sartography/cr-connect-workflow
1
0
Fork 0
mirror of https://github.com/sartography/cr-connect-workflow.git synced 2025-02-20 11:48:16 +00:00
Code Issues Packages Projects Releases Wiki Activity

Merge branch 'dev' into 321-Markdown-Macro

Browse Source
This commit is contained in:
Dan Funk 2021-05-14 12:32:41 -04:00 committed by GitHub
commit 99da502912
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
61 changed files with 850 additions and 419 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

389
Pipfile.lock generated
View File

@ -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"
],
"markers": "python_version >= '3.7'",
"version": "==1.20.2"
},
"openapi-schema-validator": {
@ -698,7 +625,6 @@
"sha256:a4b2712020284cee880b4c55faa513fbc2f8f07f365deda6098f8ab943c9f0df",
"sha256:b65d6c2242620bfe76d4c749b61cd9657e4528895a8f4fb6f916085b508ebd24"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
"version": "==0.1.5"
},
"openapi-spec-validator": {
@ -707,7 +633,6 @@
"sha256:53ba3d884e98ff2062d5ada025aa590541dcd665b8f81067dc82dd61c0923759",
"sha256:e11df7c559339027bd04f2399bc82474983129a6a7a6a0421eaa95e2c844d686"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
"version": "==0.3.0"
},
"openpyxl": {
@ -723,38 +648,29 @@
"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"
},
"pandas": {
"hashes": [
"sha256:09761bf5f8c741d47d4b8b9073288de1be39bbfccc281d70b889ade12b2aad29",
"sha256:0f27fd1adfa256388dc34895ca5437eaf254832223812afd817a6f73127f969c",
"sha256:43e00770552595c2250d8d712ec8b6e08ca73089ac823122344f023efa4abea3",
"sha256:46fc671c542a8392a4f4c13edc8527e3a10f6cb62912d856f82248feb747f06e",
"sha256:475b7772b6e18a93a43ea83517932deff33954a10d4fbae18d0c1aba4182310f",
"sha256:4d821b9b911fc1b7d428978d04ace33f0af32bb7549525c8a7b08444bce46b74",
"sha256:5e3c8c60541396110586bcbe6eccdc335a38e7de8c217060edaf4722260b158f",
"sha256:621c044a1b5e535cf7dcb3ab39fca6f867095c3ef223a524f18f60c7fee028ea",
"sha256:72ffcea00ae8ffcdbdefff800284311e155fbb5ed6758f1a6110fc1f8f8f0c1c",
"sha256:8a051e957c5206f722e83f295f95a2cf053e890f9a1fba0065780a8c2d045f5d",
"sha256:97b1954533b2a74c7e20d1342c4f01311d3203b48f2ebf651891e6a6eaf01104",
"sha256:9f5829e64507ad10e2561b60baf285c470f3c4454b007c860e77849b88865ae7",
"sha256:a93e34f10f67d81de706ce00bf8bb3798403cabce4ccb2de10c61b5ae8786ab5",
"sha256:d59842a5aa89ca03c2099312163ffdd06f56486050e641a45d926a072f04d994",
"sha256:dbb255975eb94143f2e6ec7dadda671d25147939047839cd6b8a4aff0379bb9b",
"sha256:df6f10b85aef7a5bb25259ad651ad1cc1d6bb09000595cab47e718cbac250b1d"
"sha256:167693a80abc8eb28051fbd184c1b7afd13ce2c727a5af47b048f1ea3afefff4",
"sha256:2111c25e69fa9365ba80bbf4f959400054b2771ac5d041ed19415a8b488dc70a",
"sha256:298f0553fd3ba8e002c4070a723a59cdb28eda579f3e243bc2ee397773f5398b",
"sha256:2b063d41803b6a19703b845609c0b700913593de067b552a8b24dd8eeb8c9895",
"sha256:2cb7e8f4f152f27dc93f30b5c7a98f6c748601ea65da359af734dd0cf3fa733f",
"sha256:52d2472acbb8a56819a87aafdb8b5b6d2b3386e15c95bde56b281882529a7ded",
"sha256:612add929bf3ba9d27b436cc8853f5acc337242d6b584203f207e364bb46cb12",
"sha256:649ecab692fade3cbfcf967ff936496b0cfba0af00a55dfaacd82bdda5cb2279",
"sha256:68d7baa80c74aaacbed597265ca2308f017859123231542ff8a5266d489e1858",
"sha256:8d4c74177c26aadcfb4fd1de6c1c43c2bf822b3e0fc7a9b409eeaf84b3e92aaa",
"sha256:971e2a414fce20cc5331fe791153513d076814d30a60cd7348466943e6e909e4",
"sha256:9db70ffa8b280bb4de83f9739d514cd0735825e79eef3a61d312420b9f16b758",
"sha256:b730add5267f873b3383c18cac4df2527ac4f0f0eed1c6cf37fcb437e25cf558",
"sha256:bd659c11a4578af740782288cac141a322057a2e36920016e0fc7b25c5a4b686",
"sha256:c601c6fdebc729df4438ec1f62275d6136a0dd14d332fc0e8ce3f7d2aadb4dd6",
"sha256:d0877407359811f7b853b548a614aacd7dea83b0c0c84620a9a643f180060950"
],
"index": "pypi",
"version": "==1.2.3"
},
"prompt-toolkit": {
"hashes": [
"sha256:bf00f22079f5fadc949f42ae8ff7f05702826a97059ffcc6281036ad40ac6f04",
"sha256:e1b4f11b9336a28fa11810bc623c357420f69dfdb6d2dac41ca2c21a55c033bc"
],
"markers": "python_full_version >= '3.6.1'",
"version": "==3.0.18"
"version": "==1.2.4"
},
"psycopg2-binary": {
"hashes": [
@ -799,19 +715,8 @@
},
"pyasn1": {
"hashes": [
"sha256:e89bf84b5437b532b0803ba5c9a5e054d21fec423a89952a74f87fa2c9b7bce2",
"sha256:0458773cfe65b153891ac249bcf1b5f8f320b7c2ce462151f8fa74de8934becf",
"sha256:99fcc3c8d804d1bc6d9a099921e39d827026409a58f2a720dcdb89374ea0c776",
"sha256:aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba",
"sha256:08c3c53b75eaa48d71cf8c710312316392ed40899cb34710d092e96745a358b7",
"sha256:39c7e2ec30515947ff4e87fb6f456dfc6e84857d34be479c9d4a4ba4bf46aa5d",
"sha256:78fa6da68ed2727915c4767bb386ab32cdba863caa7dbe473eaae45f9959da86",
"sha256:014c0e9976956a08139dc0712ae195324a75e142284d5f87f1a87ee1b068a359",
"sha256:03840c999ba71680a131cfaee6fab142e1ed9bbd9c693e285cc6aca0d555e576",
"sha256:5c9414dcfede6e441f7e8f81b43b34e834731003427e5b09e4e00e3172a10f00",
"sha256:7ab8a544af125fb704feadb008c99a88805126fb525280b2270bb25cc1d78a12",
"sha256:fec3e9d8e36808a28efb59b489e4528c10ad0f480e57dcc32b4de5c9d8c9fdf3",
"sha256:6e7545f1a61025a4e58bb336952c5061697da694db1cae97b116e9c46abcf7c8"
"sha256:aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba"
],
"version": "==0.4.8"
},
@ -820,56 +725,67 @@
"sha256:2d475327684562c3a96cc71adf7dc8c4f0565175cf86b6d7a404ff4c771f15f0",
"sha256:7582ad22678f0fcd81102833f60ef8d0e57288b6b5fb00323d101be910e35705"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==2.20"
},
"pygithub": {
"hashes": [
"sha256:300bc16e62886ca6537b0830e8f516ea4bc3ef12d308e0c5aff8bdbd099173d4",
"sha256:87afd6a67ea582aa7533afdbf41635725f13d12581faed7e3e04b1579c0c0627"
"sha256:1bbfff9372047ff3f21d5cd8e07720f3dbfdaf6462fcaed9d815f528f1ba7283",
"sha256:2caf0054ea079b71e539741ae56c5a95e073b81fa472ce222e81667381b9601b"
],
"index": "pypi",
"version": "==1.54.1"
"version": "==1.55"
},
"pygments": {
"hashes": [
"sha256:2656e1a6edcdabf4275f9a3640db59fd5de107d88e8663c5d4e9a0fa62f77f94",
"sha256:534ef71d539ae97d4c3a4cf7d6f110f214b0e687e92f9cb9d2a3b0d3101289c8"
"sha256:a18f47b506a429f6f4b9df81bb02beab9ca21d0a5fee38ed15aef65f0545519f",
"sha256:d66e804411278594d764fc69ec36ec13d9ae9147193a1740cd34d272ca383b8e"
],
"markers": "python_version >= '3.5'",
"version": "==2.8.1"
"version": "==2.9.0"
},
"pyjwt": {
"hashes": [
"sha256:5c6eca3c2940464d106b99ba83b00c6add741c9becaec087fb7ccdefea71350e",
"sha256:8d59a976fb773f3e6a39c85636357c4f0e242707394cadadd9814f5cbaa20e96"
"sha256:934d73fbba91b0483d3857d1aff50e96b2a892384ee2c17417ed3203f173fca1",
"sha256:fba44e7898bbca160a2b2b501f492824fc8382485d3a6f11ba5d0c1937ce6130"
],
"index": "pypi",
"version": "==1.7.1"
"version": "==2.1.0"
},
"pynacl": {
"hashes": [
"sha256:06cbb4d9b2c4bd3c8dc0d267416aaed79906e7b33f114ddbf0911969794b1cc4",
"sha256:11335f09060af52c97137d4ac54285bcb7df0cef29014a1a4efe64ac065434c4",
"sha256:2fe0fc5a2480361dcaf4e6e7cea00e078fcda07ba45f811b167e3f99e8cff574",
"sha256:30f9b96db44e09b3304f9ea95079b1b7316b2b4f3744fe3aaecccd95d547063d",
"sha256:4e10569f8cbed81cb7526ae137049759d2a8d57726d52c1a000a3ce366779634",
"sha256:511d269ee845037b95c9781aa702f90ccc36036f95d0f31373a6a79bd8242e25",
"sha256:537a7ccbea22905a0ab36ea58577b39d1fa9b1884869d173b5cf111f006f689f",
"sha256:54e9a2c849c742006516ad56a88f5c74bf2ce92c9f67435187c3c5953b346505",
"sha256:757250ddb3bff1eecd7e41e65f7f833a8405fede0194319f87899690624f2122",
"sha256:7757ae33dae81c300487591c68790dfb5145c7d03324000433d9a2c141f82af7",
"sha256:7c6092102219f59ff29788860ccb021e80fffd953920c4a8653889c029b2d420",
"sha256:8122ba5f2a2169ca5da936b2e5a511740ffb73979381b4229d9188f6dcb22f1f",
"sha256:9c4a7ea4fb81536c1b1f5cc44d54a296f96ae78c1ebd2311bd0b60be45a48d96",
"sha256:c914f78da4953b33d4685e3cdc7ce63401247a21425c16a39760e282075ac4a6",
"sha256:cd401ccbc2a249a47a3a1724c2918fcd04be1f7b54eb2a5a71ff915db0ac51c6",
"sha256:d452a6746f0a7e11121e64625109bc4468fc3100452817001dbe018bb8b08514",
"sha256:ea6841bc3a76fa4942ce00f3bda7d436fda21e2d91602b9e21b7ca9ecab8f3ff",
"sha256:f8851ab9041756003119368c1e6cd0b9c631f46d686b3904b18c0139f4419f80"
],
"version": "==1.4.0"
},
"pyparsing": {
"hashes": [
"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"
},
"pyrsistent": {
"hashes": [
"sha256:2e636185d9eb976a18a8a8e96efce62f2905fea90041958d8cc2a189756ebf3e"
],
"markers": "python_version >= '3.5'",
"version": "==0.17.3"
},
"python-box": {
"hashes": [
"sha256:4ed4ef5d34de505a65c01e3f1911de8cdb29484fcae0c035141dce535c6c194a",
"sha256:f2a531f9f5bbef078c175fad6abb31e9b59d40d121ea79993197e6bb221c6be6"
],
"markers": "python_version >= '3.6'",
"version": "==5.3.0"
},
"python-dateutil": {
"hashes": [
"sha256:73ebfe9dbf22e832286dafa60473e4cd239f8592f699aa5adaf10050e6e1823c",
@ -887,10 +803,8 @@
"python-editor": {
"hashes": [
"sha256:1bf6e860a8ad52a14c3ee1252d5dc25b2030618ed80c022598f00176adc8367d",
"sha256:ea87e17f6ec459e780e4221f295411462e0d0810858e055fc514684350a2f522",
"sha256:c3da2053dbab6b29c94e43c486ff67206eafbe7eb52dbec7390b5e2fb05aac77",
"sha256:5f98b069316ea1c2ed3f67e7f5df6c0d8f10b689964a4a811ff64f0106819ec8",
"sha256:51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b"
"sha256:51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b",
"sha256:5f98b069316ea1c2ed3f67e7f5df6c0d8f10b689964a4a811ff64f0106819ec8"
],
"version": "==1.0.4"
},
@ -940,7 +854,6 @@
"sha256:fdc842473cd33f45ff6bce46aea678a54e3d21f1b61a7750ce3c498eedfe25d6",
"sha256:fe69978f3f768926cfa37b867e3843918e012cf83f680806599ddce33c2c68b0"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'",
"version": "==5.4.1"
},
"recommonmark": {
@ -972,11 +885,10 @@
},
"six": {
"hashes": [
"sha256:30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259",
"sha256:8b74bedcbbbaca38ff6d7491d76f2b06b3592611af620f8426e82dddb04a5ced"
"sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926",
"sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==1.15.0"
"version": "==1.16.0"
},
"snowballstemmer": {
"hashes": [
@ -995,18 +907,17 @@
},
"sphinx": {
"hashes": [
"sha256:3f01732296465648da43dec8fb40dc451ba79eb3e2cc5c6d79005fd98197107d",
"sha256:ce9c228456131bab09a3d7d10ae58474de562a6f79abb3dc811ae401cf8c1abc"
"sha256:19010b7b9fa0dc7756a6e105b2aacd3a80f798af3c25c273be64d7beeb482cb1",
"sha256:2320d4e994a191f4b4be27da514e46b3d6b420f2ff895d064f52415d342461e8"
],
"index": "pypi",
"version": "==3.5.3"
"version": "==3.5.4"
},
"sphinxcontrib-applehelp": {
"hashes": [
"sha256:806111e5e962be97c29ec4c1e7fe277bfd19e9652fb1a4392105b43e01af885a",
"sha256:a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58"
],
"markers": "python_version >= '3.5'",
"version": "==1.0.2"
},
"sphinxcontrib-devhelp": {
@ -1014,7 +925,6 @@
"sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e",
"sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4"
],
"markers": "python_version >= '3.5'",
"version": "==1.0.2"
},
"sphinxcontrib-htmlhelp": {
@ -1022,7 +932,6 @@
"sha256:3c0bc24a2c41e340ac37c85ced6dafc879ab485c095b1d65d2461ac2f7cca86f",
"sha256:e8f5bb7e31b2dbb25b9cc435c8ab7a79787ebf7f906155729338f3156d93659b"
],
"markers": "python_version >= '3.5'",
"version": "==1.0.3"
},
"sphinxcontrib-jsmath": {
@ -1030,7 +939,6 @@
"sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178",
"sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"
],
"markers": "python_version >= '3.5'",
"version": "==1.0.1"
},
"sphinxcontrib-qthelp": {
@ -1038,7 +946,6 @@
"sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72",
"sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"
],
"markers": "python_version >= '3.5'",
"version": "==1.0.3"
},
"sphinxcontrib-serializinghtml": {
@ -1046,52 +953,50 @@
"sha256:eaa0eccc86e982a9b939b2b82d12cc5d013385ba5eadcc7e4fed23f4405f77bc",
"sha256:f242a81d423f59617a8e5cf16f5d4d74e28ee9a66f9e5b637a18082991db5a9a"
],
"markers": "python_version >= '3.5'",
"version": "==1.1.4"
},
"spiffworkflow": {
"git": "https://github.com/sartography/SpiffWorkflow.git",
"ref": "382048e31e872d23188fab6bec68323f593ccc19"
"ref": "1a44d004d657bc5773551254aafba88993ae6d35"
},
"sqlalchemy": {
"hashes": [
"sha256:02b039e0e7e6de2f15ea2d2de3995e31a170e700ec0b37b4eded662171711d19",
"sha256:08943201a1e3c6238e48f4d5d56c27ea1e1b39d3d9f36a9d81fc3cfb0e1b83bd",
"sha256:0ee0054d4a598d2920cae14bcbd33e200e02c5e3b47b902627f8cf5d4c9a2a4b",
"sha256:11e7a86209f69273e75d2dd64b06c0c2660e39cd942fce2170515c404ed7358a",
"sha256:1294f05916c044631fd626a4866326bbfbd17f62bd37510d000afaef4b35bd74",
"sha256:2f11b5783933bff55291ca06496124347627d211ff2e509e846af1c35de0a3fb",
"sha256:301d0cd6ef1dc73b607748183da857e712d6f743de8d92b1e1f8facfb0ba2aa2",
"sha256:344b58b4b4193b72e8b768a51ef6eb5a4c948ce313a0f23e2ea081e71ce8ac0e",
"sha256:44e11a06168782b6d485daef197783366ce7ab0d5eea0066c899ae06cef47bbc",
"sha256:45b091ccbf94374ed14abde17e9a04522b0493a17282eaaf4383efdd413f5243",
"sha256:48540072f43b3c080159ec1f24a4b014c0ee83d3b73795399974aa358a8cf71b",
"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"
}
}

