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2021-11-19Replace guix environment with guix shell.Arun Isaac
* README.md, guix.scm: Replace guix environment with guix shell.
2021-11-19Do not recommend GUIX_PACKAGE_PATH.Arun Isaac
* guix.scm: Do not recommend GUIX_PACKAGE_PATH.
2021-11-19Remove gemma specific instructions from guix.scm.Arun Isaac
* guix.scm: Remove gemma specific instructions.
2021-11-19Sort inputs in package definition.Arun Isaac
* guix.scm (genenetwork3)[propagated-inputs]: Sort.
2021-11-19Remove duplicated python-plotly dependency.Arun Isaac
* guix.scm (genenetwork3)[propagated-inputs]: Remove python-plotly.
2021-11-16Remove sqlalchemy.Arun Isaac
* gn3/settings.py (SQLALCHEMY_TRACK_MODIFICATIONS): Delete variable. * guix.scm (genenetwork3)[propagated-inputs]: Remove python-sqlalchemy-stubs. * setup.py: Remove sqlalchemy-stubs from install_requires.
2021-11-10Remove repeated input python-flask-cors.Arun Isaac
* guix.scm (genenetwork3)[propagated-inputs]: Remove python-flask-cors.
2021-11-10Indent guix.scm use-modules better.Arun Isaac
* guix.scm: Indent use-modules better, the more conventional way.
2021-11-10Set version to 0.1.0.Arun Isaac
Semantic versioning begins at 0.1.0, not 0.0.1. * guix.scm: Set genenetwork package version to 0.1.0.
2021-11-10Name source checkout in the store.Arun Isaac
* guix.scm: Name source checkout in the store to "genenetwork3-checkout".
2021-11-10Use git-predicate in guix.scm.Arun Isaac
* guix.scm: Do not import (srfi srfi-1), (srfi srfi-26), (ice-9 match), (ice-9 popen) and (ice-9 rdelim). Use git-predicate instead of git-file?. (git-file?): Delete function.
2021-10-29Feature/biweight reimplementation (#47)Alexander Kabui
* add biweight reimplementation with pingouin * delete biweight scripts and tests * add python-pingouin to guix file * delete biweight paths * mypy fix:pingouin mising imports * pep8 formatting && pylint fixes
2021-10-25add flask-socketio input to gn3Alexander Kabui
2021-10-06guix.scm: Add python-flask-cors and python-plotly dependenciesBonfaceKilz
2021-09-27fix merge conflictsAlexander Kabui
2021-09-23add rjson dependencyAlexander Kabui
2021-09-22add required wgcna dependencies to guix.scmAlexander Kabui
2021-09-20Enable Cross-Origin Resource SharingFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/api/heatmaps.py: Fix bugs in data parsing * gn3/app.py: enable CORS * gn3/settings.py: add flask-cors configurations * guix.scm: Add flask-cors dependency For easier testing of the heatmaps generation feature, this commit activates the cross-origin resource sharing for all "localhost" origins.
2021-09-15remove golang package causing build failureAlexander Kabui
2021-08-26Update imported module nameMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * guix.scm: (gn packages golang) ==> (gnu packages golang) csvdiff has moved to upstream guix and been removed from latest guix-bioinformatics.
2021-08-26Add rust-qtlreaperMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * guix.scm: new dependency (rust-qtlreaper)
2021-08-18Initialise heatmap generation moduleMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/heatmaps/heatmaps.py: Initialise the module with some code to be used to test out plotly features on the command-line. * guix.scm: Add `python-plotly` and `python-pandas` as dependencies.
2021-08-12Initialise heatmap generation moduleMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/heatmaps/heatmaps.py: Initialise the module with some code to be used to test out plotly features on the command-line. * guix.scm: Add `python-plotly` and `python-pandas` as dependencies.
