From abbf0e1af86ad572276fb43f0800d103bc27b0f8 Mon Sep 17 00:00:00 2001 From: khituras Date: Fri, 21 Oct 2022 16:01:56 +0200 Subject: [PATCH] Update version in README.md. --- gepi/README.md | 25 ++++--------------- .../dependency-reduced-pom.xml | 2 +- .../gepi-indexing-pmc/config/logback.xml | 7 ------ .../JCoRe Database Checkpoint Writer.xml | 2 +- .../JCoRe XMI Database Multiplier Reader.xml | 4 +-- 5 files changed, 9 insertions(+), 31 deletions(-) diff --git a/gepi/README.md b/gepi/README.md index 855309ba..7c1be213 100644 --- a/gepi/README.md +++ b/gepi/README.md @@ -19,8 +19,8 @@ The `production` stage expects that the complete GePI project has been built in Run the following commands to create a `development` container: ```bash -DOCKER_BUILDKIT=1 docker build -t gepi:0.9.0-SNAPSHOT --target development . -docker run -dp 8080:8080 -v {/path/to/gepi/directory}:/var/gepi/dev -e GEPI_CONFIGURATION= gepi:0.9.0-SNAPSHOT +DOCKER_BUILDKIT=1 docker build -t gepi:0.10.0-SNAPSHOT --target development . +docker run -dp 8080:8080 -v {/path/to/gepi/directory}:/var/gepi/dev -e GEPI_CONFIGURATION= gepi:0.10.0-SNAPSHOT ``` The first command builds an image of the `development` stage. This will also build the `dependencies` stage where all the Java dependencies of the GePI application are downloaded and cached. This will take a while on the first execution but should be faster afterwards thanks to caching. @@ -38,8 +38,8 @@ To run the `production` container, run ```bash mvn clean package --projects gepi-webapp --also-make -DOCKER_BUILDKIT=1 docker build -t gepi:0.9.0-SNAPSHOT --target production . -docker run -dp 8080:8080 gepi:0.9.0-SNAPSHOT +DOCKER_BUILDKIT=1 docker build -t gepi:0.10.0-SNAPSHOT --target production . +docker run -dp 8080:8080 gepi:0.10.0-SNAPSHOT ``` These commands @@ -65,19 +65,4 @@ gepi.neo4j.bolt.url=bolt://: ## GePI development -Important note: ***Do not edit the `README.md` file in the module roots*** if there exists a `readme-raw` subdirectory. The file in the root is just a Maven-filtered copy of the `readme-raw/README.md` file. The Maven filtering replaces Maven properties like the project version in the `readme-raw/README.md` file and puts the result in the module root, overriding the previous `README.md` file. - -### Development ElasticSearch - -For development purposes, an ElasticSearch Docker container can be created using the contents of the `gepi-indexing/es-docker` directory. - -In the original development, this container-ES was populated by selecting a random subset of document containing genes from the larger JeDIS database tables of a completely processed PubMed. The CoStoSys subset table for this purpose was called `gepi.dev` which might be found at appropriate places - or not if the last pipeline run was not a development run. The used pipeline was the production `gepi-indexing-pubmed` pipeline with the following adjustments: -* *JCoRe ElasticSearch Consumer* deactivated -* *Gazetteer FamPlex Dictionary* deactivated -* *JCoRe ElasticSearch Consumer Localhost* activated -* *Gazetteer FamPlex Dictionary dev* -* DB XMI reader configured to read from the `gepi.dev` subset table -* `config/costosys.xml` file must use the `DBConnection` called `pmlocalhost` - * this required that the JeDIS database runs at the localhost or there is an SSH tunnel to the database server - -The ES Consumer resources that these components use were the original resources derived from the production Neo4j gene database so that the production database could be used for development. \ No newline at end of file +Important note: ***Do not edit the `README.md` file in the module roots*** if there exists a `readme-raw` subdirectory. The file in the root is just a Maven-filtered copy of the `readme-raw/README.md` file. The Maven filtering replaces Maven properties like the project version in the `readme-raw/README.md` file and puts the result in the module root, overriding the previous `README.md` file. \ No newline at end of file diff --git a/gepi/gepi-concept-database/dependency-reduced-pom.xml b/gepi/gepi-concept-database/dependency-reduced-pom.xml index 4c7aee6d..66d4c7cd 100644 --- a/gepi/gepi-concept-database/dependency-reduced-pom.xml +++ b/gepi/gepi-concept-database/dependency-reduced-pom.xml @@ -3,7 +3,7 @@ gepi de.julielab - 0.9.0-SNAPSHOT + 0.10.0-SNAPSHOT 4.0.0 gepi-concept-database diff --git a/gepi/gepi-indexing/gepi-indexing-pmc/config/logback.xml b/gepi/gepi-indexing/gepi-indexing-pmc/config/logback.xml index 475277ba..5e08ab5a 100644 --- a/gepi/gepi-indexing/gepi-indexing-pmc/config/logback.xml +++ b/gepi/gepi-indexing/gepi-indexing-pmc/config/logback.xml @@ -8,13 +8,6 @@ - - - - - - - diff --git a/gepi/gepi-indexing/gepi-indexing-pmc/descAll/JCoRe Database Checkpoint Writer.xml b/gepi/gepi-indexing/gepi-indexing-pmc/descAll/JCoRe Database Checkpoint Writer.xml index 7d34a9cf..3eb6d5b6 100644 --- a/gepi/gepi-indexing/gepi-indexing-pmc/descAll/JCoRe Database Checkpoint Writer.xml +++ b/gepi/gepi-indexing/gepi-indexing-pmc/descAll/JCoRe Database Checkpoint Writer.xml @@ -97,7 +97,7 @@ - 50 + 5 diff --git a/gepi/gepi-indexing/gepi-indexing-pmc/descAll/JCoRe XMI Database Multiplier Reader.xml b/gepi/gepi-indexing/gepi-indexing-pmc/descAll/JCoRe XMI Database Multiplier Reader.xml index 48c88b12..02b489a5 100644 --- a/gepi/gepi-indexing/gepi-indexing-pmc/descAll/JCoRe XMI Database Multiplier Reader.xml +++ b/gepi/gepi-indexing/gepi-indexing-pmc/descAll/JCoRe XMI Database Multiplier Reader.xml @@ -283,7 +283,7 @@ - false + true @@ -295,7 +295,7 @@ - 50 + 5