From 77b225570825705c3ac26452be79e82e98252bbf Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Wed, 8 Nov 2023 14:56:43 +0000 Subject: [PATCH 01/48] Docker publish --- .github/workflows/docker-publish.yml | 94 ++++++++++++++++++++++++++++ Dockerfile | 7 +++ 2 files changed, 101 insertions(+) create mode 100644 .github/workflows/docker-publish.yml create mode 100644 Dockerfile diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml new file mode 100644 index 00000000..e2c51837 --- /dev/null +++ b/.github/workflows/docker-publish.yml @@ -0,0 +1,94 @@ +name: Docker + +# This workflow uses actions that are not certified by GitHub. +# They are provided by a third-party and are governed by +# separate terms of service, privacy policy, and support +# documentation. + +on: + push: + # Publish semver tags as releases. + branches: [master, develop, docker] + tags: [ 'v*.*.*' ] + +env: + # Use docker.io for Docker Hub if empty + REGISTRY: ghcr.io + # github.repository as / + IMAGE_NAME: ${{ github.repository }} + +jobs: + build: + + if: ${{ github.event.workflow_run.conclusion == 'success' }} + runs-on: ubuntu-latest + permissions: + contents: read + packages: write + # This is used to complete the identity challenge + # with sigstore/fulcio when running outside of PRs. + id-token: write + + steps: + - name: Checkout repository + uses: actions/checkout@v3 + + # Install the cosign tool except on PR + # https://github.com/sigstore/cosign-installer + - name: Install cosign + if: github.event_name != 'pull_request' + uses: sigstore/cosign-installer@6e04d228eb30da1757ee4e1dd75a0ec73a653e06 #v3.1.1 + with: + cosign-release: 'v2.1.1' + + # Set up BuildKit Docker container builder to be able to build + # multi-platform images and export cache + # https://github.com/docker/setup-buildx-action + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@f95db51fddba0c2d1ec667646a06c2ce06100226 # v3.0.0 + + # Login against a Docker registry except on PR + # https://github.com/docker/login-action + - name: Log into registry ${{ env.REGISTRY }} + if: github.event_name != 'pull_request' + uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d # v3.0.0 + with: + registry: ${{ env.REGISTRY }} + username: ${{ github.actor }} + password: ${{ secrets.GITHUB_TOKEN }} + + # Extract metadata (tags, labels) for Docker + # https://github.com/docker/metadata-action + - name: Extract Docker metadata + id: meta + uses: docker/metadata-action@96383f45573cb7f253c731d3b3ab81c87ef81934 # v5.0.0 + with: + images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} + + # Build and push Docker image with Buildx (don't push on PR) + # https://github.com/docker/build-push-action + - name: Build and push Docker image + id: build-and-push + uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09 # v5.0.0 + with: + context: . + push: ${{ github.event_name != 'pull_request' }} + tags: ${{ steps.meta.outputs.tags }} + labels: ${{ steps.meta.outputs.labels }} + cache-from: type=gha + cache-to: type=gha,mode=max + + # Sign the resulting Docker image digest except on PRs. + # This will only write to the public Rekor transparency log when the Docker + # repository is public to avoid leaking data. If you would like to publish + # transparency data even for private images, pass --force to cosign below. + # https://github.com/sigstore/cosign + - name: Sign the published Docker image + if: ${{ github.event_name != 'pull_request' }} + env: + # https://docs.github.com/en/actions/security-guides/security-hardening-for-github-actions#using-an-intermediate-environment-variable + TAGS: ${{ steps.meta.outputs.tags }} + DIGEST: ${{ steps.build-and-push.outputs.digest }} + # This step uses the identity token to provision an ephemeral certificate + # against the sigstore community Fulcio instance. + run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST} \ No newline at end of file diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 00000000..c4c98ec7 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,7 @@ +FROM openjdk:8 + +COPY . / + +RUN apt-get update && apt-get install -y graphviz + +CMD ["sh", "run.sh"] From e03779791da6d3739f87c41de3a2fcf7bb045c03 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Wed, 8 Nov 2023 14:57:15 +0000 Subject: [PATCH 02/48] capitalization --- .github/workflows/docker-publish.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml index e2c51837..6bac771d 100644 --- a/.github/workflows/docker-publish.yml +++ b/.github/workflows/docker-publish.yml @@ -8,7 +8,7 @@ name: Docker on: push: # Publish semver tags as releases. - branches: [master, develop, docker] + branches: [master, develop, Docker] tags: [ 'v*.*.*' ] env: From 248f28753bb08902c2b69ed955d82d360e4cbdae Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Wed, 8 Nov 2023 14:58:13 +0000 Subject: [PATCH 03/48] Unprotect yml --- .github/workflows/docker-publish.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml index 6bac771d..c2021bdd 100644 --- a/.github/workflows/docker-publish.yml +++ b/.github/workflows/docker-publish.yml @@ -20,7 +20,6 @@ env: jobs: build: - if: ${{ github.event.workflow_run.conclusion == 'success' }} runs-on: ubuntu-latest permissions: contents: read From ce1efb76e3fb22c6215844be571248545fd657a0 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Wed, 8 Nov 2023 15:08:16 +0000 Subject: [PATCH 04/48] First try multistage build --- Dockerfile | 24 +++++++++++++++++++++++- 1 file changed, 23 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index c4c98ec7..6120cb64 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,28 @@ -FROM openjdk:8 +FROM openjdk:8 as builder + +RUN git clone https://github.com/fbk/utils \ + && cd utils \ + && mvn clean install \ + && cd .. \ + && git clone https://github.com/fbk/fcw \ + && cd fcw \ + && git checkout develop \ + && mvn clean install \ + && cd .. \ + && git clone https://github.com/dhfbk/tint \ + && cd tint \ + && git checkout develop \ + && mvn clean install \ + && cd .. \ + && git clone https://github.com/dkmfbk/pikes \ + && cd pikes \ + && git checkout develop \ + && mvn clean package -DskipTests -Prelease + +FROM openjdk:8 as server COPY . / +COPY --from=build **/pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar ./pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar RUN apt-get update && apt-get install -y graphviz From dbd19f0e43cf21f232849d340fed03583d68ce75 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Wed, 8 Nov 2023 15:09:23 +0000 Subject: [PATCH 05/48] fix name --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 6120cb64..4a8a7693 100644 --- a/Dockerfile +++ b/Dockerfile @@ -22,7 +22,7 @@ RUN git clone https://github.com/fbk/utils \ FROM openjdk:8 as server COPY . / -COPY --from=build **/pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar ./pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar +COPY --from=builder **/pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar ./pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar RUN apt-get update && apt-get install -y graphviz From 7dcd967bf60358b55ae05e64900c1483a9a25c4c Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Wed, 8 Nov 2023 15:11:31 +0000 Subject: [PATCH 06/48] maven builder --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 4a8a7693..21f16a79 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM openjdk:8 as builder +FROM maven:3.9-amazoncorretto-8 as builder RUN git clone https://github.com/fbk/utils \ && cd utils \ From 1926a1b431ca77260b84c239e5512563bc58cb51 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Wed, 8 Nov 2023 15:13:10 +0000 Subject: [PATCH 07/48] Install git --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 21f16a79..fd2ccfff 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,7 @@ FROM maven:3.9-amazoncorretto-8 as builder -RUN git clone https://github.com/fbk/utils \ +RUN apt-get install -y git \ + && git clone https://github.com/fbk/utils \ && cd utils \ && mvn clean install \ && cd .. \ From 83ea67308bbfb653830fc516bd069f3531db0070 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Wed, 8 Nov 2023 15:15:47 +0000 Subject: [PATCH 08/48] specific image --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index fd2ccfff..fe9cb230 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM maven:3.9-amazoncorretto-8 as builder +FROM maven:3.9-amazoncorretto-8-debian as builder RUN apt-get install -y git \ && git clone https://github.com/fbk/utils \ From 9d7cd447b6325ea5ee125c50fa3abb4625e2aa92 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Wed, 8 Nov 2023 15:17:05 +0000 Subject: [PATCH 09/48] update --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index fe9cb230..3fe8c38e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ FROM maven:3.9-amazoncorretto-8-debian as builder -RUN apt-get install -y git \ +RUN apt-get update && apt-get install -y git \ && git clone https://github.com/fbk/utils \ && cd utils \ && mvn clean install \ From 1a98846d49b087d7ef3dadaffc135e30f825f75d Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Wed, 8 Nov 2023 15:19:21 +0000 Subject: [PATCH 10/48] install gpg --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 3fe8c38e..0ac5dddd 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ FROM maven:3.9-amazoncorretto-8-debian as builder -RUN apt-get update && apt-get install -y git \ +RUN apt-get update && apt-get install -y git gnupg \ && git clone https://github.com/fbk/utils \ && cd utils \ && mvn clean install \ From 267ef3bad7fafd7bd2c5bf62740192449c0244be Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Wed, 8 Nov 2023 15:22:16 +0000 Subject: [PATCH 11/48] fix encryption --- Dockerfile | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index 0ac5dddd..b51bdf93 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ FROM maven:3.9-amazoncorretto-8-debian as builder -RUN apt-get update && apt-get install -y git gnupg \ +RUN apt-get update && apt-get install -y git gnupg2 \ && git clone https://github.com/fbk/utils \ && cd utils \ && mvn clean install \ @@ -15,9 +15,6 @@ RUN apt-get update && apt-get install -y git gnupg \ && git checkout develop \ && mvn clean install \ && cd .. \ - && git clone https://github.com/dkmfbk/pikes \ - && cd pikes \ - && git checkout develop \ && mvn clean package -DskipTests -Prelease FROM openjdk:8 as server From 22e1e9bdc381b0dbd3340188da040ad37d8c985f Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Wed, 8 Nov 2023 15:25:39 +0000 Subject: [PATCH 12/48] Generate secret key --- Dockerfile | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/Dockerfile b/Dockerfile index b51bdf93..ef280f97 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,17 @@ FROM maven:3.9-amazoncorretto-8-debian as builder RUN apt-get update && apt-get install -y git gnupg2 \ + && gpg --batch --passphrase "pikes" --generate-key < Date: Wed, 8 Nov 2023 15:26:36 +0000 Subject: [PATCH 13/48] Spacing --- Dockerfile | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/Dockerfile b/Dockerfile index ef280f97..0617d254 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,16 +2,16 @@ FROM maven:3.9-amazoncorretto-8-debian as builder RUN apt-get update && apt-get install -y git gnupg2 \ && gpg --batch --passphrase "pikes" --generate-key < Date: Wed, 8 Nov 2023 15:29:05 +0000 Subject: [PATCH 14/48] build.sh --- .gitignore | 1 - Dockerfile | 29 ++--------------------------- build.sh | 28 ++++++++++++++++++++++++++++ 3 files changed, 30 insertions(+), 28 deletions(-) create mode 100644 build.sh diff --git a/.gitignore b/.gitignore index 28a6075c..69ec51fe 100644 --- a/.gitignore +++ b/.gitignore @@ -2,7 +2,6 @@ target mytests .DS_Store .idea -*.sh dkm-commandlist.txt *.iml */.classpath diff --git a/Dockerfile b/Dockerfile index 0617d254..3768ff6e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,32 +1,7 @@ FROM maven:3.9-amazoncorretto-8-debian as builder -RUN apt-get update && apt-get install -y git gnupg2 \ - && gpg --batch --passphrase "pikes" --generate-key < Date: Wed, 8 Nov 2023 15:31:41 +0000 Subject: [PATCH 15/48] Fix environment --- build.sh | 3 +++ 1 file changed, 3 insertions(+) diff --git a/build.sh b/build.sh index 7a58ed7e..13884d9a 100644 --- a/build.sh +++ b/build.sh @@ -11,6 +11,9 @@ Passphrase: pikes %commit EOF +GPG_TTY=$(tty) +export GPG_TTY + git clone https://github.com/fbk/utils \ && cd utils \ && mvn clean install \ From 4ba812a4ef6cd7747a116735e5f167afff5f74cb Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Wed, 8 Nov 2023 15:35:36 +0000 Subject: [PATCH 16/48] Switch to focal --- Dockerfile | 2 +- build.sh | 16 +--------------- 2 files changed, 2 insertions(+), 16 deletions(-) diff --git a/Dockerfile b/Dockerfile index 3768ff6e..4c334862 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM maven:3.9-amazoncorretto-8-debian as builder +FROM maven:3.9-amazoncorretto-8-focal as builder COPY ./build.sh / RUN sh ./build.sh diff --git a/build.sh b/build.sh index 13884d9a..3c54575e 100644 --- a/build.sh +++ b/build.sh @@ -1,18 +1,4 @@ -apt-get update && apt-get install -y git gnupg2 -gpg --batch --passphrase "pikes" --generate-key < Date: Wed, 8 Nov 2023 15:36:37 +0000 Subject: [PATCH 17/48] correct version --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 4c334862..6927ca6a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM maven:3.9-amazoncorretto-8-focal as builder +FROM maven:3.9-eclipse-temurin-8-focal as builder COPY ./build.sh / RUN sh ./build.sh From 77bf2b9810b9ff8f5531618977023b9bcf179791 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Wed, 8 Nov 2023 15:38:18 +0000 Subject: [PATCH 18/48] gpg --- build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.sh b/build.sh index 3c54575e..c0f0dd36 100644 --- a/build.sh +++ b/build.sh @@ -1,4 +1,4 @@ -apt-get update && apt-get install -y git +apt-get update && apt-get install -y git gnupg git clone https://github.com/fbk/utils \ && cd utils \ From 24550e1335dae05b688c42232a9564179d0a61e1 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Wed, 8 Nov 2023 15:39:46 +0000 Subject: [PATCH 19/48] secret key --- build.sh | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/build.sh b/build.sh index c0f0dd36..437d1511 100644 --- a/build.sh +++ b/build.sh @@ -1,4 +1,15 @@ apt-get update && apt-get install -y git gnupg +gpg --batch --passphrase "pikes" --generate-key < Date: Wed, 8 Nov 2023 15:41:22 +0000 Subject: [PATCH 20/48] Skip gpg --- build.sh | 21 +++++---------------- 1 file changed, 5 insertions(+), 16 deletions(-) diff --git a/build.sh b/build.sh index 437d1511..4edb25d4 100644 --- a/build.sh +++ b/build.sh @@ -1,28 +1,17 @@ -apt-get update && apt-get install -y git gnupg -gpg --batch --passphrase "pikes" --generate-key < Date: Wed, 8 Nov 2023 15:44:01 +0000 Subject: [PATCH 21/48] Skip tests --- build.