Graph db #111

NiklasAbraham · 2024-12-22T13:07:28Z

@haeussma please confirm

…onship for start end

* added support for remote aura neo instance * fixed types * cleaned docs, added natural language query method `chat`

…nto primaryAdapterNCBI

… ENCODES

Merge fix niklas

…tuff

…work analyssis

* added linting on pr * refactored blast service - docker and pyeed side, added test database * refactored clustal * removed in-file dev example

haeussma and others added 30 commits October 11, 2024 14:12

added new implementation

febfaf8

defined data graph model

46708db

renamed pyeed class

4eed2ae

implemented db connector with respect to neomodel

ba25ea3

added working uniprot fetcher with db transaction

e4430d2

refactored requester

ac9a9d0

😵‍💫

a1857d8

added implementation to calculate embeddings (#94)

1336942

fixed incorrect vector index size

0ff07a5

renamed project, circumventing import error

b4b9501

deleted unused

c67e5df

reorganzing work and starting with test cases

eac2373

works for uniprot

f459d57

working mapper curretly without sites and regions but mapper works

6c28472

passed site region coding seq tests

9436f94

getting dna, works, getting coding sequence withpout connection

67a5ac1

stable working version with HAS_CODING_SEQUENZE Realtion Ship

6086fbe

fixed path error from max, added new logic in region model and relati…

9a442f2

…onship for start end

fixed site Bug, and changed model relationship for site as with region

a466efd

fixed Site Bug

0783cbf

Clean stuff (#95)

da9957c

* added support for remote aura neo instance * fixed types * cleaned docs, added natural language query method `chat`

added docs

08def2b

remove old tests added DBChat unit tests

4e4500e

fixed mypy type problems

cd71389

fixed mypy stuff and fixed import of test

c252201

removed ds store

4c51d45

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

alacheim and others added 30 commits January 14, 2025 08:08

Datamodel for Clusters

61a189e

fixed to small bugs

9e171e2

fixed docstrings

110fe4c

Merge pull request #122 from PyEED/merge_fix_niklas

e53d5e6

Merge fix niklas

fixed missing types and docstrings

9e31cdb

added types

a154261

fixed bugs and added docstirng and type

467c18f

Merge branch 'graph-db' of github.com:PyEED/pyeed into graph-db

80f2350

added simple embedding example as well as mutation, fixed types and s…

319ec63

…tuff

changed ontologie setup and mutations analysis example as well as net…

18d657b

…work analyssis

proposed solution

e3de042

Refactor of docker serices and tools (#125)

72da3fd

* added linting on pr * refactored blast service - docker and pyeed side, added test database * refactored clustal * removed in-file dev example

fixed pyproject.toml

f77ce85

removed redefinition of free_memory

cf1b23c

added missing dep for esm and resolved numpy verison conflict

94ffe66

changed debug level for service url change message

bab02f5

added type annotations

3c79938

cleaned notebooks

6bbed34

added docker-compose

c8e8547

added debug statements

fe42386

added notebooks to docs

421594a

enabled site search

6911c7a

fixed lint errors

77c34b1

fixed linther issues

3375dfe

Merge branch 'graph-db' of github.com:PyEED/pyeed into graph-db

25b640d

added ignores to liter issues

f68141c

bug fix in embeddings search

eb2abad

fixed imports

e31fc30

added missing mypy dev dependency, remove incorrect line length config

f434ed9

fixed linting errors

3185acc

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Graph db #111

Graph db #111

NiklasAbraham commented Dec 22, 2024

Graph db #111

Are you sure you want to change the base?

Graph db #111

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NiklasAbraham commented Dec 22, 2024