1
config/default.py
View File

@ -60,6 +60,7 @@ PB_INVESTIGATORS_URL = environ.get('PB_INVESTIGATORS_URL', default=PB_BASE_URL +
PB_REQUIRED_DOCS_URL = environ.get('PB_REQUIRED_DOCS_URL', default=PB_BASE_URL + "required_docs?studyid=%i")
PB_STUDY_DETAILS_URL = environ.get('PB_STUDY_DETAILS_URL', default=PB_BASE_URL + "study?studyid=%i")
PB_SPONSORS_URL = environ.get('PB_SPONSORS_URL', default=PB_BASE_URL + "sponsors?studyid=%i")
PB_IRB_INFO_URL = environ.get('PB_IRB_INFO_URL', default=PB_BASE_URL + "current_irb_info/%i")
# Ldap Configuration
LDAP_URL = environ.get('LDAP_URL', default="ldap.virginia.edu").strip('/') # No trailing slash or http://

42
crc/api.yml
View File

@ -83,6 +83,8 @@ paths:
type : integer
get:
operationId: crc.api.file.get_document_directory
security:
- auth_admin: ['secret']
summary: Returns a directory of all files for study in a nested structure
tags:
- Document Categories
@ -349,6 +351,12 @@ paths:
schema:
type: integer
format: int32
- name: update_status
in: query
required: false
description: If set to true, will synch the study with protocol builder and assure the status of all workflows is up to date (expensive).
schema:
type: boolean
get:
operationId: crc.api.study.get_study
summary: Provides a single study
@ -425,7 +433,7 @@ paths:
- name: spec_id
in: path
required: true
description: The unique id of an existing workflow specification to modify.
description: The unique id of an existing workflow specification.
schema:
type: string
get:
@ -440,6 +448,18 @@ paths:
application/json:
schema:
$ref: "#/components/schemas/WorkflowSpec"
post:
operationId: crc.api.workflow.get_workflow_from_spec
summary: Creates a workflow from a workflow spec and returns the workflow
tags:
- Workflow Specifications
responses:
'200':
description: Workflow generated successfully
content:
application/json:
schema:
$ref: "#/components/schemas/Workflow"
put:
operationId: crc.api.workflow.update_workflow_specification
security:
@ -469,6 +489,21 @@ paths:
responses:
'204':
description: The workflow specification has been removed.
/workflow-specification/standalone:
get:
operationId: crc.api.workflow.standalone_workflow_specs
summary: Provides a list of workflow specifications that can be run outside a study.
tags:
- Workflow Specifications
responses:
'200':
description: A list of workflow specifications
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/WorkflowSpec"
/workflow-specification/{spec_id}/validate:
parameters:
- name: spec_id
@ -1571,6 +1606,9 @@ components:
category_id:
type: integer
nullable: true
standalone:
type: boolean
example: false
workflow_spec_category:
$ref: "#/components/schemas/WorkflowSpecCategory"
is_status:
@ -1643,6 +1681,8 @@ components:
type: integer
num_tasks_incomplete:
type: integer
study_id:
type: integer
example:
id: 291234

4
crc/api/data_store.py
View File

@ -55,7 +55,7 @@ def update_datastore(id, body):
raise ApiError('unknown_item', 'The item "' + id + '" is not recognized.')
DataStoreSchema().load(body, instance=item, session=session)
item.last_updated = datetime.now()
item.last_updated = datetime.utcnow()
session.add(item)
session.commit()
return DataStoreSchema().dump(item)
@ -87,7 +87,7 @@ def add_datastore(body):
'but not more than one of these')
item = DataStoreSchema().load(body)
item.last_updated = datetime.now()
item.last_updated = datetime.utcnow()
session.add(item)
session.commit()
return DataStoreSchema().dump(item)

10
crc/api/study.py
View File

@ -23,7 +23,7 @@ def add_study(body):
study_model = StudyModel(user_uid=UserService.current_user().uid,
title=body['title'],
primary_investigator_id=body['primary_investigator_id'],
last_updated=datetime.now(),
last_updated=datetime.utcnow(),
status=StudyStatus.in_progress)
session.add(study_model)
StudyService.add_study_update_event(study_model,
@ -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
@ -51,7 +51,7 @@ def update_study(study_id, body):
study: Study = StudyForUpdateSchema().load(body)
status = StudyStatus(study.status)
study_model.last_updated = datetime.now()
study_model.last_updated = datetime.utcnow()
if study_model.status != status:
study_model.status = status
@ -74,8 +74,8 @@ def update_study(study_id, body):
return StudySchema().dump(study)
def get_study(study_id):
study = StudyService.get_study(study_id)
def get_study(study_id, update_status=False):
study = StudyService.get_study(study_id, do_status=update_status)
if (study is None):
raise ApiError("unknown_study", 'The study "' + study_id + '" is not recognized.', status_code=404)
return StudySchema().dump(study)

