| Age | Commit message (Expand) | Author |
|---|
| 2021-09-16 | pass user input to call script | Alexander Kabui |
| 2021-09-16 | add initial endpoint for wgcna | Alexander Kabui |
| 2021-08-18 | Fix obvious linting errors...* Fix linting errors that do not change the function of the code.
| Muriithi Frederick Muriuki |
| 2021-08-11 | use normal function for correlation (#34)...* use normal function for correlation + rename functions
* update test for sample correlation
* use normal function for tissue correlation + rename functions | Alexander Kabui |
| 2021-08-07 | Add gunicorn support for production | Pjotr Prins |
| 2021-06-18 | Fixed pylint issues | zsloan |
| 2021-06-18 | Fixed issue where all bool kwargs were always being passed to generate_rqtl_c... | zsloan |
| 2021-05-25 | Include code that processes rqtl output files and returns actual results inst... | zsloan |
| 2021-05-18 | Account for boolean kwargs in compute() by storing them in a list, since they... | zsloan |
| 2021-05-18 | Fixed variety of issues detected by pylint | zsloan |
| 2021-05-17 | Read in kwargs fromrequest and pass the command, tmpdir, and kwargs to genera... | zsloan |
| 2021-05-17 | Add rqtl.py for rqtl endpoints | zsloan |
| 2021-05-13 | Add end-point for running an rQTL program...* gn3/api/general.py (run_r_qtl): New function.
* gn3/settings.py: New variable.
| BonfaceKilz |
| 2021-05-13 | Rename file_utils to fs_helpers...Generally avoid naming things with a "utils" prefix/ suffix since it
encourages contributors to dump any new functions there; and over time, as the
code grows, things get messy...
| BonfaceKilz |
| 2021-05-08 | Fix pep-8 errors | BonfaceKilz |
| 2021-05-08 | Add endpoints for (batch) entering phenotypes and genotypes | BonfaceKilz |
| 2021-05-02 | delete dataset and trait files | Alexander Kabui |
| 2021-04-16 | benchmark normal function for sample r | Alexander Kabui |
| 2021-04-15 | optimization for sample correlation | Alexander Kabui |
| 2021-04-15 | test endpoint for fetching probeset data types | Alexander Kabui |
| 2021-04-12 | replace experimental db | Alexander Kabui |
| 2021-04-12 | fix merge conflict | Alexander Kabui |
| 2021-04-12 | Integrate correlation API...- 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 | Alexander Kabui |
| 2021-04-06 | fix Docstrings | Alexander Kabui |
| 2021-04-06 | delete unnecessary functions and comments | Alexander Kabui |
| 2021-04-05 | fix for fetching dataset traits data | Alexander Kabui |
| 2021-04-04 | refactor code for trait data...modify unittest and integration tests for datasets
| Alexander Kabui |
| 2021-03-31 | add fetch dataset strain id,strain name and unittests | Alexander Kabui |
| 2021-03-31 | add temp_db setup and integration tests | Alexander Kabui |
| 2021-03-30 | refactor retrieve trait sample data and tests | Alexander Kabui |
| 2021-03-30 | initial commit for creating dataset | Alexander Kabui |
| 2021-03-23 | Use ipfs to get genotype files | BonfaceKilz |
| 2021-03-23 | Apply auto-pep8 formatting | BonfaceKilz |
| 2021-03-16 | delete unwanted correlation stuff (#5)...* 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> | Alexander Kabui |
| 2021-03-16 | 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> | Alexander Kabui |
| 2021-03-15 | Apply pep-8 formatting | BonfaceKilz |
| 2021-03-13 | Correlation api (#2)...* 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> | Alexander Kabui |
| 2021-03-10 | Rename "covariates" to "covars" in endpoints for consistency | BonfaceKilz |
| 2021-03-10 | Add extra endpoint for when TOKEN isn't provided | BonfaceKilz |
| 2021-03-08 | Remove unused imports | BonfaceKilz |
| 2021-03-08 | Remove "/k-gwa-computation" | BonfaceKilz |
| 2021-03-08 | Add "/k-gwa-compute/covars/loco/<chromosomes>/maf/<maf>/<token>"...Reviewed-by: BonfaceKilz <me@bonfacemunyoki.com>
| BonfaceKilz |
| 2021-03-08 | Add "/gemma/k-gwa-compute/loco/<chromosomes>/maf/<maf>/<token>" | BonfaceKilz |
| 2021-03-08 | Add "/k-gwa-compute/covars/<token>" | BonfaceKilz |
| 2021-03-08 | Add "/gemma/k-gwa-compute/<token>" | BonfaceKilz |
| 2021-03-08 | Replace "compute_k_values" with "generate_gemma_cmd" | BonfaceKilz |
| 2021-03-08 | Use new "compute_k_values" procedure | BonfaceKilz |
| 2021-03-08 | Add generic fn for computing k and gwa values | BonfaceKilz |
| 2021-03-08 | Apply pep-8 formatting...Began using elpy's format code fn
| BonfaceKilz |
| 2021-03-08 | Add new endpoint..."/gwa-compute/<k_filename>/loco/covariates/maf/<maf>/<token>"
| BonfaceKilz |
