From 236ca06dc4c84baecb7b090b8724db997a5d988a Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Sat, 13 Mar 2021 13:04:33 +0300 Subject: 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 --- tests/unit/correlation/__init__.py | 0 tests/unit/correlation/correlation_test_data.json | 18 + tests/unit/correlation/dataset.json | 64 + .../correlation/expected_correlation_results.json | 1902 ++++++++++++++++++++ tests/unit/correlation/group_data_test.json | 214 +++ tests/unit/correlation/my_results.json | 388 ++++ .../correlation/test_correlation_computations.py | 65 + tests/unit/correlation/test_show_corr_results.py | 226 +++ tests/unit/utility/__init__.py | 0 tests/unit/utility/test_chunks.py | 19 + tests/unit/utility/test_corr_result_helpers.py | 35 + tests/unit/utility/test_hmac.py | 51 + 12 files changed, 2982 insertions(+) create mode 100644 tests/unit/correlation/__init__.py create mode 100644 tests/unit/correlation/correlation_test_data.json create mode 100644 tests/unit/correlation/dataset.json create mode 100644 tests/unit/correlation/expected_correlation_results.json create mode 100644 tests/unit/correlation/group_data_test.json create mode 100644 tests/unit/correlation/my_results.json create mode 100644 tests/unit/correlation/test_correlation_computations.py create mode 100644 tests/unit/correlation/test_show_corr_results.py create mode 100644 tests/unit/utility/__init__.py create mode 100644 tests/unit/utility/test_chunks.py create mode 100644 tests/unit/utility/test_corr_result_helpers.py create mode 100644 tests/unit/utility/test_hmac.py (limited to 'tests/unit') diff --git a/tests/unit/correlation/__init__.py b/tests/unit/correlation/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/unit/correlation/correlation_test_data.json b/tests/unit/correlation/correlation_test_data.json new file mode 100644 index 0000000..87d24e3 --- /dev/null +++ b/tests/unit/correlation/correlation_test_data.json @@ -0,0 +1,18 @@ +{ + "primary_samples": "C57BL/6J,DBA/2J,B6D2F1,D2B6F1,BXD1,BXD2,BXD5,BXD6,BXD8,BXD9,BXD11,BXD12,BXD13,BXD14,BXD15,BXD16,BXD18,BXD19,BXD20,BXD21,BXD22,BXD23,BXD24,BXD24a,BXD25,BXD27,BXD28,BXD29,BXD30,BXD31,BXD32,BXD33,BXD34,BXD35,BXD36,BXD37,BXD38,BXD39,BXD40,BXD41,BXD42,BXD43,BXD44,BXD45,BXD48,BXD48a,BXD49,BXD50,BXD51,BXD52,BXD53,BXD54,BXD55,BXD56,BXD59,BXD60,BXD61,BXD62,BXD63,BXD64,BXD65,BXD65a,BXD65b,BXD66,BXD67,BXD68,BXD69,BXD70,BXD71,BXD72,BXD73,BXD73a,BXD73b,BXD74,BXD75,BXD76,BXD77,BXD78,BXD79,BXD81,BXD83,BXD84,BXD85,BXD86,BXD87,BXD88,BXD89,BXD90,BXD91,BXD93,BXD94,BXD95,BXD98,BXD99,BXD100,BXD101,BXD102,BXD104,BXD105,BXD106,BXD107,BXD108,BXD109,BXD110,BXD111,BXD112,BXD113,BXD114,BXD115,BXD116,BXD117,BXD119,BXD120,BXD121,BXD122,BXD123,BXD124,BXD125,BXD126,BXD127,BXD128,BXD128a,BXD130,BXD131,BXD132,BXD133,BXD134,BXD135,BXD136,BXD137,BXD138,BXD139,BXD141,BXD142,BXD144,BXD145,BXD146,BXD147,BXD148,BXD149,BXD150,BXD151,BXD152,BXD153,BXD154,BXD155,BXD156,BXD157,BXD160,BXD161,BXD162,BXD165,BXD168,BXD169,BXD170,BXD171,BXD172,BXD173,BXD174,BXD175,BXD176,BXD177,BXD178,BXD180,BXD181,BXD183,BXD184,BXD186,BXD187,BXD188,BXD189,BXD190,BXD191,BXD192,BXD193,BXD194,BXD195,BXD196,BXD197,BXD198,BXD199,BXD200,BXD201,BXD202,BXD203,BXD204,BXD205,BXD206,BXD207,BXD208,BXD209,BXD210,BXD211,BXD212,BXD213,BXD214,BXD215,BXD216,BXD217,BXD218,BXD219,BXD220", + "trait_id": "1444666_at", + "dataset": "HC_M2_0606_P", + "sample_vals": "{\"C57BL/6J\":\"6.638\",\"DBA/2J\":\"6.266\",\"B6D2F1\":\"6.494\",\"D2B6F1\":\"6.565\",\"BXD1\":\"6.357\",\"BXD2\":\"6.456\",\"BXD5\":\"6.590\",\"BXD6\":\"6.568\",\"BXD8\":\"6.581\",\"BXD9\":\"6.322\",\"BXD11\":\"6.519\",\"BXD12\":\"6.543\",\"BXD13\":\"6.636\",