2
crc/api/user.py
View File

@ -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:

21
crc/api/workflow.py
View File

@ -101,6 +101,24 @@ def delete_workflow_specification(spec_id):
session.commit()
def get_workflow_from_spec(spec_id):
workflow_model = WorkflowService.get_workflow_from_spec(spec_id, g.user)
processor = WorkflowProcessor(workflow_model)
processor.do_engine_steps()
processor.save()
WorkflowService.update_task_assignments(processor)
workflow_api_model = WorkflowService.processor_to_workflow_api(processor)
return WorkflowApiSchema().dump(workflow_api_model)
def standalone_workflow_specs():
schema = WorkflowSpecModelSchema(many=True)
specs = WorkflowService.get_standalone_workflow_specs()
return schema.dump(specs)
def get_workflow(workflow_id, do_engine_steps=True):
"""Retrieve workflow based on workflow_id, and return it in the last saved State.
If do_engine_steps is False, return the workflow without running any engine tasks or logging any events. """
@ -185,9 +203,6 @@ def update_task(workflow_id, task_id, body, terminate_loop=None, update_all=Fals
if workflow_model is None:
raise ApiError("invalid_workflow_id", "The given workflow id is not valid.", status_code=404)
elif workflow_model.study is None:
raise ApiError("invalid_study", "There is no study associated with the given workflow.", status_code=404)
processor = WorkflowProcessor(workflow_model)
task_id = uuid.UUID(task_id)
spiff_task = processor.bpmn_workflow.get_task(task_id)

9
crc/api/workflow_sync.py
View File

@ -184,9 +184,12 @@ def update_or_create_current_file(remote,workflow_spec_id,updatefile):
currentfile.content_type = updatefile['content_type']
currentfile.primary_process_id = updatefile['primary_process_id']
session.add(currentfile)
content = WorkflowSyncService.get_remote_file_by_hash(remote, updatefile['md5_hash'])
FileService.update_file(currentfile, content, updatefile['type'])
try:
content = WorkflowSyncService.get_remote_file_by_hash(remote, updatefile['md5_hash'])
FileService.update_file(currentfile, content, updatefile['type'])
except ApiError:
# Remote files doesn't exist, don't update it.
print("Remote file " + currentfile.name + " does not exist, so not syncing.")
def sync_changed_files(remote,workflow_spec_id):
"""

7
crc/models/api_models.py
View File

@ -191,7 +191,7 @@ class DocumentDirectory(object):
class WorkflowApi(object):
def __init__(self, id, status, next_task, navigation,
spec_version, is_latest_spec, workflow_spec_id, total_tasks, completed_tasks,
last_updated, is_review, title):
last_updated, is_review, title, study_id):
self.id = id
self.status = status
self.next_task = next_task # The next task that requires user input.
@ -204,13 +204,14 @@ class WorkflowApi(object):
self.last_updated = last_updated
self.title = title
self.is_review = is_review
self.study_id = study_id or ''
class WorkflowApiSchema(ma.Schema):
class Meta:
model = WorkflowApi
fields = ["id", "status", "next_task", "navigation",
"workflow_spec_id", "spec_version", "is_latest_spec", "total_tasks", "completed_tasks",
"last_updated", "is_review", "title"]
"last_updated", "is_review", "title", "study_id"]
unknown = INCLUDE
status = EnumField(WorkflowStatus)
@ -221,7 +222,7 @@ class WorkflowApiSchema(ma.Schema):
def make_workflow(self, data, **kwargs):
keys = ['id', 'status', 'next_task', 'navigation',
'workflow_spec_id', 'spec_version', 'is_latest_spec', "total_tasks", "completed_tasks",
"last_updated", "is_review", "title"]
"last_updated", "is_review", "title", "study_id"]
filtered_fields = {key: data[key] for key in keys}
filtered_fields['next_task'] = TaskSchema().make_task(data['next_task'])
return WorkflowApi(**filtered_fields)

2
crc/models/data_store.py
View File

@ -10,7 +10,7 @@ from crc import db, ma
class DataStoreModel(db.Model):
__tablename__ = 'data_store'
id = db.Column(db.Integer, primary_key=True)
last_updated = db.Column(db.DateTime(timezone=True), default=func.now())
last_updated = db.Column(db.DateTime(timezone=True), server_default=func.now())
key = db.Column(db.String, nullable=False)
workflow_id = db.Column(db.Integer)
study_id = db.Column(db.Integer, nullable=True)

14
crc/models/file.py
View File

@ -1,7 +1,7 @@
import enum
from typing import cast
from marshmallow import INCLUDE, EXCLUDE
from marshmallow import INCLUDE, EXCLUDE, fields, Schema
from marshmallow_enum import EnumField
from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
from sqlalchemy import func, Index
@ -65,11 +65,13 @@ class FileDataModel(db.Model):
md5_hash = db.Column(UUID(as_uuid=True), unique=False, nullable=False)
data = deferred(db.Column(db.LargeBinary)) # Don't load it unless you have to.
version = db.Column(db.Integer, default=0)
date_created = db.Column(db.DateTime(timezone=True), default=func.now())
size = db.Column(db.Integer, default=0)
date_created = db.Column(db.DateTime(timezone=True), server_default=func.now())
file_model_id = db.Column(db.Integer, db.ForeignKey('file.id'))
file_model = db.relationship("FileModel", foreign_keys=[file_model_id])
class FileModel(db.Model):
__tablename__ = 'file'
id = db.Column(db.Integer, primary_key=True)
@ -117,11 +119,13 @@ class File(object):
if data_model:
instance.last_modified = data_model.date_created
instance.latest_version = data_model.version
instance.size = data_model.size
else:
instance.last_modified = None
instance.latest_version = None
return instance
class FileModelSchema(SQLAlchemyAutoSchema):
class Meta:
model = FileModel
@ -132,17 +136,19 @@ class FileModelSchema(SQLAlchemyAutoSchema):
type = EnumField(FileType)
class FileSchema(ma.Schema):
class FileSchema(Schema):
class Meta:
model = File
fields = ["id", "name", "is_status", "is_reference", "content_type",
"primary", "primary_process_id", "workflow_spec_id", "workflow_id",
"irb_doc_code", "last_modified", "latest_version", "type", "categories",
"description", "category", "description", "download_name"]
"description", "category", "description", "download_name", "size"]
unknown = INCLUDE
type = EnumField(FileType)
class LookupFileModel(db.Model):
"""Gives us a quick way to tell what kind of lookup is set on a form field.
Connected to the file data model, so that if a new version of the same file is

2
crc/models/ldap.py
View File

@ -15,7 +15,7 @@ class LdapModel(db.Model):
department = db.Column(db.String)
affiliation = db.Column(db.String)
sponsor_type = db.Column(db.String)
date_cached = db.Column(db.DateTime(timezone=True), default=func.now())
date_cached = db.Column(db.DateTime(timezone=True), server_default=func.now())
@classmethod
def from_entry(cls, entry):

4
crc/models/study.py
View File

@ -41,7 +41,7 @@ class StudyModel(db.Model):
id = db.Column(db.Integer, primary_key=True)
title = db.Column(db.String)
short_title = db.Column(db.String, nullable=True)
last_updated = db.Column(db.DateTime(timezone=True), default=func.now())
last_updated = db.Column(db.DateTime(timezone=True), server_default=func.now())
status = db.Column(db.Enum(StudyStatus))
irb_status = db.Column(db.Enum(IrbStatus))
primary_investigator_id = db.Column(db.String, nullable=True)
@ -85,7 +85,7 @@ class StudyEvent(db.Model):
id = db.Column(db.Integer, primary_key=True)
study_id = db.Column(db.Integer, db.ForeignKey(StudyModel.id), nullable=False)
study = db.relationship(StudyModel, back_populates='events_history')
create_date = db.Column(db.DateTime(timezone=True), default=func.now())
create_date = db.Column(db.DateTime(timezone=True), server_default=func.now())
status = db.Column(db.Enum(StudyStatus))
comment = db.Column(db.String, default='')
event_type = db.Column(db.Enum(StudyEventType))

5
crc/models/task_event.py
View File

@ -5,12 +5,13 @@ from crc import db, ma
from crc.models.study import StudyModel, StudySchema, WorkflowMetadataSchema, WorkflowMetadata
from crc.models.workflow import WorkflowModel
from crc.services.ldap_service import LdapService
from sqlalchemy import func
class TaskEventModel(db.Model):
__tablename__ = 'task_event'
id = db.Column(db.Integer, primary_key=True)
study_id = db.Column(db.Integer, db.ForeignKey('study.id'), nullable=False)
study_id = db.Column(db.Integer, db.ForeignKey('study.id'))
user_uid = db.Column(db.String, nullable=False) # In some cases the unique user id may not exist in the db yet.
workflow_id = db.Column(db.Integer, db.ForeignKey('workflow.id'), nullable=False)
workflow_spec_id = db.Column(db.String, db.ForeignKey('workflow_spec.id'))
@ -27,7 +28,7 @@ class TaskEventModel(db.Model):
mi_count = db.Column(db.Integer)
mi_index = db.Column(db.Integer)
process_name = db.Column(db.String)
date = db.Column(db.DateTime)
date = db.Column(db.DateTime(timezone=True),default=func.now())
class TaskEventModelSchema(SQLAlchemyAutoSchema):

5
crc/models/workflow.py
View File

@ -3,6 +3,7 @@ import enum
import marshmallow
from marshmallow import EXCLUDE
from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
from sqlalchemy import func
from crc import db
from crc.models.file import FileModel, FileDataModel
@ -33,6 +34,7 @@ class WorkflowSpecModel(db.Model):
category_id = db.Column(db.Integer, db.ForeignKey('workflow_spec_category.id'), nullable=True)
category = db.relationship("WorkflowSpecCategoryModel")
is_master_spec = db.Column(db.Boolean, default=False)
standalone = db.Column(db.Boolean, default=False)
class WorkflowSpecModelSchema(SQLAlchemyAutoSchema):
@ -87,7 +89,8 @@ class WorkflowModel(db.Model):
workflow_spec = db.relationship("WorkflowSpecModel")
total_tasks = db.Column(db.Integer, default=0)
completed_tasks = db.Column(db.Integer, default=0)
last_updated = db.Column(db.DateTime)
last_updated = db.Column(db.DateTime(timezone=True), server_default=func.now())
user_id = db.Column(db.String, default=None)
# Order By is important or generating hashes on reviews.
dependencies = db.relationship(WorkflowSpecDependencyFile, cascade="all, delete, delete-orphan",
order_by="WorkflowSpecDependencyFile.file_data_id")

5
crc/scripts/complete_template.py
View File

@ -114,7 +114,10 @@ Takes two arguments:
doc_context = self.rich_text_update(doc_context)
doc_context = self.append_images(doc, doc_context, image_file_data)
jinja_env = jinja2.Environment(autoescape=True)
doc.render(doc_context, jinja_env)
try:
doc.render(doc_context, jinja_env)
except Exception as e:
print (e)
target_stream = BytesIO()
doc.save(target_stream)
target_stream.seek(0) # move to the beginning of the stream.

