Resolving an alembic conflict.

Upgrading libraries, and resolving issues from that upgrade, including changes to how we manage tokens.  This seems to be working locally.

Pipfile.lock

@@ -25,19 +25,11 @@
         },
         "alembic": {
             "hashes": [
-                "sha256:8a259f0a4c8b350b03579d77ce9e810b19c65bf0af05f84efb69af13ad50801e",
-                "sha256:e27fd67732c97a1c370c33169ef4578cf96436fa0e7dcfaeeef4a917d0737d56"
+                "sha256:3ff4f90d23dd283d7822d78ffbc07cb256344ae1d60500b933378bc13407efcc",
+                "sha256:d7f6d4dc6abed18e1591932a85349a7d621298ef0daa40021609cdca54a6047c"
             ],
             "index": "pypi",
-            "version": "==1.5.8"
-        },
-        "amqp": {
-            "hashes": [
-                "sha256:03e16e94f2b34c31f8bf1206d8ddd3ccaa4c315f7f6a1879b7b1210d229568c2",
-                "sha256:493a2ac6788ce270a2f6a765b017299f60c1998f5a8617908ee9be082f7300fb"
-            ],
-            "markers": "python_version >= '3.6'",
-            "version": "==5.0.6"
+            "version": "==1.6.0"
         },
         "aniso8601": {
             "hashes": [
@@ -51,16 +43,14 @@
                 "sha256:31b2eced602aa8423c2aea9c76a724617ed67cf9513173fd3a4f03e3a929c7e6",
                 "sha256:832aa3cde19744e49938b91fea06d69ecb9e649c93ba974535d08ad92164f700"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==20.3.0"
         },
         "babel": {
             "hashes": [
-                "sha256:9d35c22fcc79893c3ecc85ac4a56cde1ecf3f19c540bba0922308a6c06ca6fa5",
-                "sha256:da031ab54472314f210b0adcff1588ee5d1d1d0ba4dbd07b94dba82bde791e05"
+                "sha256:ab49e12b91d937cd11f0b67cb259a57ab4ad2b59ac7a3b41d6c06c0ac5b0def9",
+                "sha256:bc0c176f9f6a994582230df350aa6e05ba2ebe4b3ac317eab29d9be5d2768da0"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
-            "version": "==2.9.0"
+            "version": "==2.9.1"
         },
         "bcrypt": {
             "hashes": [
@@ -72,7 +62,6 @@
                 "sha256:cd1ea2ff3038509ea95f687256c46b79f5fc382ad0aa3664d200047546d511d1",
                 "sha256:cdcdcb3972027f83fe24a48b1e90ea4b584d35f1cc279d76de6fc4b13376239d"
             ],
-            "markers": "python_version >= '3.6'",
             "version": "==3.2.0"
         },
         "beautifulsoup4": {
@@ -83,27 +72,12 @@
             ],
             "version": "==4.9.3"
         },
-        "billiard": {
-            "hashes": [
-                "sha256:299de5a8da28a783d51b197d496bef4f1595dd023a93a4f59dde1886ae905547",
-                "sha256:87103ea78fa6ab4d5c751c4909bcff74617d985de7fa8b672cf8618afd5a875b"
-            ],
-            "version": "==3.6.4.0"
-        },
         "blinker": {
             "hashes": [
                 "sha256:471aee25f3992bd325afa3772f1063dbdbbca947a041b8b89466dc00d606f8b6"
             ],
             "version": "==1.4"
         },
-        "celery": {
-            "hashes": [
-                "sha256:5e8d364e058554e83bbb116e8377d90c79be254785f357cb2cec026e79febe13",
-                "sha256:f4efebe6f8629b0da2b8e529424de376494f5b7a743c321c8a2ddc2b1414921c"
-            ],
-            "markers": "python_version >= '3.6'",
-            "version": "==5.0.5"
-        },
         "certifi": {
             "hashes": [
                 "sha256:1a4995114262bffbc2413b159f2a1a480c969de6e6eb13ee966d470af86af59c",
@@ -158,7 +132,6 @@
                 "sha256:0d6f53a15db4120f2b08c94f11e7d93d2c911ee118b6b30a04ec3ee8310179fa",
                 "sha256:f864054d66fd9118f2e67044ac8981a54775ec5b67aed0441892edb553d21da5"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
             "version": "==4.0.0"
         },
         "click": {
@@ -166,29 +139,8 @@
                 "sha256:d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a",
                 "sha256:dacca89f4bfadd5de3d7489b7c8a566eee0d3676333fbb50030263894c38c0dc"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
             "version": "==7.1.2"
         },
-        "click-didyoumean": {
-            "hashes": [
-                "sha256:112229485c9704ff51362fe34b2d4f0b12fc71cc20f6d2b3afabed4b8bfa6aeb"
-            ],
-            "version": "==0.0.3"
-        },
-        "click-plugins": {
-            "hashes": [
-                "sha256:46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b",
-                "sha256:5d262006d3222f5057fd81e1623d4443e41dcda5dc815c06b442aa3c02889fc8"
-            ],
-            "version": "==1.1.1"
-        },
-        "click-repl": {
-            "hashes": [
-                "sha256:9c4c3d022789cae912aad8a3f5e1d7c2cdd016ee1225b5212ad3e8691563cda5",
-                "sha256:b9f29d52abc4d6059f8e276132a111ab8d94980afe6a5432b9d996544afa95d5"
-            ],
