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authorAlexander Kabui2021-03-13 13:04:33 +0300
committerGitHub2021-03-13 13:04:33 +0300
commit236ca06dc4c84baecb7b090b8724db997a5d988a (patch)
tree7fce724ae007dacfe3cf0f7511756b6064026ea3 /tests/unit/correlation
parent7f9a293929be021eb73aec35defe254351557dcb (diff)
downloadgenenetwork3-236ca06dc4c84baecb7b090b8724db997a5d988a.tar.gz
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>
Diffstat (limited to 'tests/unit/correlation')
-rw-r--r--tests/unit/correlation/__init__.py0
-rw-r--r--tests/unit/correlation/correlation_test_data.json18
-rw-r--r--tests/unit/correlation/dataset.json64
-rw-r--r--tests/unit/correlation/expected_correlation_results.json1902
-rw-r--r--tests/unit/correlation/group_data_test.json214
-rw-r--r--tests/unit/correlation/my_results.json388
-rw-r--r--tests/unit/correlation/test_correlation_computations.py65
-rw-r--r--tests/unit/correlation/test_show_corr_results.py226
8 files changed, 2877 insertions, 0 deletions
diff --git a/tests/unit/correlation/__init__.py b/tests/unit/correlation/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/tests/unit/correlation/__init__.py
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",
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+ "lrs_location": "Chr19: 16.955950",
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+ "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",
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+ "description": "histone deacetylase 5; last four exons",
+ "location": "Chr11: 102.057397",
+ "mean": "11.009",
+ "additive": "0.081",
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+ "lrs_location": "Chr7: 125.263073",
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+ "num_overlap": 67,
+ "sample_p": "1.950e-02",
+ "lit_corr": "--",
+ "tissue_corr": "0.005",
+ "tissue_pvalue": "9.823e-01"
+ },
+ {
+ "index": 10,
+ "trait_id": "1415690_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415690_at:HC_M2_0606_P:603b215ede00b6fe1104",
+ "symbol": "Mrp127",
+ "description": "39S ribosomal protein L27, mitochondrial; last three exons",
+ "location": "Chr11: 94.517922",
+ "mean": "12.569",
+ "additive": "0.063",
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+ "lrs_location": "Chr2: 164.779024",
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+ "sample_p": "2.986e-02",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
+ {
+ "index": 11,
+ "trait_id": "1415727_at",
+ "dataset": "HC_M2_0606_P",
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+ "symbol": "Apoa1bp",
+ "description": "apolipoprotein A-I binding protein; exons 3 through 6",
+ "location": "Chr3: 87.860534",
+ "mean": "11.707",
+ "additive": "-0.076",
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+ "lrs_location": "Chr3: 56.295375",
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+ "lit_corr": "--",
+ "tissue_corr": "-0.535",
+ "tissue_pvalue": "4.841e-03"
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+ {
+ "index": 12,
+ "trait_id": "1415730_at",
+ "dataset": "HC_M2_0606_P",
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+ "symbol": "Cpsf7",
+ "description": "cleavage and polyadenylation specificity factor 7; distal 3' UTR (transQTL on Chr 4 in BXD eye data)",
+ "location": "Chr19: 10.621618",
+ "mean": "10.662",
+ "additive": "-0.048",
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+ "lrs_location": "Chr1: 188.085707",
+ "sample_r": "-0.263",
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+ "sample_p": "3.164e-02",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
+ {
+ "index": 13,
+ "trait_id": "1415741_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415741_at:HC_M2_0606_P:033752be361d32960c29",
+ "symbol": "Tmem165",
+ "description": "transmembrane protein 165; 3' UTR",
+ "location": "Chr5: 76.637708",
+ "mean": "10.974",
+ "additive": "0.048",
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+ "lrs_location": "Chr4: 5.606394",
+ "sample_r": "-0.258",
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+ "sample_p": "3.489e-02",
