Clustal api #75
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Clustal api #75
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…equest errorsated example
haeussma
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May 13, 2024
* Refactored dm, added ontology terms * added example and generated lib * refactored dm * added dependencies * updated data model * enabled api generation * . * API update * added correct branch * . * corrected brach * API update * regenereated lib with ontology support from pyeed==0.2.2 * API update * Squashed commit of the following: commit 3b5495c Author: Niklas Abraham <lord.voldemort1492@gmail.com> Date: Fri Apr 19 13:47:02 2024 +0200 test commit 7e141b5 Author: Niklas Abraham <lord.voldemort1492@gmail.com> Date: Tue Apr 16 09:55:53 2024 +0200 added packages and cytoscape kinda works commit eab8b01 Author: Niklas Abraham <lord.voldemort1492@gmail.com> Date: Sun Apr 14 22:20:43 2024 +0200 kina works but aint pretty commit 6e0d42a Author: Niklas Abraham <lord.voldemort1492@gmail.com> Date: Sat Apr 13 12:11:15 2024 +0200 adding edges from list commit 4768b5c Author: Niklas Abraham <lord.voldemort1492@gmail.com> Date: Fri Apr 12 13:10:20 2024 +0200 added average commit 0a2bdf7 Author: Niklas Abraham <lord.voldemort1492@gmail.com> Date: Tue Apr 9 12:59:37 2024 +0200 graphs created within the network.py commit d2837a5 Author: Niklas Abraham <lord.voldemort1492@gmail.com> Date: Tue Apr 9 10:45:13 2024 +0200 added fields commit 67613db Author: Niklas Abraham <lord.voldemort1492@gmail.com> Date: Thu Apr 4 15:01:25 2024 +0200 working on implementing cytoscope in the network, starting with dataframe of alignements * API update * formatted imports * API update * removed unused * specified correct dir for api generation * API update * changed execution event * deleted unused * API update * added correct path * removed wrong lib * API update * 62 refactor mappers of fetcher modules (#66) * API update * removed old lib imports * changed type if taxonomy_id to int * removed deprecated imports * renamed to --> ontology * added ontology resources * started refactoring uniprot mapper * API update --------- Co-authored-by: sdRDM Bot <sdRDM@bot.com> * API update * Refactor `ProteinRecord` #55 (#67) * okay import fixed and fixed proteinRecord Test * working on fixing the fetcher not working but fixed al lot of wrong refences * okay fixeed protein record and test * API update * ruff is happy now with the test * API update * all work with simple test * API update * fix circular import * API update * move `ProteinRecord` into functions * move `ProteinRecord` into functions * added test to detect circular imports * API update * enabled tests upon PR * API update * use `psycopg2-binary` to prevent missing bins * API update * API update * all in working order * working on the pairwise alignment structres, sigle should work, not using the Aglinment object * aligment seems to start working, first simple tests are running * working aligner tests, all inorder * at least working import all functinaly broken in network * changed aligner and changed the test the id is now inculded, better for overview and better for network * API update * all with general network run fine * added good alignment test with real data * fixed potenial error with diffrence in parralel naming seq1 or se2 and floating error * simple cytoscope graph cretaed and works * running network create and working threshhold * added degree calculations, node size, node color * API update --------- Co-authored-by: Niklas Abraham <lord.voldemort1492@gmail.com> Co-authored-by: sdRDM Bot <sdRDM@bot.com> Co-authored-by: Jan Range <range.jan@web.de> * API update * Refactor sequence alignment #63 (#70) * okay import fixed and fixed proteinRecord Test * working on fixing the fetcher not working but fixed al lot of wrong refences * okay fixeed protein record and test * API update * ruff is happy now with the test * API update * all work with simple test * API update * fix circular import * API update * move `ProteinRecord` into functions * move `ProteinRecord` into functions * added test to detect circular imports * API update * enabled tests upon PR * API update * use `psycopg2-binary` to prevent missing bins * API update * API update * API update * tests for alignment * API update * fix circular import * remove literals * API update --------- Co-authored-by: Niklas Abraham <lord.voldemort1492@gmail.com> Co-authored-by: sdRDM Bot <sdRDM@bot.com> Co-authored-by: Jan Range <range.jan@web.de> Co-authored-by: Max Häußler <83341109+haeussma@users.noreply.github.com> Co-authored-by: max <max.haeussler@gmail.com> * API update * Add examples (#72) * fixed mapping of proteinmapper * API update --------- Co-authored-by: sdRDM Bot <sdRDM@bot.com> * API update * added new wokring function, inorder to bypass BUG in filter base_url * API update * added packages * API update * added base_url_fixes * API update * Fix basics (#73) * refactored pairwise aligner * API update * renaimed pairwise_aligner in pairwise * tested multipairwise aligner * added docstring * API update --------- Co-authored-by: sdRDM Bot <sdRDM@bot.com> * API update * API update * fixed test runs, some still missing * API update * all update * API update * add new fixes * API update * added new lyout * API update * Update network.py * API update * Refactor alignment notebook to use updated pyeed API and handle API request errorsated example * updated example * cleaned * formatted * implemented abstract tool with clustalo * added docstr * removed deprecated * removed * added tofasta * API update * Clustal api (#75) * Refactor alignment notebook to use updated pyeed API and handle API request errorsated example * updated example * cleaned * formatted * implemented abstract tool with clustalo * added docstr * removed deprecated * removed * added tofasta * API update --------- Co-authored-by: sdRDM Bot <sdRDM@bot.com> * API update * removed deprecated * cleaing * API update * API update * fixed service link * API update * updated docs * API update * added docs --------- Co-authored-by: sdRDM Bot <sdRDM@bot.com> Co-authored-by: Niklas Abraham <lord.voldemort1492@gmail.com> Co-authored-by: Jan Range <range.jan@web.de> Co-authored-by: Alina Lacheim <149413087+alacheim@users.noreply.github.com> Co-authored-by: NiklasAbraham <st184432@stud.uni-stuttgart.de>
haeussma
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that referenced
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Jun 21, 2024
* Refactor alignment notebook to use updated pyeed API and handle API request errorsated example * updated example * cleaned * formatted * implemented abstract tool with clustalo * added docstr * removed deprecated * removed * added tofasta * API update --------- Co-authored-by: sdRDM Bot <sdRDM@bot.com>
haeussma
added a commit
that referenced
this pull request
Jun 21, 2024
* Refactored dm, added ontology terms * added example and generated lib * refactored dm * added dependencies * updated data model * enabled api generation * . * API update * added correct branch * . * corrected brach * API update * regenereated lib with ontology support from pyeed==0.2.2 * API update * Squashed commit of the following: commit 3b5495c Author: Niklas Abraham <lord.voldemort1492@gmail.com> Date: Fri Apr 19 13:47:02 2024 +0200 test commit 7e141b5 Author: Niklas Abraham <lord.voldemort1492@gmail.com> Date: Tue Apr 16 09:55:53 2024 +0200 added packages and cytoscape kinda works commit eab8b01 Author: Niklas Abraham <lord.voldemort1492@gmail.com> Date: Sun Apr 14 22:20:43 2024 +0200 kina works but aint pretty commit 6e0d42a Author: Niklas Abraham <lord.voldemort1492@gmail.com> Date: Sat Apr 13 12:11:15 2024 +0200 adding edges from list commit 4768b5c Author: Niklas Abraham <lord.voldemort1492@gmail.com> Date: Fri Apr 12 13:10:20 2024 +0200 added average commit 0a2bdf7 Author: Niklas Abraham <lord.voldemort1492@gmail.com> Date: Tue Apr 9 12:59:37 2024 +0200 graphs created within the network.py commit d2837a5 Author: Niklas Abraham <lord.voldemort1492@gmail.com> Date: Tue Apr 9 10:45:13 2024 +0200 added fields commit 67613db Author: Niklas Abraham <lord.voldemort1492@gmail.com> Date: Thu Apr 4 15:01:25 2024 +0200 working on implementing cytoscope in the network, starting with dataframe of alignements * API update * formatted imports * API update * removed unused * specified correct dir for api generation * API update * changed execution event * deleted unused * API update * added correct path * removed wrong lib * API update * 62 refactor mappers of fetcher modules (#66) * API update * removed old lib imports * changed type if taxonomy_id to int * removed deprecated imports * renamed to --> ontology * added ontology resources * started refactoring