Question: PHG ImputePipelinePlugin `liquibaseDir` and `skipLiquibaseCheck` hardcoded variables only?
0
gravatar for dovi
23 days ago by
dovi60
dovi60 wrote:

Hi everyone,

I was reading the ImputePipelinePlugin.kt file from https://bitbucket.org/bucklerlab/practicalhaplotypegraph/src/master/src/main/kotlin/net/maizegenetics/pangenome/pipeline/ImputePipelinePlugin.kt

There is one step (~ line 123) to check if liquibase is available, however it searches for a hardcoded path var liquibaseDir = "/liquibase/changelogs", I wonder if is there any possibility to set this variable as an input parameter in the configuration file. Moreover, there is another parameter, called val skipLiquibaseCheck = false which is also hardcoded (line 124 of ImputePipelinePlugin.kt file), setting this to true would skip the error if not finding the liquibaseDir.

I wonder why are they hardcoded and if is there any possibility to overwrite them.

Thanks!

phg • 119 views
ADD COMMENTlink modified 13 days ago by lcj3430 • written 23 days ago by dovi60
3
gravatar for lcj34
13 days ago by
lcj3430
lcj3430 wrote:

Regarding the liquibaseDir: This is hardcoded to where liquiBase lives in the docker. If a user is running outside of the docker, they will probably want to skip the liquiBase update as that code expects specific directories.

in terms of the skipLiquibaseCheck value, you are correct - the code should be checking the value of the plugin parameter. I will make a note to change that.

ADD COMMENTlink written 13 days ago by lcj3430
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