\"BXD14\":\"x\",\"BXD15\":\"6.578\",\"BXD16\":\"6.636\",\"BXD18\":\"x\",\"BXD19\":\"6.562\",\"BXD20\":\"6.610\",\"BXD21\":\"6.668\",\"BXD22\":\"6.607\",\"BXD23\":\"6.513\",\"BXD24\":\"6.601\",\"BXD24a\":\"x\",\"BXD25\":\"x\",\"BXD27\":\"6.573\",\"BXD28\":\"6.639\",\"BXD29\":\"6.656\",\"BXD30\":\"x\",\"BXD31\":\"6.549\",\"BXD32\":\"6.502\",\"BXD33\":\"6.584\",\"BXD34\":\"6.261\",\"BXD35\":\"x\",\"BXD36\":\"x\",\"BXD37\":\"x\",\"BXD38\":\"6.646\",\"BXD39\":\"6.584\",\"BXD40\":\"6.790\",\"BXD41\":\"x\",\"BXD42\":\"6.536\",\"BXD43\":\"6.476\",\"BXD44\":\"6.545\",\"BXD45\":\"6.742\",\"BXD48\":\"6.393\",\"BXD48a\":\"6.618\",\"BXD49\":\"x\",\"BXD50\":\"6.496\",\"BXD51\":\"6.494\",\"BXD52\":\"x\",\"BXD53\":\"x\",\"BXD54\":\"x\",\"BXD55\":\"6.263\",\"BXD56\":\"x\",\"BXD59\":\"x\",\"BXD60\":\"6.541\",\"BXD61\":\"6.662\",\"BXD62\":\"6.628\",\"BXD63\":\"6.556\",\"BXD64\":\"6.572\",\"BXD65\":\"6.530\",\"BXD65a\":\"6.280\",\"BXD65b\":\"6.490\",\"BXD66\":\"6.608\",\"BXD67\":\"6.534\",\"BXD68\":\"6.352\",\"BXD69\":\"6.548\",\"BXD70\":\"6.520\",\"BXD71\":\"x\",\"BXD72\":\"x\",\"BXD73\":\"6.484\",\"BXD73a\":\"6.486\",\"BXD73b\":\"x\",\"BXD74\":\"6.639\",\"BXD75\":\"6.401\",\"BXD76\":\"6.452\",\"BXD77\":\"6.568\",\"BXD78\":\"x\",\"BXD79\":\"6.642\",\"BXD81\":\"x\",\"BXD83\":\"6.446\",\"BXD84\":\"6.582\",\"BXD85\":\"6.484\",\"BXD86\":\"6.877\",\"BXD87\":\"6.474\",\"BXD88\":\"x\",\"BXD89\":\"6.676\",\"BXD90\":\"6.644\",\"BXD91\":\"x\",\"BXD93\":\"6.620\",\"BXD94\":\"6.528\",\"BXD95\":\"x\",\"BXD98\":\"6.486\",\"BXD99\":\"6.530\",\"BXD100\":\"x\",\"BXD101\":\"x\",\"BXD102\":\"x\",\"BXD104\":\"x\",\"BXD105\":\"x\",\"BXD106\":\"x\",\"BXD107\":\"x\",\"BXD108\":\"x\",\"BXD109\":\"x\",\"BXD110\":\"x\",\"BXD111\":\"x\",\"BXD112\":\"x\",\"BXD113\":\"x\",\"BXD114\":\"x\",\"BXD115\":\"x\",\"BXD116\":\"x\",\"BXD117\":\"x\",\"BXD119\":\"x\",\"BXD120\":\"x\",\"BXD121\":\"x\",\"BXD122\":\"x\",\"BXD123\":\"x\",\"BXD124\":\"x\",\"BXD125\":\"x\",\"BXD126\":\"x\",\"BXD127\":\"x\",\"BXD128\":\"x\",\"BXD128a\":\"x\",\"BXD130\":\"x\",\"BXD131\":\"x\",\"BXD132\":\"x\",\"BXD133\":\"x\",\"BXD134\":\"x\",\"BXD135\":\"x\",\"BXD136\":\"x\",\"BXD137\":\"x\",\"BXD138\":\"x\",\"BXD139\":\"x\",\"BXD141\":\"x\",\"BXD142\":\"x\",\"BXD144\":\"x\",\"BXD145\":\"x\",\"BXD146\":\"x\",\"BXD147\":\"x\",\"BXD148\":\"x\",\"BXD149\":\"x\",\"BXD150\":\"x\",\"BXD151\":\"x\",\"BXD152\":\"x\",\"BXD153\":\"x\",\"BXD154\":\"x\",\"BXD155\":\"x\",\"BXD156\":\"x\",\"BXD157\":\"x\",\"BXD160\":\"x\",\"BXD161\":\"x\",\"BXD162\":\"x\",\"BXD165\":\"x\",\"BXD168\":\"x\",\"BXD169\":\"x\",\"BXD170\":\"x\",\"BXD171\":\"x\",\"BXD172\":\"x\",\"BXD173\":\"x\",\"BXD174\":\"x\",\"BXD175\":\"x\",\"BXD176\":\"x\",\"BXD177\":\"x\",\"BXD178\":\"x\",\"BXD180\":\"x\",\"BXD181\":\"x\",\"BXD183\":\"x\",\"BXD184\":\"x\",\"BXD186\":\"x\",\"BXD187\":\"x\",\"BXD188\":\"x\",\"BXD189\":\"x\",\"BXD190\":\"x\",\"BXD191\":\"x\",\"BXD192\":\"x\",\"BXD193\":\"x\",\"BXD194\":\"x\",\"BXD195\":\"x\",\"BXD196\":\"x\",\"BXD197\":\"x\",\"BXD198\":\"x\",\"BXD199\":\"x\",\"BXD200\":\"x\",\"BXD201\":\"x\",\"BXD202\":\"x\",\"BXD203\":\"x\",\"BXD204\":\"x\",\"BXD205\":\"x\",\"BXD206\":\"x\",\"BXD207\":\"x\",\"BXD208\":\"x\",\"BXD209\":\"x\",\"BXD210\":\"x\",\"BXD211\":\"x\",\"BXD212\":\"x\",\"BXD213\":\"x\",\"BXD214\":\"x\",\"BXD215\":\"x\",\"BXD216\":\"x\",\"BXD217\":\"x\",\"BXD218\":\"x\",\"BXD219\":\"x\",\"BXD220\":\"x\"}", + "corr_type": "lit", + "corr_dataset": "HC_M2_0606_P", + "corr_return_results": "100", + "corr_samples_group": "samples_primary", + "corr_sample_method": "pearson", + "min_expr": "", + "location_type": "gene", + "loc_chr": "", + "min_loc_mb": "", + "max_loc_mb": "", + "p_range_lower": "-0.60", + "p_range_upper": "0.74" +} \ No newline at end of file diff --git a/tests/unit/correlation/dataset.json b/tests/unit/correlation/dataset.json new file mode 100644 index 0000000..8a53ed5 --- /dev/null +++ b/tests/unit/correlation/dataset.json @@ -0,0 +1,64 @@ +{ + "name":"HC_M2_0606_P", + "id":112, + "shortname":"Hippocampus M430v2 BXD 06/06 PDNN", + "fullname":"Hippocampus Consortium M430v2 (Jun06) PDNN", + "type":"ProbeSet", + "data_scale":"log2", + "search_fields":[ + "Name", + "Description", + "Probe_Target_Description", + "Symbol", + "Alias", + "GenbankId", + "UniGeneId", + "RefSeq_TranscriptId" + ], + "display_fields":[ + "name", + "symbol", + "description", + "probe_target_description", + "chr", + "mb", + "alias", + "geneid", + "genbankid", + "unigeneid", + "omim", + "refseq_transcriptid", + "blatseq", + "targetseq", + "chipid", + "comments", + "strand_probe", + "strand_gene", + "proteinid", + "uniprotid", + "probe_set_target_region", + "probe_set_specificity", + "probe_set_blat_score", + "probe_set_blat_mb_start", + "probe_set_blat_mb_end", + "probe_set_strand", + "probe_set_note_by_rw", + "flag" + ], + "header_fields":[ + "Index", + "Record", + "Symbol", + "Description", + "Location", + "Mean", + "Max LRS", + "Max LRS Location", + "Additive Effect" + ], + "query_for_group":"\n SELECT\n InbredSet.Name, InbredSet.Id, InbredSet.GeneticType\n FROM\n InbredSet, ProbeSetFreeze, ProbeFreeze\n WHERE\n ProbeFreeze.InbredSetId = InbredSet.Id AND\n ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND\n ProbeSetFreeze.Name = \"HC_M2_0606_P\"\n ", + "tissue":"Hippocampus mRNA", + "group":"None", + "accession_id":"None", + "species":"None" +} \ No newline at end of file diff --git a/tests/unit/correlation/expected_correlation_results.json b/tests/unit/correlation/expected_correlation_results.json new file mode 100644 index 0000000..b5bbc2d --- /dev/null +++ b/tests/unit/correlation/expected_correlation_results.json @@ -0,0 +1,1902 @@ +[ + { + "index": 1, + "trait_id": "1415758_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415758_at:HC_M2_0606_P:da50fa1141a7d608ab20", + "symbol": "Fryl", + "description": "furry homolog-like; far 3' UTR", + "location": "Chr5: 72.964984", + "mean": "9.193", + "additive": "-0.081", + "lod_score": "4.4", + "lrs_location": "Chr1: 196.404284", + "sample_r": "-0.407", + "num_overlap": 67, + "sample_p": "6.234e-04", + "lit_corr": "--", + "tissue_corr": "-0.221", + "tissue_pvalue": "2.780e-01" + }, + { + "index": 2, + "trait_id": "1415693_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415693_at:HC_M2_0606_P:0959e913366f559ea22b", + "symbol": "Derl1", + "description": "derlin 1; proximal to mid 3' UTR", + "location": "Chr15: 57.702171", + "mean": "9.445", + "additive": "0.056", + "lod_score": "2.1", + "lrs_location": "Chr1: 193.731996", + "sample_r": "0.398", + "num_overlap": 67, + "sample_p": "8.614e-04", + "lit_corr": "--", + "tissue_corr": "0.114", + "tissue_pvalue": "5.800e-01" + }, + { + "index": 3, + "trait_id": "1415753_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415753_at:HC_M2_0606_P:d75ca42e7fa1613364bb", + "symbol": "Fam108a", + "description": "abhydrolase domain-containing protein FAM108A; last two exons and proximal 3' UTR", + "location": "Chr10: 80.046470", + "mean": "12.731", + "additive": "0.050", + "lod_score": "1.5", + "lrs_location": "ChrX: 103.404884", + "sample_r": "0.384", + "num_overlap": 67, + "sample_p": "1.344e-03", + "lit_corr": "--", + "tissue_corr": "0.108", + "tissue_pvalue": "5.990e-01" + }, + { + "index": 