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/integration/correlation_data.json | 18 + tests/integration/expected_corr_results.json | 1902 ++++++++++++++++++++++++++ tests/integration/test_correlation.py | 57 + 3 files changed, 1977 insertions(+) create mode 100644 tests/integration/correlation_data.json create mode 100644 tests/integration/expected_corr_results.json create mode 100644 tests/integration/test_correlation.py (limited to 'tests/integration') diff --git a/tests/integration/correlation_data.json b/tests/integration/correlation_data.json new file mode 100644 index 0000000..87d24e3 --- /dev/null +++ b/tests/integration/correlation_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": 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+ "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/integration/expected_corr_results.json b/tests/integration/expected_corr_results.json new file mode 100644 index 0000000..b5bbc2d --- /dev/null +++ b/tests/integration/expected_corr_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": 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"tissue_pvalue": "9.370e-01" + }, + { + "index": 74, + "trait_id": "1415755_a_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415755_a_at:HC_M2_0606_P:e23340ac6458755b9d1e", + "symbol": "Ube2v1", + "description": "ubiquitin-conjugating enzyme E2 variant 1", + "location": "Chr2: 23.477654", + "mean": "12.282", + "additive": "0.053", + "lod_score": "2.2", + "lrs_location": "Chr6: 127.954548", + "sample_r": "0.040", + "num_overlap": 67, + "sample_p": "7.490e-01", + "lit_corr": "--", + "tissue_corr": "-0.321", + "tissue_pvalue": "1.102e-01" + }, + { + "index": 75, + "trait_id": "1415694_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415694_at:HC_M2_0606_P:38c96bb74d8916f0c519", + "symbol": "Wars", + "description": "tryptophanyl-tRNA synthetase; alternative 3' UTR (short form, test Mendelian 12.109, BXD hippocampus, B high)", + "location": "Chr12: 110.098698", + "mean": "8.523", + "additive": "-0.938", + "lod_score": "32.3", + "lrs_location": "Chr12: 110.136559", + "sample_r": "-0.039", + "num_overlap": 67, + "sample_p": "7.559e-01", + "lit_corr": "--", + "tissue_corr": "-0.275", + "tissue_pvalue": "1.738e-01" + }, + { + "index": 76, + "trait_id": "1415744_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415744_at:HC_M2_0606_P:38f9abcb635f29e5871c", + "symbol": "Pfdn6", + "description": "prefoldin subunit 6 (H2-K region expressed gene 2); 5' UTR, exons 1, 3, 4, and 3' UTR", + "location": "Chr17: 34.075883", + "mean": "11.324", + "additive": "-0.157", + "lod_score": "11.0", + "lrs_location": "Chr17: 33.247164", + "sample_r": "0.038", + "num_overlap": 67, + "sample_p": "7.626e-01", + "lit_corr": "--", + "tissue_corr": "--", + "tissue_pvalue": "--" + }, + { + "index": 77, + "trait_id": "1415700_a_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415700_a_at:HC_M2_0606_P:95582b9daa0776067713", + "symbol": "Ssr3", + "description": "signal sequence receptor, gamma (translocon-associated protein gamma); mid-distal 3' UTR", + "location": "Chr3: 65.183917", + "mean": "12.068", + "additive": "0.067", + "lod_score": "2.1", + "lrs_location": "Chr7: 27.852865", + "sample_r": "0.036", + "num_overlap": 67, + "sample_p": "7.742e-01", + "lit_corr": "--", + "tissue_corr": "-0.354", + "tissue_pvalue": "7.623e-02" + }, + { + "index": 