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+ "tissue_corr": "0.271",
+ "tissue_pvalue": "1.812e-01"
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+ {
+ "index": 14,
+ "trait_id": "1415725_at",
+ "dataset": "HC_M2_0606_P",
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+ "symbol": "Rrn3",
+ "description": "RRN3 RNA polymerase I transcription factor homolog (yeast)",
+ "location": "Chr16: 13.814359",
+ "mean": "9.195",
+ "additive": "-0.085",
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+ "lrs_location": "Chr1: 148.717644",
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+ "num_overlap": 67,
+ "sample_p": "3.636e-02",
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+ "tissue_corr": "0.587",
+ "tissue_pvalue": "1.621e-03"
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+ {
+ "index": 15,
+ "trait_id": "1415717_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415717_at:HC_M2_0606_P:dd51438830e4033114f8",
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+ "description": "ring finger protein 220; mid 3' UTR",
+ "location": "Chr4: 116.944155",
+ "mean": "10.778",
+ "additive": "-0.084",
+ "lod_score": "2.4",
+ "lrs_location": "Chr4: 122.536808",
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+ "sample_p": "4.816e-02",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
+ {
+ "index": 16,
+ "trait_id": "1415703_at",
+ "dataset": "HC_M2_0606_P",
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+ "description": "HECT, UBA and WWE domain containing 1; last 3 exons and proximal 3' UTR",
+ "location": "ChrX: 148.367136",
+ "mean": "11.335",
+ "additive": "-0.094",
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+ "lrs_location": "Chr1: 135.891043",
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+ "sample_p": "5.541e-02",
+ "lit_corr": "--",
+ "tissue_corr": "0.528",
+ "tissue_pvalue": "5.576e-03"
+ },
+ {
+ "index": 17,
+ "trait_id": "1415748_a_at",
+ "dataset": "HC_M2_0606_P",
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+ "symbol": "Dctn5",
+ "description": "dynactin 5; last exon and proximal half of 3' UTR",
+ "location": "Chr7: 129.291923",
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+ "additive": "0.071",
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+ "sample_p": "6.133e-02",
+ "lit_corr": "--",
+ "tissue_corr": "0.064",
+ "tissue_pvalue": "7.557e-01"
+ },
+ {
+ "index": 18,
+ "trait_id": "1415706_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415706_at:HC_M2_0606_P:ddfffdb78d0ff84d6a1a",
+ "symbol": "Copa",
+ "description": "coatomer protein complex, subunit alpha; 3' UTR",
+ "location": "Chr1: 174.051912",
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+ "sample_p": "6.829e-02",
+ "lit_corr": "--",
+ "tissue_corr": "-0.147",
+ "tissue_pvalue": "4.739e-01"
+ },
+ {
+ "index": 19,
+ "trait_id": "1415696_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415696_at:HC_M2_0606_P:da00b2667d7c27dc76a2",
+ "symbol": "Sar1a",
+ "description": "SAR1 gene homolog A; distal 3' UTR",
+ "location": "Chr10: 61.155492",
+ "mean": "11.447",
+ "additive": "-0.051",
+ "lod_score": "2.4",
+ "lrs_location": "Chr15: 87.788313",
+ "sample_r": "0.220",
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+ "sample_p": "7.356e-02",
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+ "tissue_corr": "-0.559",
+ "tissue_pvalue": "3.015e-03"
+ },
+ {
+ "index": 20,
+ "trait_id": "1415731_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415731_at:HC_M2_0606_P:9e91e97ca1001091a5f3",
+ "symbol": "Angel2",
+ "description": "angel homolog 2; distal 3' UTR",
+ "location": "Chr1: 192.769800",
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+ "additive": "0.062",
+ "lod_score": "2.6",
+ "lrs_location": "Chr14: 124.508018",
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+ "sample_p": "7.623e-02",
+ "lit_corr": "--",
+ "tissue_corr": "0.232",
+ "tissue_pvalue": "2.544e-01"
+ },
+ {
+ "index": 21,
+ "trait_id": "1415750_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415750_at:HC_M2_0606_P:c9f757736d57e5f23aa5",