-            "version": "==0.1.6"
-        },
         "clickclick": {
             "hashes": [
                 "sha256:4efb13e62353e34c5eef7ed6582c4920b418d7dedc86d819e22ee089ba01802c",
@@ -203,14 +155,6 @@
             ],
             "version": "==0.9.1"
         },
-        "configparser": {
-            "hashes": [
-                "sha256:85d5de102cfe6d14a5172676f09d19c465ce63d6019cf0a4ef13385fc535e828",
-                "sha256:af59f2cdd7efbdd5d111c1976ecd0b82db9066653362f0962d7bf1d3ab89a1fa"
-            ],
-            "markers": "python_version >= '3.6'",
-            "version": "==5.0.2"
-        },
         "connexion": {
             "extras": [
                 "swagger-ui"
@@ -285,30 +229,29 @@
                 "sha256:08452d69b6b5bc66e8330adde0a4f8642e969b9e1702904d137eeb29c8ffc771",
                 "sha256:6d2de2de7931a968874481ef30208fd4e08da39177d61d3d4ebdf4366e7dbca1"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==1.2.12"
         },
         "docutils": {
             "hashes": [
-                "sha256:a71042bb7207c03d5647f280427f14bfbd1a65c9eb84f4b341d85fafb6bb4bdf",
-                "sha256:e2ffeea817964356ba4470efba7c2f42b6b0de0b04e66378507e3e2504bbff4c"
+                "sha256:0c5b78adfbf7762415433f5515cd5c9e762339e23369dbe8000d84a4bf4ab3af",
+                "sha256:c2de3a60e9e7d07be26b7f2b00ca0309c207e06c100f9cc2a94931fc75a478fc"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
-            "version": "==0.17"
+            "version": "==0.16"
         },
         "docxtpl": {
             "hashes": [
-                "sha256:18b81c072254b2eef3cbf878951a93515f4d287c319856d3dd7ada53a3ffd5ad",
-                "sha256:c26ad7a0e6e9aedc7dfaf6b09af60ee0a4f001a065896503056ce9171bd9024a"
+                "sha256:b7370b11fd226a712fcbf36ff45d34993253cce268846ee1c8309cef649cffa2",
+                "sha256:d7b78a5da704800c53e4434a7ef397faa19e56d21595af23f70b89a84e56ac1d"
             ],
             "index": "pypi",
-            "version": "==0.11.3"
+            "version": "==0.11.4"
         },
         "et-xmlfile": {
             "hashes": [
-                "sha256:614d9722d572f6246302c4491846d2c393c199cfa4edc9af593437691683335b"
+                "sha256:8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c",
+                "sha256:a2ba85d1d6a74ef63837eed693bcb89c3f752169b0e3e7ae5b16ca5e1b3deada"
             ],
-            "version": "==1.0.1"
+            "version": "==1.1.0"
         },
         "flask": {
             "hashes": [
@@ -320,10 +263,10 @@
         },
         "flask-admin": {
             "hashes": [
-                "sha256:145f59407d78319925e20f7c3021f60c71f0cacc98e916e52000845dc4c63621"
+                "sha256:eb06a1f31b98881dee53a55c64faebd1990d6aac38826364b280df0b2679ff74"
             ],
             "index": "pypi",
-            "version": "==1.5.7"
+            "version": "==1.5.8"
         },
         "flask-bcrypt": {
             "hashes": [
@@ -376,16 +319,8 @@
                 "sha256:2bda44b43e7cacb15d4e05ff3cc1f8bc97936cc464623424102bfc2c35e95912",
                 "sha256:f12c3d4cc5cc7fdcc148b9527ea05671718c3ea45d50c7e732cceb33f574b390"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==2.5.1"
         },
-        "future": {
-            "hashes": [
-                "sha256:b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d"
-            ],
-            "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'",
-            "version": "==0.18.2"
-        },
         "greenlet": {
             "hashes": [
                 "sha256:0a77691f0080c9da8dfc81e23f4e3cffa5accf0f5b56478951016d7cfead9196",
@@ -437,6 +372,7 @@
         },
         "gunicorn": {
             "hashes": [
+                "sha256:9dcc4547dbb1cb284accfb15ab5667a0e5d1881cc443e0677b4882a4067a807e",
                 "sha256:e0a968b5ba15f8a328fdfd7ab1fcb5af4470c28aaf7e55df02a99bc13138e6e8"
             ],
             "index": "pypi",
@@ -454,7 +390,6 @@
                 "sha256:b307872f855b18632ce0c21c5e45be78c0ea7ae4c15c828c20788b26921eb3f6",
                 "sha256:b97d804b1e9b523befed77c48dacec60e6dcb0b5391d57af6a65a312a90648c0"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==2.10"
         },
         "imagesize": {
@@ -462,7 +397,6 @@
                 "sha256:6965f19a6a2039c7d48bca7dba2473069ff854c36ae6f19d2cde309d998228a1",
                 "sha256:b1f6b5a4eab1f73479a50fb79fcf729514a900c341d8503d62a62dbc4127a2b1"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==1.2.0"
         },
         "inflection": {
@@ -470,7 +404,6 @@
                 "sha256:1a29730d366e996aaacffb2f1f1cb9593dc38e2ddd30c91250c6dde09ea9b417",
                 "sha256:f38b2b640938a4f35ade69ac3d053042959b62a0f1076a5bbaa1b9526605a8a2"