2
crc/scripts/data_store_base.py
View File

@ -76,7 +76,7 @@ class DataStoreBase(object):
workflow_id=workflow_id,
spec_id=workflow_spec_id)
study.value = args[1]
study.last_updated = datetime.now()
study.last_updated = datetime.utcnow()
overwritten = self.overwritten(study.value, prev_value)
session.add(study)
session.commit()

4
crc/scripts/file_data_get.py
View File

@ -10,7 +10,9 @@ class FileDataGet(Script, DataStoreBase):
return """Gets user data from the data store - takes only two keyword arguments arguments: 'file_id' and 'key' """
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
self.do_task(task, study_id, workflow_id, *args, **kwargs)
if self.validate_kw_args(**kwargs):
myargs = [kwargs['key']]
return True
def validate_kw_args(self,**kwargs):
if kwargs.get('key',None) is None:

6
crc/scripts/file_data_set.py
View File

@ -10,7 +10,11 @@ class FileDataSet(Script, DataStoreBase):
return """Sets data the data store - takes three keyword arguments arguments: 'file_id' and 'key' and 'value'"""
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
self.do_task(task, study_id, workflow_id, *args, **kwargs)
if self.validate_kw_args(**kwargs):
myargs = [kwargs['key'],kwargs['value']]
fileid = kwargs['file_id']
del(kwargs['file_id'])
return True
def validate_kw_args(self,**kwargs):
if kwargs.get('key',None) is None:

24
crc/scripts/get_irb_info.py Normal file
View File

@ -0,0 +1,24 @@
from crc.scripts.script import Script
from crc.api.common import ApiError
from crc.services.protocol_builder import ProtocolBuilderService
class IRBInfo(Script):
pb = ProtocolBuilderService()
def get_description(self):
return """Returns the IRB Info data for a Study"""
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
return isinstance(study_id, int)
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
irb_info = self.pb.get_irb_info(study_id)
if irb_info:
return irb_info
else:
raise ApiError.from_task(code='missing_irb_info',
message=f'There was a problem retrieving IRB Info for study {study_id}.',
task=task)

4
crc/services/cache_service.py
View File

@ -10,7 +10,7 @@ def firsttime():
def sincetime(txt,lasttime):
thistime=firsttime()
print('%s runtime was %2f'%(txt,thistime-lasttime))
print('%2.4f sec | %s' % (thistime-lasttime, txt))
return thistime
def timeit(f):
@ -20,7 +20,7 @@ def timeit(f):
ts = time.time()
result = f(*args, **kw)
te = time.time()
print('func:%r args:[%r, %r] took: %2.4f sec' % (f.__name__, args, kw, te-ts))
print('%2.4f sec | func:%r args:[%r, %r] ' % (te-ts, f.__name__, args, kw))
return result
return timed

7
crc/services/file_service.py
View File

@ -14,6 +14,7 @@ from sqlalchemy.exc import IntegrityError
from crc import session, app
from crc.api.common import ApiError
from crc.models.data_store import DataStoreModel
from crc.models.file import FileType, FileDataModel, FileModel, LookupFileModel, LookupDataModel
from crc.models.workflow import WorkflowSpecModel, WorkflowModel, WorkflowSpecDependencyFile
from crc.services.cache_service import cache
@ -175,6 +176,8 @@ class FileService(object):
order_by(desc(FileDataModel.date_created)).first()
md5_checksum = UUID(hashlib.md5(binary_data).hexdigest())
size = len(binary_data)
if (latest_data_model is not None) and (md5_checksum == latest_data_model.md5_hash):
# This file does not need to be updated, it's the same file. If it is arhived,
# then de-arvhive it.
@ -210,7 +213,8 @@ class FileService(object):
new_file_data_model = FileDataModel(
data=binary_data, file_model_id=file_model.id, file_model=file_model,
version=version, md5_hash=md5_checksum, date_created=datetime.now()
version=version, md5_hash=md5_checksum, date_created=datetime.utcnow(),
size=size
)
session.add_all([file_model, new_file_data_model])
session.commit()
@ -389,6 +393,7 @@ class FileService(object):
session.query(LookupDataModel).filter_by(lookup_file_model_id=lf.id).delete()
session.query(LookupFileModel).filter_by(id=lf.id).delete()
session.query(FileDataModel).filter_by(file_model_id=file_id).delete()
session.query(DataStoreModel).filter_by(file_id=file_id).delete()
session.query(FileModel).filter_by(id=file_id).delete()
session.commit()
except IntegrityError as ie:

5
crc/services/protocol_builder.py
View File

@ -14,6 +14,7 @@ class ProtocolBuilderService(object):
REQUIRED_DOCS_URL = app.config['PB_REQUIRED_DOCS_URL']
STUDY_DETAILS_URL = app.config['PB_STUDY_DETAILS_URL']
SPONSORS_URL = app.config['PB_SPONSORS_URL']
IRB_INFO_URL = app.config['PB_IRB_INFO_URL']
@staticmethod
def is_enabled():
@ -55,6 +56,10 @@ class ProtocolBuilderService(object):
def get_study_details(study_id) -> {}:
return ProtocolBuilderService.__make_request(study_id, ProtocolBuilderService.STUDY_DETAILS_URL)
@staticmethod
def get_irb_info(study_id) -> {}:
return ProtocolBuilderService.__make_request(study_id, ProtocolBuilderService.IRB_INFO_URL)
@staticmethod
def get_sponsors(study_id) -> {}:
return ProtocolBuilderService.__make_request(study_id, ProtocolBuilderService.SPONSORS_URL)

5
crc/services/study_service.py
View File

@ -55,7 +55,7 @@ class StudyService(object):
return studies
@staticmethod
def get_study(study_id, study_model: StudyModel = None, do_status=True):
def get_study(study_id, study_model: StudyModel = None, do_status=False):
"""Returns a study model that contains all the workflows organized by category.
IMPORTANT: This is intended to be a lightweight call, it should never involve
loading up and executing all the workflows in a study to calculate information."""
@ -508,8 +508,9 @@ class StudyService(object):
def _create_workflow_model(study: StudyModel, spec):
workflow_model = WorkflowModel(status=WorkflowStatus.not_started,
study=study,
user_id=None,
workflow_spec_id=spec.id,
last_updated=datetime.now())
last_updated=datetime.utcnow())
session.add(workflow_model)
session.commit()
return workflow_model

4
crc/services/workflow_processor.py
View File

@ -42,7 +42,7 @@ class CustomBpmnScriptEngine(BpmnScriptEngine):
"""
return self.evaluate_expression(task, expression)
@timeit
def execute(self, task: SpiffTask, script, data):
study_id = task.workflow.data[WorkflowProcessor.STUDY_ID_KEY]
@ -219,7 +219,7 @@ class WorkflowProcessor(object):
self.workflow_model.status = self.get_status()
self.workflow_model.total_tasks = len(tasks)
self.workflow_model.completed_tasks = sum(1 for t in tasks if t.state in complete_states)
self.workflow_model.last_updated = datetime.now()
self.workflow_model.last_updated = datetime.utcnow()
self.update_dependencies(self.spec_data_files)
session.add(self.workflow_model)
session.commit()

76
crc/services/workflow_service.py
View File

@ -57,13 +57,15 @@ class WorkflowService(object):
user = db.session.query(UserModel).filter_by(uid="test").first()
if not user:
db.session.add(UserModel(uid="test"))
db.session.commit()
study = db.session.query(StudyModel).filter_by(user_uid="test").first()
if not study:
db.session.add(StudyModel(user_uid="test", title="test"))
db.session.commit()
study = db.session.query(StudyModel).filter_by(user_uid="test").first()
workflow_model = WorkflowModel(status=WorkflowStatus.not_started,
workflow_spec_id=spec_id,
last_updated=datetime.now(),
last_updated=datetime.utcnow(),
study=study)
return workflow_model
@ -408,7 +410,8 @@ class WorkflowService(object):
completed_tasks=processor.workflow_model.completed_tasks,
last_updated=processor.workflow_model.last_updated,
is_review=is_review,
title=spec.display_name
title=spec.display_name,
study_id=processor.workflow_model.study_id or None
)
if not next_task: # The Next Task can be requested to be a certain task, useful for parallel tasks.
# This may or may not work, sometimes there is no next task to complete.
@ -667,30 +670,39 @@ class WorkflowService(object):
@staticmethod
def get_users_assigned_to_task(processor, spiff_task) -> List[str]:
if not hasattr(spiff_task.task_spec, 'lane') or spiff_task.task_spec.lane is None:
associated = StudyService.get_study_associates(processor.workflow_model.study.id)
return [user['uid'] for user in associated if user['access']]
if spiff_task.task_spec.lane not in spiff_task.data:
return [] # No users are assignable to the task at this moment
lane_users = spiff_task.data[spiff_task.task_spec.lane]
if not isinstance(lane_users, list):
lane_users = [lane_users]
if processor.workflow_model.study_id is None and processor.workflow_model.user_id is None:
raise ApiError.from_task(code='invalid_workflow',
message='A workflow must have either a study_id or a user_id.',
task=spiff_task)
# Standalone workflow - we only care about the current user
elif processor.workflow_model.study_id is None and processor.workflow_model.user_id is not None:
return [processor.workflow_model.user_id]
# Workflow associated with a study - get all the users
else:
if not hasattr(spiff_task.task_spec, 'lane') or spiff_task.task_spec.lane is None:
associated = StudyService.get_study_associates(processor.workflow_model.study.id)
return [user['uid'] for user in associated if user['access']]
if spiff_task.task_spec.lane not in spiff_task.data:
return [] # No users are assignable to the task at this moment
lane_users = spiff_task.data[spiff_task.task_spec.lane]
if not isinstance(lane_users, list):
lane_users = [lane_users]
lane_uids = []
for user in lane_users:
if isinstance(user, dict):
if 'value' in user and user['value'] is not None:
lane_uids.append(user['value'])
lane_uids = []
for user in lane_users:
if isinstance(user, dict):
if 'value' in user and user['value'] is not None:
lane_uids.append(user['value'])
else:
raise ApiError.from_task(code="task_lane_user_error", message="Spiff Task %s lane user dict must have a key called 'value' with the user's uid in it." %
spiff_task.task_spec.name, task=spiff_task)
elif isinstance(user, str):
lane_uids.append(user)
else:
raise ApiError.from_task(code="task_lane_user_error", message="Spiff Task %s lane user dict must have a key called 'value' with the user's uid in it." %
spiff_task.task_spec.name, task=spiff_task)
elif isinstance(user, str):
lane_uids.append(user)
else:
raise ApiError.from_task(code="task_lane_user_error", message="Spiff Task %s lane user is not a string or dict" %
spiff_task.task_spec.name, task=spiff_task)
raise ApiError.from_task(code="task_lane_user_error", message="Spiff Task %s lane user is not a string or dict" %
spiff_task.task_spec.name, task=spiff_task)
return lane_uids
return lane_uids
@staticmethod
def log_task_action(user_uid, processor, spiff_task, action):
@ -714,7 +726,7 @@ class WorkflowService(object):
mi_count=task.multi_instance_count, # This is the number of times the task could repeat.
mi_index=task.multi_instance_index, # And the index of the currently repeating task.
process_name=task.process_name,
date=datetime.now(),
date=datetime.utcnow(),
)
db.session.add(task_event)
db.session.commit()
@ -783,3 +795,19 @@ class WorkflowService(object):
for workflow in workflows:
if workflow.status == WorkflowStatus.user_input_required or workflow.status == WorkflowStatus.waiting:
WorkflowProcessor.reset(workflow, clear_data=False)
@staticmethod
def get_workflow_from_spec(workflow_spec_id, user):
workflow_model = WorkflowModel(status=WorkflowStatus.not_started,
study=None,
user_id=user.uid,
workflow_spec_id=workflow_spec_id,
last_updated=datetime.now())
db.session.add(workflow_model)
db.session.commit()
return workflow_model
@staticmethod
def get_standalone_workflow_specs():
specs = db.session.query(WorkflowSpecModel).filter_by(standalone=True).all()
return specs

