Refactor/clean up correlations (#4)

* initial commit for Refactor/clean-up-correlation

* add python scipy dependency

* initial commit for sample correlation

* initial commit for sample correlation endpoint

* initial commit for integration and unittest

* initial commit for registering  correlation blueprint

* add and modify unittest and integration tests for correlation

* Add compute compute_all_sample_corr   method for correlation

* add scipy to requirement txt file

* add tissue correlation for trait list

* add unittest for tissue correlation

* add lit correlation for trait list

* add unittests for lit correlation for trait list

* modify lit correlarion for trait list

* add unittests for lit correlation for trait list

* add correlation metho  in dynamic url

* add file format for expected structure input  while doing sample correlation

* modify input data structure -> add  trait id

* update tests for sample r correlation

* add compute all lit correlation method

* add endpoint for computing lit_corr

* add unit and integration tests for computing lit corr

* add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation

* add unittest and integration tests for tissue correlation

Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>

2 files changed, 306 insertions, 0 deletions

diff --git a/tests/unit/computations/correlation_test_data/target_dataset.json b/tests/unit/computations/correlation_test_data/target_dataset.json
new file mode 100644
index 0000000..f6757b6
--- /dev/null
+++ b/tests/unit/computations/correlation_test_data/target_dataset.json
@@ -0,0 +1,230 @@
+[
+   {
+      "trait_id":"1425637_at",
+      "sample_data":{
+         "BXD1":7.081,
+         "BXD2":6.912,
+         "BXD5":7.153,
+         "BXD6":6.92,
+         "BXD8":6.886,
+         "BXD9":7.406,
+         "BXD11":6.917,
+         "BXD12":6.914,
+         "BXD13":6.964,
+         "BXD15":6.863,
+         "BXD16":7.06,
+         "BXD19":7.002,
+         "BXD20":7.158,
+         "BXD21":7.039,
+         "BXD22":7.036,
+         "BXD23":6.962,
+         "BXD24":6.946,
+         "BXD27":7.084,
+         "BXD28":7.154,
+         "BXD29":6.932,
+         "BXD31":6.994,
+         "BXD32":6.846,
+         "BXD33":7.078,
+         "BXD34":6.94,
+         "BXD38":6.992,
+         "BXD39":7.048,
+         "BXD40":7.14,
+         "BXD42":6.98,
+         "BXD43":7.072,
+         "BXD44":7.045,
+         "BXD45":6.739,
+         "BXD48":7.07,
+         "BXD48a":6.998,
+         "BXD50":7.053,
+         "BXD51":6.922,
+         "BXD55":6.782,
+         "BXD60":7.042,
+         "BXD61":6.887,
+         "BXD62":6.86,
+         "BXD63":6.815,
+         "BXD64":7.424,
+         "BXD65":7.216,
+         "BXD65a":6.934,
+         "BXD65b":6.893,
+         "BXD66":6.935,
+         "BXD67":6.985,
+         "BXD68":7.044,
+         "BXD69":6.908,
+         "BXD70":6.864,
+         "BXD73":7.074,
+         "BXD73a":6.986,
+         "BXD74":6.914,
+         "BXD75":6.98,
+         "BXD76":6.772,