             ],
-            "markers": "python_version >= '3.5'",
             "version": "==0.5.1"
         },
         "isodate": {
@@ -485,7 +418,6 @@
                 "sha256:321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19",
                 "sha256:b12271b2047cb23eeb98c8b5622e2e5c5e9abd9784a153e9d8ef9cb4dd09d749"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==1.1.0"
         },
         "jinja2": {
@@ -493,7 +425,6 @@
                 "sha256:03e47ad063331dd6a3f04a43eddca8a966a26ba0c5b7207a9a9e4e08f1b29419",
                 "sha256:a6d58433de0ae800347cab1fa3043cebbabe8baa9d29e668f1c768cb87a333c6"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
             "version": "==2.11.3"
         },
         "jsonschema": {
@@ -503,21 +434,10 @@
             ],
             "version": "==3.2.0"
         },
-        "kombu": {
-            "hashes": [
-                "sha256:6dc509178ac4269b0e66ab4881f70a2035c33d3a622e20585f965986a5182006",
-                "sha256:f4965fba0a4718d47d470beeb5d6446e3357a62402b16c510b6a2f251e05ac3c"
-            ],
-            "markers": "python_version >= '3.6'",
-            "version": "==5.0.2"
-        },
         "ldap3": {
             "hashes": [
                 "sha256:18c3ee656a6775b9b0d60f7c6c5b094d878d1d90fc03d56731039f0a4b546a91",
-                "sha256:afc6fc0d01f02af82cd7bfabd3bbfd5dc96a6ae91e97db0a2dab8a0f1b436056",
-                "sha256:c1df41d89459be6f304e0ceec4b00fdea533dbbcd83c802b1272dcdb94620b57",
-                "sha256:8c949edbad2be8a03e719ba48bd6779f327ec156929562814b3e84ab56889c8c",
-                "sha256:4139c91f0eef9782df7b77c8cbc6243086affcb6a8a249b768a9658438e5da59"
+                "sha256:c1df41d89459be6f304e0ceec4b00fdea533dbbcd83c802b1272dcdb94620b57"
             ],
             "index": "pypi",
             "version": "==2.9"
@@ -527,18 +447,24 @@
                 "sha256:079f3ae844f38982d156efce585bc540c16a926d4436712cf4baee0cce487a3d",
                 "sha256:0fbcf5565ac01dff87cbfc0ff323515c823081c5777a9fc7703ff58388c258c3",
                 "sha256:122fba10466c7bd4178b07dba427aa516286b846b2cbd6f6169141917283aae2",
+                "sha256:1b38116b6e628118dea5b2186ee6820ab138dbb1e24a13e478490c7db2f326ae",
                 "sha256:1b7584d421d254ab86d4f0b13ec662a9014397678a7c4265a02a6d7c2b18a75f",
                 "sha256:26e761ab5b07adf5f555ee82fb4bfc35bf93750499c6c7614bd64d12aaa67927",
                 "sha256:289e9ca1a9287f08daaf796d96e06cb2bc2958891d7911ac7cae1c5f9e1e0ee3",
                 "sha256:2a9d50e69aac3ebee695424f7dbd7b8c6d6eb7de2a2eb6b0f6c7db6aa41e02b7",
+                "sha256:3082c518be8e97324390614dacd041bb1358c882d77108ca1957ba47738d9d59",
                 "sha256:33bb934a044cf32157c12bfcfbb6649807da20aa92c062ef51903415c704704f",
                 "sha256:3439c71103ef0e904ea0a1901611863e51f50b5cd5e8654a151740fde5e1cade",
+                "sha256:36108c73739985979bf302006527cf8a20515ce444ba916281d1c43938b8bb96",
                 "sha256:39b78571b3b30645ac77b95f7c69d1bffc4cf8c3b157c435a34da72e78c82468",
                 "sha256:4289728b5e2000a4ad4ab8da6e1db2e093c63c08bdc0414799ee776a3f78da4b",
                 "sha256:4bff24dfeea62f2e56f5bab929b4428ae6caba2d1eea0c2d6eb618e30a71e6d4",
+                "sha256:4c61b3a0db43a1607d6264166b230438f85bfed02e8cff20c22e564d0faff354",
                 "sha256:542d454665a3e277f76954418124d67516c5f88e51a900365ed54a9806122b83",
                 "sha256:5a0a14e264069c03e46f926be0d8919f4105c1623d620e7ec0e612a2e9bf1c04",
+                "sha256:5c8c163396cc0df3fd151b927e74f6e4acd67160d6c33304e805b84293351d16",
                 "sha256:66e575c62792c3f9ca47cb8b6fab9e35bab91360c783d1606f758761810c9791",
+                "sha256:6f12e1427285008fd32a6025e38e977d44d6382cf28e7201ed10d6c1698d2a9a",
                 "sha256:74f7d8d439b18fa4c385f3f5dfd11144bb87c1da034a466c5b5577d23a1d9b51",
                 "sha256:7610b8c31688f0b1be0ef882889817939490a36d0ee880ea562a4e1399c447a1",
                 "sha256:76fa7b1362d19f8fbd3e75fe2fb7c79359b0af8747e6f7141c338f0bee2f871a",
@@ -551,10 +477,14 @@
                 "sha256:b007cbb845b28db4fb8b6a5cdcbf65bacb16a8bd328b53cbc0698688a68e1caa",
                 "sha256:bc4313cbeb0e7a416a488d72f9680fffffc645f8a838bd2193809881c67dd106",
                 "sha256:bccbfc27563652de7dc9bdc595cb25e90b59c5f8e23e806ed0fd623755b6565d",
+                "sha256:c47ff7e0a36d4efac9fd692cfa33fbd0636674c102e9e8d9b26e1b93a94e7617",
                 "sha256:c4f05c5a7c49d2fb70223d0d5bcfbe474cf928310ac9fa6a7c6dddc831d0b1d4",
+                "sha256:cdaf11d2bd275bf391b5308f86731e5194a21af45fbaaaf1d9e8147b9160ea92",
                 "sha256:ce256aaa50f6cc9a649c51be3cd4ff142d67295bfc4f490c9134d0f9f6d58ef0",