4, + "trait_id": "1415740_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415740_at:HC_M2_0606_P:755cdc41d0d50a03b647", + "symbol": "Psmc5", + "description": "protease (prosome, macropain) 26S subunit, ATPase 5; exons 7, 8, 9", + "location": "Chr11: 106.123450", + "mean": "12.424", + "additive": "0.059", + "lod_score": "2.6", + "lrs_location": "Chr9: 34.013550", + "sample_r": "0.364", + "num_overlap": 67, + "sample_p": "2.476e-03", + "lit_corr": "--", + "tissue_corr": "0.333", + "tissue_pvalue": "9.696e-02" + }, + { + "index": 5, + "trait_id": "1415757_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415757_at:HC_M2_0606_P:8bbf06aa2e3aa5530934", + "symbol": "Gbf1", + "description": "Golgi-specific brefeldin A-resistance factor 1; last exon and proximal 3' UTR", + "location": "Chr19: 46.360410", + "mean": "9.800", + "additive": "-0.062", + "lod_score": "2.0", + "lrs_location": "Chr17: 52.750885", + "sample_r": "0.363", + "num_overlap": 67, + "sample_p": "2.539e-03", + "lit_corr": "--", + "tissue_corr": "-0.059", + "tissue_pvalue": "7.741e-01" + }, + { + "index": 6, + "trait_id": "1415768_a_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415768_a_at:HC_M2_0606_P:5e67109eee04f5da3393", + "symbol": "Ube2r2", + "description": "ubiquitin-conjugating enzyme E2R 2", + "location": "Chr4: 41.137929", + "mean": "9.811", + "additive": "-0.087", + "lod_score": "3.3", + "lrs_location": "Chr12: 114.553844", + "sample_r": "-0.312", + "num_overlap": 67, + "sample_p": "1.019e-02", + "lit_corr": "--", + "tissue_corr": "-0.007", + "tissue_pvalue": "9.711e-01" + }, + { + "index": 7, + "trait_id": "1415670_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415670_at:HC_M2_0606_P:4f82d7374f29ebfacaaf", + "symbol": "Copg", + "description": "coatomer protein complex, subunit gamma 1; two of the three last exons and proximal 3' UTR", + "location": "Chr6: 87.859681", + "mean": "11.199", + "additive": "-0.113", + "lod_score": "3.7", + "lrs_location": "Chr1: 157.588921", + "sample_r": "0.305", + "num_overlap": 67, + "sample_p": "1.200e-02", + "lit_corr": "--", + "tissue_corr": "-0.405", + "tissue_pvalue": "4.032e-02" + }, + { + "index": 8, + "trait_id": "1415742_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415742_at:HC_M2_0606_P:b72a582a1f840a18c3e7", + "symbol": "Aup1", + "description": "ancient ubiquitous protein 1", + "location": "Chr6: 83.006784", + "mean": "9.529", + "additive": "-0.062", + "lod_score": "2.4", + "lrs_location": "Chr19: 16.955950", + "sample_r": "0.295", + "num_overlap": 67, + "sample_p": "1.523e-02", + "lit_corr": "--", + "tissue_corr": "-0.033", + "tissue_pvalue": "8.716e-01" + }, + { + "index": 9, + "trait_id": "1415743_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415743_at:HC_M2_0606_P:3187245a079e824b4236", + "symbol": "Hdac5", + "description": "histone deacetylase 5; last four exons", + "location": "Chr11: 102.057397", + "mean": "11.009", + "additive": "0.081", + "lod_score": "2.1", + "lrs_location": "Chr7: 125.263073", + "sample_r": "0.285", + "num_overlap": 67, + "sample_p": "1.950e-02", + "lit_corr": "--", + "tissue_corr": "0.005", + "tissue_pvalue": "9.823e-01" + }, + { + "index": 10, + 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"--", + "tissue_corr": "0.028", + "tissue_pvalue": "8.923e-01" + }, + { + "index": 17, + "trait_id": "1419755_at", + "dataset": "HC_M2_0606_P", + "hmac": "1419755_at:HC_M2_0606_P:15fea7c69b0d5faa1298", + "symbol": "Mfi2", + "description": "antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5", + "location": "Chr16: 31.898518", + "mean": "6.697", + "additive": "-0.038", + "lod_score": "2.0", + "lrs_location": "Chr4: 50.881071", + "sample_r": "-0.654", + "num_overlap": 