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+ "description": "transducin (beta)-like 3",
+ "location": "Chr17: 24.838067",
+ "mean": "8.703",
+ "additive": "-0.132",
+ "lod_score": "10.0",
+ "lrs_location": "Chr17: 23.322636",
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+ "sample_p": "8.332e-02",
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+ "tissue_corr": "0.312",
+ "tissue_pvalue": "1.211e-01"
+ },
+ {
+ "index": 22,
+ "trait_id": "1415680_at",
+ "dataset": "HC_M2_0606_P",
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+ "description": "anaphase promoting complex subunit 1; last 3 exons and 3' UTR",
+ "location": "Chr2: 128.438499",
+ "mean": "9.180",
+ "additive": "-0.102",
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+ "sample_p": "8.734e-02",
+ "lit_corr": "--",
+ "tissue_corr": "0.367",
+ "tissue_pvalue": "6.539e-02"
+ },
+ {
+ "index": 23,
+ "trait_id": "1415712_at",
+ "dataset": "HC_M2_0606_P",
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+ "description": "zinc finger, RAN-binding domain containing 1 (ubiquitin thioesterase, TRAF-binding protein); far 3' UTR (M430AB control duplicate)",
+ "location": "Chr7: 140.175988",
+ "mean": "9.923",
+ "additive": "-0.079",
+ "lod_score": "2.8",
+ "lrs_location": "Chr5: 143.642242",
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+ "sample_p": "9.125e-02",
+ "lit_corr": "--",
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+ "tissue_pvalue": "7.413e-01"
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+ "index": 24,
+ "trait_id": "1415674_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415674_a_at:HC_M2_0606_P:c8e7fb1fcad21d73fcfd",
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+ "description": "trafficking protein particle complex 4; exons 3 and 4",
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+ "additive": "-0.065",
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+ "lrs_location": "Chr5: 69.527298",
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+ "sample_p": "1.028e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.334",
+ "tissue_pvalue": "9.587e-02"
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+ "index": 25,
+ "trait_id": "1415747_s_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415747_s_at:HC_M2_0606_P:5d86584be55f6cec47ab",
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+ "description": "RIO kinase 3 (yeast); mid to distal 3' UTR",
+ "location": "Chr18: 12.314783",
+ "mean": "10.906",
+ "additive": "0.068",
+ "lod_score": "2.1",
+ "lrs_location": "Chr4: 13.764991",
+ "sample_r": "-0.198",
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+ "sample_p": "1.081e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.282",
+ "tissue_pvalue": "1.628e-01"
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+ "index": 26,
+ "trait_id": "1415682_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415682_at:HC_M2_0606_P:d02febdf17a279a71088",
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+ "description": "exportin 7",
+ "location": "Chr14: 71.064730",
+ "mean": "9.075",
+ "additive": "-0.073",
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+ "lrs_location": "Chr17: 68.421021",
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+ "lit_corr": "--",
+ "tissue_corr": "-0.322",
+ "tissue_pvalue": "1.084e-01"
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+ "index": 27,
+ "trait_id": "1415732_at",
+ "dataset": "HC_M2_0606_P",
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+ "description": "abhydrolase domain containing 16A; last five exons including proximal 3' UTR",
+ "location": "Chr17: 35.238940",
+ "mean": "10.798",
+ "additive": "-0.132",
+ "lod_score": "6.1",
+ "lrs_location": "Chr17: 37.015392",
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+ "sample_p": "1.527e-01",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
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+ "index": 28,
+ "trait_id": "1415688_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415688_at:HC_M2_0606_P:4c3b6c7cd3d447f2346c",