                 "sha256:d2e35d7bf1c1ac8c538f88d26b396e73dd81440d59c1ef8522e1ea77b345ede4",
+                "sha256:d916d31fd85b2f78c76400d625076d9124de3e4bda8b016d25a050cc7d603f24",
                 "sha256:df7c53783a46febb0e70f6b05df2ba104610f2fb0d27023409734a3ecbb78fb2",
+                "sha256:e1cbd3f19a61e27e011e02f9600837b921ac661f0c40560eefb366e4e4fb275e",
                 "sha256:efac139c3f0bf4f0939f9375af4b02c5ad83a622de52d6dfa8e438e8e01d0eb0",
                 "sha256:efd7a09678fd8b53117f6bae4fa3825e0a22b03ef0a932e070c0bdbb3a35e654",
                 "sha256:f2380a6376dfa090227b663f9678150ef27543483055cc327555fb592c5967e2",
@@ -569,7 +499,6 @@
                 "sha256:17831f0b7087c313c0ffae2bcbbd3c1d5ba9eeac9c38f2eb7b50e8c99fe9d5ab",
                 "sha256:aea166356da44b9b830c8023cd9b557fa856bd8b4035d6de771ca027dfc5cc6e"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==1.1.4"
         },
         "markdown": {
@@ -635,7 +564,6 @@
                 "sha256:e8313f01ba26fbbe36c7be1966a7b7424942f670f38e666995b88d012765b9be",
                 "sha256:feb7b34d6325451ef96bc0e36e1a6c0c1c64bc1fbec4b854f4529e51887b1621"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==1.1.1"
         },
         "marshmallow": {
@@ -656,11 +584,11 @@
         },
         "marshmallow-sqlalchemy": {
             "hashes": [
-                "sha256:b217c6327bcf291e843dc1c2c20f0915061d4ecc303f0c5be40f23206607f702",
-                "sha256:ee3ead3b83de6608c6850ff60515691b0dc556ca226680f8a82b9f785cdb71b1"
+                "sha256:f1491f83833ac9c8406ba603458b1447fdfd904194833aab4b3cc01ef3646944",
+                "sha256:f861888ae3299f2c1f18cd94f02147ced70cd1b4986b2c5077e4a1036018d2a2"
             ],
             "index": "pypi",
-            "version": "==0.24.2"
+            "version": "==0.25.0"
         },
         "numpy": {
             "hashes": [
@@ -689,7 +617,6 @@
                 "sha256:e9459f40244bb02b2f14f6af0cd0732791d72232bbb0dc4bab57ef88e75f6935",
                 "sha256:edb1f041a9146dcf02cd7df7187db46ab524b9af2515f392f337c7cbbf5b52cd"
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@@ -698,7 +625,6 @@
                 "sha256:a4b2712020284cee880b4c55faa513fbc2f8f07f365deda6098f8ab943c9f0df",
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             "version": "==0.1.5"
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@@ -707,7 +633,6 @@
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@@ -723,38 +648,29 @@
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             "version": "==20.9"
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@@ -799,19 +715,8 @@
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@@ -820,56 +725,67 @@
                 "sha256:2d475327684562c3a96cc71adf7dc8c4f0565175cf86b6d7a404ff4c771f15f0",
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             "version": "==2.20"
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-            "version": "==1.54.1"
+            "version": "==1.55"
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-            "version": "==2.8.1"
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@@ -887,10 +803,8 @@
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@@ -940,7 +854,6 @@
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@@ -975,7 +888,6 @@
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@@ -995,18 +907,17 @@
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@@ -1014,7 +925,6 @@
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@@ -1022,7 +932,6 @@
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@@ -1030,7 +939,6 @@
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@@ -1038,7 +946,6 @@
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@@ -1046,52 +953,50 @@
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-                "sha256:4df07161897191ed8d4a0cfc92425c81296160e5c5f76c9256716d3085172883",
-                "sha256:4f7ce3bfdab6520554af4a5b1df4513d45388624d015ba4d921daf48ce1d6503",
-                "sha256:5361e25181b9872d6906c8c9be7dc05cb0a0951d71ee59ee5a71c1deb301b8a8",
-                "sha256:6f8fdad2f335d2f3ca2f3ee3b01404f7abcf519b03de2c510f1f42d16e39ffb4",
-                "sha256:70a1387396ea5b3022539b560c287daf79403d8b4b365f89b56d660e625a4457",
-                "sha256:7481f9c2c832a3bf37c80bee44d91ac9938b815cc06f7e795b976e300914aab9",
-                "sha256:7c0c7bb49167ac738ca6ee6e7f94a9988a7e4e261d8da335341e8c8c8f3b2e9b",
-                "sha256:7de84feb31af3d8fdf819cac2042928d0b60d3cb16f49c4b2f48d88db46e79f6",
-                "sha256:7f5087104c3c5af11ea59e49ae66c33ca98b14a47d3796ae97498fca53f84aef",
-                "sha256:81badd7d3e0e6aba70a5d1b50fabe8112e9835a6fdb0684054c3fe5378ce0d01",
-                "sha256:82f11b679df91275788be6734dd4a9dfa29bac67b85326992609f62b05bdab37",