2
crc/services/workflow_sync.py
View File

@ -47,6 +47,6 @@ class WorkflowSyncService(object):
return json.loads(response.text)
else:
raise ApiError("workflow_sync_error",
"Received an invalid response from the protocol builder (status %s): %s when calling "
"Received an invalid response from the remote CR-Connect API (status %s): %s when calling "
"url '%s'." %
(response.status_code, response.text, url))

5
example_data.py
View File

@ -266,7 +266,7 @@ class ExampleDataLoader:
from_tests=True)
def create_spec(self, id, name, display_name="", description="", filepath=None, master_spec=False,
category_id=None, display_order=None, from_tests=False):
category_id=None, display_order=None, from_tests=False, standalone=False):
"""Assumes that a directory exists in static/bpmn with the same name as the given id.
further assumes that the [id].bpmn is the primary file for the workflow.
returns an array of data models to be added to the database."""
@ -278,7 +278,8 @@ class ExampleDataLoader:
description=description,
is_master_spec=master_spec,
category_id=category_id,
display_order=display_order)
display_order=display_order,
standalone=standalone)
db.session.add(spec)
db.session.commit()
if not filepath and not from_tests:

28
migrations/versions/62910318009f_.py Normal file
View File

@ -0,0 +1,28 @@
"""empty message
Revision ID: 62910318009f
Revises: 665624ac29f1
Create Date: 2021-04-28 14:09:57.648732
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '62910318009f'
down_revision = '665624ac29f1'
branch_labels = None
depends_on = None
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.add_column('file_data', sa.Column('size', sa.Integer(), nullable=True))
# ### end Alembic commands ###
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.drop_column('file_data', 'size')
# ### end Alembic commands ###

5
migrations/versions/665624ac29f1_.py
View File

@ -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 ###

30
migrations/versions/8b976945a54e_.py Normal file
View File

@ -0,0 +1,30 @@
"""empty message
Revision ID: 8b976945a54e
Revises: c872232ebdcb
Create Date: 2021-04-18 11:42:41.894378
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '8b976945a54e'
down_revision = 'c872232ebdcb'
branch_labels = None
depends_on = None
def upgrade():
op.add_column('workflow', sa.Column('user_id', sa.String(), nullable=True))
op.add_column('workflow_spec', sa.Column('standalone', sa.Boolean(), default=False))
op.execute("UPDATE workflow_spec SET standalone=False WHERE standalone is null;")
op.execute("ALTER TABLE task_event ALTER COLUMN study_id DROP NOT NULL")
def downgrade():
op.execute("UPDATE workflow SET user_id=NULL WHERE user_id is not NULL")
op.drop_column('workflow', 'user_id')
op.drop_column('workflow_spec', 'standalone')
op.execute("ALTER TABLE task_event ALTER COLUMN study_id SET NOT NULL ")

28
migrations/versions/abeffe547305_update_type_on_task_events_table.py Normal file
View File

@ -0,0 +1,28 @@
"""update type on task_events table and workflow table
Revision ID: abeffe547305
Revises: 665624ac29f1
Create Date: 2021-04-28 08:51:16.220260
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = 'abeffe547305'
down_revision = '665624ac29f1'
branch_labels = None
depends_on = None
def upgrade():
op.execute("alter table task_event alter column date type timestamp with time zone")
op.execute("alter table workflow alter column last_updated type timestamp with time zone")
pass
def downgrade():
op.execute("alter table task_event alter column date type timestamp without time zone")
op.execute("alter table workflow alter column last_updated type timestamp without time zone")
pass

38
migrations/versions/bbf064082623_.py Normal file
View File

@ -0,0 +1,38 @@
"""empty message
Revision ID: bbf064082623
Revises: c1449d1d1681
Create Date: 2021-05-13 15:07:44.463757
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
from sqlalchemy import func
revision = 'bbf064082623'
down_revision = 'c1449d1d1681'
branch_labels = None
depends_on = None
def upgrade():
op.alter_column('data_store', 'last_updated', server_default=func.now())
op.alter_column('file_data', 'date_created', server_default=func.now())
op.alter_column('data_store', 'last_updated', server_default=func.now())
op.alter_column('ldap_model', 'date_cached', server_default=func.now())
op.alter_column('study', 'last_updated', server_default=func.now())
op.alter_column('study_event', 'create_date', server_default=func.now())
op.alter_column('workflow', 'last_updated', server_default=func.now())
def downgrade():
op.alter_column('data_store', 'last_updated', server_default=None)
op.alter_column('file_data', 'date_created', server_default=None)
op.alter_column('data_store', 'last_updated', server_default=None)
op.alter_column('ldap_model', 'date_cached', server_default=None)
op.alter_column('study', 'last_updated', server_default=None)
op.alter_column('study_event', 'create_date', server_default=None)
op.alter_column('workflow', 'last_updated', server_default=None)

24
migrations/versions/c1449d1d1681_.py Normal file
View File

@ -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

2
postgres/docker-compose.yml
View File

@ -10,3 +10,5 @@ services:
- POSTGRES_USER=${DB_USER}
- POSTGRES_PASSWORD=${DB_PASS}
- POSTGRES_MULTIPLE_DATABASES=crc_dev,crc_test,pb,pb_test
- TZ=America/New_York
- PGTZ=America/New_York

18
tests/base_test.py
View File

@ -70,7 +70,7 @@ class BaseTest(unittest.TestCase):
{
'id': 0,
'title': 'The impact of fried pickles on beer consumption in bipedal software developers.',
'last_updated': datetime.datetime.now(),
'last_updated': datetime.datetime.utcnow(),
'status': StudyStatus.in_progress,
'primary_investigator_id': 'dhf8r',
'sponsor': 'Sartography Pharmaceuticals',
@ -80,7 +80,7 @@ class BaseTest(unittest.TestCase):
{
'id': 1,
'title': 'Requirement of hippocampal neurogenesis for the behavioral effects of soft pretzels',
'last_updated': datetime.datetime.now(),
'last_updated': datetime.datetime.utcnow(),
'status': StudyStatus.in_progress,
'primary_investigator_id': 'dhf8r',
'sponsor': 'Makerspace & Co.',
@ -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):
"""
@ -175,11 +175,6 @@ class BaseTest(unittest.TestCase):
specs = session.query(WorkflowSpecModel).all()
self.assertIsNotNone(specs)
for spec in specs:
files = session.query(FileModel).filter_by(workflow_spec_id=spec.id).all()
self.assertIsNotNone(files)
self.assertGreater(len(files), 0)
for spec in specs:
files = session.query(FileModel).filter_by(workflow_spec_id=spec.id).all()
self.assertIsNotNone(files)
@ -379,6 +374,10 @@ class BaseTest(unittest.TestCase):
def complete_form(self, workflow_in, task_in, dict_data, update_all=False, error_code=None, terminate_loop=None,
user_uid="dhf8r"):
# workflow_in should be a workflow, not a workflow_api
# we were passing in workflow_api in many of our tests, and
# this caused problems testing standalone workflows
standalone = getattr(workflow_in.workflow_spec, 'standalone', False)
prev_completed_task_count = workflow_in.completed_tasks
if isinstance(task_in, dict):
task_id = task_in["id"]
@ -421,7 +420,8 @@ class BaseTest(unittest.TestCase):
.order_by(TaskEventModel.date.desc()).all()
self.assertGreater(len(task_events), 0)
event = task_events[0]
self.assertIsNotNone(event.study_id)
if not standalone:
self.assertIsNotNone(event.study_id)
self.assertEqual(user_uid, event.user_uid)
self.assertEqual(workflow.id, event.workflow_id)
self.assertEqual(workflow.workflow_spec_id, event.workflow_spec_id)

58
tests/data/hello_world/hello_world.bpmn Normal file
View File

@ -0,0 +1,58 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" id="Definitions_0ixyfs0" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
<bpmn:process id="Process_HelloWorld" name="Hello World Process" isExecutable="true">
<bpmn:documentation>This workflow asks for a name and says hello</bpmn:documentation>
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_0qyd2b7</bpmn:outgoing>
</bpmn:startEvent>
<bpmn:sequenceFlow id="SequenceFlow_0qyd2b7" sourceRef="StartEvent_1" targetRef="Task_GetName" />
<bpmn:userTask id="Task_GetName" name="Get Name" camunda:formKey="Name">
<bpmn:documentation>Hello</bpmn:documentation>
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="name" label="Name" type="string" defaultValue="World" />
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>SequenceFlow_0qyd2b7</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_1h46b40</bpmn:outgoing>
</bpmn:userTask>
<bpmn:sequenceFlow id="SequenceFlow_1h46b40" sourceRef="Task_GetName" targetRef="Task_SayHello" />
<bpmn:manualTask id="Task_SayHello" name="Say Hello">
<bpmn:documentation>Hello {{name}}</bpmn:documentation>
<bpmn:incoming>SequenceFlow_1h46b40</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_0lqrc6e</bpmn:outgoing>
</bpmn:manualTask>
<bpmn:endEvent id="EndEvent_1l03lqw">
<bpmn:incoming>SequenceFlow_0lqrc6e</bpmn:incoming>
</bpmn:endEvent>
<bpmn:sequenceFlow id="SequenceFlow_0lqrc6e" sourceRef="Task_SayHello" targetRef="EndEvent_1l03lqw" />
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_HelloWorld">
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="179" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="SequenceFlow_0qyd2b7_di" bpmnElement="SequenceFlow_0qyd2b7">
<di:waypoint x="215" y="117" />
<di:waypoint x="270" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="UserTask_0fbucz7_di" bpmnElement="Task_GetName">
<dc:Bounds x="270" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="SequenceFlow_1h46b40_di" bpmnElement="SequenceFlow_1h46b40">
<di:waypoint x="370" y="117" />
<di:waypoint x="430" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="ManualTask_1tia2zr_di" bpmnElement="Task_SayHello">
<dc:Bounds x="430" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="EndEvent_1l03lqw_di" bpmnElement="EndEvent_1l03lqw">
<dc:Bounds x="592" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="SequenceFlow_0lqrc6e_di" bpmnElement="SequenceFlow_0lqrc6e">
<di:waypoint x="530" y="117" />
<di:waypoint x="592" y="117" />
</bpmndi:BPMNEdge>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