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+ "description": "ubiquitin-conjugating enzyme E2 G1; mid to distal 3' UTR",
+ "location": "Chr11: 72.497627",
+ "mean": "11.494",
+ "additive": "-0.116",
+ "lod_score": "7.1",
+ "lrs_location": "Chr11: 72.486317",
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+ "sample_p": "1.605e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.365",
+ "tissue_pvalue": "6.671e-02"
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+ "index": 29,
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+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415698_at:HC_M2_0606_P:4d8988a8fac8bdbce9c2",
+ "symbol": "Golm1",
+ "description": "Golgi membrane protein 1; distal 3' UTR",
+ "location": "Chr13: 59.736417",
+ "mean": "11.367",
+ "additive": "0.113",
+ "lod_score": "2.9",
+ "lrs_location": "Chr7: 36.124856",
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+ "sample_p": "2.221e-01",
+ "lit_corr": "--",
+ "tissue_corr": "-0.053",
+ "tissue_pvalue": "7.958e-01"
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+ "index": 30,
+ "trait_id": "1415697_at",
+ "dataset": "HC_M2_0606_P",
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+ "symbol": "G3bp2",
+ "description": "GTPase activating protein (SH3 domain) binding protein 2; mid proximal 3' UTR",
+ "location": "Chr5: 92.482845",
+ "mean": "10.768",
+ "additive": "0.137",
+ "lod_score": "3.6",
+ "lrs_location": "Chr5: 138.337847",
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+ "sample_p": "2.504e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.107",
+ "tissue_pvalue": "6.032e-01"
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+ "trait_id": "1415676_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415676_a_at:HC_M2_0606_P:b236ce0b2af4408662b6",
+ "symbol": "Psmb5",
+ "description": "proteasome (prosome, macropain) subunit, beta type 5; coding exons 2 and 3",
+ "location": "Chr14: 55.233131",
+ "mean": "14.199",
+ "additive": "0.130",
+ "lod_score": "6.9",
+ "lrs_location": "Chr14: 54.987777",
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+ "sample_p": "2.725e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.152",
+ "tissue_pvalue": "4.580e-01"
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+ "index": 32,
+ "trait_id": "1415723_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415723_at:HC_M2_0606_P:8672294efc1c30e220c2",
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+ "description": "eukaryotic translation initiation factor 5; distal 3' UTR",
+ "location": "Chr12: 112.784258",
+ "mean": "12.507",
+ "additive": "-0.196",
+ "lod_score": "12.9",
+ "lrs_location": "Chr12: 112.426348",
+ "sample_r": "-0.134",
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+ "sample_p": "2.795e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.105",
+ "tissue_pvalue": "6.104e-01"
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+ {
+ "index": 33,
+ "trait_id": "1415692_s_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415692_s_at:HC_M2_0606_P:a30c9243d16dd6d28826",
+ "symbol": "Canx",
+ "description": "calnexin; mid 3' UTR",
+ "location": "Chr11: 50.108505",
+ "mean": "13.862",
+ "additive": "0.090",
+ "lod_score": "3.3",
+ "lrs_location": "Chr9: 15.693672",
+ "sample_r": "0.133",
+ "num_overlap": 67,
+ "sample_p": "2.828e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.298",
+ "tissue_pvalue": "1.388e-01"
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+ {
+ "index": 34,
+ "trait_id": "1415728_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415728_at:HC_M2_0606_P:449a770634eff3bac9f5",
+ "symbol": "Pabpn1",
+ "description": "polyadenylate-binding protein 2; far 3' UTR",
+ "location": "Chr14: 55.517242",
+ "mean": "10.510",
+ "additive": "0.150",
+ "lod_score": "2.3",
+ "lrs_location": "Chr19: 53.933992",
+ "sample_r": "-0.130",
+ "num_overlap": 67,
+ "sample_p": "2.942e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.132",
+ "tissue_pvalue": "5.194e-01"
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+ {
+ "index": 35,