-                "sha256:8301ecf3e819eb5dbc171e84654ff60872807775301a55fe35b0ab2ba3742031",
-                "sha256:8d6a9feb5efd2fdab25c6d5a0a5589fed9d789f5ec57ec12263fd0e60ce1dea6",
-                "sha256:915d4fa08776c0252dc5a34fa15c6490f66f411ea1ac9492022f98875d6baf20",
-                "sha256:94040a92b6676f9ffdab6c6b479b3554b927a635c90698c761960b266b04fc88",
-                "sha256:a08027ae84efc563f0f2f341dda572eadebeca38c0ae028a009988f27e9e6230",
-                "sha256:a103294583383660d9e06dbd82037dc8e94c184bdcb27b2be44ae4457dafc6b4",
-                "sha256:c22bfac8d3b955cdb13f0fcd6343156bf56d925196cf7d9ab9ce9f61d3f1e11c",
-                "sha256:c3810ebcf1d42c532c8f5c3f442c705d94442a27a32f2df5344f0857306ab321",
-                "sha256:ee4ddc904fb6414b5118af5b8d45e428aac2ccda01326b2ba2fe4354b0d8d1ae",
-                "sha256:f16801795f1ffe9472360589a04301018c79e4582a85e68067275bb4f765e4e2",
-                "sha256:f62c57ceadedeb8e7b98b48ac4d684bf2b0f73b9d882fed3ca260d9aedf6403f",
-                "sha256:fbb0fda1c574975807aceb0e2332e0ecfe9e5656c191ed482c1a5eafe7a33823"
+                "sha256:08a00a955c5cb1d3a610f9735e0e9ca64f2fd2540c942ab84dc9a71433940f86",
+                "sha256:1b2b0199153a4ecbb57ec09ff8a3693dcb2c134fef217379e2761f27bccf3a14",
+                "sha256:1d8a71c2bf21437d6216ba1963507d4d1a37920429eafd09d85387d0d078fa5a",
+                "sha256:36bcf7530ca070e89f29e2f6e05c5566c9ab3a2e493608437a230253ecf112a7",
+                "sha256:375cde7038d3c4493e2e61273ed2a3be04b5845e9bea5c662543c22935fb439b",
+                "sha256:384c0ecc845b597eda2519de2f8dd66770e76f8f39e0d21f00dd5affaf293787",
+                "sha256:46737cd87a57e03ab20e79d29ad931b842e7b3226a169ae9b36babe69d92256f",
+                "sha256:49fc18facca9ecb29308e486de53e7d9ab7d7b02d6705158fa34af0c1a6c3b0b",
+                "sha256:4b9e7764638910c43eea6e6e367395dce3d1c6acc17f8550e66cd913725491d2",
+                "sha256:50dba4adb0f7cafb5c05e3e9734b7d84f0b009daf17ca5a3c1560be7dbcaaba7",
+                "sha256:586eb3698e616fe044472e7a249d24a5b05dc5c714dc0b9744417031988df3af",
+                "sha256:58bee8384a7e32846e560da0ad595cf0dd5046b286aafa8d000312c5db8899bf",
+                "sha256:5e7e9a7092aea03c68318d390f39dab75422143354543244b6e1b2b31848a494",
+                "sha256:6adf973e7e27bce34c6bb14f62368b99e53a55226836ac93ff1352fe467dc966",
+                "sha256:6d01d83d290db9e27ea02183e56ba548a48143b3b1b7977d07cedafc3606f91d",
+                "sha256:6f0bd9b2cf1c555c6bfbb71d58750d096f7462a582abf6994cff80fbfe0d8c94",
+                "sha256:74cd7afd1789eabe42c838747c5680d78317aee448a22de75638ac0735ae3284",
+                "sha256:79286d63e5f92340357bc2a0801637b2accc95d7e0044768c3eea5e8271cc300",
+                "sha256:8162f379edc3c1c0c4ac7436b3a8baa8ca7754913ed81002f631bc066486803e",
+                "sha256:85bd128ebb3c47615496778fedbe334094cf6133c6933804e237c741fce4f20c",
+                "sha256:8a00c3494a1553e171c77505653cca22f5fadf09a0af4a020243f1baaad412b3",
+                "sha256:8dd79b534516b9b792dbb319324962d02c69a50a390cb2387e360bebe5d7b280",
+                "sha256:938e819bc74c95466c7f6d5dc7e2d08142c116c380992aa36d60e64e7a62ffe7",
+                "sha256:98270f1c52dc4a62279aee7c0a134e84182372e4b3c7ee35cafd906c11f4e218",
+                "sha256:9c2afd9ad52387d32b2a856b19352d605213a06b4684a3b469ff8f39a27fb3a2",
+                "sha256:a35d909327a1c3bc407689179101af93de34bc6af8c6f07d5d29e4eaab54a9f4",
+                "sha256:a63848afe8f909d1dcea286c3856c1cc1de6e8908e9ce1bdb672c9f19b2d2aa7",
+                "sha256:b12b39ded8cee6c4fdd0b8aa5afdb8cb5641098f2625acc9175effdc064b5c9f",
+                "sha256:b53a0faf32cde49eb04ad81f8ff60cfa1dcc024aa6a6bb8b545621339395e640",
+                "sha256:c9937cb1061042fb09c4b622884407525a0a595e300ef199d80a7290ca2c71ea",
+                "sha256:e21ca6ecf2a48a53856562af3380f2a64a1ce08ae2d17c800095f4685ab499b1",
+                "sha256:e25d48233f5501b41c7d561cfd9ec9c89a891643aaf282750c129d627cc5a547",
+                "sha256:e288a3640c3c9311bb223c13e6ecb2ae4c5fb018756b5fbf82b9a1f13c6c6111",
+                "sha256:ed96e1f28708c5a00fb371971d6634210afdcabb439dd488d41e1cfc2c906459"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'",
-            "version": "==1.4.5"
+            "version": "==1.4.13"
         },
         "swagger-ui-bundle": {
             "hashes": [
@@ -1106,38 +1011,20 @@
                 "sha256:2f4da4594db7e1e110a944bb1b551fdf4e6c136ad42e4234131391e21eb5b0df",
                 "sha256:e7b021f7241115872f92f43c6508082facffbd1c048e3c6e2bb9c2a157e28937"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'",
             "version": "==1.26.4"