78, + "trait_id": "1415687_a_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415687_a_at:HC_M2_0606_P:f15bcfef7839d22ca5a3", + "symbol": "Psap", + "description": "prosaposin; mid and distal 3' UTR", + "location": "Chr10: 59.764772", + "mean": "14.976", + "additive": "0.121", + "lod_score": "2.0", + "lrs_location": "Chr5: 4.468199", + "sample_r": "0.035", + "num_overlap": 67, + "sample_p": "7.777e-01", + "lit_corr": "--", + "tissue_corr": "0.078", + "tissue_pvalue": "7.058e-01" + }, + { + "index": 79, + "trait_id": "1415729_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415729_at:HC_M2_0606_P:08dc70633663e17111dd", + "symbol": "Pdpk1", + "description": "3-phosphoinositide dependent protein kinase-1; distal 3' UTR", + "location": "Chr17: 24.210667", + "mean": "12.376", + "additive": "-0.081", + "lod_score": "3.0", + "lrs_location": "Chr2: 55.266330", + "sample_r": "-0.029", + "num_overlap": 67, + "sample_p": "8.147e-01", + "lit_corr": "--", + "tissue_corr": "0.290", + "tissue_pvalue": "1.506e-01" + }, + { + "index": 80, + "trait_id": "1415672_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415672_at:HC_M2_0606_P:d6a7286d4957f3487196", + "symbol": "Golga7", + "description": "golgi autoantigen, golgin subfamily a, 7", + "location": "Chr8: 24.351869", + "mean": "13.218", + "additive": "0.063", + "lod_score": "2.6", + "lrs_location": "Chr13: 120.059030", + "sample_r": "-0.027", + "num_overlap": 67, + "sample_p": "8.305e-01", + "lit_corr": "--", + "tissue_corr": "-0.456", + "tissue_pvalue": "1.919e-02" + }, + { + "index": 81, + "trait_id": "1415713_a_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415713_a_at:HC_M2_0606_P:e22be15fd9ade623e3bb", + "symbol": "Ddx24", + "description": "DEAD (Asp-Glu-Ala-Asp) box polypeptide 24; last two exons", + "location": "Chr12: 104.646500", + "mean": "11.808", + "additive": "0.052", + "lod_score": "3.1", + "lrs_location": "Chr9: 15.693672", + "sample_r": "-0.026", + "num_overlap": 67, + "sample_p": "8.322e-01", + "lit_corr": "--", + "tissue_corr": "0.338", + "tissue_pvalue": "9.077e-02" + }, + { + "index": 82, + "trait_id": "1415683_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415683_at:HC_M2_0606_P:f544e88da2dd8adb0b3f", + "symbol": "Nmt1", + "description": "N-myristoyltransferase 1; exons 10 and 11, and 3' UTR", + "location": "Chr11: 102.926047", + "mean": "12.261", + "additive": "-0.070", + "lod_score": "2.6", + "lrs_location": "Chr6: 101.797292", + "sample_r": "0.026", + "num_overlap": 67, + "sample_p": "8.375e-01", + "lit_corr": "--", + "tissue_corr": "0.366", + "tissue_pvalue": "6.559e-02" + }, + { + "index": 83, + "trait_id": "1415701_x_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415701_x_at:HC_M2_0606_P:8faa1e92ec8fc8cf33b5", + "symbol": "Rpl23", + "description": "ribosomal protein L23; spans exons 1, 2, 3, 4, and intron 4, and proximal 3' UTR", + "location": "Chr11: 97.639386", + "mean": "16.236", + "additive": "0.067", + "lod_score": "2.7", + "lrs_location": "Chr2: 162.502590", + "sample_r": "0.024", + "num_overlap": 67, + "sample_p": "8.474e-01", + "lit_corr": "--", + "tissue_corr": "-0.036", + "tissue_pvalue": "8.630e-01" + }, + { + "index": 84, + "trait_id": "1415681_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415681_at:HC_M2_0606_P:96ceed972f5f3da9d52d", + "symbol": "Mrpl43", + "description": "mitochondrial ribosomal protein L43", + "location": "Chr19: 45.079983", + "mean": "10.604", + "additive": "-0.058", + "lod_score": "2.1", + "lrs_location": "Chr7: 