67, + "sample_p": "1.950e-09", + "lit_corr": "--", + "tissue_corr": "0.244", + "tissue_pvalue": "2.305e-01" + }, + { + "index": 18, + "trait_id": "1425457_a_at", + "dataset": "HC_M2_0606_P", + "hmac": "1425457_a_at:HC_M2_0606_P:669c485b158c0207026c", + "symbol": "Grb10", + "description": "growth factor receptor bound protein 10", + "location": "Chr11: 11.833500", + "mean": "6.515", + "additive": "0.081", + "lod_score": "3.9", + "lrs_location": "Chr5: 133.538653", + "sample_r": "-0.652", + "num_overlap": 67, + "sample_p": "2.295e-09", + "lit_corr": "--", + "tissue_corr": "-0.090", + "tissue_pvalue": "6.617e-01" + }, + { + "index": 19, + "trait_id": "1431329_at", + "dataset": "HC_M2_0606_P", + "hmac": "1431329_at:HC_M2_0606_P:a6df7ed818ea0042c550", + "symbol": "Nphp4", + "description": "nephronophthisis 4 (renal tubular development and function)", + "location": "Chr4: 151.863271", + "mean": "6.191", + "additive": "0.039", + "lod_score": "1.9", + "lrs_location": "ChrX: 112.637353", + "sample_r": "-0.652", + "num_overlap": 67, + "sample_p": "2.330e-09", + "lit_corr": "--", + "tissue_corr": "-0.104", + "tissue_pvalue": "6.144e-01" + }, + { + "index": 20, + "trait_id": "1443987_at", + "dataset": "HC_M2_0606_P", + "hmac": "1443987_at:HC_M2_0606_P:681e6c787b4d652d0c07", + "symbol": "Klhl18", + "description": "kelch-like 18 (Drosophila)", + "location": "Chr9: 110.330597", + "mean": "7.244", + "additive": "-0.070", + "lod_score": "2.1", + "lrs_location": "Chr15: 13.149248", + "sample_r": "-0.650", + "num_overlap": 67, + "sample_p": "2.561e-09", + "lit_corr": "--", + "tissue_corr": "-0.200", + "tissue_pvalue": "3.270e-01" + } +] \ No newline at end of file diff --git a/tests/unit/correlation/test_correlation_computations.py b/tests/unit/correlation/test_correlation_computations.py new file mode 100644 index 0000000..dbb2587 --- /dev/null +++ b/tests/unit/correlation/test_correlation_computations.py @@ -0,0 +1,65 @@ +"""module for testing correlation/correlation_computations""" + +import unittest +from gn3.correlation.correlation_computations import compute_correlation + + +# mock for calculating correlation function + +def mock_get_loading_page_data(initial_start_vars): + """function to mock filtering input""" + results = {'start_vars': + {'genofile': 'SAMPLE:X', 'dataset': 'HC_M2_0606_P', + 'sample_vals': '{"C57BL/6J":"7.197","DBA/2J":"7.148","B6D2F1":"6.999"}', + 'primary_samples': 'C57BL/6J,DBA/2J,B6D2F1', + 'n_samples': 3, + 'wanted_inputs': "sample_vals,dataset,genofile,primary_samples"}} + + return results + + +class MockCorrelationResults: + """mock class for CorrelationResults""" + + def __init__(self, start_vars): + for _key, value in start_vars.items(): + self.value = value + + self.assert_start_vars(start_vars) + + @staticmethod + def assert_start_vars(start_vars): + """assert data required is supplied""" + assert "wanted_inputs" in start_vars + + def do_correlation(self, start_vars): + """mock method for doing correlation""" + + return { + "results": "success" + } + + +class TestCorrelationUtility(unittest.TestCase): + """tests for correlation computations""" + + def test_compute_correlation(self): + """test function for doing correlation""" + + sample_vals = """{"C57BL/6J":"7.197","DBA/2J":"7.148","B6D2F1":"6.999"}""" + + correlation_input_data = { + "wanted_inputs": "sample_vals,dataset,genofile,primary_samples", + "genofile": "SAMPLE:X", + "dataset": "HC_M2_0606_P", + + "sample_vals": sample_vals, + "primary_samples": "C57BL/6J,DBA/2J,B6D2F1" + + } + correlation_results = compute_correlation( + correlation_input_data=correlation_input_data, + correlation_results=MockCorrelationResults) + results = {"results": "success"} + + self.assertEqual(results,correlation_results) diff --git a/tests/unit/correlation/test_show_corr_results.py b/tests/unit/correlation/test_show_corr_results.py new file mode 100644 index 0000000..4846f5e --- /dev/null +++ b/tests/unit/correlation/test_show_corr_results.py @@ -0,0 +1,226 @@ +"""module contains code for testing creating show correlation object""" + +import unittest +import json +import os +from unittest import mock +from types import SimpleNamespace +from gn3.correlation.show_corr_results import CorrelationResults +from gn3.correlation.show_corr_results import get_header_fields +from gn3.correlation.show_corr_results import generate_corr_json +# pylint: disable=unused-argument + + + +class ObjectMixin: + """object for adding other methods""" + def __str__(self): + raise NotImplementedError + + def get_dict(self): + raise NotImplementedError + +class MockGroup(ObjectMixin): + """mock class for Group""" + + def __init__(self): + self.samplelist = "add a mock for this" + self.parlist = None + + self.filist = None + +class MockCreateTrait(ObjectMixin): + """mock class for create trait""" + + def __init__(self): + pass + + def get_dict(self): + """class for getting dict items""" + return self.__dict__ + + def __str__(self): + return self.__class__.__name__ + + +class MockCreateDataset: + """mock class for create dataset""" + + def __init__(self): + + self.group = MockGroup() + + def get_trait_data(self, sample_keys): + """method for getting trait data""" + raise NotImplementedError() + + def retrieve_genes(self, symbol): + """method for retrieving genes""" + raise NotImplementedError() + + +def file_path(relative_path): + """getting abs path for file """ + # adopted from github + dir_name = os.path.dirname(os.path.abspath(__file__)) + split_path = relative_path.split("/") + new_path = os.path.join(dir_name, *split_path) + return new_path + + +def create_trait(dataset="Temp", name=None, cellid=None): + """mock function for creating trait""" + return "trait results" + + +def create_dataset(dataset_name="Temp", dataset_type="Temp", group_name=None): + """mock function to create dataset """ + return "dataset results" + + +def get_species(self, start_vars): + """ + how this function works is that it sets the self.dataset and self.species and self.this_trait + """ + + with open(file_path("./dataset.json")) as dataset_file: + results = json.load(dataset_file) + self.dataset = SimpleNamespace(**results) + + with open(file_path("./group_data_test.json")) as group_file: + results = json.load(group_file) + self.group = SimpleNamespace(**results) + + self.dataset.group = self.group + + trait_dict = {'name': '1434568_at', 'dataset': self.dataset, 'cellid': None, + 'identification': 'un-named trait', 'haveinfo': True, 'sequence': None} + + trait_obj = SimpleNamespace(**trait_dict) + + self.this_trait = trait_obj + + self.species = "this species data" + + +class TestCorrelationResults(unittest.TestCase): + """unittests for Correlation Results""" + + def setUp(self): + + with open(file_path("./correlation_test_data.json")) as json_file: + self.correlation_data = json.load(json_file) + + def tearDown(self): + + self.correlation_data = "" + + def test_for_assertion(self): + """test for assertion failures""" + with self.assertRaises(AssertionError): + _corr_results_object = CorrelationResults(start_vars={}) + + @mock.patch("gn3.correlation.show_corr_results.CorrelationResults.process_samples") + def test_do_correlation(self, process_samples): + """test for doing correlation""" + process_samples.return_value = None + corr_object = CorrelationResults(start_vars=self.correlation_data) + + with self.assertRaises(Exception) as _error: + + # xtodo;to be completed + + _corr_results = corr_object.do_correlation(start_vars=self.correlation_data, + create_dataset=create_dataset, + create_trait=None, + get_species_dataset_trait=get_species) + + + + def test_get_header_fields(self): + expected = [ + ['Index', + 'Record', + 'Symbol', + 'Description', + 'Location', + 'Mean', + 'Sample rho', + 'N', + 'Sample p(rho)', + 'Lit rho', + 'Tissue rho', + 'Tissue p(rho)', + 'Max LRS', + 'Max LRS Location', + 'Additive Effect'], + + ['Index', + 'ID', + 'Location', + 'Sample r', + 'N', + 'Sample p(r)'] + + ] + result1 = get_header_fields("ProbeSet", "spearman") + result2 = get_header_fields("Other", "Other") + self.assertEqual(result1, expected[0]) + self.assertEqual(result2, expected[1]) + + + + @mock.patch("gn3.utility.hmac.data_hmac") + def test_generate_corr_json(self, mock_data_hmac): + mock_data_hmac.return_value = "hajsdiau" + + dataset = SimpleNamespace(**{"name": "the_name"}) + this_trait = SimpleNamespace(**{"name": "trait_test", "dataset": dataset}) + target_dataset = SimpleNamespace(**{"type": "Publish"}) + corr_trait_1 = SimpleNamespace(**{ + "name": "trait_1", + "dataset": SimpleNamespace(**{"name": "dataset_1"}), + "view": True, + "abbreviation": "T1", + "description_display": "Trait I description", + "authors": "JM J,JYEW", + "pubmed_id": "34n4nn31hn43", + "pubmed_text": "2016", + "pubmed_link": "https://www.load", + "lod_score": "", + "mean": "", + "LRS_location_repr": "BXBS", + "additive": "", + "sample_r": 10.5, + "num_overlap": 2, + "sample_p": 5 + + + + + }) + corr_results = [corr_trait_1] + + dataset_type_other = { + "location": "cx-3-4", + "sample_4": 12.32, + "num_overlap": 3, + "sample_p": 10.34 + } + + expected_results = '[{"index": 1, "trait_id": "trait_1", "dataset": "dataset_1", "hmac": "hajsdiau", "abbreviation_display": "T1", "description": "Trait I description", "mean": "N/A", "authors_display": "JM J,JYEW", "additive": "N/A", "pubmed_id": "34n4nn31hn43", "year": "2016", "lod_score": "N/A", "lrs_location": "BXBS", "sample_r": "10.500", "num_overlap": 2, "sample_p": "5.000e+00"}]' + + results1 = generate_corr_json(corr_results=corr_results, this_trait=this_trait, + dataset=dataset, target_dataset=target_dataset, for_api=True) + self.assertEqual(expected_results, results1) + + + def test_generate_corr_json_view_false(self): + trait = SimpleNamespace(**{"view": False}) + corr_results = [trait] + this_trait = SimpleNamespace(**{"name": "trait_test"}) + dataset = SimpleNamespace(**{"name": "the_name"}) + + results_where_view_is_false = generate_corr_json( + corr_results=corr_results, this_trait=this_trait, dataset={}, target_dataset={}, for_api=False) + self.assertEqual(results_where_view_is_false, "[]") \ No newline at end of file diff --git a/tests/unit/utility/__init__.py b/tests/unit/utility/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/unit/utility/test_chunks.py b/tests/unit/utility/test_chunks.py new file mode 100644 index 0000000..7c42b44 --- /dev/null +++ b/tests/unit/utility/test_chunks.py @@ -0,0 +1,19 @@ +"""Test chunking""" + +import unittest + +from gn3.utility.chunks import divide_into_chunks + + +class TestChunks(unittest.TestCase): + "Test Utility method for chunking" + def test_divide_into_chunks(self): + "Check that a list is chunked correctly" + self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3), + [[1, 2, 7], [3, 22, 8], [5, 22, 333]]) + self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 4), + [[1, 2, 7], [3, 22, 8], [5, 22, 333]]) + self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 