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/build.sh b/build.sh index 4edb25d4..f42e82e5 100644 --- a/build.sh +++ b/build.sh @@ -2,16 +2,16 @@ apt-get update && apt-get install -y git git clone https://github.com/fbk/utils \ && cd utils \ - && mvn clean install -Dgpg.skip \ + && mvn clean install -DskipTests -Dgpg.skip \ && cd .. \ && git clone https://github.com/fbk/fcw \ && cd fcw \ && git checkout develop \ - && mvn clean install -Dgpg.skip \ + && mvn clean install -DskipTests -Dgpg.skip \ && cd .. \ && git clone https://github.com/dhfbk/tint \ && cd tint \ && git checkout develop \ - && mvn clean install -Dgpg.skip \ + && mvn clean install -DskipTests -Dgpg.skip \ && cd .. \ && mvn clean package -DskipTests -Dgpg.skip -Prelease From c678a95c1aaf44d30bf720d6fe5f41558dddf165 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Wed, 8 Nov 2023 15:48:04 +0000 Subject: [PATCH 22/48] master tint --- build.sh | 1 - 1 file changed, 1 deletion(-) diff --git a/build.sh b/build.sh index f42e82e5..15ab68a9 100644 --- a/build.sh +++ b/build.sh @@ -11,7 +11,6 @@ git clone https://github.com/fbk/utils \ && cd .. \ && git clone https://github.com/dhfbk/tint \ && cd tint \ - && git checkout develop \ && mvn clean install -DskipTests -Dgpg.skip \ && cd .. \ && mvn clean package -DskipTests -Dgpg.skip -Prelease From 3b770f649f01f9391581d6895f1918c4139c28fc Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 11:40:00 +0000 Subject: [PATCH 23/48] Add missing files --- Dockerfile | 2 +- run.sh | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) create mode 100644 run.sh diff --git a/Dockerfile b/Dockerfile index 6927ca6a..6436c468 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ FROM maven:3.9-eclipse-temurin-8-focal as builder -COPY ./build.sh / +COPY . / RUN sh ./build.sh FROM openjdk:8 as server diff --git a/run.sh b/run.sh new file mode 100644 index 00000000..661f6d78 --- /dev/null +++ b/run.sh @@ -0,0 +1,6 @@ +#!/bin/bash +CLASSPATH=pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar +CONF=config-pikes.prop +PORT=8011 +RAM=-Xmx8G +java $RAM -cp $CLASSPATH eu.fbk.dkm.pikes.tintop.server.PipelineServer -p $PORT -c $CONF From 79bebbd25af8dd3877bcfc120842a81e8011a279 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 11:52:48 +0000 Subject: [PATCH 24/48] Install rdfpro as well --- build.sh | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/build.sh b/build.sh index 15ab68a9..4ef6a247 100644 --- a/build.sh +++ b/build.sh @@ -4,6 +4,10 @@ git clone https://github.com/fbk/utils \ && cd utils \ && mvn clean install -DskipTests -Dgpg.skip \ && cd .. \ + && git clone https://github.com/dkmfbk/rdfpro \ + && cd rdfpro \ + && mvn clean install -DskipTests -Dgpg.skip \ + && cd .. \ && git clone https://github.com/fbk/fcw \ && cd fcw \ && git checkout develop \ From 9b22f518d0886f1078daadf6a71c8c775393db6b Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 11:58:27 +0000 Subject: [PATCH 25/48] Version adaptions --- build.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/build.sh b/build.sh index 4ef6a247..89947976 100644 --- a/build.sh +++ b/build.sh @@ -6,7 +6,7 @@ git clone https://github.com/fbk/utils \ && cd .. \ && git clone https://github.com/dkmfbk/rdfpro \ && cd rdfpro \ - && mvn clean install -DskipTests -Dgpg.skip \ + && mvn clean install -DskipTests -Dgpg.skip -Prelease \ && cd .. \ && git clone https://github.com/fbk/fcw \ && cd fcw \ @@ -17,4 +17,4 @@ git clone https://github.com/fbk/utils \ && cd tint \ && mvn clean install -DskipTests -Dgpg.skip \ && cd .. \ - && mvn clean package -DskipTests -Dgpg.skip -Prelease + && mvn clean package -DskipTests -Dgpg.skip -Prelease versions:use-latest-versions From 4a92249be3a5f87fbb593432c52dca486e347e68 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 12:10:12 +0000 Subject: [PATCH 26/48] Setting versions --- build.sh | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/build.sh b/build.sh index 89947976..950d0ce1 100644 --- a/build.sh +++ b/build.sh @@ -2,11 +2,12 @@ apt-get update && apt-get install -y git git clone https://github.com/fbk/utils \ && cd utils \ - && mvn clean install -DskipTests -Dgpg.skip \ + && mvn clean install -DskipTests -Dgpg.skip -Prelease \ && cd .. \ && git clone https://github.com/dkmfbk/rdfpro \ && cd rdfpro \ - && mvn clean install -DskipTests -Dgpg.skip -Prelease \ + && mvn versions:set -DnewVersion=0.7-SNAPSHOT \ + && mvn clean install -DskipTests -Dgpg.skip \ && cd .. \ && git clone https://github.com/fbk/fcw \ && cd fcw \ From acad0f694ecea45fea01a545a9468be8afee27fb Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 12:16:25 +0000 Subject: [PATCH 27/48] Correct utils version --- build.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/build.sh b/build.sh index 950d0ce1..3d49cc80 100644 --- a/build.sh +++ b/build.sh @@ -2,7 +2,8 @@ apt-get update && apt-get install -y git git clone https://github.com/fbk/utils \ && cd utils \ - && mvn clean install -DskipTests -Dgpg.skip -Prelease \ + && mvn versions:set -DnewVersion=3.2-SNAPSHOT \ + && mvn clean install -DskipTests -Dgpg.skip \ && cd .. \ && git clone https://github.com/dkmfbk/rdfpro \ && cd rdfpro \ From 620897e9fe12184d13b08c526683222cdb85fd56 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 12:55:50 +0000 Subject: [PATCH 28/48] Update build sh --- build.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/build.sh b/build.sh index 3d49cc80..5c221df1 100644 --- a/build.sh +++ b/build.sh @@ -7,6 +7,7 @@ git clone https://github.com/fbk/utils \ && cd .. \ && git clone https://github.com/dkmfbk/rdfpro \ && cd rdfpro \ + && git checkout develop \ && mvn versions:set -DnewVersion=0.7-SNAPSHOT \ && mvn clean install -DskipTests -Dgpg.skip \ && cd .. \ From 4dafb65b29a688bcade669da5ffac7949bf043ef Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 13:07:32 +0000 Subject: [PATCH 29/48] Add parent for deployment --- build.sh | 12 +++++++++--- parent | 1 + rdfpro | 1 + utils | 1 + 4 files changed, 12 insertions(+), 3 deletions(-) create mode 160000 parent create mode 160000 rdfpro create mode 160000 utils diff --git a/build.sh b/build.sh index 5c221df1..de0f61c3 100644 --- a/build.sh +++ b/build.sh @@ -4,13 +4,19 @@ git clone https://github.com/fbk/utils \ && cd utils \ && mvn versions:set -DnewVersion=3.2-SNAPSHOT \ && mvn clean install -DskipTests -Dgpg.skip \ + && cd .. \ + && git clone https://github.com/fbk/parent \ + && cd parent \ + && git checkout develop \ + && mvn versions:set -DnewVersion=2.3-SNAPSHOT \ + && mvn clean install -DskipTests -Dgpg.skip \ && cd .. \ - && git clone https://github.com/dkmfbk/rdfpro \ - && cd rdfpro \ + && git clone https://github.com/dkmfbk/rdfpro parent/rdfpro \ + && cd parent/rdfpro \ && git checkout develop \ && mvn versions:set -DnewVersion=0.7-SNAPSHOT \ && mvn clean install -DskipTests -Dgpg.skip \ - && cd .. \ + && cd ../.. \ && git clone https://github.com/fbk/fcw \ && cd fcw \ && git checkout