From d7c28d8b5ddcd6f03d3a15eaa31a5c4ebb833647 Mon Sep 17 00:00:00 2001 From: khituras Date: Sun, 18 Dec 2022 18:02:54 +0100 Subject: [PATCH] Release 2.6.0. Fix deployment script to actually only deploy releases that do not already exist. The problem was that when '.' was deployed, this means the whole project, no matter what the actually new components are. --- .../src/main/resources/LICENSE | 166 ------------------ .../jcore/ae/banner/config/banner_progene.xml | 46 ----- .../jcore-banner-ae-biomedical-english.xml | 81 --------- pom.xml | 1 - scripts/deploy.sh | 65 +++++++ 5 files changed, 65 insertions(+), 294 deletions(-) delete mode 100644 jcore-banner-progene-ae/src/main/resources/LICENSE delete mode 100644 jcore-banner-progene-ae/src/main/resources/de/julielab/jcore/ae/banner/config/banner_progene.xml delete mode 100644 jcore-banner-progene-ae/src/main/resources/de/julielab/jcore/ae/banner/desc/jcore-banner-ae-biomedical-english.xml create mode 100755 scripts/deploy.sh diff --git a/jcore-banner-progene-ae/src/main/resources/LICENSE b/jcore-banner-progene-ae/src/main/resources/LICENSE deleted file mode 100644 index 341c30b..0000000 --- a/jcore-banner-progene-ae/src/main/resources/LICENSE +++ /dev/null @@ -1,166 +0,0 @@ - GNU LESSER GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - - This version of the GNU Lesser General Public License incorporates -the terms and conditions of version 3 of the GNU General Public -License, supplemented by the additional permissions listed below. - - 0. Additional Definitions. - - As used herein, "this License" refers to version 3 of the GNU Lesser -General Public License, and the "GNU GPL" refers to version 3 of the GNU -General Public License. - - "The Library" refers to a covered work governed by this License, -other than an Application or a Combined Work as defined below. - - An "Application" is any work that makes use of an interface provided -by the Library, but which is not otherwise based on the Library. -Defining a subclass of a class defined by the Library is deemed a mode -of using an interface provided by the Library. - - A "Combined Work" is a work produced by combining or linking an -Application with the Library. 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Such new -versions will be similar in spirit to the present version, but may -differ in detail to address new problems or concerns. - - Each version is given a distinguishing version number. If the -Library as you received it specifies that a certain numbered version -of the GNU Lesser General Public License "or any later version" -applies to it, you have the option of following the terms and -conditions either of that published version or of any later version -published by the Free Software Foundation. If the Library as you -received it does not specify a version number of the GNU Lesser -General Public License, you may choose any version of the GNU Lesser -General Public License ever published by the Free Software Foundation. - - If the Library as you received it specifies that a proxy can decide -whether future versions of the GNU Lesser General Public License shall -apply, that proxy's public statement of acceptance of any version is -permanent authorization for you to choose that version for the -Library. - diff --git a/jcore-banner-progene-ae/src/main/resources/de/julielab/jcore/ae/banner/config/banner_progene.xml b/jcore-banner-progene-ae/src/main/resources/de/julielab/jcore/ae/banner/config/banner_progene.xml deleted file mode 100644 index 43c5704..0000000 --- a/jcore-banner-progene-ae/src/main/resources/de/julielab/jcore/ae/banner/config/banner_progene.xml +++ /dev/null @@ -1,46 +0,0 @@ - - - - - de.julielab.jcore.banner.dataset.JCoReEntityDataset - - /var/data/data_corpora/genomics/Genes/banner-tagging/data/conversions/ProGene/progene_sentences.tsv - /var/data/data_corpora/genomics/Genes/banner-tagging/data/conversions/ProGene/progene_genes.tsv - - output/ids.txt - output/raw.txt - output/training.txt - output/output.txt - output/contextAnalysis.html - output/mention.txt - de/julielab/jcore/ae/banner/resources/banner-progene-dictbannerdefaultbin - nlpdata/lemmatiser - nlpdata/tagger - dragon.nlp.tool.HeppleTagger - banner.tokenization.SimpleTokenizer - true - true - true - IOB - 2 - Required - Exception - Exception - banner.tagging.dictionary.DictionaryTagger - - - - - true - false - false - false - true - false - /dict/single.txt - protein - - - - - \ No newline at end of file diff --git a/jcore-banner-progene-ae/src/main/resources/de/julielab/jcore/ae/banner/desc/jcore-banner-ae-biomedical-english.xml b/jcore-banner-progene-ae/src/main/resources/de/julielab/jcore/ae/banner/desc/jcore-banner-ae-biomedical-english.xml deleted file mode 100644 index 196db07..0000000 --- a/jcore-banner-progene-ae/src/main/resources/de/julielab/jcore/ae/banner/desc/jcore-banner-ae-biomedical-english.xml +++ /dev/null @@ -1,81 +0,0 @@ - - - org.apache.uima.java - true - de.julielab.jcore.ae.banner.BANNERAnnotator - - JCoRe BANNER AE for Biomedical English - This component uses the BANNER named entity recognizer with a model trained on the complete (train and test) dataset of the BioCreative II gene mention challenge. - 2.6.0 - - - - ConfigFile - An XML configuration file that does all settings for the BANNER AnalysisEngine. May point - to a regular file or a classpath resource. - - String - false - true - - - TypeMapping - A list of mappings from entity labels to UIMA types in the form <label>=<fully - qualified type name>. If not given, all entities will be realized as EntityMention instances. - - String - true - false - - - - - ConfigFile - - de/julielab/jcore/ae/banner/config/banner_biomed_english.xml - - - - TypeMapping - - - Gene=de.julielab.jcore.types.Gene - - - - - ComponentId - - BANNERAnnotatorProGene - - - - - - - - - - - - - - - - - de.julielab.jcore.types.Sentence - - - de.julielab.jcore.types.Gene - - - - - - true - true - false - - - - \ No newline at end of file diff --git a/pom.xml b/pom.xml index cd08caa..ce2124d 100644 --- a/pom.xml +++ b/pom.xml @@ -51,7 +51,6 @@ jcore-pubmed-db-reader jcore-pubmed-reader jcore-lingscope-negation-ae - jcore-banner-progene-ae jcore-gnormplus-pubmed-db-reader diff --git a/scripts/deploy.sh b/scripts/deploy.sh new file mode 100755 index 0000000..f0efae8 --- /dev/null +++ b/scripts/deploy.sh @@ -0,0 +1,65 @@ +#!/usr/bin/env bash +# This script is useful when the whole project should be deployed but some modules have already +# been deployed with the current version, e.g. due to bug fixes. Then, just deploying the base project +# with all its modules would fail due to the already deployed releases. +# If, however, all versions are newly deployed, just use a mvn deploy command on the project root, +# this is much quicker and also results in a single staging repository in Nexus instead of one project +# for each module. +# An alternative is to do the deployment of the root in any case - even with already deployed modules - and +# remove those modules manually in the Nexus UI from the staging repository. One can open the contents of +# a repository and browse it. With a right click on an item one can select to delete it. + + +echo "Executing deploy" +if [ ! -f julie-xml-tools.jar ]; then + wget https://repo1.maven.org/maven2/de/julielab/julie-xml-tools/0.6.0/julie-xml-tools-0.6.0-xml-tools-assembly.jar --output-document julie-xml-tools.jar +else + echo "julie-xml-tools.jar already exists and is not downloaded." +fi +if [ ! -f julielab-maven-aether-utilities.jar ]; then + wget https://oss.sonatype.org/content/repositories/releases/de/julielab/julielab-maven-aether-utilities/1.1.4/julielab-maven-aether-utilities-1.1.4-cli-assembly.jar --output-document julielab-maven-aether-utilities.jar + else + echo "julielab-maven-aether-utilities.jar already exists and is not downloaded." + fi + + modulestodeploy= + + + echo "Collecting direct child modules of jcore-base and jcore-base itself for deployment" +for i in . `java -jar julie-xml-tools.jar pom.xml //module`; do + java -cp julielab-maven-aether-utilities.jar de.julielab.utilities.aether.apps.GetCoordinatesFromRawPom $i/pom.xml > coords.txt; + if [ ! "$?" -eq "0" ]; then + exit 1 + fi + groupId=`grep 'GROUPID:' coords.txt | sed 's/^GROUPID: //'` + artifactId=`grep 'ARTIFACTID:' coords.txt | sed 's/^ARTIFACTID: //'` + version=`grep 'VERSION:' coords.txt | sed 's/^VERSION: //'` + packaging=`grep 'PACKAGING:' coords.txt | sed 's/^PACKAGING: //'` + artifactFile=$i/target/$artifactId-$version.$packaging + # SNAPSHOTS are deployed always anyway + if [[ ! $version =~ .*SNAPSHOT.* ]]; then + echo "Checking if $groupId:$artifactId:$packaging:$version exists" + csNotFound=`java -cp julielab-maven-aether-utilities.jar de.julielab.utilities.aether.apps.GetRemoteChecksums $groupId:$artifactId:$packaging:$version | grep ''` + fi + if [[ $version =~ .*SNAPSHOT.* ]] || [ "$csNotFound" == "" ]; then + echo "This is a SNAPSHOT or a release that has not yet been deployed. Deploying." + modulestodeploy=$modulestodeploy,$i + fi + done + + + + if [ ! -z "$modulestodeploy" ]; then + echo "Deploying the following projects: $modulestodeploy" + if [[ "${modulestodeploy}" =~ ".," ]]; then + echo "Deploying parent POM" + mvn clean deploy -P sonatype-nexus-deployment -N + modulestodeploy=$(printf '%s\n' "${modulestodeploy//.,/}") + echo "Modules to deploy after removal of parent POM: $modulestodeploy" + else + echo "Parent POM was not included in the deployment list." + fi + mvn clean deploy -B -P sonatype-nexus-deployment -DskipTests=true -pl $modulestodeploy + else + echo "All modules up to date, skipping deployment." + fi