5), + [[1, 2], [7, 3], [22, 8], [5, 22], [333]]) + self.assertEqual(divide_into_chunks([], 5), + [[]]) diff --git a/tests/unit/utility/test_corr_result_helpers.py b/tests/unit/utility/test_corr_result_helpers.py new file mode 100644 index 0000000..ce5891f --- /dev/null +++ b/tests/unit/utility/test_corr_result_helpers.py @@ -0,0 +1,35 @@ +""" Test correlation helper methods """ + +import unittest +from gn3.utility.corr_result_helpers import normalize_values +from gn3.utility.corr_result_helpers import common_keys +from gn3.utility.corr_result_helpers import normalize_values_with_samples + + +class TestCorrelationHelpers(unittest.TestCase): + """Test methods for normalising lists""" + + def test_normalize_values(self): + """Test that a list is normalised correctly""" + self.assertEqual( + normalize_values([2.3, None, None, 3.2, 4.1, 5],\ + [3.4, 7.2, 1.3, None, 6.2, 4.1]), + ([2.3, 4.1, 5], [3.4, 6.2, 4.1], 3) + ) + + def test_common_keys(self): + """Test that common keys are returned as a list""" + test_a = dict(BXD1=9.113, BXD2=9.825, BXD14=8.985, BXD15=9.300) + test_b = dict(BXD1=9.723, BXD3=9.825, BXD14=9.124, BXD16=9.300) + self.assertEqual(sorted(common_keys(test_a, test_b)), + ['BXD1', 'BXD14']) + + def test_normalize_values_with_samples(self): + """Test that a sample(dict) is normalised correctly""" + self.assertEqual( + normalize_values_with_samples( + dict(BXD1=9.113, BXD2=9.825, BXD14=8.985, + BXD15=9.300, BXD20=9.300), + dict(BXD1=9.723, BXD3=9.825, BXD14=9.124, BXD16=9.300)), + (({'BXD1': 9.113, 'BXD14': 8.985}, {'BXD1': 9.723, 'BXD14': 9.124}, 2)) + ) diff --git a/tests/unit/utility/test_hmac.py b/tests/unit/utility/test_hmac.py new file mode 100644 index 0000000..eba25a3 --- /dev/null +++ b/tests/unit/utility/test_hmac.py @@ -0,0 +1,51 @@ +"""Test hmac utility functions""" +# pylint: disable-all +import unittest +from unittest import mock + +from gn3.utility.hmac import data_hmac +from gn3.utility.hmac import url_for_hmac +from gn3.utility.hmac import hmac_creation + + +class TestHmacUtil(): + """Test Utility method for hmac creation""" + + @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"}) + def test_hmac_creation(self): + """Test hmac creation with a utf-8 string""" + self.assertEqual(hmac_creation("ファイ"), "7410466338cfe109e946") + + @mock.patch("utility.hmac.app.config", + {'SECRET_HMAC_CODE': ('\x08\xdf\xfa\x93N\x80' + '\xd9\\H@\\\x9f`\x98d^' + '\xb4a;\xc6OM\x946a\xbc' + '\xfc\x80:*\xebc')}) + def test_hmac_creation_with_cookie(self): + """Test hmac creation with a cookie""" + cookie = "3f4c1dbf-5b56-4260-87d6-f35445bda37e:af4fcf5eace9e7c864ce" + uuid_, _, signature = cookie.partition(":") + self.assertEqual( + hmac_creation(uuid_), + "af4fcf5eace9e7c864ce") + + @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"}) + def test_data_hmac(self): + """Test data_hmac fn with a utf-8 string""" + self.assertEqual(data_hmac("ファイ"), "ファイ:7410466338cfe109e946") + + @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"}) + @mock.patch("utility.hmac.url_for") + def test_url_for_hmac_with_plain_url(self, mock_url): + """Test url_for_hmac without params""" + mock_url.return_value = "https://mock_url.com/ファイ/" + self.assertEqual(url_for_hmac("ファイ"), + "https://mock_url.com/ファイ/?hm=05bc39e659b1948f41e7") + + @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"}) + @mock.patch("utility.hmac.url_for") + def test_url_for_hmac_with_param_in_url(self, mock_url): + """Test url_for_hmac with params""" + mock_url.return_value = "https://mock_url.com/?ファイ=1" + self.assertEqual(url_for_hmac("ファイ"), + "https://mock_url.com/?ファイ=1&hm=4709c1708270644aed79") -- cgit v1.2.3