issues that were discovered during biohackathon 2019 in Paris (!1028) · Merge requests · minerva / core · GitLab

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Merged Piotr Gawron requested to merge wikipathways-issues into master 5 years ago

Dec 16, 2019
- changelog updated · 8a36b4eb
  Piotr Gawron authored 5 years ago
  
  8a36b4eb
- lines in generated layout end on the border (don't go to the center of the element) · 9a835bb3
  Piotr Gawron authored 5 years ago
  
  9a835bb3
- dimension doesn't depend on number of reactions · 50eb0c93
  Piotr Gawron authored 5 years ago
  
  50eb0c93
- simple layout generator provides z-index · 9611bc5e
  Piotr Gawron authored 5 years ago
  
  9611bc5e
- allow to provide z-index only for selected bioentites · 87cb50b0
  Piotr Gawron authored 5 years ago
  
  87cb50b0
- when moving element structural state and modification residue is also moved · 15d88f35
  Piotr Gawron authored 5 years ago
  
  15d88f35
Dec 12, 2019
- moving element moves also central line · 281f5f5a
  Piotr Gawron authored 5 years ago
  
  281f5f5a
- code that verfies if string properties are valid · ecc76e18
  Piotr Gawron authored 5 years ago
  
  ecc76e18
Dec 07, 2019
- ignore invalid biopax references · 870761ea
  Piotr Gawron authored 5 years ago
  
  870761ea
- missing type added · dfbc3953
  Piotr Gawron authored 5 years ago
  
  dfbc3953
- provide warning when trying export of reaction to compartment · 2e96d72a
  Piotr Gawron authored 5 years ago
  
  2e96d72a
- simplify error handling · c5b1dd3e
  Piotr Gawron authored 5 years ago
  
  c5b1dd3e
- provide warning when exporting reaction to compartment instead of exception · 543da80f
  Piotr Gawron authored 5 years ago
  
  543da80f
- test produce less warnings · ae57573b
  Piotr Gawron authored 5 years ago
  
  ae57573b
- handle properly situation when product line for some reason is reversed · 28fd4540
  Piotr Gawron authored 5 years ago
  
  28fd4540
Dec 06, 2019
- proper prefix for kegg.drugs · 4ca58810
  Piotr Gawron authored 5 years ago
  
  4ca58810
- when product start and end on the main interaction chose starting point as the product anchor point · 4b557efc
  Piotr Gawron authored 5 years ago
  
  4b557efc
- import export of unknown type of annotations produce warning, not error · cfd7971b
  Piotr Gawron authored 5 years ago
  
  cfd7971b
- self loops are removed from model · 3f52f470
  Piotr Gawron authored 5 years ago
  
  3f52f470
- element dimension must be positive · 2e7e0f1f
  Piotr Gawron authored 5 years ago
  
  2e7e0f1f
Dec 05, 2019
- export of reaction to compartment doesn't crash · df770df1
  Piotr Gawron authored 5 years ago
  
  df770df1
- reactions to empty complexes are removed together with complexes · b15278eb
  Piotr Gawron authored 5 years ago
  
  b15278eb
- ensembl plants is exported properly · 0f2e2a75
  Piotr Gawron authored 5 years ago
  
  0f2e2a75
- only process lines that are not considered as parts of interactions · 3ac1fbdf
  Piotr Gawron authored 5 years ago
  
  3ac1fbdf
- import from cell designer doesn't round dimension to integer · 51cbcbfc
  Piotr Gawron authored 5 years ago
  
  51cbcbfc
- groups don't have size equal to 0 when there are lines drawn in it · 87923589
  Piotr Gawron authored 5 years ago
  
  87923589
- method for obtainging line bounds · 567b2174
  Piotr Gawron authored 5 years ago
  
  567b2174
- width and height was cast to int but floating number should be used · 0d428510
  Piotr Gawron authored 5 years ago
  
  0d428510
- reverse mapping for wikipathways annotations added · 44c27094
  Piotr Gawron authored 5 years ago
  
  44c27094
Dec 04, 2019
- explicit length limit added in the model · 2da35d98
  Piotr Gawron authored 5 years ago
  
  2da35d98
- layer text length is not restricted to 255 characters · 3f3acc6c
  Piotr Gawron authored 5 years ago
  
  3f3acc6c
- Merge remote-tracking branch 'origin/master' into wikipathways-issues · d7863692
  Piotr Gawron authored 5 years ago
  
  d7863692
- missing mappings · 5a00d1fc
  Piotr Gawron authored 5 years ago
  
  5a00d1fc
- the prefix is unnecessary · 23494d29
  Piotr Gawron authored 5 years ago
  
  23494d29
- prefixes were invalid for chebi and mgd · 62febc32
  Piotr Gawron authored 5 years ago
  
  62febc32
- allow to extend invalid lines · 33110ed0
  Piotr Gawron authored 5 years ago
  
  33110ed0
Dec 03, 2019
- when products starts at beginning of the interaction there was a problem with... · c386853b
  Piotr Gawron authored 5 years ago
  
  when products starts at beginning of the interaction there was a problem with finding connection points
  c386853b
- ignore some shapes in the complexes · f812ed3d
  Piotr Gawron authored 5 years ago
  
  f812ed3d
- putting species in Pathways doesn't break the code · cdadc90d
  Piotr Gawron authored 5 years ago
  
  cdadc90d
- check of group type should be reversed (due to nulls) · 90aea75d
  Piotr Gawron authored 5 years ago
  
  90aea75d
- support for Pathway group added · 08d96b5a
  Piotr Gawron authored 5 years ago
  
  08d96b5a
Nov 29, 2019
- throw warning when there are elements without id (instead of crash) · 82146a40
  Piotr Gawron authored 5 years ago
  
  82146a40
- unused parameter removed · 216ca3d1
  Piotr Gawron authored 5 years ago
  
  216ca3d1
- positions change to mutations and everything else is changed to structural state · e852cdbf
  Piotr Gawron authored 5 years ago
  
  e852cdbf
- improve logging · 5803d5dc
  Piotr Gawron authored 5 years ago
  
  5803d5dc
- support for additional annotataions added: RGD, SPIKE, TTD Drug, ZFIN BioEntity · f8a70f0e
  Piotr Gawron authored 5 years ago
  
  f8a70f0e
- support for LIPID MAPS, NCBI Protein, PATO annotations added · fc5e99ee
  Piotr Gawron authored 5 years ago
  
  fc5e99ee
- support for Intact, Kegg Drug, KNApSAcK annotations added · f5afa709
  Piotr Gawron authored 5 years ago
  
  f5afa709
Nov 28, 2019
- support for GeneDB added · 4815918b
  Piotr Gawron authored 5 years ago
  
  4815918b
- tests for unsupported database types added · 6f65a0ca
  Piotr Gawron authored 5 years ago
  
  6f65a0ca
- support for FlyBase added · b6740311
  Piotr Gawron authored 5 years ago
  
  b6740311
- support for ecogene added · 9dfc59b5
  Piotr Gawron authored 5 years ago
  
  9dfc59b5
- database parsing test refactored · 7fbcb827
  Piotr Gawron authored 5 years ago
  
  7fbcb827
- support for chembl compound and mir mature sequences added · ec0a82fb
  Piotr Gawron authored 5 years ago
  
  ec0a82fb
- support for ChemIDplus annotations added · d72ef91f
  Piotr Gawron authored 5 years ago
  
  d72ef91f