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Graph db#111

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haeussma merged 155 commits intomainPyEED/pyeed:mainfrom graph-dbPyEED/pyeed:graph-dbCopy head branch name to clipboardFeb 7, 2025

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Commits on Oct 11, 2024

• added new implementation

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• defined data graph model

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• renamed pyeed class

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• implemented db connector with respect to neomodel

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• added working uniprot fetcher with db transaction

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Commits on Oct 12, 2024

• refactored requester

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Commits on Oct 13, 2024

• 😵‍💫

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Commits on Oct 14, 2024

• added implementation to calculate embeddings (#94)

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• fixed incorrect vector index size

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Commits on Oct 15, 2024

• renamed project, circumventing import error

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• deleted unused

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Commits on Oct 18, 2024

• reorganzing work and starting with test cases

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• works for uniprot

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• working mapper curretly without sites and regions but mapper works

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• passed site region coding seq tests

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Commits on Oct 19, 2024

• getting dna, works, getting coding sequence withpout connection

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• stable working version with HAS_CODING_SEQUENZE Realtion Ship

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• fixed path error from max, added new logic in region model and relationship for start end

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

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• fixed Site Bug

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Commits on Oct 24, 2024

• Clean stuff (#95)

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• added docs

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• remove old tests added DBChat unit tests

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Commits on Oct 25, 2024

• fixed mypy type problems

  

  Niklas Abraham - INFlux

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• fixed mypy stuff and fixed import of test

  

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• removed ds store

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• Merge branch 'primaryAdapterNCBI' of https://github.com/PyEED/pyeed into primaryAdapterNCBI

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Commits on Oct 26, 2024

• all working

  

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• added cds mapping, but unsure, very work in progres

  

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• big logic mistake in region to dna to protein, added new realtionship ENCODES

  

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• Merge branch 'primaryAdapterNCBI' of github.com:PyEED/pyeed into primaryAdapterNCBI

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Commits on Oct 27, 2024

• changed update logic for proteins are now updated reagrdless

  

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• added align multpairwise, used old code, works, strucutre still in beta

  

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Commits on Oct 28, 2024

• a lot happend, added clustalo, works, added mulpitsequence alignment, and added simple standard numbering allows standrad numbering based on base sequence

  

  Niklas Abraham - INFlux

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• changed fallback value of mol_weight to none

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• Merge branch 'primaryAdapterNCBI' of https://github.com/PyEED/pyeed into primaryAdapterNCBI

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• removed unused imports, added type hints

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Commits on Nov 2, 2024

• update

  

  Niklas Abraham - INFlux

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• Merge branch 'primaryAdapterNCBI' of github.com:PyEED/pyeed into primaryAdapterNCBI

  

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Commits on Nov 10, 2024

• added test.py

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• add pytest-loguru dependency to pyproject.toml

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• simplified sorting and enhanced patterns

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• - moved alignment logic and interaction of pairwise aligner into scope of PairwiseAlignment

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• - moved definition of StrictStructuredNode into own file nodes_and_relations.py

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• add StrictStructuredNode class for enhanced property validation in nodes_and_relations.py

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• formatting

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• formatting

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• - added pyeed db interface to respective align methods

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• add utility function to yield n-sized chunks from a list

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• refactor test_dnafetch.py to comment out unproductive tests

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Commits on Nov 11, 2024

• fixed naming of dna fetching with protein nucletidoe id, fixed model bug constarins

  

  Niklas Abraham - INFlux

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• fixed nest bug, and removed HAS_CODINGSEQUENCE realtionship, all runs now with encodes, start and end added in protei node

  

  Niklas Abraham - INFlux

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• working standard numerbing with clustalo and db connection

  

  Niklas Abraham - INFlux

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• removed old clustal o function

  

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• naming

  

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Commits on Nov 19, 2024

• updated model diagram

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• sorted imports

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Commits on Nov 25, 2024

• fixed standard numbering external tool

  

  Niklas Abraham - INFlux

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• Merge branch 'primaryAdapterNCBI' of github.com:PyEED/pyeed into primaryAdapterNCBI

  

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• Merge pull request #96 from PyEED/primaryAdapterNCBI

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Commits on Nov 27, 2024

• Implementation of blast search

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Commits on Nov 29, 2024

• imporrting OWL and adding in description

  

  Niklas Abraham - INFlux

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• include custom realtionships

  

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• added labels and synonym

  

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Commits on Nov 30, 2024

• onotlogy works

  

  Niklas Abraham - INFlux

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• Merge pull request #105 from PyEED/97-owl-file-including-and-loading-in-db

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• added embedding tools, analsis

  

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Commits on Dec 1, 2024

• chnage in model.py for multplte mutaions

  

  Niklas Abraham - INFlux

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Commits on Dec 6, 2024

• fixing bugs in blast

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• added big visualziation lotter for TSNE

  