         },
-        "vine": {
-            "hashes": [
-                "sha256:4c9dceab6f76ed92105027c49c823800dd33cacce13bdedc5b914e3514b7fb30",
-                "sha256:7d3b1624a953da82ef63462013bbd271d3eb75751489f9807598e8f340bd637e"
-            ],
-            "markers": "python_version >= '3.6'",
-            "version": "==5.0.0"
-        },
         "waitress": {
             "hashes": [
                 "sha256:29af5a53e9fb4e158f525367678b50053808ca6c21ba585754c77d790008c746",
                 "sha256:69e1f242c7f80273490d3403c3976f3ac3b26e289856936d1f620ed48f321897"
             ],
-            "markers": "python_full_version >= '3.6.0'",
             "version": "==2.0.0"
         },
-        "wcwidth": {
-            "hashes": [
-                "sha256:beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784",
-                "sha256:c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83"
-            ],
-            "version": "==0.2.5"
-        },
         "webob": {
             "hashes": [
                 "sha256:73aae30359291c14fa3b956f8b5ca31960e420c28c1bec002547fb04928cf89b",
                 "sha256:b64ef5141be559cfade448f044fa45c2260351edcb6a8ef6b7e00c7dcef0c323"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==1.8.7"
         },
         "webtest": {
@@ -1179,11 +1066,11 @@
         },
         "xlsxwriter": {
             "hashes": [
-                "sha256:2b7e22b1268c2ed85d73e5629097c9a63357f2429667ada9863cd05ff8ee33aa",
-                "sha256:30ebc19d0f201fafa34a6c622050ed2a268ac8dee24037a61605caa801dc8af5"
+                "sha256:1a6dd98892e8010d3e089d1cb61385baa8f76fa547598df2c221cc37238c72d3",
+                "sha256:82be5a58c09bdc2ff8afc25acc815c465275239ddfc56d6e7b2a7e6c5d2e213b"
             ],
             "index": "pypi",
-            "version": "==1.3.8"
+            "version": "==1.4.0"
         }
     },
     "develop": {
@@ -1192,7 +1079,6 @@
                 "sha256:31b2eced602aa8423c2aea9c76a724617ed67cf9513173fd3a4f03e3a929c7e6",
                 "sha256:832aa3cde19744e49938b91fea06d69ecb9e649c93ba974535d08ad92164f700"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==20.3.0"
         },
         "coverage": {
@@ -1265,23 +1151,21 @@
                 "sha256:5b327ac1320dc863dca72f4514ecc086f31186744b84a230374cc1fd776feae5",
                 "sha256:67714da7f7bc052e064859c05c595155bd1ee9f69f76557e21f051443c20947a"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==20.9"
         },
         "pbr": {
             "hashes": [
-                "sha256:5fad80b613c402d5b7df7bd84812548b2a61e9977387a80a5fc5c396492b13c9",
-                "sha256:b236cde0ac9a6aedd5e3c34517b423cd4fd97ef723849da6b0d2231142d89c00"
+                "sha256:42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd",
+                "sha256:c68c661ac5cc81058ac94247278eeda6d2e6aecb3e227b0387c30d277e7ef8d4"
             ],
             "index": "pypi",
-            "version": "==5.5.1"
+            "version": "==5.6.0"
         },
         "pluggy": {
             "hashes": [
                 "sha256:15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0",
                 "sha256:966c145cd83c96502c3c3868f50408687b38434af77734af1e9ca461a4081d2d"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==0.13.1"
         },
         "py": {
@@ -1289,7 +1173,6 @@
                 "sha256:21b81bda15b66ef5e1a777a21c4dcd9c20ad3efd0b3f817e7a809035269e1bd3",
                 "sha256:3b80836aa6d1feeaa108e046da6423ab8f6ceda6468545ae8d02d9d58d18818a"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==1.10.0"
         },
         "pyparsing": {
@@ -1297,23 +1180,21 @@
                 "sha256:c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1",
                 "sha256:ef9d7589ef3c200abe66653d3f1ab1033c3c419ae9b9bdb1240a85b024efc88b"
             ],
-            "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==2.4.7"
         },
         "pytest": {
             "hashes": [
-                "sha256:671238a46e4df0f3498d1c3270e5deb9b32d25134c99b7d75370a68cfbe9b634",
-                "sha256:6ad9c7bdf517a808242b998ac20063c41532a570d088d77eec1ee12b0b5574bc"
+                "sha256:50bcad0a0b9c5a72c8e4e7c9855a3ad496ca6a881a3641b4260605450772c54b",
+                "sha256:91ef2131a9bd6be8f76f1f08eac5c5317221d6ad1e143ae03894b862e8976890"
             ],
             "index": "pypi",
-            "version": "==6.2.3"
+            "version": "==6.2.4"
         },
         "toml": {
             "hashes": [
                 "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b",
                 "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"
             ],
-            "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==0.10.2"
         }
     }