develop \ diff --git a/parent b/parent new file mode 160000 index 00000000..030405ee --- /dev/null +++ b/parent @@ -0,0 +1 @@ +Subproject commit 030405ee8ccbaaf7fd502403361193fef3bd69bd diff --git a/rdfpro b/rdfpro new file mode 160000 index 00000000..382da1fb --- /dev/null +++ b/rdfpro @@ -0,0 +1 @@ +Subproject commit 382da1fbf8f58d1d5b747a3f6b9f53642d7be844 diff --git a/utils b/utils new file mode 160000 index 00000000..08e5c343 --- /dev/null +++ b/utils @@ -0,0 +1 @@ +Subproject commit 08e5c343f8826086b0d435ee89fad2f0855cbfc8 From 8fd942fbf7a407499a35421cd37148962fe42456 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 13:12:39 +0000 Subject: [PATCH 30/48] Remove spaces --- build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.sh b/build.sh index de0f61c3..b0fbe91e 100644 --- a/build.sh +++ b/build.sh @@ -4,7 +4,7 @@ git clone https://github.com/fbk/utils \ && cd utils \ && mvn versions:set -DnewVersion=3.2-SNAPSHOT \ && mvn clean install -DskipTests -Dgpg.skip \ - && cd .. \ + && cd .. \ && git clone https://github.com/fbk/parent \ && cd parent \ && git checkout develop \ From 3379e91f6ddbd11b80c2b4cfb663dc898b7f4b7b Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 13:20:08 +0000 Subject: [PATCH 31/48] Add version --- build.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/build.sh b/build.sh index b0fbe91e..bf66ff41 100644 --- a/build.sh +++ b/build.sh @@ -20,6 +20,7 @@ git clone https://github.com/fbk/utils \ && git clone https://github.com/fbk/fcw \ && cd fcw \ && git checkout develop \ + && mvn versions:set -DnewVersion=1.0-SNAPSHOT \ && mvn clean install -DskipTests -Dgpg.skip \ && cd .. \ && git clone https://github.com/dhfbk/tint \ From 975dde9fdefb41eff30bc4d102d82b942279d9b6 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 13:21:32 +0000 Subject: [PATCH 32/48] Remove wrongly added refs --- parent | 1 - rdfpro | 1 - utils | 1 - 3 files changed, 3 deletions(-) delete mode 160000 parent delete mode 160000 rdfpro delete mode 160000 utils diff --git a/parent b/parent deleted file mode 160000 index 030405ee..00000000 --- a/parent +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 030405ee8ccbaaf7fd502403361193fef3bd69bd diff --git a/rdfpro b/rdfpro deleted file mode 160000 index 382da1fb..00000000 --- a/rdfpro +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 382da1fbf8f58d1d5b747a3f6b9f53642d7be844 diff --git a/utils b/utils deleted file mode 160000 index 08e5c343..00000000 --- a/utils +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 08e5c343f8826086b0d435ee89fad2f0855cbfc8 From 65e605a9ad39b0608d5d96a3a157169c0d0a072b Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 13:34:02 +0000 Subject: [PATCH 33/48] Small dockerfile fixes --- .devcontainer/devcontainer.json | 20 +++++++++++++++++++ Dockerfile | 5 +++-- config-pikes.prop | 35 +++++++++++++++++++++++++++++++++ 3 files changed, 58 insertions(+), 2 deletions(-) create mode 100644 .devcontainer/devcontainer.json create mode 100644 config-pikes.prop diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 00000000..a2b2ab18 --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,20 @@ +// For format details, see https://aka.ms/devcontainer.json. For config options, see the +// README at: https://github.com/devcontainers/templates/tree/main/src/python +{ + "name": "Java 8", + // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile + "image": "mcr.microsoft.com/devcontainers/java:8", + + // Configure tool-specific properties. + "customizations": { + // Configure properties specific to VS Code. + "vscode": { + "settings": {}, + "extensions": [ + "github.vscode-github-actions", + "ms-azuretools.vscode-docker", + "streetsidesoftware.code-spell-checker" + ] + } + } +} \ No newline at end of file diff --git a/Dockerfile b/Dockerfile index 6436c468..976fbce3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -5,8 +5,9 @@ RUN sh ./build.sh FROM openjdk:8 as server -COPY . / -COPY --from=builder **/pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar ./pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar +COPY run.sh ./ +COPY config-pikes.prop ./ +COPY --from=builder pikes-tintop/target/pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar ./pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar RUN apt-get update && apt-get install -y graphviz diff --git a/config-pikes.prop b/config-pikes.prop new file mode 100644 index 00000000..40c0f731 --- /dev/null +++ b/config-pikes.prop @@ -0,0 +1,35 @@ +stanford.dbps.annotator = dbpedia-annotate +stanford.dbps.address = http://api.dbpedia-spotlight.org +stanford.dbps.min_confidence = 0.0 +stanford.dbps.first_confidence = 0.5 +stanford.dbps.extract_types = 0 + +enable_predicate_matrix = 1 +enable_naf_filter = 1 +enable_on_filter = 1 + +max_text_len = 1000000 + +stanford.annotators = tokenize, ssplit, dbps, pos, simple_pos, lemma, ukb, ner_custom, parse, conll_parse, mst_fake, mate, semafor, dcoref + +stanford.ssplit.newlineIsSentenceBreak = two + +filter.termSenseCompletion = true +filter.entityRemoveOverlaps = true +filter.entitySpanFixing = true +filter.entityAddition = true +filter.entityValueNormalization = true +filter.linkingCompletion = true +filter.linkingFixing = true +filter.corefSpanFixing = true +filter.corefForRoleDependencies = true +filter.srlRemoveWrongRefs = true +filter.srlRemoveUnknownPredicates = true +filter.srlPredicateAddition = true +filter.srlSelfArgFixing = true +filter.srlSenseMapping = false +filter.srlRoleLinking = none +filter.opinionLinking = none + +stanford.parse.maxlen = 50 +stanford.dcoref.maxdist = 5 From aa15d5188673ebb4defa55f2be91988146cbc584 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 13:39:13 +0000 Subject: [PATCH 34/48] devcontainer fix --- .devcontainer/devcontainer.json | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index a2b2ab18..feeb9897 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -16,5 +16,8 @@ "streetsidesoftware.code-spell-checker" ] } - } + }, + + // Use 'onCreateCommand' to run commands before the container is created. + "onCreateCommand": "sudo apt-get update && sudo apt-get install -y maven" } \ No newline at end of file From dd52946fd085d042c7453e2f49621df7855093fc Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 14:04:53 +0000 Subject: [PATCH 35/48] Add necessary dependencies to Dockerfile --- Dockerfile | 9 +++++++++ build.sh | 0 run.sh | 0 3 files changed, 9 insertions(+) mode change 100644 => 100755 build.sh mode change 100644 => 100755 run.sh diff --git a/Dockerfile b/Dockerfile index 976fbce3..a010da20 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,12 +2,21 @@ FROM maven:3.9-eclipse-temurin-8-focal as builder COPY . / RUN sh ./build.sh +RUN wget https://wordnetcode.princeton.edu/wn3.1.dict.tar.gz +RUN tar -zxvf wn3.1.dict.tar.gz +RUN wget https://git.rwth-aachen.de/coscine/research/pikesdocker/-/archive/main/pikesdocker-main.tar.gz?path=models +RUN tar -zxvf pikesdocker-main.tar.gz?path=models +RUN wget https://git.rwth-aachen.de/coscine/research/pikesdocker/-/archive/main/pikesdocker-main.tar.gz?path=ukb +RUN tar -zxvf pikesdocker-main.tar.gz?path=ukb FROM openjdk:8 as server COPY run.sh ./ COPY config-pikes.prop ./ COPY --from=builder