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Lotus_bot

This is a Bot for Wikidata. It is used to import the data for the LOTUS and the Wikidata Natural Products Chemistry project

It is written in Kotlin and uses:

Requires Java >=11

Build

Run

Import lotus Data

Replace <> and <> by your users and password. Notice the space in front of that command to not store them in your shell history.

This will run a single entry from the file in test mode:

 export WIKIDATA_USER=<<foo>>
 export WIKIDATA_PASSWORD=<<bar>>
./gradlew :uploadLotus:run --args="../data/validated_referenced_structure_organism_pairs.tsv"

This will run the full file in test mode:

 export WIKIDATA_USER=<<foo>>
 export WIKIDATA_PASSWORD=<<bar>>
./gradlew :uploadLotus:run --args="../data/validated_referenced_structure_organism_pairs.tsv -l -1"

This will run the first line of the file in real mode (you will likely need bot rights to do that:

 export WIKIDATA_USER=<<foo>>
 export WIKIDATA_PASSWORD=<<bar>>
./gradlew :uploadLotus:run --args="../data/validated_referenced_structure_organism_pairs.tsv -r"

If you need to produce a jar file (to use on a different machine for example)

./gradlew build

The distribution will be available in build/distributions (.zip and .tar.gz)

There is work to do to reduce the size of the distribution (use java modules, use only the parts of cdk and rdf4j we are really using).

Allow the creation of new species

This is only for LOTUS developers, please use with caution as it is not perfect yet

export CREATE_SPECIES=yes_and_I_understand_that_I_will_not_complain_if_things_are_wrong

Developers

If you need to upgrade wiki-java

You need to make sure you did a recursive clone of this repository with

git clone --recursive

You can then update the repo and update the jars:

git submodule update
cd external/wiki-java
mvn package  # You need to have maven installed obviously, and this will take some time (2 min on a Ryzen 3700X)
rm ../../libs/wiki-java-*.jar
cp target/wiki-java-*.jar ../../libs

Don't forget to update build.gradle.kts if the version changed.