52
tests/data/irb_info_script/irb_info_script.bpmn Normal file
View File

@ -0,0 +1,52 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1e8c8os" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
<bpmn:process id="Process_GetIRBInfo" name="Get IRB Info" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_0xey0zw</bpmn:outgoing>
</bpmn:startEvent>
<bpmn:sequenceFlow id="SequenceFlow_0xey0zw" sourceRef="StartEvent_1" targetRef="Task_GetInfo" />
<bpmn:scriptTask id="Task_GetInfo" name="Get IRB Info">
<bpmn:incoming>SequenceFlow_0xey0zw</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_03hympo</bpmn:outgoing>
<bpmn:script>irb_info = get_irb_info()</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="SequenceFlow_03hympo" sourceRef="Task_GetInfo" targetRef="Task_PrintInfo" />
<bpmn:endEvent id="EndEvent_0qdzlqr">
<bpmn:incoming>SequenceFlow_1s6cthx</bpmn:incoming>
</bpmn:endEvent>
<bpmn:sequenceFlow id="SequenceFlow_1s6cthx" sourceRef="Task_PrintInfo" targetRef="EndEvent_0qdzlqr" />
<bpmn:manualTask id="Task_PrintInfo" name="Print IRB Info">
<bpmn:documentation>IRB Info: {{irb_info}}</bpmn:documentation>
<bpmn:incoming>SequenceFlow_03hympo</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_1s6cthx</bpmn:outgoing>
</bpmn:manualTask>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_GetIRBInfo">
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="179" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="SequenceFlow_0xey0zw_di" bpmnElement="SequenceFlow_0xey0zw">
<di:waypoint x="215" y="117" />
<di:waypoint x="270" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="ScriptTask_0xmrk10_di" bpmnElement="Task_GetInfo">
<dc:Bounds x="270" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="SequenceFlow_03hympo_di" bpmnElement="SequenceFlow_03hympo">
<di:waypoint x="370" y="117" />
<di:waypoint x="430" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="EndEvent_0qdzlqr_di" bpmnElement="EndEvent_0qdzlqr">
<dc:Bounds x="592" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="SequenceFlow_1s6cthx_di" bpmnElement="SequenceFlow_1s6cthx">
<di:waypoint x="530" y="117" />
<di:waypoint x="592" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="ManualTask_1uh1r6q_di" bpmnElement="Task_PrintInfo">
<dc:Bounds x="430" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

38
tests/data/pb_responses/irb_info.json Normal file
View File

@ -0,0 +1,38 @@
[
{
"AGENDA_DATE": "2021-04-15T00:00:00+00:00",
"DATE_MODIFIED": "2021-04-15T00:00:00+00:00",
"IRBEVENT": "IRB Event 1",
"IRB_ADMINISTRATIVE_REVIEWER": "IRB Admin Reviewer 1",
"IRB_OF_RECORD": "IRB of Record 1",
"IRB_REVIEW_TYPE": "IRB Review Type 1",
"IRB_STATUS": "IRB Status 1",
"STUDYIRBREVIEWERADMIN": "Study IRB Review Admin 1",
"UVA_IRB_HSR_IS_IRB_OF_RECORD_FOR_ALL_SITES": 1,
"UVA_STUDY_TRACKING": "UVA Study Tracking 1"
},
{
"AGENDA_DATE": "2021-04-15T00:00:00+00:00",
"DATE_MODIFIED": "2021-04-15T00:00:00+00:00",
"IRBEVENT": "IRB Event 2",
"IRB_ADMINISTRATIVE_REVIEWER": "IRB Admin Reviewer 2",
"IRB_OF_RECORD": "IRB of Record 2",
"IRB_REVIEW_TYPE": "IRB Review Type 2",
"IRB_STATUS": "IRB Status 2",
"STUDYIRBREVIEWERADMIN": "Study IRB Review Admin 2",
"UVA_IRB_HSR_IS_IRB_OF_RECORD_FOR_ALL_SITES": 2,
"UVA_STUDY_TRACKING": "UVA Study Tracking 2"
},
{
"AGENDA_DATE": "2021-04-15T00:00:00+00:00",
"DATE_MODIFIED": "2021-04-15T00:00:00+00:00",
"IRBEVENT": "IRB Event 3",
"IRB_ADMINISTRATIVE_REVIEWER": "IRB Admin Reviewer 3",
"IRB_OF_RECORD": "IRB of Record 3",
"IRB_REVIEW_TYPE": "IRB Review Type 3",
"IRB_STATUS": "IRB Status 3",
"STUDYIRBREVIEWERADMIN": "Study IRB Review Admin 3",
"UVA_IRB_HSR_IS_IRB_OF_RECORD_FOR_ALL_SITES": 3,
"UVA_STUDY_TRACKING": "UVA Study Tracking 3"
}
]

4
tests/files/test_file_service.py
View File

@ -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()
@ -72,7 +72,7 @@ class TestFileService(BaseTest):
file_data = FileService.get_workflow_data_files(workflow_id=workflow.id)
self.assertEqual(1, len(file_data))
self.assertEqual(2, file_data[0].version)
self.assertEquals(4, file_data[0].size) # File dat size is included.
def test_add_file_from_form_increments_version_and_replaces_on_subsequent_add_with_same_name(self):
self.load_example_data()

12
tests/files/test_files_api.py
View File

@ -181,11 +181,11 @@ class TestFilesApi(BaseTest):
data['file'] = io.BytesIO(self.minimal_bpmn("abcdef")), 'my_new_file.bpmn'
rv = self.app.post('/v1.0/file?workflow_spec_id=%s' % spec.id, data=data, follow_redirects=True,
content_type='multipart/form-data', headers=self.logged_in_headers())
json_data = json.loads(rv.get_data(as_text=True))
file = FileModelSchema().load(json_data, session=session)
file_json = json.loads(rv.get_data(as_text=True))
self.assertEquals(80, file_json['size'])
data['file'] = io.BytesIO(self.minimal_bpmn("efghijk")), 'my_new_file.bpmn'
rv = self.app.put('/v1.0/file/%i/data' % file.id, data=data, follow_redirects=True,
rv = self.app.put('/v1.0/file/%i/data' % file_json['id'], data=data, follow_redirects=True,
content_type='multipart/form-data', headers=self.logged_in_headers())
self.assert_success(rv)
self.assertIsNotNone(rv.get_data())
@ -193,14 +193,14 @@ class TestFilesApi(BaseTest):
self.assertEqual(2, file_json['latest_version'])
self.assertEqual(FileType.bpmn.value, file_json['type'])
self.assertEqual("application/octet-stream", file_json['content_type'])
self.assertEqual(spec.id, file.workflow_spec_id)
self.assertEqual(spec.id, file_json['workflow_spec_id'])
# Assure it is updated in the database and properly persisted.
file_model = session.query(FileModel).filter(FileModel.id == file.id).first()
file_model = session.query(FileModel).filter(FileModel.id == file_json['id']).first()
file_data = FileService.get_file_data(file_model.id)
self.assertEqual(2, file_data.version)
rv = self.app.get('/v1.0/file/%i/data' % file.id, headers=self.logged_in_headers())
rv = self.app.get('/v1.0/file/%i/data' % file_json['id'], headers=self.logged_in_headers())
self.assert_success(rv)
data = rv.get_data()
self.assertIsNotNone(data)

9
tests/study/test_study_api.py
View File

@ -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
@ -25,7 +25,7 @@ class TestStudyApi(BaseTest):
TEST_STUDY = {
"title": "Phase III Trial of Genuine People Personalities (GPP) Autonomous Intelligent Emotional Agents "
"for Interstellar Spacecraft",
"last_updated": datetime.now(tz=timezone.utc),
"last_updated": datetime.utcnow(),
"primary_investigator_id": "tmm2x",
"user_uid": "dhf8r",
}
@ -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)

12
tests/study/test_study_cancellations.py
View File

@ -72,7 +72,7 @@ class TestStudyCancellations(BaseTest):
workflow, study_id = self.load_workflow()
workflow_api, first_task = self.get_first_task(workflow)
self.complete_form(workflow_api, first_task, {})
self.complete_form(workflow, first_task, {})
study_result = self.put_study_on_hold(study_id)
self.assertEqual('New Title', study_result.title)
@ -82,10 +82,10 @@ class TestStudyCancellations(BaseTest):
workflow, study_id = self.load_workflow()
workflow_api, first_task = self.get_first_task(workflow)
self.complete_form(workflow_api, first_task, {})
self.complete_form(workflow, first_task, {})
workflow_api, next_task = self.get_second_task(workflow)
self.complete_form(workflow_api, next_task, {'how_many': 3})
self.complete_form(workflow, next_task, {'how_many': 3})
study_result = self.put_study_on_hold(study_id)
self.assertEqual('Second Title', study_result.title)
@ -95,13 +95,13 @@ class TestStudyCancellations(BaseTest):
workflow, study_id = self.load_workflow()
workflow_api, first_task = self.get_first_task(workflow)
self.complete_form(workflow_api, first_task, {})
self.complete_form(workflow, first_task, {})
workflow_api, second_task = self.get_second_task(workflow)
self.complete_form(workflow_api, second_task, {'how_many': 3})
self.complete_form(workflow, second_task, {'how_many': 3})
workflow_api, third_task = self.get_third_task(workflow)
self.complete_form(workflow_api, third_task, {})
self.complete_form(workflow, third_task, {})
study_result = self.put_study_on_hold(study_id)
self.assertEqual('Beer consumption in the bipedal software engineer', study_result.title)

2
tests/study/test_study_service.py
View File

@ -47,7 +47,7 @@ class TestStudyService(BaseTest):
self.assertIsNotNone(study.id)
workflow = WorkflowModel(workflow_spec_id="random_fact", study_id=study.id,
status=WorkflowStatus.not_started, last_updated=datetime.now())
status=WorkflowStatus.not_started, last_updated=datetime.utcnow())
db.session.add(workflow)
db.session.commit()
# Assure there is a master specification, one standard spec, and lookup tables.