90.186486", + "sample_r": "-0.021", + "num_overlap": 67, + "sample_p": "8.669e-01", + "lit_corr": "--", + "tissue_corr": "0.362", + "tissue_pvalue": "6.958e-02" + }, + { + "index": 85, + "trait_id": "1415691_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415691_at:HC_M2_0606_P:c6a3213115c205f73f86", + "symbol": "Dlg1", + "description": "discs, large homolog 1 (presynaptic protein SAP97); distal 3' UTR", + "location": "Chr16: 31.872849", + "mean": "11.782", + "additive": "0.088", + "lod_score": "2.9", + "lrs_location": "Chr17: 55.490261", + "sample_r": "-0.020", + "num_overlap": 67, + "sample_p": "8.731e-01", + "lit_corr": "--", + "tissue_corr": "0.015", + "tissue_pvalue": "9.426e-01" + }, + { + "index": 86, + "trait_id": "1415715_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415715_at:HC_M2_0606_P:8c7d719635beb0f7a9f5", + "symbol": "Slbp", + "description": "stem-loop binding protein", + "location": "Chr5: 33.995959", + "mean": "9.003", + "additive": "0.051", + "lod_score": "2.2", + "lrs_location": "Chr11: 69.415410", + "sample_r": "-0.020", + "num_overlap": 67, + "sample_p": "8.749e-01", + "lit_corr": "--", + "tissue_corr": "0.090", + "tissue_pvalue": "6.621e-01" + }, + { + "index": 87, + "trait_id": "1415751_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415751_at:HC_M2_0606_P:d0d8a9fa8a2b142d4374", + "symbol": "Hb1bp3", + "description": "heterochromatin protein 1-binding protein 3", + "location": "Chr4: 137.798500", + "mean": "12.239", + "additive": "-0.168", + "lod_score": "14.7", + "lrs_location": "Chr4: 138.152371", + "sample_r": "0.019", + "num_overlap": 67, + "sample_p": "8.773e-01", + "lit_corr": "--", + "tissue_corr": "--", + "tissue_pvalue": "--" + }, + { + "index": 88, + "trait_id": "1415764_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415764_at:HC_M2_0606_P:8a23b78d5d55a0026ceb", + "symbol": "Cpsf7", + "description": "cleavage and polyadenylation specificity factor 7", + "location": "Chr1: 135.516541", + "mean": "11.499", + "additive": "-0.352", + "lod_score": "28.8", + "lrs_location": "Chr1: 135.115363", + "sample_r": "-0.019", + "num_overlap": 67, + "sample_p": "8.787e-01", + "lit_corr": "--", + "tissue_corr": "--", + "tissue_pvalue": "--" + }, + { + "index": 89, + "trait_id": "1415724_a_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415724_a_at:HC_M2_0606_P:4ff4b2d244043dc3b03e", + "symbol": "Cdc42", + "description": "cell division cycle 42 (activator of Rac); mid-distal 3' UTR", + "location": "Chr4: 136.876012", + "mean": "11.795", + "additive": "-0.120", + "lod_score": "5.5", + "lrs_location": "Chr1: 172.981863", + "sample_r": "0.019", + "num_overlap": 67, + "sample_p": "8.792e-01", + "lit_corr": "--", + "tissue_corr": "0.073", + "tissue_pvalue": "7.233e-01" + }, + { + "index": 90, + "trait_id": "1415737_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415737_at:HC_M2_0606_P:c667a35a9b2b78172117", + "symbol": "Rfk", + "description": "riboflavin kinase; distal 3' UTR", + "location": "Chr19: 17.475267", + "mean": "11.552", + "additive": "0.414", + "lod_score": "35.4", + "lrs_location": "Chr19: 16.955950", + "sample_r": "0.019", + "num_overlap": 67, + "sample_p": "8.810e-01", + "lit_corr": "--", + "tissue_corr": "0.117", + "tissue_pvalue": "5.681e-01" + }, + { + "index": 91, + "trait_id": "1415738_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415738_at:HC_M2_0606_P:304349c531fb99926720", + "symbol": "Txndc12", + "description": "thioredoxin