crc/api/study.py

@@ -33,7 +33,7 @@ def add_study(body):
 
     errors = StudyService._add_all_workflow_specs_to_study(study_model)
     session.commit()
-    study = StudyService().get_study(study_model.id)
+    study = StudyService().get_study(study_model.id, do_status=True)
     study_data = StudySchema().dump(study)
     study_data["errors"] = ApiErrorSchema(many=True).dump(errors)
     return study_data

crc/api/user.py

@@ -214,7 +214,7 @@ def _handle_login(user_info: LdapModel, redirect_url=None):
     g.user = user
 
     # Return the frontend auth callback URL, with auth token appended.
-    auth_token = user.encode_auth_token().decode()
+    auth_token = user.encode_auth_token()
     g.token = auth_token
 
     if redirect_url is not None:

migrations/versions/665624ac29f1_.py

@@ -19,12 +19,11 @@ depends_on = None
 def upgrade():
     # ### commands auto generated by Alembic - please adjust! ###
     op.add_column('data_store', sa.Column('file_id', sa.Integer(), nullable=True))
-    op.create_foreign_key(None, 'data_store', 'file', ['file_id'], ['id'])
+    op.create_foreign_key('file_id_key', 'data_store', 'file', ['file_id'], ['id'])
     # ### end Alembic commands ###
 
-
 def downgrade():
     # ### commands auto generated by Alembic - please adjust! ###
-    op.drop_constraint(None, 'data_store', type_='foreignkey')
+    op.drop_constraint('file_id_key', 'data_store', type_='foreignkey')
     op.drop_column('data_store', 'file_id')
     # ### end Alembic commands ###

migrations/versions/c1449d1d1681_.py

@@ -0,0 +1,24 @@
+"""empty message
+
+Revision ID: c1449d1d1681
+Revises: abeffe547305, 8b976945a54e, 62910318009f
+Create Date: 2021-05-04 13:20:55.447143
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'c1449d1d1681'
+down_revision = ('abeffe547305', '8b976945a54e', '62910318009f')
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    pass
+
+
+def downgrade():
+    pass

tests/base_test.py

@@ -131,7 +131,7 @@ class BaseTest(unittest.TestCase):
         user = UserService.current_user(allow_admin_impersonate=True)
         self.assertEqual(uid, user.uid, 'Logged in user should match given user uid')
 
