| Age | Commit message (Expand) | Author |
|---|
| 2021-11-19 | Replace guix environment with guix shell....* README.md, guix.scm: Replace guix environment with guix shell.
| Arun Isaac |
| 2021-11-19 | Do not recommend GUIX_PACKAGE_PATH....* guix.scm: Do not recommend GUIX_PACKAGE_PATH.
| Arun Isaac |
| 2021-11-19 | Remove gemma specific instructions from guix.scm....* guix.scm: Remove gemma specific instructions.
| Arun Isaac |
| 2021-11-19 | Sort inputs in package definition....* guix.scm (genenetwork3)[propagated-inputs]: Sort.
| Arun Isaac |
| 2021-11-19 | Remove duplicated python-plotly dependency....* guix.scm (genenetwork3)[propagated-inputs]: Remove python-plotly.
| Arun Isaac |
| 2021-11-16 | Remove sqlalchemy....* 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.
| Arun Isaac |
| 2021-11-10 | Remove repeated input python-flask-cors....* guix.scm (genenetwork3)[propagated-inputs]: Remove python-flask-cors.
| Arun Isaac |
| 2021-11-10 | Indent guix.scm use-modules better....* guix.scm: Indent use-modules better, the more conventional way.
| Arun Isaac |
| 2021-11-10 | Set version to 0.1.0....Semantic versioning begins at 0.1.0, not 0.0.1.
* guix.scm: Set genenetwork package version to 0.1.0.
| Arun Isaac |
| 2021-11-10 | Name source checkout in the store....* guix.scm: Name source checkout in the store to "genenetwork3-checkout".
| Arun Isaac |
| 2021-11-10 | Use git-predicate in guix.scm....* 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.
| Arun Isaac |
| 2021-10-29 | Feature/biweight reimplementation (#47)...* 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 | Alexander Kabui |
| 2021-10-25 | add flask-socketio input to gn3 | Alexander Kabui |
| 2021-10-06 | guix.scm: Add python-flask-cors and python-plotly dependencies | BonfaceKilz |
| 2021-09-27 | fix merge conflicts | Alexander Kabui |
| 2021-09-23 | add rjson dependency | Alexander Kabui |
| 2021-09-22 | add required wgcna dependencies to guix.scm | Alexander Kabui |
| 2021-09-20 | Enable Cross-Origin Resource Sharing...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.
| Frederick Muriuki Muriithi |
| 2021-09-15 | remove golang package causing build failure | Alexander Kabui |
| 2021-08-26 | Update imported module name...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.
| Muriithi Frederick Muriuki |
| 2021-08-26 | Add rust-qtlreaper...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* guix.scm: new dependency (rust-qtlreaper)
| Muriithi Frederick Muriuki |
| 2021-08-18 | Initialise heatmap generation module...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.
| Muriithi Frederick Muriuki |
| 2021-08-12 | Initialise heatmap generation module...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.
| Muriithi Frederick Muriuki |
| 2021-08-07 | Add gunicorn support for production | Pjotr Prins |
| 2021-08-07 | Update info on running guix container | Pjotr Prins |
| 2021-08-03 | guix.scm: Add csvdiff as a propagated input | BonfaceKilz |
| 2021-06-29 | guix: Add diffutils as a propagated input | BonfaceKilz |
| 2021-06-29 | guix: Remove commented out hunk | BonfaceKilz |
| 2021-06-20 | fix conflict | Alexander Kabui |
| 2021-06-16 | add r-wgna package | Alexander Kabui |
| 2021-06-16 | add r_testthatpackage | Alexander Kabui |
| 2021-05-19 | Add r-optparse to guix.scm | Pjotr Prins |
| 2021-05-19 | Added R and r-qtl | Pjotr Prins |
| 2021-05-10 | guix.scm: Add missing comma in propagated-input | BonfaceKilz |
| 2021-05-08 | guix.scm: Add python-numpy and python-requests | BonfaceKilz |
| 2021-05-08 | Add python-mysqlclient as a dependency | BonfaceKilz |
| 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 |
| 2021-03-23 | guix.scm: Add missing module | BonfaceKilz |
| 2021-03-17 | guix.scm: Add ipfs-httpclient & sqlalchemy-stubs and sort the inputs | 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 | Add sqlalchemy-stubs as a requirement | 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 |
| 2021-03-08 | guix.scm: Add jupyter deps | BonfaceKilz |
| 2021-02-17 | Add gemma-wrapper...* guix.scm: New package propagated-input.
* README.md: Mention that you require "guix-bioinformatics" package, because
of the addition of "gemma-wrapper".
| BonfaceKilz |
| 2021-02-16 | Add python-bcrypt as a dependency...* guix.scm: Add python-bcrypt.
* requirements.txt: Ditto.
| BonfaceKilz |
| 2021-02-15 | Add genenetwork3 package definition | BonfaceKilz |
