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MassBank / MassBank-data

Official repository of open data MassBank records
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Unable to run MassBank validation: Missing MassBank-lib-0.0.1-SNAPSHOT-jar-with-dependencies.jar #135

Closed MaliRemorker closed 4 years ago

MaliRemorker commented 4 years ago

After successfully running maven build per README instructions, we encountered two issues.

Firstly, cloning the repository as,

git clone --depth 1 -q https://github.com/MassBank/MassBank-web.git .scripts/MassBank-web

is not going to fetch the validation scripts. One needs to download the scripts from here, https://github.com/MassBank/MassBank-data/tree/main/.scripts

This is not clear from the README, someone should change this.

Secondly, the validation.sh calls test.sh which calls

$DIR/MassBank-web/MassBank-Project/MassBank-lib/target/MassBank-lib-0.0.1-SNAPSHOT-jar-with-dependencies.jar

After executing the build command suggested in the README, this is the content of the target subdirectory,

user@host:~/scratch/sources$ ls .scripts/MassBank-web/MassBank-Project/MassBank-lib/target/
MassBank-lib            archive-tmp  generated-sources  maven-status
MassBank-lib-2.1.5.jar  classes      maven-archiver

The SNAPSHOT file has clearly not have been built.

Are we doing something wrong?

Notes

Maven and Java

user@host:~$ mvn -v
Apache Maven 3.6.1 (guix_build; 1970-01-01T01:00:00+01:00)
Maven home: [censored]
Java version: 11.0.8, vendor: Ubuntu, runtime: /usr/lib/jvm/java-11-openjdk-amd64
Default locale: en, platform encoding: UTF-8
OS name: "linux", version: "4.15.0-1087-oem", arch: "amd64", family: "unix"
MaliRemorker commented 4 years ago

@schymane @anjuraj15 for your info

meier-rene commented 4 years ago

That's a test on my machine starting in an empty directory listing all commands: git clone git@github.com:MassBank/MassBank-data.git -> a MassBank-data repo is created cd MassBank-data/ git clone --depth 1 https://github.com/MassBank/MassBank-web.git .scripts/MassBank-web -> this should create a directory .scripts/MassBank-web in your MassBank-data repo mvn -f .scripts/MassBank-web/MassBank-Project/MassBank-lib/pom.xml install ./.scripts/validate.sh AAFC -> no errors, successful validation

I see that there are some minor problems in the docs, because they were written from the perspective of the MassBank-data repo and now they should be more general because they moved to a separate documentation repo. Please check which step does not work in your place.

MaliRemorker commented 4 years ago

Thank you!