+         "BXD77":7.121,
+         "BXD79":6.829,
+         "BXD83":7.018,
+         "BXD84":6.948,
+         "BXD85":7.112,
+         "BXD86":6.858,
+         "BXD87":6.865,
+         "BXD89":7.034,
+         "BXD90":6.901,
+         "BXD93":6.97,
+         "BXD94":7.112,
+         "BXD98":6.954,
+         "BXD99":6.912,
+         "C57BL/6J":7.121,
+         "DBA/2J":6.821,
+         "B6D2F1":6.998,
+         "D2B6F1":6.967
+      }
+   },
+   {
+      "trait_id":"1455376_at",
+      "trait_sample_data":{
+         "BXD1":10.929,
+         "BXD2":11.279,
+         "BXD5":11.941,
+         "BXD6":11.407,
+         "BXD8":12.048,
+         "BXD9":11.694,
+         "BXD11":11.534,
+         "BXD12":11.048,
+         "BXD13":12.274,
+         "BXD15":12.077,
+         "BXD16":11.91,
+         "BXD19":11.797,
+         "BXD20":11.67,
+         "BXD21":12.062,
+         "BXD22":12.49,
+         "BXD23":11.957,
+         "BXD24":11.766,
+         "BXD27":13.026,
+         "BXD28":12.184,
+         "BXD29":11.792,
+         "BXD31":12.36,
+         "BXD32":10.608,
+         "BXD33":11.817,
+         "BXD34":11.213,
+         "BXD38":11.212,
+         "BXD39":12.023,
+         "BXD40":12.892,
+         "BXD42":11.518,
+         "BXD43":12.306,
+         "BXD44":11.932,
+         "BXD45":10.982,
+         "BXD48":12.055,
+         "BXD48a":12.572,
+         "BXD50":11.696,
+         "BXD51":11.828,
+         "BXD55":10.523,
+         "BXD60":11.403,
+         "BXD61":11.378,
+         "BXD62":11.887,
+         "BXD63":11.776,
+         "BXD64":12.37,
+         "BXD65":11.122,
+         "BXD65a":10.853,
+         "BXD65b":11.46,
+         "BXD66":11.546,
+         "BXD67":12.198,
+         "BXD68":13.21,
+         "BXD69":11.581,
+         "BXD70":12.338,
+         "BXD73":11.876,
+         "BXD73a":11.75,
+         "BXD74":11.898,
+         "BXD75":11.718,
+         "BXD76":11.926,
+         "BXD77":12.326,
+         "BXD79":12.052,
+         "BXD83":11.478,
+         "BXD84":11.494,
+         "BXD85":11.435,
+         "BXD86":11.476,
+         "BXD87":11.456,
+         "BXD89":11.547,
+         "BXD90":12.452,
+         "BXD93":12.921,
+         "BXD94":11.892,
+         "BXD98":12.614,
+         "BXD99":13.142,
+         "C57BL/6J":12.138,
+         "DBA/2J":11.394,
+         "B6D2F1":11.615,
+         "D2B6F1":11.918
+      }
+   },
+   {
+      "trait_id":"1444351_at",
+      "trait_sample_data":{
+         "BXD1":17.847,
+         "BXD2":15.262,
+         "BXD5":18.054,
+         "BXD6":17.24,
+         "BXD8":15.735,
+         "BXD9":17.876,
+         "BXD11":17.359,
+         "BXD12":17.906,
+         "BXD13":16.084,
+         "BXD15":17.173,
+         "BXD16":15.941,
+         "BXD19":17.721,
+         "BXD20":17.548,
+         "BXD21":17.242,
+         "BXD22":17.012,
+         "BXD23":17.139,
+         "BXD24":17.904,
+         "BXD27":17.008,
+         "BXD28":17.441,
+         "BXD29":17.606,
+         "BXD31":17.35,
+         "BXD32":17.859,
+         "BXD33":17.453,