+ "trait_id": "1415675_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415675_at:HC_M2_0606_P:9712db695d534370b0d9",
+ "symbol": "Dpm2",
+ "description": "dolichol-phosphate (beta-D) mannosyltransferase 2; last exon and proximal to mid 3' UTR",
+ "location": "Chr2: 32.428524",
+ "mean": "10.207",
+ "additive": "-0.043",
+ "lod_score": "2.6",
+ "lrs_location": "Chr13: 30.769380",
+ "sample_r": "-0.129",
+ "num_overlap": 67,
+ "sample_p": "2.966e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.102",
+ "tissue_pvalue": "6.201e-01"
+ },
+ {
+ "index": 36,
+ "trait_id": "1415721_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415721_a_at:HC_M2_0606_P:fd804230fcc3400d6b4b",
+ "symbol": "Naa60",
+ "description": "N(alpha)-acetyltransferase 60, NatF catalytic subunit; distal 3' UTR",
+ "location": "Chr16: 3.904169",
+ "mean": "10.153",
+ "additive": "-0.059",
+ "lod_score": "3.6",
+ "lrs_location": "Chr2: 159.368724",
+ "sample_r": "0.128",
+ "num_overlap": 67,
+ "sample_p": "3.004e-01",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
+ {
+ "index": 37,
+ "trait_id": "1415733_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1415733_a_at:HC_M2_0606_P:4eff33f3ecd4c0dd418e",
+ "symbol": "Shb",
+ "description": "Src homology 2 domain containing adaptor protein B; putative far 3' UTR (or intercalated neighbor)",
+ "location": "Chr4: 45.118127",
+ "mean": "10.756",
+ "additive": "-0.044",
+ "lod_score": "1.9",
+ "lrs_location": "Chr5: 69.527298",
+ "sample_r": "0.126",
+ "num_overlap": 67,
+ "sample_p": "3.103e-01",
+ "lit_corr": "--",
+ "tissue_corr": "0.149",
+ "tissue_pvalue": "4.678e-01"
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+ {
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+ {
+ "index": 40,
+ "trait_id": "1415762_x_at",
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+ "dataset": "HC_M2_0606_P",
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+ "tissue_pvalue": "--"
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+ "trait_id": "1415677_at",
+ "dataset": "HC_M2_0606_P",
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+ "additive": "0.070",
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+ "lrs_location": "Chr1: 29.231425",
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+ "sample_p": "6.785e-01",
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+ "tissue_corr": "-0.238",
+ "tissue_pvalue": "2.422e-01"
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+ "index": 66,
+ "trait_id": "1415756_a_at",
+ "dataset": "HC_M2_0606_P",
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+ "mean": "9.902",
+ "additive": "-0.155",
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+ "lrs_location": "Chr3: 89.894692",
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+ "sample_p": "6.788e-01",
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+ "tissue_corr": "0.179",
+ "tissue_pvalue": "3.809e-01"
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+ "dataset": "HC_M2_0606_P",
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+ "location": "Chr12: 73.894951",
+ "mean": "11.586",
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+ "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/unit/correlation/group_data_test.json b/tests/unit/correlation/group_data_test.json
new file mode 100644
index 0000000..9a73a46
--- /dev/null
+++ b/tests/unit/correlation/group_data_test.json
@@ -0,0 +1,214 @@
+{
+ "name":"BXD",
+ "id":1,
+ "genetic_type":"riset",
+ "f1list":"None",
+ "parlist":"None",
+ "mapping_id":"1",
+ "mapping_names":[
+ "GEMMA",
+ "QTLReaper",
+ "R/qtl"
+ ],
+ "species":"mouse",
+ "samplelist":[
+ "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"
+ ]
+} \ No newline at end of file
diff --git a/tests/unit/correlation/my_results.json b/tests/unit/correlation/my_results.json
new file mode 100644
index 0000000..2061c6e
--- /dev/null
+++ b/tests/unit/correlation/my_results.json
@@ -0,0 +1,388 @@
+[
+
+ {
+ "sample_r_correlation_using_genenetwork3":"Results",
+
+ },
+
+ {
+ "index": 1,
+ "trait_id": "1445813_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1445813_at:HC_M2_0606_P:ca1b85915ccba7198af3",