12
tests/test_authentication.py
View File

@ -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)
@ -273,7 +273,7 @@ class TestAuthentication(BaseTest):
def _make_fake_study(self, uid):
return {
"title": "blah",
"last_updated": datetime.now(tz=timezone.utc),
"last_updated": datetime.utcnow(),
"status": StudyStatus.in_progress,
"primary_investigator_id": uid,
"user_uid": uid,

3
tests/test_auto_set_primary_bpmn.py
View File

@ -13,7 +13,8 @@ class TestAutoSetPrimaryBPMN(BaseTest):
category_id = session.query(WorkflowSpecCategoryModel).first().id
# Add a workflow spec
spec = WorkflowSpecModel(id='make_cookies', name='make_cookies', display_name='Cooooookies',
description='Om nom nom delicious cookies', category_id=category_id)
description='Om nom nom delicious cookies', category_id=category_id,
standalone=False)
rv = self.app.post('/v1.0/workflow-specification',
headers=self.logged_in_headers(),
content_type="application/json",

3
tests/test_email_script.py
View File

@ -23,7 +23,6 @@ class TestEmailScript(BaseTest):
first_task = self.get_workflow_api(workflow).next_task
workflow = self.get_workflow_api(workflow)
self.complete_form(workflow, first_task, {'subject': 'My Email Subject', 'recipients': 'test@example.com'})
self.assertEqual(1, len(outbox))
@ -49,7 +48,6 @@ class TestEmailScript(BaseTest):
def test_bad_email_address_1(self):
workflow = self.create_workflow('email_script')
first_task = self.get_workflow_api(workflow).next_task
workflow = self.get_workflow_api(workflow)
with self.assertRaises(AssertionError):
self.complete_form(workflow, first_task, {'recipients': 'test@example'})
@ -57,7 +55,6 @@ class TestEmailScript(BaseTest):
def test_bad_email_address_2(self):
workflow = self.create_workflow('email_script')
first_task = self.get_workflow_api(workflow).next_task
workflow = self.get_workflow_api(workflow)
with self.assertRaises(AssertionError):
self.complete_form(workflow, first_task, {'recipients': 'test'})

21
tests/test_irb_info_script.py Normal file
View File

@ -0,0 +1,21 @@
from tests.base_test import BaseTest
from crc import app, session
from crc.services.protocol_builder import ProtocolBuilderService
from unittest.mock import patch
class TestIRBInfo(BaseTest):
@patch('crc.services.protocol_builder.requests.get')
def test_irb_info_script(self, mock_get):
app.config['PB_ENABLED'] = True
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response('irb_info.json')
workflow = self.create_workflow('irb_info_script')
irb_info = ProtocolBuilderService.get_irb_info(workflow.study_id)
workflow_api = self.get_workflow_api(workflow)
first_task = workflow_api.next_task
self.assertEqual('Task_PrintInfo', first_task.name)
self.assertEqual(f'IRB Info: {irb_info}', first_task.documentation)

23
tests/test_launch_workflow_outside_study.py Normal file
View File

@ -0,0 +1,23 @@
from tests.base_test import BaseTest
from crc import session
from crc.models.user import UserModel
from crc.services.workflow_service import WorkflowService
from example_data import ExampleDataLoader
class TestNoStudyWorkflow(BaseTest):
def test_no_study_workflow(self):
self.load_example_data()
spec = ExampleDataLoader().create_spec('hello_world', 'Hello World', standalone=True, from_tests=True)
user = session.query(UserModel).first()
self.assertIsNotNone(user)
workflow_model = WorkflowService.get_workflow_from_spec(spec.id, user)
workflow_api = self.get_workflow_api(workflow_model)
first_task = workflow_api.next_task
self.complete_form(workflow_model, first_task, {'name': 'Big Guy'})
workflow_api = self.get_workflow_api(workflow_model)
second_task = workflow_api.next_task
self.assertEqual(second_task.documentation, 'Hello Big Guy')

6
tests/test_message_event.py
View File

@ -13,10 +13,10 @@ class TestMessageEvent(BaseTest):
# Start the workflow.
first_task = self.get_workflow_api(workflow).next_task
self.assertEqual('Activity_GetData', first_task.name)
workflow = self.get_workflow_api(workflow)
self.complete_form(workflow, first_task, {'formdata': 'asdf'})
workflow = self.get_workflow_api(workflow)
self.assertEqual('Activity_HowMany', workflow.next_task.name)
workflow_api = self.get_workflow_api(workflow)
self.assertEqual('Activity_HowMany', workflow_api.next_task.name)
# reset the workflow
# this ultimately calls crc.api.workflow.set_current_task

10
tests/test_multi_instance_tasks_api.py
View File

@ -67,14 +67,14 @@ class TestMultiinstanceTasksApi(BaseTest):
content_type="application/json")
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
workflow = WorkflowApiSchema().load(json_data)
data = workflow.next_task.data
workflow_api = WorkflowApiSchema().load(json_data)
data = workflow_api.next_task.data
data['investigator']['email'] = "dhf8r@virginia.edu"
self.complete_form(workflow, workflow.next_task, data)
self.complete_form(workflow, workflow_api.next_task, data)
#tasks = self.get_workflow_api(workflow).user_tasks
workflow = self.get_workflow_api(workflow)
self.assertEqual(WorkflowStatus.complete, workflow.status)
workflow_api = self.get_workflow_api(workflow)
self.assertEqual(WorkflowStatus.complete, workflow_api.status)
@patch('crc.services.protocol_builder.requests.get')

12
tests/test_protocol_builder.py
View File

@ -60,3 +60,15 @@ class TestProtocolBuilder(BaseTest):
self.assertEqual(2, response[0]["SS_STUDY"])
self.assertEqual(2453, response[0]["SPONSOR_ID"])
self.assertEqual("Abbott Ltd", response[0]["SP_NAME"])
@patch('crc.services.protocol_builder.requests.get')
def test_get_irb_info(self, mock_get):
app.config['PB_ENABLED'] = True
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response('irb_info.json')
response = ProtocolBuilderService.get_irb_info(self.test_study_id)
self.assertIsNotNone(response)
self.assertEqual(3, len(response))
self.assertEqual('IRB Event 1', response[0]["IRBEVENT"])
self.assertEqual('IRB Event 2', response[1]["IRBEVENT"])
self.assertEqual('IRB Event 3', response[2]["IRBEVENT"])

22
tests/test_tasks_api.py
View File

@ -386,15 +386,15 @@ class TestTasksApi(BaseTest):
# Start the workflow.
first_task = self.get_workflow_api(workflow).next_task
self.complete_form(workflow, first_task, {"has_bananas": True})
workflow = self.get_workflow_api(workflow)
self.assertEqual('Task_Num_Bananas', workflow.next_task.name)
workflow_api = self.get_workflow_api(workflow)
self.assertEqual('Task_Num_Bananas', workflow_api.next_task.name)
# Trying to re-submit the initial task, and answer differently, should result in an error.
self.complete_form(workflow, first_task, {"has_bananas": False}, error_code="invalid_state")
# Go ahead and set the number of bananas.
workflow = self.get_workflow_api(workflow)
task = workflow.next_task
workflow_api = self.get_workflow_api(workflow)
task = workflow_api.next_task
self.complete_form(workflow, task, {"num_bananas": 4})
# We are now at the end of the workflow.
@ -405,19 +405,19 @@ class TestTasksApi(BaseTest):
content_type="application/json")
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
workflow = WorkflowApiSchema().load(json_data)
workflow_api = WorkflowApiSchema().load(json_data)
# Assure the Next Task is the one we just reset the token to be on.
self.assertEqual("Task_Has_Bananas", workflow.next_task.name)
self.assertEqual("Task_Has_Bananas", workflow_api.next_task.name)
# Go ahead and get that workflow one more time, it should still be right.
workflow = self.get_workflow_api(workflow)
workflow_api = self.get_workflow_api(workflow)
# Assure the Next Task is the one we just reset the token to be on.
self.assertEqual("Task_Has_Bananas", workflow.next_task.name)
self.assertEqual("Task_Has_Bananas", workflow_api.next_task.name)
# The next task should be a different value.
self.complete_form(workflow, workflow.next_task, {"has_bananas": False})
workflow = self.get_workflow_api(workflow)
self.assertEqual('Task_Why_No_Bananas', workflow.next_task.name)
self.complete_form(workflow, workflow_api.next_task, {"has_bananas": False})
workflow_api = self.get_workflow_api(workflow)
self.assertEqual('Task_Why_No_Bananas', workflow_api.next_task.name)

10
tests/test_workflow_sync.py
View File

@ -52,7 +52,7 @@ class TestWorkflowSync(BaseTest):
self.load_example_data()
othersys = get_all_spec_state()
rf2pos = get_random_fact_pos(othersys)
othersys[rf2pos]['date_created'] = str(datetime.now())
othersys[rf2pos]['date_created'] = str(datetime.utcnow())
othersys[rf2pos]['md5_hash'] = '12345'
mock_get.return_value = othersys
response = get_changed_workflows('localhost:0000') #endpoint is not used due to mock
@ -69,7 +69,7 @@ class TestWorkflowSync(BaseTest):
self.load_example_data()
othersys = get_all_spec_state()
othersys.append({'workflow_spec_id':'my_new_workflow',
'date_created':str(datetime.now()),
'date_created':str(datetime.utcnow()),
'md5_hash': '12345'})
mock_get.return_value = othersys
response = get_changed_workflows('localhost:0000') #endpoint is not used due to mock
@ -121,7 +121,7 @@ class TestWorkflowSync(BaseTest):
self.load_example_data()
othersys = get_workflow_spec_files('random_fact')
rf2pos = get_random_fact_2_pos(othersys)
othersys[rf2pos]['date_created'] = str(datetime.now())
othersys[rf2pos]['date_created'] = str(datetime.utcnow())
othersys[rf2pos]['md5_hash'] = '12345'
mock_get.return_value = othersys
response = get_changed_files('localhost:0000','random_fact',as_df=False) #endpoint is not used due to mock
@ -145,7 +145,7 @@ class TestWorkflowSync(BaseTest):
# change the remote file date and hash
othersys = get_workflow_spec_files('random_fact')
rf2pos = get_random_fact_2_pos(othersys)
othersys[rf2pos]['date_created'] = str(datetime.now())
othersys[rf2pos]['date_created'] = str(datetime.utcnow())
othersys[rf2pos]['md5_hash'] = '12345'
spec_files_mock.return_value = othersys
# actually go get a different file
@ -179,7 +179,7 @@ class TestWorkflowSync(BaseTest):
'primary':False,
'content_type':'text/text',
'primary_process_id':None,
'date_created':str(datetime.now()),
'date_created':str(datetime.utcnow()),
'md5_hash':'12345'
}
othersys.append(newfile)

2
tests/workflow/test_workflow_boolean_default.py
View File

@ -7,7 +7,7 @@ class TestBooleanDefault(BaseTest):
workflow = self.create_workflow('boolean_default_value')
workflow_api = self.get_workflow_api(workflow)
set_default_task = workflow_api.next_task
result = self.complete_form(workflow_api, set_default_task, {'yes_no': yes_no})
result = self.complete_form(workflow, set_default_task, {'yes_no': yes_no})
return result
def test_boolean_true_string(self):