2021-08-07Add gunicorn support for productionPjotr Prins
2021-08-07Update info on running guix containerPjotr Prins
2021-08-03guix.scm: Add csvdiff as a propagated inputBonfaceKilz
2021-06-29guix: Add diffutils as a propagated inputBonfaceKilz
2021-06-29guix: Remove commented out hunkBonfaceKilz
2021-06-20fix conflictAlexander Kabui
2021-06-16add r-wgna packageAlexander Kabui
2021-06-16add r_testthatpackageAlexander Kabui
2021-05-19Add r-optparse to guix.scmPjotr Prins
2021-05-19Added R and r-qtlPjotr Prins
2021-05-10guix.scm: Add missing comma in propagated-inputBonfaceKilz
2021-05-08guix.scm: Add python-numpy and python-requestsBonfaceKilz
2021-05-08Add python-mysqlclient as a dependencyBonfaceKilz
2021-04-12Integrate correlation APIAlexander Kabui
- add new api for gn2-gn3 sample r integration - delete map for sample list to values - add db util file - add python msql-client dependency - add db for fetching lit correlation results - add unittests for db utils - add tests for db_utils - modify api for fetching lit correlation results - refactor Mock Database Connector and unittests - add sql url parser - add SQL URI env variable - refactor code for db utils - modify return data for lit correlation - refactor tissue correlation endpoint - replace db_instance with conn
2021-03-23guix.scm: Add missing moduleBonfaceKilz
2021-03-17guix.scm: Add ipfs-httpclient & sqlalchemy-stubs and sort the inputsBonfaceKilz
2021-03-16delete unwanted correlation stuff (#5)Alexander Kabui
* delete unwanted correlation stuff * Refactor/clean up correlations (#4) * initial commit for Refactor/clean-up-correlation * add python scipy dependency * initial commit for sample correlation * initial commit for sample correlation endpoint * initial commit for integration and unittest * initial commit for registering correlation blueprint * add and modify unittest and integration tests for correlation * Add compute compute_all_sample_corr method for correlation * add scipy to requirement txt file * add tissue correlation for trait list * add unittest for tissue correlation * add lit correlation for trait list * add unittests for lit correlation for trait list * modify lit correlarion for trait list * add unittests for lit correlation for trait list * add correlation metho in dynamic url * add file format for expected structure input while doing sample correlation * modify input data structure -> add trait id * update tests for sample r correlation * add compute all lit correlation method * add endpoint for computing lit_corr * add unit and integration tests for computing lit corr * add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation * add unittest and integration tests for tissue correlation Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com> * update guix scm file * fix pylint error for correlations api Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>
2021-03-16Refactor/clean up correlations (#4)Alexander Kabui
* initial commit for Refactor/clean-up-correlation * add python scipy dependency * initial commit for sample correlation * initial commit for sample correlation endpoint * initial commit for integration and unittest * initial commit for registering correlation blueprint * add and modify unittest and integration tests for correlation * Add compute compute_all_sample_corr method for correlation * add scipy to requirement txt file * add tissue correlation for trait list * add unittest for tissue correlation * add lit correlation for trait list * add unittests for lit correlation for trait list * modify lit correlarion for trait list * add unittests for lit correlation for trait list * add correlation metho in dynamic url * add file format for expected structure input while doing sample correlation * modify input data structure -> add trait id * update tests for sample r correlation * add compute all lit correlation method * add endpoint for computing lit_corr * add unit and integration tests for computing lit corr * add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation * add unittest and integration tests for tissue correlation Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>
2021-03-15Add sqlalchemy-stubs as a requirementBonfaceKilz
2021-03-13Correlation api (#2)Alexander Kabui
* add file for correlation api * register initial correlation api * add correlation package * add function for getting page data * delete loading page api * modify code for correlation * add tests folder for correlations * fix error in correlation api * add tests for correlation * add tests for correlation loading data * add module for correlation computations * modify api to return json when computing correlation * add tests for computing correlation * modify code for loading correlation data * modify tests for correlation computation * test loading correlation data using api endpoint * add tests for asserting error in creating Correlation object * add do correlation method * add dummy tests for do_correlation method * delete unused modules * add tests for creating trait and dataset * add intergration test for correlation api * add tests for correlation api * edit docorrelation method * modify integration tests for correlation api * modify tests for show_corr_results * add create dataset function * pep8 formatting and fix return value for api * add more test data for doing correlation * modify tests for correlation * pep8 formatting * add getting formatted corr type method * import json library add process samples method for correlation * fix issue with sample_vals key_error * create utility module for correlation * refactor endpoint for /corr_compute * add test and mocks for