+ "symbol": "0610012K18Rik",
+ "description": "RIKEN cDNA 0610012H03 (no human homolog defined)",
+ "location": "Chr17: 14.966404",
+ "mean": "6.643",
+ "additive": "0.042",
+ "lod_score": "2.6",
+ "lrs_location": "Chr5: 133.538653",
+ "sample_r": "-0.694",
+ "num_overlap": 67,
+ "sample_p": "7.244e-11",
+ "lit_corr": "--",
+ "tissue_corr": "--",
+ "tissue_pvalue": "--"
+ },
+ {
+ "index": 2,
+ "trait_id": "1439910_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1439910_a_at:HC_M2_0606_P:0c4c7a3cb088699af36c",
+ "symbol": "Tradd",
+ "description": "TNFRSF1A-associated via death domain",
+ "location": "Chr8: 107.783836",
+ "mean": "7.449",
+ "additive": "0.039",
+ "lod_score": "1.7",
+ "lrs_location": "Chr1: 195.987783",
+ "sample_r": "-0.692",
+ "num_overlap": 67,
+ "sample_p": "9.012e-11",
+ "lit_corr": "--",
+ "tissue_corr": "-0.285",
+ "tissue_pvalue": "1.575e-01"
+ },
+ {
+ "index": 3,
+ "trait_id": "1421499_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1421499_a_at:HC_M2_0606_P:b807253e0829c2592ceb",
+ "symbol": "Ptpn14",
+ "description": "protein tyrosine phosphatase, non-receptor type 14",
+ "location": "Chr1: 191.689356",
+ "mean": "6.655",
+ "additive": "0.049",
+ "lod_score": "2.4",
+ "lrs_location": "Chr1: 197.014645",
+ "sample_r": "-0.691",
+ "num_overlap": 67,
+ "sample_p": "1.009e-10",
+ "lit_corr": "--",
+ "tissue_corr": "-0.242",
+ "tissue_pvalue": "2.337e-01"
+ },
+ {
+ "index": 4,
+ "trait_id": "1421167_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1421167_at:HC_M2_0606_P:d7b29d02c306e1ae105a",
+ "symbol": "Atp11a",
+ "description": "ATPase, class VI, type 11A; last four exons and 3' UTR",
+ "location": "Chr8: 12.856932",
+ "mean": "7.341",
+ "additive": "0.050",
+ "lod_score": "1.7",
+ "lrs_location": "Chr9: 62.226499",
+ "sample_r": "-0.690",
+ "num_overlap": 67,
+ "sample_p": "1.059e-10",
+ "lit_corr": "--",
+ "tissue_corr": "0.154",
+ "tissue_pvalue": "4.522e-01"
+ },
+ {
+ "index": 5,
+ "trait_id": "1436525_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1436525_at:HC_M2_0606_P:b36b6c4053c40cc5b25b",
+ "symbol": "Ap3s2",
+ "description": "adaptor-related protein complex 3, sigma 2 subunit",
+ "location": "Chr7: 87.022674",
+ "mean": "8.227",
+ "additive": "-0.070",
+ "lod_score": "3.0",
+ "lrs_location": "Chr4: 63.346622",
+ "sample_r": "-0.679",
+ "num_overlap": 67,
+ "sample_p": "2.627e-10",
+ "lit_corr": "--",
+ "tissue_corr": "-0.059",
+ "tissue_pvalue": "7.750e-01"
+ },
+ {
+ "index": 6,
+ "trait_id": "1450824_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1450824_at:HC_M2_0606_P:fa9b15d1d4a2d629decb",
+ "symbol": "Ptch1",
+ "description": "patched homolog 1",
+ "location": "Chr13: 63.612887",
+ "mean": "7.105",
+ "additive": "0.070",
+ "lod_score": "3.9",
+ "lrs_location": "Chr5: 133.538653",
+ "sample_r": "-0.679",
+ "num_overlap": 67,
+ "sample_p": "2.771e-10",
+ "lit_corr": "--",
+ "tissue_corr": "-0.360",
+ "tissue_pvalue": "7.075e-02"
+ },
+ {
+ "index": 7,
+ "trait_id": "1450540_x_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1450540_x_at:HC_M2_0606_P:0836630187705e0a98ed",
+ "symbol": "Krtap5-1",
+ "description": "keratin associated protein 5-1",
+ "location": "Chr7: 149.482282",
+ "mean": "7.584",
+ "additive": "0.059",
+ "lod_score": "2.2",
+ "lrs_location": "Chr5: 140.893042",
+ "sample_r": "-0.678",
+ "num_overlap": 67,
+ "sample_p": "2.828e-10",
+ "lit_corr": "--",
+ "tissue_corr": "-0.486",
+ "tissue_pvalue": "1.174e-02"
+ },
+ {
+ "index": 8,
+ "trait_id": "1454403_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1454403_at:HC_M2_0606_P:d6625a44bb78d0c9a7bc",
+ "symbol": "Fgd5",
+ "description": "FYVE, RhoGEF and PH domain containing 5",
+ "location": "Chr6: 91.964079",
+ "mean": "6.447",
+ "additive": "-0.036",
+ "lod_score": "1.8",
+ "lrs_location": "Chr8: 7.701081",
+ "sample_r": "-0.669",
+ "num_overlap": 67,
+ "sample_p": "5.895e-10",
+ "lit_corr": "--",
+ "tissue_corr": "-0.209",
+ "tissue_pvalue": "3.062e-01"
+ },
+ {
+ "index": 9,
+ "trait_id": "1444162_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1444162_at:HC_M2_0606_P:fea27946a4ed1ee2b47a",
