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2021-05-08Add extra genotype test fileBonfaceKilz
* tests/unit/test_data/genotype.txt: New file. * tests/unit/test_file_utils.py: Update failing test.
2021-05-03minor fixes for tiss correlation tests and namingAlexander Kabui
2021-05-03replace database with connAlexander Kabui
2021-05-02delete dataset and trait filesAlexander Kabui
2021-04-18refactor:return trait_name in corr_resultsAlexander Kabui
2021-04-17ad pep8 formattingAlexander Kabui
2021-04-17refactor tests for litAlexander Kabui
2021-04-15optimization for sample correlationAlexander Kabui
2021-04-12fix tests for lit correlationAlexander Kabui
2021-04-12fix merge conflictAlexander Kabui
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
2021-04-06fix DocstringsAlexander Kabui
2021-04-06delete unnecessary functions and commentsAlexander Kabui
2021-04-05fix for fetching dataset traits dataAlexander Kabui
2021-04-04refactor code for trait dataAlexander Kabui
modify unittest and integration tests for datasets
2021-04-03add tests for getting trait dataAlexander Kabui
2021-03-31add fetch dataset strain id,strain name and unittestsAlexander Kabui
2021-03-31add datasets functions and endpointsAlexander Kabui
2021-03-30refactor retrieve trait sample data and testsAlexander Kabui
2021-03-30modify getting sample data from dbAlexander Kabui
2021-03-30initial commit for creating datasetAlexander Kabui
2021-03-30initial commit for creating trait and datasetsAlexander Kabui
2021-03-23Convert Path object to a strBonfaceKilz
* gn3/file_utils.py (cache_ipfs_file): Return a str instead of a path object. * tests/unit/test_file_utils.py: Update failing tests.
2021-03-23Add function to cache ipfs filesBonfaceKilz
2021-03-23Apply autopep-8BonfaceKilz
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>
2021-03-13Correlation 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>
2021-03-10Fix k-compute command when "loco" is trueBonfaceKilz
2021-03-10Update test to ensure redis.hset is called correctlyBonfaceKilz
2021-03-10Apply yapf file formatting to fileBonfaceKilz
2021-03-10Add extra tests for file utilsBonfaceKilz
In test server, files were not extracted properly. This test exposes the bug.
2021-03-10Run yapf-formatter against fileBonfaceKilz
2021-03-08Delete "generate_gemma_computation_cmd"BonfaceKilz
2021-03-08Replace "compute_k_values" with "generate_gemma_cmd"BonfaceKilz
2021-03-08Add generic fn for computing k and gwa valuesBonfaceKilz
2021-03-08Apply pep-8 formattingBonfaceKilz
Began using elpy's format code fn
2021-03-08bug: Put a space between gemma-wrapper argsBonfaceKilz
2021-03-08Delete "lookup_file" procedureBonfaceKilz
2021-03-08Extract files to "/TMPDIR/TOKEN"BonfaceKilz
TOKEN is the user token * gn3/file_utils.py (extract_uploaded_file): Add extra param "token". If a token is empty, create a new directory based off that token. * tests/unit/test_file_utils.py: Update failing tests.
2021-03-08Fix failing testsBonfaceKilz
2021-03-08Make the name of the redis job queue configurableBonfaceKilz
2021-02-24Create a new helper function for generating k_values and GWABonfaceKilz
2021-02-24Add new procedure that computes the hash of an array of stringsBonfaceKilz
2021-02-24Create a new method for generating a valid phenotype file on the flyBonfaceKilz
2021-02-24Update "compose_gemma_cmd" testsBonfaceKilz
2021-02-16Add procedure for uploading gzipped fileBonfaceKilz
* gn3/file_utils.py (extract_uploaded_file): New procedure. * tests/unit/test_file_utils.py: Test cases for ^^. * tests/unit/upload-data.tar.gz: New test data.
2021-02-16Add extra option to set email when queueing CMDBonfaceKilz
The e-mail field will be used to send the results of the computation when it is completed.
2021-02-16Add new test cases for run_cmdBonfaceKilz
2021-02-12Use sorted list of files when calculating md5sums of directoryBonfaceKilz
* gn3/file_utils.py (get_dir_hash): Sort list of files before calculating their md5sums. * tests/unit/test_file_utils.py (test_get_dir_hash): Update test-case md5sum.
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