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2021-06-07gn3: db: Make "WHERE" clause optionalBonfaceKilz
* gn3/db/__init__.py (fetchone): Make "WHERE" an Optional arg.
2021-06-07gn3: db: Use correct DATACLASSMAP entry from metadata_auditBonfaceKilz
2021-06-07gn3: db: sort importsBonfaceKilz
2021-06-03gn3: db: Remove "escape_string" from importsBonfaceKilz
We use prepared statements, so no need to have this.
2021-06-03Use prepared statements for FETCH sql functionBonfaceKilz
2021-06-03gn3: db: Replace items() with keys()BonfaceKilz
* gn3/db/__init__.py (diff_from_dict): We only use the keys of the dict!
2021-06-03Use prepared statements for UPDATE sql functionBonfaceKilz
2021-06-03gn3: db: Add new function for doing sql INSERTBonfaceKilz
2021-06-03Add data structures for the table metadata_auditBonfaceKilz
2021-06-03gn3: db: Add spacing before around "AND" in sql clauseBonfaceKilz
2021-06-03Get the diff between 2 dicts and return that as a dictBonfaceKilz
2021-06-03gn3: db: Return None if data and where are emptyBonfaceKilz
2021-05-26Move the methods, "update" and "fetch", to gn3.dbBonfaceKilz
2021-05-26db: phenotypes: Fix publication_mappingBonfaceKilz
2021-05-26db: phenotypes: Fix typoBonfaceKilz
2021-05-20db: phenotypes: Add function for fetching a single resultBonfaceKilz
* gn3/db/phenotypes.py (fetchone): New function.
2021-05-20db: phenotypes: Add a dataclass mapBonfaceKilz
Maps a string to it's dataclass.
2021-05-20db: phenotypes: Add Publication table mappingBonfaceKilz
2021-05-20db: phenotypes: Rename phenotype_column_mappingBonfaceKilz
2021-05-20db: phenotypes: Add Publication dataclass and mappingBonfaceKilz
2021-05-20db: phenotypes: Generalise the update functionBonfaceKilz
* gn3/db/phenotypes.py (update_phenotype): Delete it. (update): New, more general function.
2021-05-20db: phenotypes: Map a table to it's relevant dict mappingBonfaceKilz
2021-05-20db: phenotypes: Add type for DataclassBonfaceKilz
See: https://www.py4u.net/discuss/188952
2021-05-20db: phenotypes: Put mapping def after dataclassBonfaceKilz
2021-05-20db: phenotypes: Add phenotype table mappingBonfaceKilz
2021-05-20db: phenotypes: Add dataclass to represent PublishXRefBonfaceKilz
2021-05-20db: phenotype: Make "pylint: disable=[R0902]" global for fileBonfaceKilz
2021-05-20db: phenotypes: Add a way of updating the Phenotype tableBonfaceKilz
* gn3/db/phenotypes.py (Phenotype): New dataclass. (update_phenotype): New function. [phenotype_column_mapping]: New variable.
2021-05-10db: species: Add method for fetching all speciesBonfaceKilz
2021-05-08db: species: Fetch chromosomes using a group or species nameBonfaceKilz
* gn3/db/species.py (get_chromosome): New function.
2021-05-08Fix pep-8 errorsBonfaceKilz
2021-05-08db: traits: Add extra method for looking up webqtl datasetsBonfaceKilz
2021-05-08db: traits: Update method for inserting publication methodBonfaceKilz
2021-05-08Add method for inserting publication_dataBonfaceKilz
2021-05-08Add webqtlCaseData DS to keep track of case data in one traitBonfaceKilz
2021-05-08Replace namedtuple with a dataclassBonfaceKilz
2021-05-08Add method for inserting phenotypesBonfaceKilz
2021-05-08Add method for inserting publicationsBonfaceKilz
2021-05-08Add method to fetch riset name and idBonfaceKilz
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>
2021-03-13Correlation 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>
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