uniprot mapper * API update --------- Co-authored-by: sdRDM Bot <sdRDM@bot.com> * API update * Refactor `ProteinRecord` #55 (#67) * okay import fixed and fixed proteinRecord Test * working on fixing the fetcher not working but fixed al lot of wrong refences * okay fixeed protein record and test * API update * ruff is happy now with the test * API update * all work with simple test * API update * fix circular import * API update * move `ProteinRecord` into functions * move `ProteinRecord` into functions * added test to detect circular imports * API update * enabled tests upon PR * API update * use `psycopg2-binary` to prevent missing bins * API update * API update * all in working order * working on the pairwise alignment structres, sigle should work, not using the Aglinment object * aligment seems to start working, first simple tests are running * working aligner tests, all inorder * at least working import all functinaly broken in network * changed aligner and changed the test the id is now inculded, better for overview and better for network * API update * all with general network run fine * added good alignment test with real data * fixed potenial error with diffrence in parralel naming seq1 or se2 and floating error * simple cytoscope graph cretaed and works * running network create and working threshhold * added degree calculations, node size, node color * API update --------- Co-authored-by: Niklas Abraham <lord.voldemort1492@gmail.com> Co-authored-by: sdRDM Bot <sdRDM@bot.com> Co-authored-by: Jan Range <range.jan@web.de> * API update * Refactor sequence alignment #63 (#70) * okay import fixed and fixed proteinRecord Test * working on fixing the fetcher not working but fixed al lot of wrong refences * okay fixeed protein record and test * API update * ruff is happy now with the test * API update * all work with simple test * API update * fix circular import * API update * move `ProteinRecord` into functions * move `ProteinRecord` into functions * added test to detect circular imports * API update * enabled tests upon PR * API update * use `psycopg2-binary` to prevent missing bins * API update * API update * API update * tests for alignment * API update * fix circular import * remove literals * API update --------- Co-authored-by: Niklas Abraham <lord.voldemort1492@gmail.com> Co-authored-by: sdRDM Bot <sdRDM@bot.com> Co-authored-by: Jan Range <range.jan@web.de> Co-authored-by: Max Häußler <83341109+haeussma@users.noreply.github.com> Co-authored-by: max <max.haeussler@gmail.com> * API update * Add examples (#72) * fixed mapping of proteinmapper * API update --------- Co-authored-by: sdRDM Bot <sdRDM@bot.com> * API update * added new wokring function, inorder to bypass BUG in filter base_url * API update * added packages * API update * added base_url_fixes * API update * Fix basics (#73) * refactored pairwise aligner * API update * renaimed pairwise_aligner in pairwise * tested multipairwise aligner * added docstring * API update --------- Co-authored-by: sdRDM Bot <sdRDM@bot.com> * API update * API update * fixed test runs, some still missing * API update * all update * API update * add new fixes * API update * added new lyout * API update * Update network.py * API update * Refactor alignment notebook to use updated pyeed API and handle API request errorsated example * updated example * cleaned * formatted * implemented abstract tool with clustalo * added docstr * removed deprecated * removed * added tofasta * API update * Clustal api (#75) * Refactor alignment notebook to use updated pyeed API and handle API request errorsated example * updated example * cleaned * formatted * implemented abstract tool with clustalo * added docstr * removed deprecated * removed * added tofasta * API update --------- Co-authored-by: sdRDM Bot <sdRDM@bot.com> * API update * removed deprecated * cleaing * API update * API update * fixed service link * API update * updated docs * API update * added docs --------- Co-authored-by: sdRDM Bot <sdRDM@bot.com> Co-authored-by: Niklas Abraham <lord.voldemort1492@gmail.com> Co-authored-by: Jan Range <range.jan@web.de> Co-authored-by: Alina Lacheim <149413087+alacheim@users.noreply.github.com> Co-authored-by: NiklasAbraham <st184432@stud.uni-stuttgart.de>
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External tools require now docker service hosting REST endpoints for tools (e.g. clustalo)