+ "symbol": "Frs2",
+ "description": "fibroblast growth factor receptor substrate 2",
+ "location": "Chr10: 116.521472",
+ "mean": "5.677",
+ "additive": "-0.040",
+ "lod_score": "1.8",
+ "lrs_location": "Chr4: 66.843058",
+ "sample_r": "-0.666",
+ "num_overlap": 67,
+ "sample_p": "7.946e-10",
+ "lit_corr": "--",
+ "tissue_corr": "-0.241",
+ "tissue_pvalue": "2.352e-01"
+ },
+ {
+ "index": 10,
+ "trait_id": "1451876_a_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1451876_a_at:HC_M2_0606_P:eb879785591c3c2addeb",
+ "symbol": "Trp63",
+ "description": "transformation related protein 63",
+ "location": "Chr16: 25.884897",
+ "mean": "6.207",
+ "additive": "0.059",
+ "lod_score": "2.0",
+ "lrs_location": "Chr9: 74.382952",
+ "sample_r": "-0.664",
+ "num_overlap": 67,
+ "sample_p": "8.743e-10",
+ "lit_corr": "--",
+ "tissue_corr": "-0.187",
+ "tissue_pvalue": "3.601e-01"
+ },
+ {
+ "index": 11,
+ "trait_id": "1457795_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1457795_at:HC_M2_0606_P:617d62e702f1f04b065d",
+ "symbol": "Scamp4",
+ "description": "secretory carrier membrane protein 4",
+ "location": "Chr10: 80.076487",
+ "mean": "7.060",
+ "additive": "-0.042",
+ "lod_score": "2.4",
+ "lrs_location": "Chr11: 58.923978",
+ "sample_r": "-0.663",
+ "num_overlap": 67,
+ "sample_p": "9.806e-10",
+ "lit_corr": "--",
+ "tissue_corr": "-0.040",
+ "tissue_pvalue": "8.462e-01"
+ },
+ {
+ "index": 12,
+ "trait_id": "1439472_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1439472_at:HC_M2_0606_P:f52f356bf5d00add1ba9",
+ "symbol": "Gcn1l1",
+ "description": "general control of amino-acid synthesis 1-like 1",
+ "location": "Chr5: 116.033483",
+ "mean": "7.325",
+ "additive": "0.058",
+ "lod_score": "3.1",
+ "lrs_location": "Chr1: 196.404284",
+ "sample_r": "-0.662",
+ "num_overlap": 67,
+ "sample_p": "1.075e-09",
+ "lit_corr": "--",
+ "tissue_corr": "-0.205",
+ "tissue_pvalue": "3.157e-01"
+ },
+ {
+ "index": 13,
+ "trait_id": "1422074_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1422074_at:HC_M2_0606_P:4acd73cfd3d194327d79",
+ "symbol": "Cdx2",
+ "description": "caudal type homeo box 2",
+ "location": "Chr5: 148.113293",
+ "mean": "6.415",
+ "additive": "-0.037",
+ "lod_score": "1.8",
+ "lrs_location": "Chr2: 180.825581",
+ "sample_r": "-0.661",
+ "num_overlap": 67,
+ "sample_p": "1.140e-09",
+ "lit_corr": "--",
+ "tissue_corr": "0.002",
+ "tissue_pvalue": "9.926e-01"
+ },
+ {
+ "index": 14,
+ "trait_id": "1429140_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1429140_at:HC_M2_0606_P:16116d150fd7a8d09687",
+ "symbol": "Spns3",
+ "description": "spinster homolog 3; exons 10, 12, and proximal 3' UTR",
+ "location": "Chr11: 72.311676",
+ "mean": "7.194",
+ "additive": "0.050",
+ "lod_score": "2.1",
+ "lrs_location": "Chr9: 69.810185",
+ "sample_r": "-0.661",
+ "num_overlap": 67,
+ "sample_p": "1.175e-09",
+ "lit_corr": "--",
+ "tissue_corr": "0.557",
+ "tissue_pvalue": "3.116e-03"
+ },
+ {
+ "index": 15,
+ "trait_id": "1437477_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1437477_at:HC_M2_0606_P:990d16df933d7bb03428",
+ "symbol": "Lrrfip1",
+ "description": "leucine rich repeat (in FLII) interacting protein 1",
+ "location": "Chr1: 93.011523",
+ "mean": "7.597",
+ "additive": "0.068",
+ "lod_score": "2.3",
+ "lrs_location": "Chr5: 133.538653",
+ "sample_r": "-0.658",
+ "num_overlap": 67,
+ "sample_p": "1.393e-09",
+ "lit_corr": "--",
+ "tissue_corr": "0.132",
+ "tissue_pvalue": "5.204e-01"
+ },
+ {
+ "index": 16,
+ "trait_id": "1440212_at",
+ "dataset": "HC_M2_0606_P",
+ "hmac": "1440212_at:HC_M2_0606_P:01ae82e4856177dd9d89",
+ "symbol": "Slc12a1",
+ "description": "solute carrier family 12, member 1",
+ "location": "Chr2: 124.990152",
+ "mean": "7.061",
+ "additive": "0.038",
+ "lod_score": "2.2",
+ "lrs_location": "Chr1: 193.731996",
+ "sample_r": "-0.655",
+ "num_overlap": 67,
+ "sample_p": "1.769e-09",
+ "lit_corr": "--",
+ "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
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 22:34:18 +0000