Update createOrganism.py to use python-apollo library for web service calls

[mpoelchau]

Vern discovered that there is a python apollo library (https://pypi.org/project/apollo/), and that it is much better for forming the web service calls to Apollo. He suggested updating createOrganism.py to use this library.

[mpoelchau]

I loaded the data to apollo2-stage, installed the apollo python library, checked out the new refactor branch and ran it with the following command from my mac:

(base) ARSMDBE22WAHMP1:bin mpoelchau$ python3 createOrganism.py -host https://apollo2-stage-node1.nal.usda.gov/apollo -organism Photinus_pyralis -genus Photinus -species pyralis -directory /app/data/other_species/phopyr/Ppyr1.3/jbrowse/data -blatdb /usr/local/blat/db/phopyr/GCF_008802855.1_Ppyr1.3_genomic.fna.2bi -publicMode -token ignore -username secretusername -password secretpassword
Create organism: Organism Photinus_pyralis does not exist
Error Createing Organism 'Photinus_pyralis' see error below:
Apollo Error in function "add_organism":
	-problem saving organism: org.codehaus.groovy.grails.web.converters.exceptions.ConverterException: Error parsing JSON

@g8tor any ideas what's going on?

[mpoelchau]

D'oh, it was the problem with the mal-formatted trackList.json file, totally unrelated... Fixed the tracklist, and the script worked like a charm!

One improvement suggestion - could you update the script so that it automatically appends /apollo to the URL (e.g. the user specifies -host http://localhost:8080, the script turns it into http://localhost:8080/apollo/[webservice function here]. If it's not appropriate here we'll need to update the cwl script to add it, and the documentation of this script to add it.

[mpoelchau]

I'll note for future reference that createOrganism.py/apollo's web services are veeeery particular about the host URL: for our staging server it should be https://apollo2-stage-node1.nal.usda.gov/apollo (NO Backslash at the end!)