Improvements
Databases support (See #4 for stats):
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Rewrite reactions generator to handle classes inheritance -
Rewrite transitions generator -
Handle empty complexes -
Handle classes complexes -
Handle classes in controls (conditions) (PID, Reactome) -
Handle AND/OR relationships for controls (specific of Reactome ? #2) -
Handle multiple controllers (Kegg #3) -
Handle nested controllers (Reactome/CTD #2) -
Handle Controls without controlType attribute -
Fix transfer features/locations in case of conflict (Reactome) (Fixed: will not be implemented) -
Handle nested classes (PID, Reactome) -
Limit duplications in developComplexEntity() (set of components instead of list) -
Check merge of complexes after merge of entities (check unicity on flat_components/primitives once they are replaced?) -
Handle conversionDirection attr of reactions (currently assume LEFT_TO_RIGHT) (PID, Reactome, etc.) (according to the small number of cases and the low interest of supporting reactions other than LEFT_TO_RIGHT (except for Kegg), we just display an alert when loading reactions with different directions) -
Handle cofactors of Catalysis reactions (?) Currently implemented as controllers
, they can/should be added incofactor
attributes. This is currently not supported (should be just added into controllers set). -
Found a way to give up classes in reactions (?) (limitation of combinatory in the final model, combinatorial) -
Cell designer support; See #6 -
Handle BIG models (ctd) => need to rewrite the functions used to export models; see commits taged [cadbiom writer] starting f845a0b8
Documentation & tests:
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Finish doc in reactions.py -
Clean the code in reactions.py -
Add the last cases of tests to the unit tests -
12-> 14 ? -
VirtualCase17 -
VirtualCase18 -
VirtualCase19
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Add the last cases of tests to the doc (examples section) -
VirtualCase17 -
VirtualCase18 -
VirtualCase19
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Update examples section of the doc (update images and comments of old tests) -
Cover the project by unit tests to facilitate bug detection and secure its future maintenance by avoiding regressions -
get_classes_from_reactants() -
develop_complexes() -
update_reactions()
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Roadmap:
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Pre-alpha: Rewrite generator of functions, first re-implementation of the suppression of classes inheritance. -
Alpha: Support of unit and functional tests. -
Beta1: 100% Support of PID -
Beta2: 100% Support of Kegg -
Beta3: 100% Support of Reactome -
Beta4: 100% Support of Cell Designer -
Release Candidate: Doc, tests, major improvements implemented ...
Perpectives:
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See tab format; https://acsn.curie.fr/ACSN2/downloads.html (abandoned) -
See Binom biopax export from sbg-ml: https://en.wikipedia.org/wiki/BioPAX (find cell-designer map and format it to biopax via Binom)
Edited by VIGNET Pierre