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Roadmap: Integrate HaploBlocker into Database objects #23

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josiahseaman opened this issue Aug 13, 2019 · 0 comments
Open

Roadmap: Integrate HaploBlocker into Database objects #23

josiahseaman opened this issue Aug 13, 2019 · 0 comments
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josiahseaman commented Aug 13, 2019 •
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Followup #19.
https://docs.google.com/document/d/1o_IWThHWK4qyyXk3-X4rZ2KJNGTbf-pPCRhzVmnQ1Xg/edit#
Much of haplonetwork.py needs to be rewritten to use Graph.models objects. Strand support could come at the same time or as a separate step.

Haplonetwork.py should use Graph.Node.

  • upstream/downstream compared to Paths
  • Should allow copy number variation in a Node to work inside Haploblocker

What does downstream mean in a graph context?
@josiahseaman josiahseaman added the enhancement New feature or request label Aug 13, 2019
@josiahseaman josiahseaman self-assigned this Aug 13, 2019
@josiahseaman josiahseaman mentioned this issue Aug 13, 2019
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josiahseaman added a commit that referenced this issue Aug 15, 2019
@josiahseaman
#23 WIP: Transitioning all code over to using Django Database and que…
650736e 
…ries in persistent memory. Tests still broken.
josiahseaman added a commit that referenced this issue Aug 15, 2019
@josiahseaman
#23 Use Django test runner which creates a temporary database.
d94bb94
@josiahseaman josiahseaman changed the title Integrate HaploBlocker into Database objects Roadmap: Integrate HaploBlocker into Database objects Aug 15, 2019
josiahseaman added a commit that referenced this issue Aug 15, 2019
@josiahseaman
#23 WIP: Transitioning all code over to using Django Database and que…
3d558b6 
…ries in persistent memory. Tests still broken.
josiahseaman added a commit that referenced this issue Aug 15, 2019
@josiahseaman
#23 Use Django test runner which creates a temporary database.
29b84d2
josiahseaman added a commit that referenced this issue Aug 19, 2019
@josiahseaman
#23 Graph.test.GFATest is migrated to DB versions. All GFATests passing.
40811bd
josiahseaman added a commit that referenced this issue Aug 19, 2019
@josiahseaman
#23 MAJOR: Removed Obsolete Classes: Slice, Graph. Replaced Slices ex…
b891006 
…ample_graph with factory_input.gfa file written by hand. build_from_test_slices() converted for quick test declarations. GraphTest shows GFA file and slices declaration are the same.
josiahseaman added a commit that referenced this issue Aug 20, 2019
@josiahseaman
#23 Testing Travis builds with Django
dbc5d07
josiahseaman added a commit that referenced this issue Aug 20, 2019
@josiahseaman
#23 Testing Travis builds with Django: removed erroneous django_templ…
6dc055c 
…ate mention
josiahseaman added a commit that referenced this issue Aug 20, 2019
@josiahseaman
#23 WIP: First round of conversions moving halponetwork to Graph.Node…
9884ea3 
…. Getters for .specimens, .upstream, .downstream. Now comes the harder work of thinking through the algorithm in database terms.
josiahseaman added a commit that referenced this issue Aug 22, 2019
@josiahseaman
#23 #3 #4 MAJOR: Added Zoom layer concept by giving Path.zoom so Path…
a2bbcef 
…s can visit Nodes from any zoom layer. There is one path per accession per zoom layer. Paths and nodes contain links to their parent/child summaries.
josiahseaman added a commit that referenced this issue Aug 23, 2019
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#23 WIP: Converting Haploblocker, automating transitions simplifies t…
c02b7f1 
…he code. But zoom filtering is becoming cumbersome.
josiahseaman added a commit that referenced this issue Aug 23, 2019
@josiahseaman
#23 ZoomLevel objects, custom create() methods for consistency and co…
52c5c0f 
…nvenience. WIP: Converting all tests and code to database queries. GraphTest now passing.
josiahseaman added a commit that referenced this issue Aug 23, 2019
@josiahseaman
#23 test_export_as_gfa now working with example fast queries for fetc…
005d1d8 
…hing the whole graph.
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