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Graph db #111

Merged
merged 155 commits into from
Feb 7, 2025
Merged

Graph db #111

merged 155 commits into from
Feb 7, 2025

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NiklasAbraham
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@haeussma please confirm

haeussma and others added 30 commits October 11, 2024 14:12
@haeussma
added new implementation
febfaf8
@haeussma
defined data graph model
46708db
@haeussma
renamed pyeed class
4eed2ae
@haeussma
implemented db connector with respect to neomodel
ba25ea3
@haeussma
added working uniprot fetcher with db transaction
e4430d2
@haeussma
refactored requester
ac9a9d0
@haeussma
😵‍💫
a1857d8
@haeussma
added implementation to calculate embeddings (#94)
1336942
@haeussma
fixed incorrect vector index size
0ff07a5
@haeussma
renamed project, circumventing import error
b4b9501
@haeussma
deleted unused
c67e5df
@NiklasAbraham
reorganzing work and starting with test cases
eac2373
@NiklasAbraham
works for uniprot
f459d57
@NiklasAbraham
working mapper curretly without sites and regions but mapper works
6c28472
@NiklasAbraham
passed site region coding seq tests
9436f94
@NiklasAbraham
getting dna, works, getting coding sequence withpout connection
67a5ac1
@NiklasAbraham
stable working version with HAS_CODING_SEQUENZE Realtion Ship
6086fbe
@NiklasAbraham
fixed path error from max, added new logic in region model and relati…
9a442f2 
…onship for start end
@NiklasAbraham
fixed site Bug, and changed model relationship for site as with region
a466efd
@NiklasAbraham
fixed Site Bug
0783cbf
@haeussma
Clean stuff (#95)
da9957c 
* added support for remote aura neo instance

* fixed types

* cleaned docs, added natural language query method `chat`
@haeussma
added docs
08def2b
@haeussma
remove old tests added DBChat unit tests
4e4500e
fixed mypy type problems
cd71389
fixed mypy stuff and fixed import of test
c252201
@haeussma
removed ds store
4c51d45
@haeussma
Merge branch 'primaryAdapterNCBI' of https://github.com/PyEED/pyeed i…
5240f6c 
…nto primaryAdapterNCBI
all working
cd90bf5
added cds mapping, but unsure, very work in progres
66b94f2
big logic mistake in region to dna to protein, added new realtionship…
dd29d9f 
… ENCODES
NiklasAbraham and others added 27 commits February 1, 2025 11:20
@NiklasAbraham
added docker blast start command with a new storage space
56c7c66
@NiklasAbraham
fixed bug in embedding calcualtions
b9fd6eb
@NiklasAbraham
update
df109a5
@NiklasAbraham
update in vector index serach fro embeddings
b1af7e6
@NiklasAbraham
fixed enabling of non qunatization measures, bette recall
7d6143e
@haeussma
Fix adapter linting (#136)
ca67dd9 
* refactored fetchers

* added fetch response test data

* fixed blast service url issue
@NiklasAbraham
niklas doing update becasue clusatlo is broken
87a77d9
@NiklasAbraham
Merge branch 'graph-db' of github.com:PyEED/pyeed into graph-db
1016428
@haeussma
Fix network linting (#137)
d30090b 
* refactored fetchers

* added fetch response test data

* fixed blast service url issue

* type hints
@haeussma
Fix network linting (#138)
9c714e7 
* refactored fetchers

* added fetch response test data

* fixed blast service url issue

* type hints
@NiklasAbraham
fixed mutations notebook and with it fixed the standardnumbering type…
1170194 
… errors
@NiklasAbraham
Merge branch 'niklas_fixes_2' into 116-alpha-score-implemntation-and-…
7906fb1 
…alpha-fold-implmeted-as-tools
@NiklasAbraham
Merge pull request #139 from PyEED/116-alpha-score-implemntation-and-…
1c2cc26 
…alpha-fold-implmeted-as-tools

116 alpha score implemntation and alpha fold implmeted as tools
@NiklasAbraham
Merge branch 'niklas_fixes_2' of github.com:PyEED/pyeed into niklas_f…
d5e1374 
…ixes_2
@NiklasAbraham
docs and linter issues in starandardnumbering and embeddings nalysis
6afc93b
@NiklasAbraham
Merge branch 'graph-db' into niklas_fixes_2
f45cf42
@NiklasAbraham
Merge pull request #140 from PyEED/niklas_fixes_2
4046634 
Niklas fixes 2
@NiklasAbraham
fixed typo in dict
bf551b6
@NiklasAbraham
fix for ontology loading
e452980
@haeussma
removed embedding section
f84c0db
@haeussma
moved example ids from notebook to file
440c8c3
@haeussma
removed meaningless sections
76728fa
@haeussma
fixed log config
b54ccb8
@haeussma
removed unecessary sections
7b7c67d
@haeussma
fixed logging
c201544
@haeussma
Refactor network analysis and logging methods
e44b7f4 
- Changed molecular weight logging from warning to debug in ncbi_protein_mapper
- Updated network analysis methods to improve variable naming and return types
- Removed unused placeholder methods in NetworkAnalysis class
@haeussma
added dummy huggingface token for pytests
d8603d5
@haeussma haeussma merged commit f718a27 into main Feb 7, 2025
7 checks passed
@haeussma haeussma deleted the graph-db branch February 7, 2025 17:22
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3 participants
@NiklasAbraham @haeussma @alacheim