+         "BXD34":15.924,
+         "BXD38":17.271,
+         "BXD39":18.034,
+         "BXD40":17.844,
+         "BXD42":17.444,
+         "BXD43":17.676,
+         "BXD44":17.71,
+         "BXD45":17.059,
+         "BXD48":17.334,
+         "BXD48a":17.398,
+         "BXD50":17.343,
+         "BXD51":17.514,
+         "BXD55":14.995,
+         "BXD60":18.03,
+         "BXD61":17.628,
+         "BXD62":17.431,
+         "BXD63":16.96,
+         "BXD64":18.199,
+         "BXD65":17.593,
+         "BXD65a":17.49,
+         "BXD65b":17.268,
+         "BXD66":16.602,
+         "BXD67":17.306,
+         "BXD68":17.167,
+         "BXD69":17.706,
+         "BXD70":17.287,
+         "BXD73":17.412,
+         "BXD73a":16.224,
+         "BXD74":16.873,
+         "BXD75":17.202,
+         "BXD76":16.934,
+         "BXD77":17.926,
+         "BXD79":16.55,
+         "BXD83":17.042,
+         "BXD84":17.134,
+         "BXD85":18.021,
+         "BXD86":17.194,
+         "BXD87":17.075,
+         "BXD89":17.511,
+         "BXD90":17.168,
+         "BXD93":17.817,
+         "BXD94":18.04,
+         "BXD98":16.744,
+         "BXD99":17.304,
+         "C57BL/6J":17.084,
+         "DBA/2J":17.316,
+         "B6D2F1":16.964,
+         "D2B6F1":17.086
+      }
+   }
+]
\ No newline at end of file
diff --git a/tests/unit/computations/correlation_test_data/this_trait_data.json b/tests/unit/computations/correlation_test_data/this_trait_data.json
new file mode 100644
index 0000000..7c57fdb
--- /dev/null
+++ b/tests/unit/computations/correlation_test_data/this_trait_data.json
@@ -0,0 +1,76 @@
+{
+  "trait_id":"1457784_at",
+  "trait_sample_data":{
+  "BXD1": 6.03,
+  "BXD2": 6.001,
+  "BXD5": 6.154,
+  "BXD6": 6.179,
+  "BXD8": 6.2,
+  "BXD9": 6.062,
+  "BXD11": 6.12,
+  "BXD12": 6.159,
+  "BXD13": 6.153,
+  "BXD15": 6.144,
+  "BXD16": 6.212,
+  "BXD19": 6.206,
+  "BXD20": 6.008,
+  "BXD21": 6.062,
+  "BXD22": 6.042,
+  "BXD23": 6.135,
+  "BXD24": 6.144,
+  "BXD27": 6.316,
+  "BXD28": 6.14,
+  "BXD29": 6.222,
+  "BXD31": 6.211,
+  "BXD32": 5.984,
+  "BXD33": 6.128,
+  "BXD34": 6.086,
+  "BXD38": 6.342,
+  "BXD39": 6.111,
+  "BXD40": 6.136,
+  "BXD42": 6.201,
+  "BXD43": 5.934,
+  "BXD44": 6.116,
+  "BXD45": 6.226,
+  "BXD48": 6.228,
+  "BXD48a": 6.16,
+  "BXD50": 5.92,
+  "BXD51": 6.227,
+  "BXD55": 6.137,
+  "BXD60": 5.932,
+  "BXD61": 6.18,
+  "BXD62": 6.188,
+  "BXD63": 6.134,
+  "BXD64": 6.102,
+  "BXD65": 6.258,
+  "BXD65a": 6.031,
+  "BXD65b": 6.088,
+  "BXD66": 6.07,
+  "BXD67": 6.275,
+  "BXD68": 6.116,
+  "BXD69": 6.031,
+  "BXD70": 6.14,
+  "BXD73": 6.089,
+  "BXD73a": 6.195,
+  "BXD74": 5.971,
+  "BXD75": 5.972,
+  "BXD76": 6.125,
+  "BXD77": 6.107,
+  "BXD79": 6.288,
+  "BXD83": 6.119,
+  "BXD84": 6.102,
+  "BXD85": 5.959,
+  "BXD86": 6.249,
+  "BXD87": 6.172,
+  "BXD89": 6.13,
+  "BXD90": 6.162,
+  "BXD93": 6.19,
+  "BXD94": 6.068,
+  "BXD98": 6.137,
+  "BXD99": 6.252,
+  "C57BL/6J": 6.255,
+  "DBA/2J": 6.14,
+  "B6D2F1": 6.223,
+  "D2B6F1": 6.038
+}
+}
\ No newline at end of file