domain-containing protein 12; 3' UTR", + "location": "Chr4: 108.534146", + "mean": "9.375", + "additive": "-0.103", + "lod_score": "3.2", + "lrs_location": "Chr1: 172.981863", + "sample_r": "-0.016", + "num_overlap": 67, + "sample_p": "9.004e-01", + "lit_corr": "--", + "tissue_corr": "0.135", + "tissue_pvalue": "5.114e-01" + }, + { + "index": 92, + "trait_id": "1415735_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415735_at:HC_M2_0606_P:f30f5a5f571c8c61d459", + "symbol": "Ddb1", + "description": "damage-specific DNA binding protein 1, 127 kDa", + "location": "Chr19: 10.703737", + "mean": "10.647", + "additive": "-0.085", + "lod_score": "5.1", + "lrs_location": "Chr16: 28.990480", + "sample_r": "0.016", + "num_overlap": 67, + "sample_p": "9.008e-01", + "lit_corr": "--", + "tissue_corr": "0.248", + "tissue_pvalue": "2.217e-01" + }, + { + "index": 93, + "trait_id": "1415684_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415684_at:HC_M2_0606_P:710753b49f7e38406e4b", + "symbol": "Atg5", + "description": "autophagy related 5; mid 3' UTR", + "location": "Chr10: 44.083511", + "mean": "8.854", + "additive": "-0.068", + "lod_score": "2.2", + "lrs_location": "Chr6: 145.406059", + "sample_r": "-0.014", + "num_overlap": 67, + "sample_p": "9.086e-01", + "lit_corr": "--", + "tissue_corr": "-0.109", + "tissue_pvalue": "5.954e-01" + }, + { + "index": 94, + "trait_id": "1415686_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415686_at:HC_M2_0606_P:455a84fffcd7a0997580", + "symbol": "Rab14", + "description": "Rab GTPase family member 14", + "location": "Chr2: 35.036216", + "mean": "12.112", + "additive": "0.110", + "lod_score": "3.6", + "lrs_location": "Chr14: 124.508018", + "sample_r": "-0.013", + "num_overlap": 67, + "sample_p": "9.139e-01", + "lit_corr": "--", + "tissue_corr": "-0.056", + "tissue_pvalue": "7.850e-01" + }, + { + "index": 95, + "trait_id": "1415685_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415685_at:HC_M2_0606_P:60c84786fe2f4a62d13d", + "symbol": "Mtif2", + "description": "mitochondrial translational initiation factor 2", + "location": "Chr11: 29.442428", + "mean": "9.271", + "additive": "-0.367", + "lod_score": "23.1", + "lrs_location": "Chr11: 28.975002", + "sample_r": "0.012", + "num_overlap": 67, + "sample_p": "9.259e-01", + "lit_corr": "--", + "tissue_corr": "-0.358", + "tissue_pvalue": "7.272e-02" + }, + { + "index": 96, + "trait_id": "1415679_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415679_at:HC_M2_0606_P:513339a6b22faab7d8f6", + "symbol": "Psenen", + "description": "presenilin enhancer 2; 5' UTR, all exons, and 3' UTR", + "location": "Chr7: 31.346914", + "mean": "11.480", + "additive": "-0.283", + "lod_score": "19.1", + "lrs_location": "Chr7: 31.505577", + "sample_r": "-0.011", + "num_overlap": 67, + "sample_p": "9.286e-01", + "lit_corr": "--", + "tissue_corr": "-0.002", + "tissue_pvalue": "9.929e-01" + }, + { + "index": 97, + "trait_id": "1415710_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415710_at:HC_M2_0606_P:4b8e32a96cf0e9bb30d3", + "symbol": "Cox18", + "description": "cytochrome c oxidase assembly protein 18; last three exons and proximal 3' UTR", + "location": "Chr5: 90.644087", + "mean": "9.513", + "additive": "0.402", + "lod_score": "33.4", + "lrs_location": "Chr5: 90.500265", + "sample_r": "0.010", + "num_overlap": 