16
tests/workflow/test_workflow_enum_default_value_expression.py
View File

@ -7,35 +7,35 @@ class TestWorkflowEnumDefault(BaseTest):
def test_enum_default_from_value_expression(self):
workflow = self.create_workflow('enum_value_expression')
first_task = self.get_workflow_api(workflow).next_task
self.assertEqual('Activity_UserInput', first_task.name)
workflow_api = self.get_workflow_api(workflow)
first_task = workflow_api.next_task
self.assertEqual('Activity_UserInput', first_task.name)
result = self.complete_form(workflow_api, first_task, {'user_input': True})
result = self.complete_form(workflow, first_task, {'user_input': True})
self.assertIn('user_input', result.next_task.data)
self.assertEqual(True, result.next_task.data['user_input'])
self.assertIn('lookup_output', result.next_task.data)
self.assertEqual('black', result.next_task.data['lookup_output'])
workflow_api = self.get_workflow_api(workflow)
self.assertEqual('Activity_PickColor', self.get_workflow_api(workflow_api).next_task.name)
self.assertEqual('Activity_PickColor', workflow_api.next_task.name)
self.assertEqual({'value': 'black', 'label': 'Black'}, workflow_api.next_task.data['color_select'])
#
workflow = self.create_workflow('enum_value_expression')
first_task = self.get_workflow_api(workflow).next_task
self.assertEqual('Activity_UserInput', first_task.name)
workflow_api = self.get_workflow_api(workflow)
first_task = workflow_api.next_task
self.assertEqual('Activity_UserInput', first_task.name)
result = self.complete_form(workflow_api, first_task, {'user_input': False})
result = self.complete_form(workflow, first_task, {'user_input': False})
self.assertIn('user_input', result.next_task.data)
self.assertEqual(False, result.next_task.data['user_input'])
self.assertIn('lookup_output', result.next_task.data)
self.assertEqual('white', result.next_task.data['lookup_output'])
workflow_api = self.get_workflow_api(workflow)
self.assertEqual('Activity_PickColor', self.get_workflow_api(workflow_api).next_task.name)
self.assertEqual('Activity_PickColor', workflow_api.next_task.name)
self.assertEqual({'value': 'white', 'label': 'White'}, workflow_api.next_task.data['color_select'])
def test_enum_value_expression_and_default(self):

2
tests/workflow/test_workflow_form_field_name.py
View File

@ -18,7 +18,7 @@ class TestFormFieldName(BaseTest):
workflow_api = self.get_workflow_api(workflow)
first_task = workflow_api.next_task
self.complete_form(workflow_api, first_task, {})
self.complete_form(workflow, first_task, {})
workflow_api = self.get_workflow_api(workflow)
second_task = workflow_api.next_task

5
tests/workflow/test_workflow_hidden_required_field.py
View File

@ -34,14 +34,13 @@ class TestWorkflowHiddenRequiredField(BaseTest):
first_task = workflow_api.next_task
self.assertEqual('Activity_Hello', first_task.name)
workflow_api = self.get_workflow_api(workflow)
self.complete_form(workflow_api, first_task, {})
self.complete_form(workflow, first_task, {})
workflow_api = self.get_workflow_api(workflow)
second_task = workflow_api.next_task
self.assertEqual('Activity_HiddenField', second_task.name)
self.complete_form(workflow_api, second_task, {})
self.complete_form(workflow, second_task, {})
workflow_api = self.get_workflow_api(workflow)
# The color field is hidden and required. Make sure we use the default value

28
tests/workflow/test_workflow_restart.py
View File

@ -12,20 +12,20 @@ class TestWorkflowRestart(BaseTest):
workflow = self.create_workflow('message_event')
first_task = self.get_workflow_api(workflow).next_task
self.assertEqual('Activity_GetData', first_task.name)
workflow_api = self.get_workflow_api(workflow)
first_task = workflow_api.next_task
self.assertEqual('Activity_GetData', first_task.name)
result = self.complete_form(workflow_api, first_task, {'formdata': 'asdf'})
result = self.complete_form(workflow, first_task, {'formdata': 'asdf'})
self.assertIn('formdata', result.next_task.data)
self.assertEqual('asdf', result.next_task.data['formdata'])
workflow_api = self.get_workflow_api(workflow)
self.assertEqual('Activity_HowMany', self.get_workflow_api(workflow_api).next_task.name)
self.assertEqual('Activity_HowMany', workflow_api.next_task.name)
# restart with data. should land at beginning with data
workflow_api = self.restart_workflow_api(result)
first_task = self.get_workflow_api(workflow_api).next_task
first_task = workflow_api.next_task
self.assertEqual('Activity_GetData', first_task.name)
self.assertIn('formdata', workflow_api.next_task.data)
self.assertEqual('asdf', workflow_api.next_task.data['formdata'])
@ -36,7 +36,6 @@ class TestWorkflowRestart(BaseTest):
self.assertEqual('Activity_GetData', first_task.name)
self.assertNotIn('formdata', workflow_api.next_task.data)
def test_workflow_restart_delete_files(self):
self.load_example_data()
irb_code = 'Study_Protocol_Document'
@ -80,14 +79,14 @@ class TestWorkflowRestart(BaseTest):
study_id = workflow.study_id
# Start the workflow.
first_task = self.get_workflow_api(workflow).next_task
self.assertEqual('Activity_GetData', first_task.name)
workflow_api = self.get_workflow_api(workflow)
self.complete_form(workflow_api, first_task, {'formdata': 'asdf'})
first_task = workflow_api.next_task
self.assertEqual('Activity_GetData', first_task.name)
self.complete_form(workflow, first_task, {'formdata': 'asdf'})
workflow_api = self.get_workflow_api(workflow)
self.assertEqual('Activity_HowMany', workflow_api.next_task.name)
workflow_api = self.restart_workflow_api(workflow)
self.restart_workflow_api(workflow)
study_result = session.query(StudyModel).filter(StudyModel.id == study_id).first()
self.assertEqual('New Title', study_result.title)
@ -106,17 +105,16 @@ class TestWorkflowRestart(BaseTest):
study_id = workflow.study_id
# Start the workflow.
first_task = self.get_workflow_api(workflow).next_task
self.assertEqual('Activity_GetData', first_task.name)
workflow_api = self.get_workflow_api(workflow)
self.complete_form(workflow_api, first_task, {'formdata': 'asdf'})
first_task = workflow_api.next_task
self.assertEqual('Activity_GetData', first_task.name)
self.complete_form(workflow, first_task, {'formdata': 'asdf'})
workflow_api = self.get_workflow_api(workflow)
next_task = workflow_api.next_task
self.assertEqual('Activity_HowMany', next_task.name)
self.complete_form(workflow_api, next_task, {'how_many': 3})
self.complete_form(workflow, next_task, {'how_many': 3})
workflow_api = self.restart_workflow_api(workflow)
study_result = session.query(StudyModel).filter(StudyModel.id == study_id).first()
self.assertEqual('Beer consumption in the bipedal software engineer', study_result.title)

64
tests/workflow/test_workflow_spec_api.py
View File

@ -3,7 +3,9 @@ import json
from tests.base_test import BaseTest
from crc import session
from crc.models.file import FileModel
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowSpecCategoryModel
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowSpecCategoryModel, WorkflowSpecCategoryModelSchema
from example_data import ExampleDataLoader
class TestWorkflowSpec(BaseTest):
@ -28,7 +30,8 @@ class TestWorkflowSpec(BaseTest):
category_id = session.query(WorkflowSpecCategoryModel).first().id
category_count = session.query(WorkflowSpecModel).filter_by(category_id=category_id).count()
spec = WorkflowSpecModel(id='make_cookies', name='make_cookies', display_name='Cooooookies',
description='Om nom nom delicious cookies', category_id=category_id)
description='Om nom nom delicious cookies', category_id=category_id,
standalone=False)
rv = self.app.post('/v1.0/workflow-specification',
headers=self.logged_in_headers(),
content_type="application/json",
@ -101,3 +104,60 @@ class TestWorkflowSpec(BaseTest):
num_workflows_after = session.query(WorkflowModel).filter_by(workflow_spec_id=spec_id).count()
self.assertEqual(num_files_after + num_workflows_after, 0)
def test_get_standalone_workflow_specs(self):
self.load_example_data()
category = session.query(WorkflowSpecCategoryModel).first()
ExampleDataLoader().create_spec('hello_world', 'Hello World', category_id=category.id,
standalone=True, from_tests=True)
rv = self.app.get('/v1.0/workflow-specification/standalone', headers=self.logged_in_headers())
self.assertEqual(1, len(rv.json))
ExampleDataLoader().create_spec('email_script', 'Email Script', category_id=category.id,
standalone=True, from_tests=True)
rv = self.app.get('/v1.0/workflow-specification/standalone', headers=self.logged_in_headers())
self.assertEqual(2, len(rv.json))
def test_get_workflow_from_workflow_spec(self):
self.load_example_data()
spec = ExampleDataLoader().create_spec('hello_world', 'Hello World', standalone=True, from_tests=True)
rv = self.app.post(f'/v1.0/workflow-specification/{spec.id}', headers=self.logged_in_headers())
self.assert_success(rv)
self.assertEqual('hello_world', rv.json['workflow_spec_id'])
self.assertEqual('Task_GetName', rv.json['next_task']['name'])
def test_add_workflow_spec_category(self):
self.load_example_data()
count = session.query(WorkflowSpecCategoryModel).count()
category = WorkflowSpecCategoryModel(
id=count,
name='another_test_category',
display_name='Another Test Category',
display_order=0
)
rv = self.app.post(f'/v1.0/workflow-specification-category',
headers=self.logged_in_headers(),
content_type="application/json",
data=json.dumps(WorkflowSpecCategoryModelSchema().dump(category))
)
self.assert_success(rv)
result = session.query(WorkflowSpecCategoryModel).filter(WorkflowSpecCategoryModel.name=='another_test_category').first()
self.assertEqual('Another Test Category', result.display_name)
self.assertEqual(count, result.id)
def test_update_workflow_spec_category(self):
self.load_example_data()
category = session.query(WorkflowSpecCategoryModel).first()
category_name_before = category.name
new_category_name = category_name_before + '_asdf'
self.assertNotEqual(category_name_before, new_category_name)
category.name = new_category_name
rv = self.app.put(f'/v1.0/workflow-specification-category/{category.id}',
content_type="application/json",
headers=self.logged_in_headers(),
data=json.dumps(WorkflowSpecCategoryModelSchema().dump(category)))
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
self.assertEqual(new_category_name, json_data['name'])

4
tests/workflow/test_workflow_value_expression.py
View File

@ -9,7 +9,7 @@ class TestValueExpression(BaseTest):
workflow_api = self.get_workflow_api(workflow)
first_task = workflow_api.next_task
self.complete_form(workflow_api, first_task, {'value_expression_value': ''})
self.complete_form(workflow, first_task, {'value_expression_value': ''})
workflow_api = self.get_workflow_api(workflow)
second_task = workflow_api.next_task
@ -26,7 +26,7 @@ class TestValueExpression(BaseTest):
workflow_api = self.get_workflow_api(workflow)
first_task = workflow_api.next_task
self.complete_form(workflow_api, first_task, {'value_expression_value': 'black'})
self.complete_form(workflow, first_task, {'value_expression_value': 'black'})
workflow_api = self.get_workflow_api(workflow)
second_task = workflow_api.next_task