Schmoho

I am also having the "unable to follow journal" "Timeout expired" issue. It applies to all my journald scrapers and thereby fully undermines confidence in journald scraping. [Here](https://github.com/grafana/loki/blob/main/clients/pkg/promtail/targets/journal/journaltarget.go#L208) is the...

While this is not as straightforward, please note that the latest database dumps can still be obtained. They have been baked into the images available [here](https://hub.docker.com/r/mephenor/bigg_docker/tags) (thanks to user _mephenor_)....

It seems like this requirements file is at least suitable for running the setup and load_db scripts. [requirements.txt](https://github.com/SBRG/cobradb/files/8854638/requirements.txt)

If I am not mistaken the ModelPolisher just draws this from AnnotateDB, right? [See here](https://github.com/draeger-lab/ModelPolisher/blob/master/src/main/java/edu/ucsd/sbrg/db/AnnotateDB.java#L81): this is called via ```BiGGAnnotation::setCVTermResources BiGGAnnotation::annotateSpecies BiGGAnnotation::annotateListOfSpecies BiGGAnnotation::annotate(Model) BiGGAnnotation::annotate(SBMLDocument) ModelPolisher::polish(SBMLDocument ...) ``` If so, and...

@NantiaL I'll close this for now then

I just realized this is also an issue with the data in BiGG too, so this issue is very much unresolved anyways. [see here](http://bigg.ucsd.edu/universal/metabolites/10fthfglu__L)

I could not reproduce this behaviour using the current state of the 2.1 branch, however I am not quite certain at what point it has been changed/fixed. I'll add the...

Here is the relevant test: https://github.com/draeger-lab/ModelPolisher/blob/113b46764b2df15a0333e6a1244fa1215cee7c39/lib/src/test/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGSpeciesAnnotatorTest.java#L233

In the end, the strict attribute is set on the model according to this inference. I guess the idea might be to allow to set strictness where possible - I...

Unfortunately, I could not get the JSBML Validator to work properly. I have, preliminarily, implemented this as a Predicate here: https://github.com/draeger-lab/ModelPolisher/blob/master/lib/src/main/java/de/uni_halle/informatik/biodata/mp/polishing/ext/fbc/StrictnessPredicate.java So I will close this issue