pikes-tintop/target/pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar ./pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar +COPY --from=builder dict/* ./wordnet/ +COPY --from=builder pikesdocker-main-models/models/* ./models/ +COPY --from=builder pikesdocker-main-ukb/ukb/* ./ukb/ RUN apt-get update && apt-get install -y graphviz diff --git a/build.sh b/build.sh old mode 100644 new mode 100755 diff --git a/run.sh b/run.sh old mode 100644 new mode 100755 From cfa231ee90e01a1df174b33797efb55c50595674 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 14:17:47 +0000 Subject: [PATCH 36/48] Simplify build --- .devcontainer/devcontainer.json | 19 +++++++++++++++++-- Dockerfile | 13 ++++--------- fcw | 1 + getDependencies.sh | 9 +++++++++ parent | 1 + tint | 1 + utils | 1 + 7 files changed, 34 insertions(+), 11 deletions(-) create mode 160000 fcw create mode 100755 getDependencies.sh create mode 160000 parent create mode 160000 tint create mode 160000 utils diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index feeb9897..1986fcc6 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -18,6 +18,21 @@ } }, + // Use 'forwardPorts' to make a list of ports inside the container available locally. + "forwardPorts": [8011], + + // Use 'portsAttributes' to set default properties for specific forwarded ports. + // More info: https://containers.dev/implementors/json_reference/#port-attributes + "portsAttributes": { + "8011": { + "label": "Server", + "onAutoForward": "notify" + } + }, + // Use 'onCreateCommand' to run commands before the container is created. - "onCreateCommand": "sudo apt-get update && sudo apt-get install -y maven" -} \ No newline at end of file + "onCreateCommand": "sudo apt-get update && sudo apt-get install -y maven", + + // Use 'postStartCommand' to run commands after the container is started. + "postStartCommand": "chmod 777 build.sh && sudo sh build.sh && chmod 777 getDependencies.sh && sudo sh getDependencies.sh && cp pikes-tintop/target/pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar ./pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar" +} diff --git a/Dockerfile b/Dockerfile index a010da20..cbb1e3b6 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,21 +2,16 @@ FROM maven:3.9-eclipse-temurin-8-focal as builder COPY . / RUN sh ./build.sh -RUN wget https://wordnetcode.princeton.edu/wn3.1.dict.tar.gz -RUN tar -zxvf wn3.1.dict.tar.gz -RUN wget https://git.rwth-aachen.de/coscine/research/pikesdocker/-/archive/main/pikesdocker-main.tar.gz?path=models -RUN tar -zxvf pikesdocker-main.tar.gz?path=models -RUN wget https://git.rwth-aachen.de/coscine/research/pikesdocker/-/archive/main/pikesdocker-main.tar.gz?path=ukb -RUN tar -zxvf pikesdocker-main.tar.gz?path=ukb +RUN sh ./getDependencies.sh FROM openjdk:8 as server COPY run.sh ./ COPY config-pikes.prop ./ COPY --from=builder pikes-tintop/target/pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar ./pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar -COPY --from=builder dict/* ./wordnet/ -COPY --from=builder pikesdocker-main-models/models/* ./models/ -COPY --from=builder pikesdocker-main-ukb/ukb/* ./ukb/ +COPY --from=builder wordnet/* ./wordnet/ +COPY --from=builder models/* ./models/ +COPY --from=builder ukb/* ./ukb/ RUN apt-get update && apt-get install -y graphviz diff --git a/fcw b/fcw new file mode 160000 index 00000000..aafa3d6f --- /dev/null +++ b/fcw @@ -0,0 +1 @@ +Subproject commit aafa3d6f1c309827a51a2ad2921fb7ec9d083b61 diff --git a/getDependencies.sh b/getDependencies.sh new file mode 100755 index 00000000..c3ed8b6c --- /dev/null +++ b/getDependencies.sh @@ -0,0 +1,9 @@ +wget https://wordnetcode.princeton.edu/wn3.1.dict.tar.gz +tar -zxvf wn3.1.dict.tar.gz +mv dict wordnet +wget https://git.rwth-aachen.de/coscine/research/pikesdocker/-/archive/main/pikesdocker-main.tar.gz?path=models +tar -zxvf pikesdocker-main.tar.gz?path=models +mv pikesdocker-main-models/models models +wget https://git.rwth-aachen.de/coscine/research/pikesdocker/-/archive/main/pikesdocker-main.tar.gz?path=ukb +tar -zxvf pikesdocker-main.tar.gz?path=ukb +mv pikesdocker-main-ukb/ukb ukb diff --git a/parent b/parent new file mode 160000 index 00000000..030405ee --- /dev/null +++ b/parent @@ -0,0 +1 @@ +Subproject commit 030405ee8ccbaaf7fd502403361193fef3bd69bd diff --git a/tint b/tint new file mode 160000 index 00000000..e11ab721 --- /dev/null +++ b/tint @@ -0,0 +1 @@ +Subproject commit e11ab72107f2b60bfe21b637ac00022167b6fbdb diff --git a/utils b/utils new file mode 160000 index 00000000..08e5c343 --- /dev/null +++ b/utils @@ -0,0 +1 @@ +Subproject commit 08e5c343f8826086b0d435ee89fad2f0855cbfc8 From 55dd681c6fa4c43be2e7bbc9e3718e6b96c83031 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 14:18:24 +0000 Subject: [PATCH 37/48] Remove git repos --- fcw | 1 - parent | 1 - tint | 1 - utils | 1 - 4 files changed, 4 deletions(-) delete mode 160000 fcw delete mode 160000 parent delete mode 160000 tint delete mode 160000 utils diff --git a/fcw b/fcw deleted file mode 160000 index aafa3d6f..00000000 --- a/fcw +++ /dev/null @@ -1 +0,0 @@ -Subproject commit aafa3d6f1c309827a51a2ad2921fb7ec9d083b61 diff --git a/parent b/parent deleted file mode 160000 index 030405ee..00000000 --- a/parent +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 030405ee8ccbaaf7fd502403361193fef3bd69bd diff --git a/tint b/tint deleted file mode 160000 index e11ab721..00000000 --- a/tint +++ /dev/null @@ -1 +0,0 @@ -Subproject commit e11ab72107f2b60bfe21b637ac00022167b6fbdb diff --git a/utils b/utils deleted file mode 160000 index 08e5c343..00000000 --- a/utils +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 08e5c343f8826086b0d435ee89fad2f0855cbfc8 From 7299b68fe000497a8207f10bcda9c92c37abcdf4 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 14:34:30 +0000 Subject: [PATCH 38/48] Small adaptions --- .devcontainer/devcontainer.json | 2 +- Dockerfile | 1 + build.sh | 2 -- 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 1986fcc6..86ce2eb3 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -34,5 +34,5 @@ "onCreateCommand": "sudo apt-get update && sudo apt-get install -y maven", // Use 'postStartCommand' to run commands after the container is started. - "postStartCommand": "chmod 777 build.sh && sudo sh build.sh && chmod 777 getDependencies.sh && sudo sh getDependencies.sh && cp pikes-tintop/target/pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar ./pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar" + "postStartCommand": "chmod 777 build.sh && sh build.sh && chmod 777 getDependencies.sh && sudo sh getDependencies.sh && cp pikes-tintop/target/pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar ./pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar" } diff --git a/Dockerfile b/Dockerfile index cbb1e3b6..f731d925 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,7 @@ FROM maven:3.9-eclipse-temurin-8-focal as builder COPY . / +RUN apt-get update && apt-get install -y git RUN sh ./build.sh RUN sh ./getDependencies.sh diff --git a/build.sh b/build.sh index bf66ff41..e8fef244 100755 --- a/build.sh +++ b/build.sh @@ -1,5 +1,3 @@ -apt-get update && apt-get install -y git - git clone https://github.com/fbk/utils \ && cd utils \ && mvn versions:set -DnewVersion=3.2-SNAPSHOT \ From 230024bd97cc34957205a6a5e98fbaca3062d91e Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 16:39:10 +0000 Subject: [PATCH 39/48] Fix dockerfile --- Dockerfile | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index f731d925..a478636b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -10,10 +10,10 @@ FROM openjdk:8 as server COPY run.sh ./ COPY config-pikes.prop ./ COPY --from=builder pikes-tintop/target/pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar ./pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar -COPY --from=builder wordnet/* ./wordnet/ -COPY --from=builder models/* ./models/ -COPY --from=builder ukb/* ./ukb/ +COPY --from=builder wordnet ./wordnet/ +COPY --from=builder models ./models/ +COPY --from=builder ukb ./ukb/ -RUN apt-get update && apt-get install -y graphviz +RUN apt-get update && apt-get install -y graphviz && chmod 777 ukb CMD ["sh", "run.sh"] From 91b3e1ce2ab4fd88e3fb349da4bca017f15a7a46 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 18:00:09 +0100 Subject: [PATCH 40/48] Sudo in Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index a478636b..954ef355 100644 --- a/Dockerfile +++ b/Dockerfile @@ -16,4 +16,4 @@ COPY --from=builder ukb ./ukb/ RUN apt-get update && apt-get install -y graphviz && chmod 777 ukb -CMD ["sh", "run.sh"] +CMD ["sudo", "sh", "run.sh"] From bee08bed712db91ca6b3c5b64ddaf40c8717f4eb Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Mon, 13 Nov 2023 18:18:05 +0100 Subject: [PATCH 41/48] Fix ukb permissions --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 954ef355..5049e117 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,6 +14,6 @@ COPY --from=builder wordnet ./wordnet/ COPY --from=builder models ./models/ COPY --from=builder ukb ./ukb/ -RUN apt-get update && apt-get install -y graphviz && chmod 777 ukb +RUN apt-get update && apt-get install -y graphviz && chmod -R 777 ukb -CMD ["sudo", "sh", "run.sh"] +CMD ["sh", "run.sh"] From 6b0b5a5f295f67edf858770f966f9d4a47de8da7 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Tue, 14 Nov 2023 09:33:26 +0000 Subject: [PATCH 42/48] Update versions --- .devcontainer/devcontainer.json | 2 +- .gitignore | 13 ++++++++++++- config-pikes.prop | 4 +++- getDependencies.sh | 6 +++--- pikes-raid/pom.xml | 9 +++++---- pikes-rdf/pom.xml | 4 ++-- pikes-resources/pom.xml | 32 ++++++++++++++++---------------- pikes-tintop-client/pom.xml | 2 +- pikes-tintop/pom.xml | 14 +++++++------- pom.xml | 2 +- 10 files changed, 51 insertions(+), 37 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 86ce2eb3..2220425e 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -31,7 +31,7 @@ }, // Use 'onCreateCommand' to run commands before the container is created. - "onCreateCommand": "sudo apt-get update && sudo apt-get install -y maven", + "onCreateCommand": "sudo apt-get update && sudo apt-get install -y maven graphviz", // Use 'postStartCommand' to run commands after the container is started. "postStartCommand": "chmod 777 build.sh && sh build.sh && chmod 777 getDependencies.sh && sudo sh getDependencies.sh && cp pikes-tintop/target/pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar ./pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar" diff --git a/.gitignore b/.gitignore index 69ec51fe..1300c9c9 100644 --- a/.gitignore +++ b/.gitignore @@ -9,4 +9,15 @@ dkm-commandlist.txt */.settings *.versionsBackup pikes.ipr -pikes.iws \ No newline at end of file +pikes.iws +utils +parent +fcw +tint +wordnet +ukb +ukb-3.2 +models +*.tgz* +*.tar.gz* +pikes-tintop-1.0-SNAPSHOT-jar-with-dependencies.jar diff --git a/config-pikes.prop b/config-pikes.prop index 40c0f731..2ea253ec 100644 --- a/config-pikes.prop +++ b/config-pikes.prop @@ -10,7 +10,9 @@ enable_on_filter = 1 max_text_len = 1000000 -stanford.annotators = tokenize, ssplit, dbps, pos, simple_pos, lemma, ukb, ner_custom, parse, conll_parse, mst_fake, mate, semafor, dcoref +#stanford.annotators = tokenize, ssplit, dbps, pos, simple_pos, lemma, ukb, ner_custom, parse, conll_parse, mst_fake, mate, semafor, dcoref +#stanford.annotators = tokenize, ssplit, dbps, pos, simple_pos, lemma, ukb, ner, depparse, conll_parse, mst_fake, mate, semafor, coref +stanford.annotators = tokenize, ssplit, dbps, pos, simple_pos, lemma, ukb, ner, parse, conll_parse, mst_fake, mate, semafor, coref, entitylink, kbp stanford.ssplit.newlineIsSentenceBreak = two diff --git a/getDependencies.sh b/getDependencies.sh index c3ed8b6c..f4860292 100755 --- a/getDependencies.sh +++ b/getDependencies.sh @@ -4,6 +4,6 @@ mv dict wordnet wget https://git.rwth-aachen.de/coscine/research/pikesdocker/-/archive/main/pikesdocker-main.tar.gz?path=models tar -zxvf pikesdocker-main.tar.gz?path=models mv pikesdocker-main-models/models models -wget https://git.rwth-aachen.de/coscine/research/pikesdocker/-/archive/main/pikesdocker-main.tar.gz?path=ukb -tar -zxvf pikesdocker-main.tar.gz?path=ukb -mv pikesdocker-main-ukb/ukb ukb +wget --no-check-certificate https://ixa2.si.ehu.eus/ukb/ukb_3.2.tgz +tar -zxvf ukb_3.2.tgz +mv ukb-3.2/bin ukb diff --git a/pikes-raid/pom.xml b/pikes-raid/pom.xml index e42651fa..cdedd547 100644 --- a/pikes-raid/pom.xml +++ b/pikes-raid/pom.xml @@ -66,18 +66,19 @@ edu.stanford.nlp stanford-corenlp - 3.4 + 4.5.5 edu.stanford.nlp stanford-corenlp models + 4.5.5 runtime org.apache.jena jena-core - 2.13.0 + 4.10.0 @@ -93,12 +94,12 @@ xml-apis xml-apis - 1.4.01 + 2.0.2 ch.qos.logback logback-classic - 1.1.3 + 1.4.11 eu.fbk.utils diff --git a/pikes-rdf/pom.xml b/pikes-rdf/pom.xml index ab5c0dc9..e60755ba 100644 --- a/pikes-rdf/pom.xml +++ b/pikes-rdf/pom.xml @@ -126,7 +126,7 @@ xml-apis xml-apis - 1.4.01 + 2.0.2 @@ -162,7 +162,7 @@ com.spotify.sparkey sparkey - 2.1.2 + 3.2.5 test diff --git a/pikes-resources/pom.xml b/pikes-resources/pom.xml index 2e82431e..0fb470ff 100644 --- a/pikes-resources/pom.xml +++ b/pikes-resources/pom.xml @@ -25,12 +25,12 @@ javax.xml.bind jaxb-api - 2.2.7 + 2.4.0-b180830.0359 org.jooq joox - 1.3.0 + 2.0.0 commons-io @@ -113,7 +113,7 @@ xml-apis xml-apis - 1.4.01 + 2.0.2 org.slf4j @@ -122,19 +122,19 @@ com.fasterxml.jackson.core jackson-databind - 2.3.1 + 2.16.0-rc1 org.apache.commons commons-csv - 1.2 + 1.10.0 ch.qos.logback logback-classic - 1.1.3 + 1.4.11 runtime @@ -142,21 +142,21 @@ org.apache.tika tika-parsers - 1.12 + 2.9.1 true net.sourceforge.htmlcleaner htmlcleaner - 2.16 + 2.29 true org.unbescape unbescape - 1.1.3.RELEASE + 1.1.6.RELEASE true @@ -165,7 +165,7 @@ org.apache.commons commons-email - 1.4 + 1.5 @@ -178,12 +178,12 @@ org.jsoup jsoup - 1.7.2 + 1.16.2 org.apache.tika tika-core - 1.12 + 2.9.1 @@ -193,7 +193,7 @@ com.sun.mail javax.mail - 1.5.2 + 1.6.2 @@ -240,21 +240,21 @@ org.apache.tika tika-parsers - 1.12 + 2.9.1 net.sourceforge.htmlcleaner htmlcleaner - 2.16 + 2.29 org.unbescape unbescape - 1.1.3.RELEASE + 1.1.6.RELEASE diff --git a/pikes-tintop-client/pom.xml b/pikes-tintop-client/pom.xml index 2999d336..5c0ebd30 100644 --- a/pikes-tintop-client/pom.xml +++ b/pikes-tintop-client/pom.xml @@ -56,7 +56,7 @@ org.apache.httpcomponents httpclient - 4.4 + 4.5.14 eu.fbk.utils diff --git a/pikes-tintop/pom.xml b/pikes-tintop/pom.xml index 00940393..7a507b72 100644 --- a/pikes-tintop/pom.xml +++ b/pikes-tintop/pom.xml @@ -74,7 +74,7 @@ com.fasterxml.jackson.core jackson-databind - 2.3.1 + 2.16.0-rc1 @@ -84,28 +84,28 @@ org.jdom jdom2 - 2.0.6 + 2.0.6.1 javax.xml.bind jaxb-api - 2.2.7 + 2.4.0-b180830.0359 runtime xml-apis xml-apis - 1.4.01 + 2.0.2 ch.qos.logback logback-classic - 1.1.3 + 1.4.11 org.glassfish.grizzly grizzly-http-server - 2.3.21 + 4.0.1 org.eclipse.rdf4j @@ -203,7 +203,7 @@ org.jooq joox - 1.3.0 + 2.0.0 diff --git a/pom.xml b/pom.xml index fc0e8960..6457cfae 100644 --- a/pom.xml +++ b/pom.xml @@ -138,7 +138,7 @@ 3.2-SNAPSHOT 0.7-SNAPSHOT 1.0-SNAPSHOT - 3.9.2 + 4.5.5 2.2.4 http://pikes.fbk.eu/ From af4ec6ba726190f49fc5e5cba34eeab106fd6b58 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Tue, 14 Nov 2023 10:43:38 +0100 Subject: [PATCH 43/48] Add maven central --- pom.xml | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/pom.xml b/pom.xml index 6457cfae..49c2aa58 100644 --- a/pom.xml +++ b/pom.xml @@ -42,6 +42,15 @@ fbk-repo https://raw.githubusercontent.com/fbk/mvn-repo/master/releases + + central + Maven Central + default + https://repo1.maven.org/maven2 + + false + + From 6182c16afa6d6d2fd5b72042cb98c780f958f824 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Tue, 14 Nov 2023 11:23:27 +0000 Subject: [PATCH 44/48] Update dependencies --- build.sh | 2 +- pikes-raid/pom.xml | 4 ++-- .../eu/fbk/dkm/pikes/raid/mdfsa/APIManager.java | 2 +- .../eu/fbk/dkm/pikes/raid/mdfsa/MaxEntTagger.java | 4 ++-- .../raid/mdfsa/parser/DependenciesBuilder.java | 13 +++++++------ pikes-resources/pom.xml | 12 ++++++------ pikes-tintop/pom.xml | 6 +++--- pom.xml | 8 ++++---- 8 files changed, 26 insertions(+), 25 deletions(-) diff --git a/build.sh b/build.sh index e8fef244..7f0e7684 100755 --- a/build.sh +++ b/build.sh @@ -25,4 +25,4 @@ git clone https://github.com/fbk/utils \ && cd tint \ && mvn clean install -DskipTests -Dgpg.skip \ && cd .. \ - && mvn clean package -DskipTests -Dgpg.skip -Prelease versions:use-latest-versions + && mvn clean package -DskipTests -Dgpg.skip -Prelease diff --git a/pikes-raid/pom.xml b/pikes-raid/pom.xml index cdedd547..00b8a89d 100644 --- a/pikes-raid/pom.xml +++ b/pikes-raid/pom.xml @@ -78,7 +78,7 @@ org.apache.jena jena-core - 4.10.0 + 2.13.0 @@ -99,7 +99,7 @@ ch.qos.logback logback-classic - 1.4.11 + 1.1.3 eu.fbk.utils diff --git a/pikes-raid/src/main/java/eu/fbk/dkm/pikes/raid/mdfsa/APIManager.java b/pikes-raid/src/main/java/eu/fbk/dkm/pikes/raid/mdfsa/APIManager.java index a447fa66..6c80050a 100644 --- a/pikes-raid/src/main/java/eu/fbk/dkm/pikes/raid/mdfsa/APIManager.java +++ b/pikes-raid/src/main/java/eu/fbk/dkm/pikes/raid/mdfsa/APIManager.java @@ -204,7 +204,7 @@ public double evaluateSentence(String text) { public double evaluateSentence(CoreMap sentence, int startNodeId, ArrayList blockedNodes) { SemanticGraph dependencies = sentence.get(BasicDependenciesAnnotation.class); - String[] dependenciesList = dependencies.toString("list").split("\n"); + String[] dependenciesList = dependencies.toString(SemanticGraph.OutputFormat.LIST).split("\n"); return evaluateSentence(dependenciesList, startNodeId, blockedNodes); } diff --git a/pikes-raid/src/main/java/eu/fbk/dkm/pikes/raid/mdfsa/MaxEntTagger.java b/pikes-raid/src/main/java/eu/fbk/dkm/pikes/raid/mdfsa/MaxEntTagger.java index 040709c0..e739ed05 100644 --- a/pikes-raid/src/main/java/eu/fbk/dkm/pikes/raid/mdfsa/MaxEntTagger.java +++ b/pikes-raid/src/main/java/eu/fbk/dkm/pikes/raid/mdfsa/MaxEntTagger.java @@ -1,7 +1,7 @@ package eu.fbk.dkm.pikes.raid.mdfsa; import edu.stanford.nlp.ling.HasWord; -import edu.stanford.nlp.ling.Sentence; +import edu.stanford.nlp.ling.SentenceUtils; import edu.stanford.nlp.ling.TaggedWord; import edu.stanford.nlp.tagger.maxent.MaxentTagger; @@ -36,7 +36,7 @@ public String tag(String fn) { List> sentences = MaxentTagger.tokenizeText(new BufferedReader(new StringReader(fn))); for (List sentence : sentences) { ArrayList tSentence = (ArrayList) tagger.tagSentence(sentence); - taggedString = taggedString.concat(Sentence.listToString(tSentence, false)); + taggedString = taggedString.concat(SentenceUtils.listToString(tSentence, false)); } return taggedString; } catch(Exception e) { diff --git a/pikes-raid/src/main/java/eu/fbk/dkm/pikes/raid/mdfsa/parser/DependenciesBuilder.java b/pikes-raid/src/main/java/eu/fbk/dkm/pikes/raid/mdfsa/parser/DependenciesBuilder.java index 1e722007..cd0dad9e 100644 --- a/pikes-raid/src/main/java/eu/fbk/dkm/pikes/raid/mdfsa/parser/DependenciesBuilder.java +++ b/pikes-raid/src/main/java/eu/fbk/dkm/pikes/raid/mdfsa/parser/DependenciesBuilder.java @@ -1,7 +1,8 @@ package eu.fbk.dkm.pikes.raid.mdfsa.parser; import edu.stanford.nlp.ling.HasWord; -import edu.stanford.nlp.ling.Sentence; +import edu.stanford.nlp.ling.IndexedWord; +import edu.stanford.nlp.ling.SentenceUtils; import edu.stanford.nlp.parser.lexparser.LexicalizedParser; import edu.stanford.nlp.process.DocumentPreprocessor; import edu.stanford.nlp.trees.*; @@ -58,8 +59,8 @@ public void buildDependeciesTree(String text) { DependencyTree dt = new DependencyTree(); for(TypedDependency td: tdl) { - TreeGraphNode dep = td.dep(); - TreeGraphNode gov = td.gov(); + IndexedWord dep = td.dep(); + IndexedWord gov = td.gov(); GrammaticalRelation gr = td.reln(); String depString = gr.toString() + "^^^" + gov.toString() + "^^^" + dep.toString(); //System.out.println(depString); @@ -78,13 +79,13 @@ public ArrayList buildDependeciesTrees(ArrayList texts) for(String text: texts) { System.out.println(textId); String[] sent = text.split(" "); - Tree parse = this.lp.apply(Sentence.toWordList(sent)); + Tree parse = this.lp.apply(SentenceUtils.toWordList(sent)); GrammaticalStructure gs = this.gsf.newGrammaticalStructure(parse); Collection tdl = gs.typedDependenciesCCprocessed(); DependencyTree curDT = new DependencyTree(); for(TypedDependency td: tdl) { - TreeGraphNode dep = td.dep(); - TreeGraphNode gov = td.gov(); + IndexedWord dep = td.dep(); + IndexedWord gov = td.gov(); GrammaticalRelation gr = td.reln(); String depString = gr.toString() + "^^^" + gov.toString() + "^^^" + dep.toString(); curDT.addDependency(depString); diff --git a/pikes-resources/pom.xml b/pikes-resources/pom.xml index 0fb470ff..4bfcea11 100644 --- a/pikes-resources/pom.xml +++ b/pikes-resources/pom.xml @@ -30,7 +30,7 @@ org.jooq joox - 2.0.0 + 1.3.0 commons-io @@ -134,7 +134,7 @@ ch.qos.logback logback-classic - 1.4.11 + 1.1.3 runtime @@ -142,7 +142,7 @@ org.apache.tika tika-parsers - 2.9.1 + 1.28.5 true @@ -178,12 +178,12 @@ org.jsoup jsoup - 1.16.2 + 1.7.2 org.apache.tika tika-core - 2.9.1 + 1.28.5 @@ -240,7 +240,7 @@ org.apache.tika tika-parsers - 2.9.1 + 1.28.5 diff --git a/pikes-tintop/pom.xml b/pikes-tintop/pom.xml index 7a507b72..8f2a818b 100644 --- a/pikes-tintop/pom.xml +++ b/pikes-tintop/pom.xml @@ -100,12 +100,12 @@ ch.qos.logback logback-classic - 1.4.11 + 1.1.3 org.glassfish.grizzly grizzly-http-server - 4.0.1 + 2.4.4 org.eclipse.rdf4j @@ -203,7 +203,7 @@ org.jooq joox - 2.0.0 + 1.3.0 diff --git a/pom.xml b/pom.xml index 49c2aa58..ffaee251 100644 --- a/pom.xml +++ b/pom.xml @@ -38,10 +38,6 @@ - - fbk-repo - https://raw.githubusercontent.com/fbk/mvn-repo/master/releases - central Maven Central @@ -51,6 +47,10 @@ false + + fbk-repo + https://raw.githubusercontent.com/fbk/mvn-repo/master/releases + From 9140cd66aafa686aeb26643d86e9393a0ddfee59 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Tue, 14 Nov 2023 11:50:53 +0000 Subject: [PATCH 45/48] Enhanced Standford Corenlp models --- config-pikes.prop | 3 ++- pikes-raid/pom.xml | 13 ++++++++++--- pikes-tintop/pom.xml | 10 +++++++++- 3 files changed, 21 insertions(+), 5 deletions(-) diff --git a/config-pikes.prop b/config-pikes.prop index 2ea253ec..e5a71bca 100644 --- a/config-pikes.prop +++ b/config-pikes.prop @@ -12,7 +12,8 @@ max_text_len = 1000000 #stanford.annotators = tokenize, ssplit, dbps, pos, simple_pos, lemma, ukb, ner_custom, parse, conll_parse, mst_fake, mate, semafor, dcoref #stanford.annotators = tokenize, ssplit, dbps, pos, simple_pos, lemma, ukb, ner, depparse, conll_parse, mst_fake, mate, semafor, coref -stanford.annotators = tokenize, ssplit, dbps, pos, simple_pos, lemma, ukb, ner, parse, conll_parse, mst_fake, mate, semafor, coref, entitylink, kbp +stanford.annotators = tokenize, ssplit, dbps, pos, simple_pos, lemma, ukb, ner, parse, conll_parse, mst_fake, mate, semafor, coref, kbp +#, entitylink stanford.ssplit.newlineIsSentenceBreak = two diff --git a/pikes-raid/pom.xml b/pikes-raid/pom.xml index 00b8a89d..1a597455 100644 --- a/pikes-raid/pom.xml +++ b/pikes-raid/pom.xml @@ -66,13 +66,20 @@ edu.stanford.nlp stanford-corenlp - 4.5.5 + ${corenlp-version} + + edu.stanford.nlp + stanford-corenlp + models + ${corenlp-version} + runtime + edu.stanford.nlp stanford-corenlp - models - 4.5.5 + models-english-kbp + ${corenlp-version} runtime diff --git a/pikes-tintop/pom.xml b/pikes-tintop/pom.xml index 8f2a818b..b6f1fc60 100644 --- a/pikes-tintop/pom.xml +++ b/pikes-tintop/pom.xml @@ -47,6 +47,7 @@ edu.stanford.nlp stanford-corenlp + ${corenlp-version} @@ -57,7 +58,14 @@ edu.stanford.nlp stanford-corenlp models - + ${corenlp-version} + runtime + + + edu.stanford.nlp + stanford-corenlp + models-english-kbp + ${corenlp-version} runtime From 2d0bc626428d97bf40f4cd9029a06d9673f7a615 Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Tue, 14 Nov 2023 11:55:03 +0000 Subject: [PATCH 46/48] Older version of xml-apis --- pikes-raid/pom.xml | 2 +- pikes-rdf/pom.xml | 2 +- pikes-resources/pom.xml | 2 +- pikes-tintop/pom.xml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/pikes-raid/pom.xml b/pikes-raid/pom.xml index 1a597455..44e8028e 100644 --- a/pikes-raid/pom.xml +++ b/pikes-raid/pom.xml @@ -101,7 +101,7 @@ xml-apis xml-apis - 2.0.2 + 1.4.01 ch.qos.logback diff --git a/pikes-rdf/pom.xml b/pikes-rdf/pom.xml index e60755ba..49fb16ce 100644 --- a/pikes-rdf/pom.xml +++ b/pikes-rdf/pom.xml @@ -126,7 +126,7 @@ xml-apis xml-apis - 2.0.2 + 1.4.01 diff --git a/pikes-resources/pom.xml b/pikes-resources/pom.xml index 4bfcea11..1ca98d07 100644 --- a/pikes-resources/pom.xml +++ b/pikes-resources/pom.xml @@ -113,7 +113,7 @@ xml-apis xml-apis - 2.0.2 + 1.4.01 org.slf4j diff --git a/pikes-tintop/pom.xml b/pikes-tintop/pom.xml index b6f1fc60..aaca5d23 100644 --- a/pikes-tintop/pom.xml +++ b/pikes-tintop/pom.xml @@ -103,7 +103,7 @@ xml-apis xml-apis - 2.0.2 + 1.4.01 ch.qos.logback From 1a1156c8927d1db73a2f4ba1832e95b26667825b Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Tue, 14 Nov 2023 12:51:35 +0000 Subject: [PATCH 47/48] Correct DBPedia API Url --- build.sh | 1 + config-pikes.prop | 15 ++++++--------- 2 files changed, 7 insertions(+), 9 deletions(-) diff --git a/build.sh b/build.sh index 7f0e7684..ec5bc5ae 100755 --- a/build.sh +++ b/build.sh @@ -17,6 +17,7 @@ git clone https://github.com/fbk/utils \ && cd ../.. \ && git clone https://github.com/fbk/fcw \ && cd fcw \ + && grep -rl "http://model.dbpedia-spotlight.org/en" . | xargs sed -i 's/http:\/\/model.dbpedia-spotlight.org\/en/https:\/\/api.dbpedia-spotlight.org\/en/g' \ && git checkout develop \ && mvn versions:set -DnewVersion=1.0-SNAPSHOT \ && mvn clean install -DskipTests -Dgpg.skip \ diff --git a/config-pikes.prop b/config-pikes.prop index e5a71bca..02beaef2 100644 --- a/config-pikes.prop +++ b/config-pikes.prop @@ -1,8 +1,8 @@ -stanford.dbps.annotator = dbpedia-annotate -stanford.dbps.address = http://api.dbpedia-spotlight.org -stanford.dbps.min_confidence = 0.0 -stanford.dbps.first_confidence = 0.5 -stanford.dbps.extract_types = 0 +stanford.customAnnotatorClass.dbps.annotator = dbpedia-annotate +stanford.customAnnotatorClass.dbps.address = http://api.dbpedia-spotlight.org/en +stanford.customAnnotatorClass.dbps.min_confidence = 0.0 +stanford.customAnnotatorClass.dbps.first_confidence = 0.5 +stanford.customAnnotatorClass.dbps.extract_types = 0 enable_predicate_matrix = 1 enable_naf_filter = 1 @@ -10,10 +10,7 @@ enable_on_filter = 1 max_text_len = 1000000 -#stanford.annotators = tokenize, ssplit, dbps, pos, simple_pos, lemma, ukb, ner_custom, parse, conll_parse, mst_fake, mate, semafor, dcoref -#stanford.annotators = tokenize, ssplit, dbps, pos, simple_pos, lemma, ukb, ner, depparse, conll_parse, mst_fake, mate, semafor, coref -stanford.annotators = tokenize, ssplit, dbps, pos, simple_pos, lemma, ukb, ner, parse, conll_parse, mst_fake, mate, semafor, coref, kbp -#, entitylink +stanford.annotators = tokenize, ssplit, dbps, pos, simple_pos, lemma, ukb, ner, parse, depparse, conll_parse, mst_fake, mate, semafor, dcoref stanford.ssplit.newlineIsSentenceBreak = two From 841449904f9998b6205d191bb60998ec9952ef4d Mon Sep 17 00:00:00 2001 From: Benedikt Heinrichs <49311227+BenediktHeinrichs@users.noreply.github.com> Date: Tue, 14 Nov 2023 13:29:21 +0000 Subject: [PATCH 48/48] Add README --- README.md | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 00000000..69a5c562 --- /dev/null +++ b/README.md @@ -0,0 +1,36 @@ +# Pikes - Knowledge Extraction Suite + +## Overview +Pikes is a Knowledge Extraction Suite designed to process and analyze text data, extracting valuable insights and information. This suite is developed as part of a collaborative effort, showcasing the power of combining various technologies and methodologies in natural language processing and semantic web. + +## Features +- **Text Analysis and Processing:** Pikes is equipped to handle complex text analysis, leveraging advanced natural language processing techniques. +- **Knowledge Extraction:** The suite excels in extracting structured knowledge from unstructured text data. +- **Semantic Web Integration:** Pikes integrates seamlessly with semantic web technologies, enhancing data interoperability and usability. + +## Modules +The Pikes project consists of several modules, each contributing to its robust functionality: +- `pikes-naflib` +- `pikes-resources` +- `pikes-tintop` +- `pikes-raid` +- `pikes-rdf` +- `pikes-tintop-client` + +## Docker + +If you want to run the image, you can execute the following command: + +```sh +docker run -p 8011:8011 ghcr.io/benediktheinrichs/pikes:Docker +``` + +## Development + +You can run the included dev container to get a full dev environment (use a machine with at least 4 cores). + +## License +Pikes is licensed under the [GNU General Public License (GPL) version 3](http://www.gnu.org/licenses/gpl.txt). + +## More Information +For more details about Pikes and its capabilities, please visit the [official website](https://pikes.fbk.eu/).