  Niklas Abraham - INFlux

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Commits on Dec 8, 2024

• fixed bug

  

  Niklas Abraham - INFlux

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Commits on Dec 11, 2024

• blast works for local NCBI db

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• deleted blast_search in analysis

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Commits on Dec 12, 2024

• fixed pandas output format

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• working blast with mydb and with ncbi local blast

  

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• Merge pull request #108 from PyEED/blast-search

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Commits on Dec 13, 2024

• fixed standard numbering model and fixed standard numbering

  

  Niklas Abraham - INFlux

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Commits on Dec 14, 2024

• added mutational detection and fixed standardnumerbing

  

  Niklas Abraham - INFlux

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Commits on Dec 16, 2024

• smaller corrections in a few places

  

  Niklas Abraham - INFlux

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Commits on Dec 17, 2024

• include RHEA in uniprot mapper

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• fixed catalytic activity mapper

  alacheim

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• Merge branch 'graph-db' into uniprot_mapper

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• Merge pull request #109 from PyEED/uniprot_mapper

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Commits on Dec 22, 2024

• added plotting function

  

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• added uasge examples

  

  Niklas Abraham - INFlux

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• Merge pull request #110 from PyEED/100-add-features-for-mutation-detection-in-dna-and-proteins

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• test works

  

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Commits on Dec 23, 2024

• Delete logging.conf

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• feature update

  

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• Merge pull request #118 from PyEED/113-embedding-analysis-has-to-have-non-mean-polling-features-jans-code-ideas

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Commits on Dec 28, 2024

• added standard numbering counting from 0.0 to 0.1, added new standadn numbering based on pairwise alignment

  

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• Merge pull request #120 from PyEED/112-implement-new-way-of-standardnumbering-based-on-pairwise-alingment

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Commits on Jan 5, 2025

• added easycluster to mmseqs- still doesn't work

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Commits on Jan 9, 2025

• added simple network_analysis works just like before

  

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Commits on Jan 13, 2025

• added final touches and finished

  

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• Merge pull request #121 from PyEED/115-network-feaures-to-build-the-new-networks-1

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• added some type hints, removed unused code, and parameterized plotting method

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Commits on Jan 14, 2025

• Added return function. Easy clustering works

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• Datamodel for Clusters

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Commits on Jan 16, 2025

• fixed to small bugs

  

  Niklas Abraham - INFlux

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• fixed docstrings

  

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• Merge pull request #122 from PyEED/merge_fix_niklas

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Commits on Jan 18, 2025

• fixed missing types and docstrings

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Commits on Jan 19, 2025

• added types

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• fixed bugs and added docstirng and type

  

  Niklas Abraham - INFlux

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

  

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• added simple embedding example as well as mutation, fixed types and stuff

  

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Commits on Jan 20, 2025

• changed ontologie setup and mutations analysis example as well as network analyssis

  

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• proposed solution

  

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Commits on Jan 22, 2025

• Refactor of docker serices and tools (#125)

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• fixed pyproject.toml

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• removed redefinition of free_memory

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• added missing dep for esm and resolved numpy verison conflict

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• changed debug level for service url change message

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• added type annotations

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• cleaned notebooks

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• added docker-compose

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• added debug statements

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• added notebooks to docs

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• enabled site search

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Commits on Jan 28, 2025

• fixed lint errors

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• fixed linther issues

  

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

  

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• added ignores to liter issues

  

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• bug fix in embeddings search

  

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• fixed imports

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• added missing mypy dev dependency, remove incorrect line length config

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• fixed linting errors

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Commits on Feb 1, 2025

• added docker blast start command with a new storage space

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• fixed bug in embedding calcualtions

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Commits on Feb 2, 2025

• update

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Commits on Feb 6, 2025

• update in vector index serach fro embeddings

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Commits on Feb 7, 2025

• fixed enabling of non qunatization measures, bette recall

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• Fix adapter linting (#136)

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• niklas doing update becasue clusatlo is broken

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

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• Fix network linting (#137)

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• Fix network linting (#138)

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• fixed mutations notebook and with it fixed the standardnumbering type errors

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• Merge branch 'niklas_fixes_2' into 116-alpha-score-implemntation-and-alpha-fold-implmeted-as-tools

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• Merge pull request #139 from PyEED/116-alpha-score-implemntation-and-alpha-fold-implmeted-as-tools

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• Merge branch 'niklas_fixes_2' of github.com:PyEED/pyeed into niklas_fixes_2

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• docs and linter issues in starandardnumbering and embeddings nalysis

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• Merge branch 'graph-db' into niklas_fixes_2

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• Merge pull request #140 from PyEED/niklas_fixes_2

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• fixed typo in dict

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• fix for ontology loading

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• removed embedding section

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• moved example ids from notebook to file

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• removed meaningless sections

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• fixed log config

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• removed unecessary sections

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• fixed logging

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• Refactor network analysis and logging methods

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• added dummy huggingface token for pytests

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