</artifactId>-->
+<!-- <version>${ctakes.version}</version>-->
+<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dependency-parser</artifactId>
<version>${ctakes.version}</version>
</dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-dependency-parser-models</artifactId>
- <version>${ctakes.version}</version>
- </dependency>
+<!-- <dependency>-->
+<!-- <groupId>org.apache.ctakes</groupId>-->
+<!-- <artifactId>ctakes-dependency-parser-models</artifactId>-->
+<!-- <version>${ctakes.version}</version>-->
+<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-relation-extractor</artifactId>
<version>${ctakes.version}</version>
</dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-relation-extractor-models</artifactId>
- <version>${ctakes.version}</version>
- </dependency>
+<!-- <dependency>-->
+<!-- <groupId>org.apache.ctakes</groupId>-->
+<!-- <artifactId>ctakes-relation-extractor-models</artifactId>-->
+<!-- <version>${ctakes.version}</version>-->
+<!-- </dependency>-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-temporal</artifactId>
<version>${ctakes.version}</version>
</dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-temporal-models</artifactId>
- <version>${ctakes.version}</version>
- </dependency>
+<!-- <dependency>-->
+<!-- <groupId>org.apache.ctakes</groupId>-->
+<!-- <artifactId>ctakes-temporal-models</artifactId>-->
+<!-- <version>${ctakes.version}</version>-->
+<!-- </dependency>-->
<!-- ctakes-user-resources exists specifically for standalone products
like ctakes-web-rest -->
<dependency>
<groupId>org.apache.ctakes</groupId>
@@ -291,7 +291,6 @@
</configuration>
</plugin>
-
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.4</version>
@@ -302,33 +301,6 @@
</configuration>
</plugin>
- <!-- !!! TODO !!! This is a snippet from the
ctakes-dockhand pom.
- There should not be complete copies of
all resources from other modules.
- Instead, those resources should be copied
when this artifact is built.
- Doing so saves space and keeps the
resources up-to-date. -->
-<!-- <plugin>-->
-<!-- <artifactId>maven-resources-plugin</artifactId>-->
-<!-- <version>3.0.2</version>-->
-<!-- <executions>-->
-<!-- <execution>-->
-<!-- <id>copy-resources</id>-->
-<!-- <phase>compile</phase>-->
-<!-- <goals>-->
-<!-- <goal>copy-resources</goal>-->
-<!-- </goals>-->
-<!-- <configuration>-->
-<!--
<outputDirectory>${basedir}/target/classes/org/apache/ctakes/dockhand/goal/rest/webapp</outputDirectory>-->
-<!-- <resources>-->
-<!-- <resource>-->
-<!--
<directory>${basedir}/../ctakes-tiny-rest/src/main/webapp</directory>-->
-<!-- <filtering>true</filtering>-->
-<!-- </resource>-->
-<!-- </resources>-->
-<!-- </configuration>-->
-<!-- </execution>-->
-<!-- </executions>-->
-<!-- </plugin>-->
-
</plugins>
</build>
</project>
diff --git a/ctakes-ytex-uima/pom.xml b/ctakes-ytex-uima/pom.xml
index af097d8..7aaffd0 100644
--- a/ctakes-ytex-uima/pom.xml
+++ b/ctakes-ytex-uima/pom.xml
@@ -147,7 +147,7 @@
</goals>
<configuration>
<includeScope>compile</includeScope>
-
<outputDirectory>${basedir}/target/lib</outputDirectory>
+
<outputDirectory>${project.basedir}/target/lib</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>false</overWriteSnapshots>
<overWriteIfNewer>true</overWriteIfNewer>
@@ -181,7 +181,7 @@
<target>
<!-- default to
hsql, override via -D -->
<property
name="db.type" value="hsql" />
- <ant
antfile="build-setup.xml" dir="${basedir}/../ctakes-ytex/scripts"
target="test.setup">
+ <ant
antfile="build-setup.xml" dir="${project.basedir}/../ctakes-ytex/scripts"
target="test.setup">
<property name="config.local" value="${project.build.testOutputDirectory}" />
<property name="db.type" value="${db.type}" />
<property name="ytex.test" value="true" />
diff --git a/ctakes-ytex-web/pom.xml b/ctakes-ytex-web/pom.xml
index 4d0513b..0be17f2 100644
--- a/ctakes-ytex-web/pom.xml
