Merge pull request #139 from asherpasha/dev

Fixed ATTED service.

Author: asherpasha

requirements.txt

@@ -3,20 +3,22 @@ appdirs==1.4.4
 async-timeout==4.0.2
 attrs==21.4.0
 black==22.3.0
-certifi==2021.10.8
+cachelib==0.7.0
+certifi==2022.5.18.1
 cffi==1.15.0
 chardet==4.0.0
 charset-normalizer==2.0.12
-click==8.1.2
-coverage==6.3.2
-cryptography==36.0.2
+click==8.1.3
+commonmark==0.9.1
+coverage==6.4.1
+cryptography==37.0.2
 Deprecated==1.2.13
 docopt==0.6.2
 flake8==4.0.1
-Flask==2.1.1
-Flask-Caching==1.10.1
+Flask==2.1.2
+Flask-Caching==1.11.1
 Flask-Cors==3.0.10
-Flask-Limiter==2.3.2
+Flask-Limiter==2.4.5.1
 flask-marshmallow==0.14.0
 flask-restx==0.5.1
 Flask-SQLAlchemy==2.5.1
@@ -25,13 +27,13 @@ idna==3.3
 importlib-metadata==4.2.0
 iniconfig==1.1.1
 itsdangerous==2.1.2
-Jinja2==3.1.1
-jsonschema==4.4.0
-limits==2.5.2
+Jinja2==3.1.2
+jsonschema==4.6.0
+limits==2.6.3
 MarkupSafe==2.1.1
-marshmallow==3.15.0
+marshmallow==3.16.0
 mccabe==0.6.1
-more-itertools==8.12.0
+more-itertools==8.13.0
 mypy-extensions==0.4.3
 mysqlclient==2.1.0
 numpy==1.21.5
@@ -44,23 +46,25 @@ py==1.11.0
 pycodestyle==2.8.0
 pycparser==2.21
 pyflakes==2.4.0
-pyparsing==3.0.8
+Pygments==2.12.0
+pyparsing==3.0.9
 pyrsistent==0.18.1
-pytest==7.1.1
+pytest==7.1.2
 python-dateutil==2.8.2
 pytz==2022.1
-redis==4.2.2
-regex==2022.3.15
+redis==4.3.3
+regex==2022.6.2
 requests==2.27.1
+rich==12.4.4
 scour==0.38.2
 six==1.16.0
-SQLAlchemy==1.4.35
+SQLAlchemy==1.4.37
 toml==0.10.2
 tomli==2.0.1
-typed-ast==1.5.3
+typed-ast==1.5.4
 typing_extensions==4.2.0
 urllib3==1.26.9
 wcwidth==0.2.5
-Werkzeug==2.1.1
-wrapt==1.14.0
+Werkzeug==2.1.2
+wrapt==1.14.1
 zipp==3.8.0

tests/data/get_atted_api4.json

@@ -8,8 +8,8 @@
     "type": null,
     "value": null,
     "topN": 5,
-    "database": "Ath-u.c2-0",
-    "database_version": "c2-0"
+    "database": "Ath-u.c3-0",
+    "database_version": "c3-0"
   },
   "result_set": [
     {
@@ -18,32 +18,32 @@
         {
           "gene": 831644,
           "other_id": "AT5G17760",
-          "mutual_rank": 482.65,
-          "logit_score": 5.2584
+          "mutual_rank": 509.98,
+          "logit_score": 5.1768
         },
         {
           "gene": 842367,
           "other_id": "AT1G60730",
-          "mutual_rank": 767.19,
-          "logit_score": 4.5674
+          "mutual_rank": 807.94,
+          "logit_score": 4.4895
         },
         {
           "gene": 837321,
           "other_id": "AT1G08050",
-          "mutual_rank": 1076.41,
-          "logit_score": 4.0541
+          "mutual_rank": 1125.71,
+          "logit_score": 3.9855
         },
         {
-          "gene": 814770,
-          "other_id": "AT2G02390",
-          "mutual_rank": 1148.08,
-          "logit_score": 3.9553
+          "gene": 844034,
+          "other_id": "AT1G76980",
+          "mutual_rank": 1134.11,
+          "logit_score": 3.9741
         },
         {
-          "gene": 832064,
-          "other_id": "AT5G19440",
-          "mutual_rank": 1148.08,
-          "logit_score": 3.9553
+          "gene": 814770,
+          "other_id": "AT2G02390",
+          "mutual_rank": 1186.04,
+          "logit_score": 3.9053
         }
       ],
       "other_id": "AT1G01010"