-        return dict(Authorization='Bearer ' + user_model.encode_auth_token().decode())
+        return dict(Authorization='Bearer ' + user_model.encode_auth_token())
 
     def delete_example_data(self, use_crc_data=False, use_rrt_data=False):
         """

tests/files/test_file_service.py

@@ -15,7 +15,7 @@ class FakeGithubCreates(Mock):
             def get_repo(var, name):
                 class FakeRepo(Mock):
                     def get_contents(var, filename, ref):
-                        raise UnknownObjectException(status='Failure', data='Failed data')
+                        raise UnknownObjectException(status='Failure', data='Failed data', headers=[])
                     def update_file(var, path, message, content, sha, branch):
                         pass
                 return FakeRepo()

tests/study/test_study_api.py

@@ -1,8 +1,8 @@
 import json
 from profile import Profile
+from tests.base_test import BaseTest
 
 from crc.services.ldap_service import LdapService
-from tests.base_test import BaseTest
 
 from datetime import datetime, timezone
 from unittest.mock import patch
@@ -113,10 +113,9 @@ class TestStudyApi(BaseTest):
         self.assertEqual(study["ind_number"], db_study.ind_number)
         self.assertEqual(study["user_uid"], db_study.user_uid)
 
-        workflow_spec_count =session.query(WorkflowSpecModel).filter(WorkflowSpecModel.is_master_spec == False).count()
+        workflow_spec_count =session.query(WorkflowSpecModel).count()
         workflow_count = session.query(WorkflowModel).filter(WorkflowModel.study_id == study['id']).count()
-        error_count = len(study["errors"])
-        self.assertEqual(workflow_spec_count, workflow_count + error_count)
+        self.assertEqual(workflow_spec_count, workflow_count)
 
         study_event = session.query(StudyEvent).first()
         self.assertIsNotNone(study_event)

tests/test_authentication.py

@@ -33,7 +33,7 @@ class TestAuthentication(BaseTest):
         user_1 = UserModel(uid="dhf8r")
         expected_exp_1 = timegm((datetime.utcnow() + timedelta(hours=new_ttl)).utctimetuple())
         auth_token_1 = user_1.encode_auth_token()
-        self.assertTrue(isinstance(auth_token_1, bytes))
+        self.assertTrue(isinstance(auth_token_1, str))
         self.assertEqual("dhf8r", user_1.decode_auth_token(auth_token_1).get("sub"))
         #actual_exp_1 = user_1.decode_auth_token(auth_token_1).get("exp")
         #self.assertTrue(expected_exp_1 - 1000 <= actual_exp_1 <= expected_exp_1 + 1000)
@@ -131,7 +131,7 @@ class TestAuthentication(BaseTest):
 
         admin_user = self._login_as_admin()
         admin_study = self._make_fake_study(admin_user.uid)
-        admin_token_headers = dict(Authorization='Bearer ' + admin_user.encode_auth_token().decode())
+        admin_token_headers = dict(Authorization='Bearer ' + admin_user.encode_auth_token())
 
         rv_add_study = self.app.post(
             '/v1.0/study',
@@ -164,7 +164,7 @@ class TestAuthentication(BaseTest):
 
         # Non-admin user should not be able to delete a study
         non_admin_user = self._login_as_non_admin()
-        non_admin_token_headers = dict(Authorization='Bearer ' + non_admin_user.encode_auth_token().decode())
+        non_admin_token_headers = dict(Authorization='Bearer ' + non_admin_user.encode_auth_token())
         non_admin_study = self._make_fake_study(non_admin_user.uid)
 
         rv_add_study = self.app.post(
@@ -211,7 +211,7 @@ class TestAuthentication(BaseTest):
         self.load_example_data()
 
         admin_user = self._login_as_admin()
-        admin_token_headers = dict(Authorization='Bearer ' + admin_user.encode_auth_token().decode())
+        admin_token_headers = dict(Authorization='Bearer ' + admin_user.encode_auth_token())
 
         # User should not be in the system yet.
         non_admin_user = session.query(UserModel).filter(UserModel.uid == self.non_admin_uid).first()
@@ -230,7 +230,7 @@ class TestAuthentication(BaseTest):
         self.logout()
         non_admin_user = self._login_as_non_admin()
         self.assertEqual(non_admin_user.uid, self.non_admin_uid)
-        non_admin_token_headers = dict(Authorization='Bearer ' + non_admin_user.encode_auth_token().decode())
+        non_admin_token_headers = dict(Authorization='Bearer ' + non_admin_user.encode_auth_token())
 
         # Add a study for the non-admin user
         non_admin_study = self._make_fake_study(self.non_admin_uid)