Age | Commit message (Expand) | Author |
2021-06-18 | tests: test_phenotypes: New test cases for loading phenotypes | BonfaceKilz |
2021-05-18 | Added test for compose_rqtl_cmd in tests/unit/test_commands.py | zsloan |
2021-05-18 | Added unit test for computations/rqtl.py | zsloan |
2021-05-15 | Merge branch 'main' into feature/minor-fixes | Alexander Kabui |
2021-05-15 | index lit tuple result | Alexander Kabui |
2021-05-13 | tests: test_general: Add test case for run_r_qtl endpoint | 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 |
2021-05-12 | delete unused functions | Alexander Kabui |
2021-05-12 | rename lit_correlation_for_trait_list to lit_correlation_for_trait | Alexander Kabui |
2021-05-12 | rename tissue_correlation_for_trait_list with tissue_correlation_for_trait | Alexander Kabui |
2021-05-12 | rename p_val ro tissue_p_value for tissue_results | Alexander Kabui |
2021-05-10 | tests: test_species: Add test for `get_all_species` | BonfaceKilz |
2021-05-10 | tests: test_gemma: Add TMPDIR to test_client() | BonfaceKilz |
2021-05-08 | Fix typo | BonfaceKilz |
2021-05-08 | tests: test_species: New tests | BonfaceKilz |
2021-05-08 | Add extra procedure for parsing a genotype file...* gn3/computations/parsers.py (parse_genofile): New procedure.
* tests/unit/computations/test_parsers.py: New test files for above.
| BonfaceKilz |
2021-05-08 | Add extra genotype test file...* tests/unit/test_data/genotype.txt: New file.
* tests/unit/test_file_utils.py: Update failing test.
| BonfaceKilz |
2021-05-03 | minor fixes for tiss correlation tests and naming | Alexander Kabui |
2021-05-03 | replace database with conn | Alexander Kabui |
2021-05-02 | delete dataset and trait files | Alexander Kabui |
2021-04-18 | refactor:return trait_name in corr_results | Alexander Kabui |
2021-04-17 | ad pep8 formatting | Alexander Kabui |
2021-04-17 | refactor tests for lit | Alexander Kabui |
2021-04-15 | optimization for sample correlation | Alexander Kabui |
2021-04-12 | fix tests for lit correlation | 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 | add mock db for tests | 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 |
2021-04-03 | add tests for getting trait data | 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 |
2021-03-31 | add datasets functions and endpoints | Alexander Kabui |
2021-03-30 | refactor retrieve trait sample data and tests | Alexander Kabui |
2021-03-30 | modify getting sample data from db | Alexander Kabui |
2021-03-30 | initial commit for creating dataset | Alexander Kabui |
2021-03-30 | initial commit for creating trait and datasets | Alexander Kabui |
2021-03-23 | Convert Path object to a str...* gn3/file_utils.py (cache_ipfs_file): Return a str instead of a path object.
* tests/unit/test_file_utils.py: Update failing tests.
| BonfaceKilz |
2021-03-23 | Use ipfs to get genotype files | BonfaceKilz |
2021-03-23 | Add function to cache ipfs files | BonfaceKilz |
2021-03-23 | Apply autopep-8 | 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 | Add missing "/" in URL in docstring | BonfaceKilz |
2021-03-10 | Rename "covariates" to "covars" in endpoints for consistency | BonfaceKilz |