67, + "sample_p": "9.360e-01", + "lit_corr": "--", + "tissue_corr": "0.420", + "tissue_pvalue": "3.257e-02" + }, + { + "index": 98, + "trait_id": "1415702_a_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415702_a_at:HC_M2_0606_P:7ef725f27498e294d14a", + "symbol": "Ctbp1", + "description": "C-terminal binding protein 1; 3' UTR", + "location": "Chr5: 33.590456", + "mean": "12.530", + "additive": "-0.056", + "lod_score": "2.3", + "lrs_location": "Chr12: 76.993653", + "sample_r": "-0.010", + "num_overlap": 67, + "sample_p": "9.372e-01", + "lit_corr": "--", + "tissue_corr": "0.514", + "tissue_pvalue": "7.288e-03" + }, + { + "index": 99, + "trait_id": "1415711_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415711_at:HC_M2_0606_P:f71bb40cdefd07ae95d6", + "symbol": "Arfgef1", + "description": "ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited); 3' UTR", + "location": "Chr18: 22.122655", + "mean": "11.617", + "additive": "-0.055", + "lod_score": "3.3", + "lrs_location": "Chr2: 50.500580", + "sample_r": "-0.003", + "num_overlap": 67, + "sample_p": "9.802e-01", + "lit_corr": "--", + "tissue_corr": "-0.020", + "tissue_pvalue": "9.216e-01" + }, + { + "index": 100, + "trait_id": "1415726_at", + "dataset": "HC_M2_0606_P", + "hmac": "1415726_at:HC_M2_0606_P:89e8ab5b988a202a2fb0", + "symbol": "Ankrd17", + "description": "ankyrin repeat domain protein 17; last exon and proximal 3' UTR", + "location": "Chr5: 90.657781", + "mean": "11.533", + "additive": "0.046", + "lod_score": "2.0", + "lrs_location": "Chr14: 42.819085", + "sample_r": "0.000", + "num_overlap": 67, + "sample_p": "9.991e-01", + "lit_corr": "--", + "tissue_corr": "0.530", + "tissue_pvalue": "5.382e-03" + } +] \ No newline at end of file diff --git a/tests/integration/test_correlation.py b/tests/integration/test_correlation.py new file mode 100644 index 0000000..b94487a --- /dev/null +++ b/tests/integration/test_correlation.py @@ -0,0 +1,57 @@ +"""Integration tests for correlation api""" + +import os +import json +import pickle +import unittest +from unittest import mock + +from gn3.app import create_app + + +def file_path(relative_path): + """getting abs path for file """ + 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 + + +class CorrelationAPITest(unittest.TestCase): + # currently disable + """Test cases for the Correlation API""" + + def setUp(self): + self.app = create_app().test_client() + + with open(file_path("correlation_data.json")) as json_file: + self.correlation_data = json.load(json_file) + + with open(file_path("expected_corr_results.json")) as results_file: + self.correlation_results = json.load(results_file) + + def tearDown(self): + self.correlation_data = "" + + self.correlation_results = "" + + @mock.patch("gn3.api.correlation.compute_correlation") + def test_corr_compute(self, compute_corr): + """Test that the correct response in correlation""" + + compute_corr.return_value = self.correlation_results + response = self.app.post( + "/api/correlation/corr_compute", json=self.correlation_data, follow_redirects=True) + + self.assertEqual(response.status_code, 200) + + @mock.patch("gn3.api.correlation.compute_correlation") + def test_corr_compute_failed_request(self,compute_corr): + """test taht cormpute requests fails """ + + compute_corr.return_value = self.correlation_results + + response = self.app.post( + "/api/correlation/corr_compute", json=None, follow_redirects=True) + + self.assertEqual(response.status_code,400) -- cgit v1.2.3