+++ b/ctakes-ytex-web/pom.xml
@@ -144,10 +144,10 @@
<goal>copy-resources</goal>
</goals>
<configuration>
-
<outputDirectory>${basedir}/target/classes</outputDirectory>
+
<outputDirectory>${project.basedir}/target/classes</outputDirectory>
<resources>
<resource>
-
<directory>${basedir}/../ctakes-ytex/src/main/resources</directory>
+
<directory>${project.basedir}/../ctakes-ytex/src/main/resources</directory>
<filtering>true</filtering>
</resource>
</resources>
diff --git a/ctakes-ytex/pom.xml b/ctakes-ytex/pom.xml
index 575f30d..c69cfc7 100644
--- a/ctakes-ytex/pom.xml
+++ b/ctakes-ytex/pom.xml
@@ -247,7 +247,7 @@
<goal>copy-dependencies</goal>
</goals>
<configuration>
-
<outputDirectory>${basedir}/target/lib</outputDirectory>
+
<outputDirectory>${project.basedir}/target/lib</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>false</overWriteSnapshots>
<overWriteIfNewer>true</overWriteIfNewer>
diff --git a/ctakes-ytex/scripts/data/build.xml
b/ctakes-ytex/scripts/data/build.xml
index 049a47b..040694e 100644
--- a/ctakes-ytex/scripts/data/build.xml
+++ b/ctakes-ytex/scripts/data/build.xml
@@ -75,7 +75,7 @@ Database connection parameters are taken from ytex.properties.
<condition property="hsql">
<equals arg1="${db.type}" arg2="hsql" />
</condition>
- <condition property="umls.data" value="${java.io.tmpdir}"
else="${basedir}/umls">
+ <condition property="umls.data" value="${java.io.tmpdir}"
else="${project.basedir}/umls">
<isset property="umls.zip.available" />
</condition>
<!-- what to do when errors occur while dropping tables.
ignore these for oracle -->
@@ -200,7 +200,7 @@ Database connection parameters are taken from
ytex.properties.
<sequential>
<antcall target="jdl">
<param name="jdl.data"
value="${rrf.home}/META/@{rrf.base}.RRF" />
- <param name="jdl.format"
value="${basedir}/umls/@{rrf.base}.xml" />
+ <param name="jdl.format"
value="${project.basedir}/umls/@{rrf.base}.xml" />
</antcall>
</sequential>
</for>
@@ -208,7 +208,7 @@ Database connection parameters are taken from
ytex.properties.
<sequential>
<antcall target="jdl">
<param name="jdl.data"
value="${rrf.home}/NET/@{rrf.base}" />
- <param name="jdl.format"
value="${basedir}/umls/@{rrf.base}.xml" />
+ <param name="jdl.format"
value="${project.basedir}/umls/@{rrf.base}.xml" />
</antcall>
</sequential>
</for>
@@ -229,12 +229,12 @@ Database connection parameters are taken from
ytex.properties.
<echo>import MRCONSO</echo>
<antcall target="jdl">
<param name="jdl.data" value="${umls.data}/MRCONSO.RRF"
/>
- <param name="jdl.format"
value="${basedir}/umls/MRCONSO.xml" />
+ <param name="jdl.format"
value="${project.basedir}/umls/MRCONSO.xml" />
</antcall>
<echo>import MRSTY</echo>
<antcall target="jdl">
<param name="jdl.data" value="${umls.data}/MRSTY.RRF" />
- <param name="jdl.format"
value="${basedir}/umls/MRSTY.xml" />
+ <param name="jdl.format"
value="${project.basedir}/umls/MRSTY.xml" />
</antcall>
<echo>index umls tables</echo>
<antcall target="jdbc.sqlcmd">
@@ -283,7 +283,7 @@ Database connection parameters are taken from
ytex.properties.
</delete>
</target>
<target name="umls.import.view" depends="init.conn" description="load
v_snomed_fword_lookup.txt. Use file from resources directory if it exists and
if ytex.test is not defined">
- <condition property="view.jdl.data"
value="${ytex.resources.home}/org/apache/ctakes/ytex/dictionary/lookup/v_snomed_fword_lookup.txt"
else="${basedir}/umls/v_snomed_fword_lookup.txt">
+ <condition property="view.jdl.data"
value="${ytex.resources.home}/org/apache/ctakes/ytex/dictionary/lookup/v_snomed_fword_lookup.txt"
else="${project.basedir}/umls/v_snomed_fword_lookup.txt">
<and>
<available
file="${ytex.resources.home}/org/apache/ctakes/ytex/dictionary/lookup/v_snomed_fword_lookup.txt"
/>
<not>
@@ -294,7 +294,7 @@ Database connection parameters are taken from
ytex.properties.