compute_correlation function * add compute correlation function and pep8 formatting * move get genofile samplelist to utility module * refactor code for CorrelationResults object * pep8 formatting for module * remove CorrelationResults from Api * add base package initialize data_set module with create_dataset,redis and Dataset_Getter * set dataset_structure if redis is empty * add callable for DatsetType * add set_dataset_key method If name is not in the object's dataset dictionary * add Dataset object and MrnaAssayDataSet * add db_tools * add mysql client * add DatasetGroup object * add species module * get mapping method * import helper functions and new dataset * add connection to db before request * add helper functions * add logger module * add get_group_samplelists module * add logger for debug * add code for adding sample_data * pep8 formatting * Add chunks module * add correlation helper module * add get_sample_r_and_p_values method add get_header_fields function * add generate corr json method * add function to retrieve_trait_info * remove comments and clean up code in show_corr_results * remove comments and clean up code for data_set module * pep8 formatting for helper_functions module * pep8 formatting for trait module * add module for species * add Temp Dataset Object * add Phenotype Dataset * add Genotype Dataset * add rettrieve sample_sample_data method * add webqtlUtil module * add do lit correlation for all traits * add webqtlCaseData:Settings not ported * return the_trait for create trait method * add correlation_test json data * add tests fore show corr results * add dictfier package * add tests for show_corr_results * add assertion for trait_id * refactor code for show_corr_results * add test file for compute_corr intergration tests * add scipy dependency * refactor show_corr_results object add do lit correlation for trait_list * add hmac module * add bunch module:Dictionary using object notation * add correlation functions * add rpy2 dependency * add hmac module * add MrnaAssayTissueData object and get_symbol_values_pairs function * add config module * add get json_results method * pep8 formatting remove comments * add config file * add db package * refactor correlatio compuatation module * add do tissue correlation for trait list * add do lit correlation for all traits * add do tissue correlation for all traits * add do_bicor for bicor method * raise error for when initital start vars is None * add support for both form and json data when for correlation input * remove print statement and pep8 formatting * add default settings file * add tools module for locate_ignore_error * refactor code remove comments for trait module * Add new test data for computing correlation * pep8 formatting and use pickle * refactor function for filtering form/json data * remove unused imports * remove mock functions in correlation_utility module * refactor tests for compute correlation and pep8 formatting * add tests for show_correlation results * modify tests for show_corr_results * add json files for tests * pep8 formatting for show_corr_results * Todo:Lint base files * pylint for intergration tests * add test module for test_corr_helpers * Add test chunk module * lint utility package * refactoring and pep8 formatting * implement simple metric for correlation * add hmac utility file * add correlation prefix * fix merge conflict * minor fixes for endpoints * import:python-scipy,python-sqlalchemy from guix * add python mysqlclient * remove pkg-resources from requirements * add python-rpy3 from guix * refactor code for species module * pep8 formatting and refactor code * add tests for genereating correlation results * lint correlation functions * fix failing tests for show_corr_results * add new correlation test data fix errors * fix issues related to getting group samplelists * refactor intergration tests for correlation * add todo for refactoring_wanted_inputs * replace custom Attribute setter with SimpleNamespace * comparison of sample r correlation results btwn genenenetwork2 and genenetwork3 * delete AttributeSetter * test request for /api/correlation/compute_correlation took 18.55710196495056 Seconds * refactor tests and show_correlation results * remove unneccessary comments and print statements * edit requirement txt file * api/correlation took 114.29814600944519 Seconds for correlation resullts:20000 - corr-type:lit - corr-method:pearson corr-dataset:corr_dataset:HC_M2_0606_P * capture SQL_URI and GENENETWORK FILES path * pep8 formatting edit && remove print statements * delete filter_input function update test and data for correlation * add docstring for required correlation_input * /api/correlation took 12.905632972717285 Seconds * pearson * lit *dataset:HX_M2_0606_P trait_id :1444666 p_range:(lower->-0.60,uppper->0.74) corr_return_results: 100 * update integration and unittest for correlation * add simple markdown docs for correlation * update docs * add tests and catch for invalid correlation_input * minor fix for api * Remove jupyter from deps * guix.scm: Remove duplicate entry * guix.scm: Add extra action items as comments * Trim requirements.txt file Co-authored-by: BonfaceKilz <me@bonfacemunyoki.com>
2021-03-08guix.scm: Add jupyter depsBonfaceKilz
2021-02-17Add gemma-wrapperBonfaceKilz
* guix.scm: New package propagated-input. * README.md: Mention that you require "guix-bioinformatics" package, because of the addition of "gemma-wrapper".
2021-02-16Add python-bcrypt as a dependencyBonfaceKilz
* guix.scm: Add python-bcrypt. * requirements.txt: Ditto.
2021-02-15Add genenetwork3 package definitionBonfaceKilz
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