Fail to analyze with certain part libraries

[Duncan-Britt]

Using the cryptococcus neoformans Database causes it to crash.

root@3462c3b17772:/workspaces/SeqImprove/apps/server# waitress-serve --port=5001 --call app:create_app
INFO:waitress:Serving on http://0.0.0.0:5001
Initializing the app...
Failed to retrieve data from SynBioHub: 502
./assets/synbict/feature-libraries/Excel2SBOL_collection.xml
./assets/synbict/feature-libraries/CIDAR_MoClo_Extension_Kit_Volume_I_Murray_Lab_collection.xml
./assets/synbict/feature-libraries/sbksactivities_collection.xml
./assets/synbict/feature-libraries/Digitalizer_collection.xml
WARNING:synbict:https://synbiohub.org/public/Digitalizer/Ter/1 not loaded since its DNA sequence was not found
WARNING:synbict:https://synbiohub.org/public/Digitalizer/CDS/1 not loaded since its DNA sequence was not found
WARNING:synbict:https://synbiohub.org/public/Digitalizer/PA1_04s_cassette/1 not loaded since its DNA sequence was not found
./assets/synbict/feature-libraries/EcoFlex_MoClo_Toolkit_Freemont_Lab_collection.xml
./assets/synbict/feature-libraries/Natural_and_Synthetic_Terminators_Voigt_Lab_collection.xml
./assets/synbict/feature-libraries/SBOLCompliantSoftware_collection.xml
./assets/synbict/feature-libraries/CnDatabase_collection.xml
./assets/synbict/feature-libraries/SEGA_collection.xml
./assets/synbict/feature-libraries/Itaconic_Acid_Pathway_Voigt_Lab_collection.xml
./assets/synbict/feature-libraries/Intein_assisted_Bisection_Mapping_collection.xml
./assets/synbict/feature-libraries/cello_library.xml
WARNING:synbict:https://synbiohub.programmingbiology.org/public/Cello_Parts/YFP_reporter/1 not loaded since its DNA sequence was not found
./assets/synbict/feature-libraries/iGEM_2016_interlab_collection.xml
./assets/synbict/feature-libraries/Anderson_Promoters_Anderson_Lab_collection.xml
./assets/synbict/feature-libraries/free_genes_feature_libraries_collection.xml
./assets/synbict/feature-libraries/Pichia_MoClo_Toolkit_Lu_Lab_collection.xml
./assets/synbict/feature-libraries/MoClo_Yeast_Toolkit_Dueber_Lab_collection.xml
./assets/synbict/feature-libraries/CIDAR_MoClo_Toolkit_Densmore_Lab_collection.xml
./assets/synbict/feature-libraries/Eco1C1G1T1_collection.xml
hi
['java', '-jar', 'SynBio2Easy.jar', 'clean', '--input-file=/tmp/tmpwhl8b3q3', '--output-file=/tmp/tmpqlsyn_vo', '--namespace=https://seqimprove.synbiohub.org', '--remove-collections=Y']
   _____                   ____    _           ___  
  / ____|                 |  _ \  (_)         |__ \ 
 | (___    _   _   _ __   | |_) |  _    ___      ) |
  \___ \  | | | | | '_ \  |  _ <  | |  / _ \    / / 
  ____) | | |_| | | | | | | |_) | | | | (_) |  / /_ 
 |_____/   \__, | |_| |_| |____/  |_|  \___/  |____|
            __/ |                                   
           |___/            

  ______                       
 |  ____|                      
 | |__      __ _   ___   _   _ 
 |  __|    / _` | / __| | | | |
 | |____  | (_| | \__ \ | |_| |
 |______|  \__,_| |___/  \__, |
                          __/ |
                         |___/ 

Successfully cleaned SBOL file located at '/tmp/tmpqlsyn_vo'

Running SYNBICT...
Caught exception
'./assets/synbict/feature-libraries/https://synbiohub.org/public/CnDatabase/CnDatabase_collection/1'

[Duncan-Britt]

This appears to happen with other libraries as well. I tried SeqImprove local libraries and that worked.

[Duncan-Britt]

Fixed: https://github.com/MyersResearchGroup/SeqImprove/commit/1dccf50d8b5348314afbdebb83dfda36d63617f4