<echo>import v_snomed_fword_lookup from ${view.jdl.data}. Be
patient, this can take a while.</echo>
<antcall target="jdl">
<param name="jdl.data" value="${view.jdl.data}" />
- <param name="jdl.format"
value="${basedir}/umls/v_snomed_fword_lookup.xml" />
+ <param name="jdl.format"
value="${project.basedir}/umls/v_snomed_fword_lookup.xml" />
</antcall>
</target>
<target name="umls.insert.view" depends="init.conn" description="create
view by joining the mrconso, mrsty and umls_aui_fword tables">
@@ -346,7 +346,7 @@ Database connection parameters are taken from
ytex.properties.
<echo>import umls tables into ${umls.schema} schema. Be
patient, this can take a while.</echo>
<antcall target="jdl">
<param name="jdl.data"
value="${umls.data}/umls_aui_fword.txt" />
- <param name="jdl.format"
value="${basedir}/umls/umls_aui_fword.xml" />
+ <param name="jdl.format"
value="${project.basedir}/umls/umls_aui_fword.xml" />
</antcall>
</target>
<target name="umls.drop.view" depends="init" description="drop and
create umls tables">
@@ -528,7 +528,7 @@ ${sql.delimiter}
</antcall>
</target>
<target name="init.conn">
- <copy file="${basedir}/conn.xml.template"
tofile="${java.io.tmpdir}/conn.xml" overwrite="yes">
+ <copy file="${project.basedir}/conn.xml.template"
tofile="${java.io.tmpdir}/conn.xml" overwrite="yes">
<filterset>
<filter token="db.driver" value="${db.driver}"
/>
<filter token="db.url" value="${db.url}" />
@@ -584,15 +584,15 @@ ${sql.delimiter}
<property name="prefix" value="sct2" />
<antcall target="jdl">
<param name="jdl.data"
value="${sct.home}/${prefix}_Concept_Snapshot_INT_${sct.version}.txt" />
- <param name="jdl.format"
value="${basedir}/snomedct/${prefix}_concept.xml" />
+ <param name="jdl.format"
value="${project.basedir}/snomedct/${prefix}_concept.xml" />
</antcall>
<antcall target="jdl">
<param name="jdl.data"
value="${sct.home}/${prefix}_Relationship_Snapshot_INT_${sct.version}.txt" />
- <param name="jdl.format"
value="${basedir}/snomedct/${prefix}_relationship.xml" />
+ <param name="jdl.format"
value="${project.basedir}/snomedct/${prefix}_relationship.xml" />
</antcall>
<antcall target="jdl">
<param name="jdl.data"
value="${sct.home}/${prefix}_Description_Snapshot-en_INT_${sct.version}.txt" />
- <param name="jdl.format"
value="${basedir}/snomedct/${prefix}_description.xml" />
+ <param name="jdl.format"
value="${project.basedir}/snomedct/${prefix}_description.xml" />
</antcall>
<antcall target="jdbc.sqlcmd">
<param name="sqlcmd.dir" value="snomedct" />
diff --git a/pom.xml b/pom.xml
index 76d4a75..6c6b8e9 100644
--- a/pom.xml
+++ b/pom.xml
@@ -812,24 +812,6 @@
<outputDirectory>${project.basedir}/../resources</outputDirectory>
</configuration>
</execution>
- <execution>
- <!-- Copy resources
that should be user-editable to ctakes-user-resources -->
- <!-- This makes
these resources available as a jar in maven central. -->
-
<id>copy-to-user-resources</id>
-<!--
<phase>package</phase>-->
-
<phase>prepare-package</phase>
- <goals>
-
<goal>copy-resources</goal>
- </goals>
- <configuration>
- <resources>
-
<resource>
-
<directory>src/user/resources</directory>
-
</resource>
- </resources>
-
<outputDirectory>${project.basedir}/../ctakes-user-resources/target/classes</outputDirectory>
- </configuration>
- </execution>
</executions>
</plugin>
<!-- TODO: remove dependency upon Apache Ant -->
