Lots and lots of random stuff as I organize code and get things to make sense.
This commit is contained in:
Dan Funk
parent
d4a138e943
commit
9861f6baf3
4
Pipfile
4
Pipfile
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@ -7,7 +7,7 @@ verify_ssl = true
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pytest = "*"
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[packages]
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connexion = {version = "*",extras = ["swagger-ui"]}
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connexion = {extras = ["swagger-ui"],version = "*"}
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swagger-ui-bundle = "*"
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flask = "*"
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flask-bcrypt = "*"
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@ -26,6 +26,8 @@ requests = "*"
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xlsxwriter = "*"
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webtest = "*"
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spiffworkflow = {editable = true,git = "https://github.com/sartography/SpiffWorkflow.git",ref = "master"}
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alembic = "*"
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coverage = "*"
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[requires]
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python_version = "3.7"
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@ -1,7 +1,7 @@
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{
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"_meta": {
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"hash": {
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"sha256": "0f69f2039d61b7ce74169d57d17f78d7d32708f22135d13f7a453656a13e8825"
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"sha256": "9a98e8870797e0de005154d479ed668e6f23a1a912621f87d020e6d86d9fcf59"
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},
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"pipfile-spec": 6,
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"requires": {
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@ -18,9 +18,10 @@
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"default": {
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"alembic": {
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"hashes": [
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"sha256:49277bb7242192bbb9eac58fed4fe02ec6c3a2a4b4345d2171197459266482b2"
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"sha256:3b0cb1948833e062f4048992fbc97ecfaaaac24aaa0d83a1202a99fb58af8c6d"
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],
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"version": "==1.3.1"
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"index": "pypi",
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"version": "==1.3.2"
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},
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"aniso8601": {
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"hashes": [
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@ -145,11 +146,48 @@
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"swagger-ui"
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],
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"hashes": [
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"sha256:6e0569b646f2e6229923dc4e4c6e0325e223978bd19105779fd81e16bcb22fdf",
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"sha256:7b4268e9ea837241e530738b35040345b78c8748d05d2c22805350aca0cd5b1c"
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"sha256:0fa5776a44b32668f20d59e6e478f15a1dc19def8e4d07d837e10d837379c2ba",
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"sha256:4b643821a775927b2ec6220c427779b6d9c3a83ddf43662d69e68dcdad4be603"
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],
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"index": "pypi",
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"version": "==2.4.0"
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"version": "==2.5.0"
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},
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"coverage": {
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"hashes": [
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"sha256:0cd13a6e98c37b510a2d34c8281d5e1a226aaf9b65b7d770ef03c63169965351",
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"sha256:1a4b6b6a2a3a6612e6361130c2cc3dc4378d8c221752b96167ccbad94b47f3cd",
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"sha256:2ee55e6dba516ddf6f484aa83ccabbb0adf45a18892204c23486938d12258cde",
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"sha256:3be5338a2eb4ef03c57f20917e1d12a1fd10e3853fed060b6d6b677cb3745898",
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"sha256:44b783b02db03c4777d8cf71bae19eadc171a6f2a96777d916b2c30a1eb3d070",
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"sha256:475bf7c4252af0a56e1abba9606f1e54127cdf122063095c75ab04f6f99cf45e",
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"sha256:47c81ee687eafc2f1db7f03fbe99aab81330565ebc62fb3b61edfc2216a550c8",
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"sha256:4a7f8e72b18f2aca288ff02255ce32cc830bc04d993efbc87abf6beddc9e56c0",
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"sha256:50197163a22fd17f79086e087a787883b3ec9280a509807daf158dfc2a7ded02",
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"sha256:56b13000acf891f700f5067512b804d1ec8c301d627486c678b903859d07f798",
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"sha256:79388ae29c896299b3567965dbcd93255f175c17c6c7bca38614d12718c47466",
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"sha256:79fd5d3d62238c4f583b75d48d53cdae759fe04d4fb18fe8b371d88ad2b6f8be",
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"sha256:7fe3e2fde2bf1d7ce25ebcd2d3de3650b8d60d9a73ce6dcef36e20191291613d",
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"sha256:81042a24f67b96e4287774014fa27220d8a4d91af1043389e4d73892efc89ac6",
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"sha256:81326f1095c53111f8afc95da281e1414185f4a538609a77ca50bdfa39a6c207",
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"sha256:8873dc0d8f42142ea9f20c27bbdc485190fff93823c6795be661703369e5877d",
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"sha256:88d2cbcb0a112f47eef71eb95460b6995da18e6f8ca50c264585abc2c473154b",
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"sha256:91f2491aeab9599956c45a77c5666d323efdec790bfe23fcceafcd91105d585a",
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"sha256:979daa8655ae5a51e8e7a24e7d34e250ae8309fd9719490df92cbb2fe2b0422b",
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"sha256:9c871b006c878a890c6e44a5b2f3c6291335324b298c904dc0402ee92ee1f0be",
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"sha256:a6d092545e5af53e960465f652e00efbf5357adad177b2630d63978d85e46a72",
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"sha256:b5ed7837b923d1d71c4f587ae1539ccd96bfd6be9788f507dbe94dab5febbb5d",
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"sha256:ba259f68250f16d2444cbbfaddaa0bb20e1560a4fdaad50bece25c199e6af864",
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"sha256:be1d89614c6b6c36d7578496dc8625123bda2ff44f224cf8b1c45b810ee7383f",
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"sha256:c1b030a79749aa8d1f1486885040114ee56933b15ccfc90049ba266e4aa2139f",
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"sha256:c95bb147fab76f2ecde332d972d8f4138b8f2daee6c466af4ff3b4f29bd4c19e",
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"sha256:d52c1c2d7e856cecc05aa0526453cb14574f821b7f413cc279b9514750d795c1",
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"sha256:d609a6d564ad3d327e9509846c2c47f170456344521462b469e5cb39e48ba31c",
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"sha256:e1bad043c12fb58e8c7d92b3d7f2f49977dcb80a08a6d1e7a5114a11bf819fca",
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"sha256:e5a675f6829c53c87d79117a8eb656cc4a5f8918185a32fc93ba09778e90f6db",
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"sha256:fec32646b98baf4a22fdceb08703965bd16dea09051fbeb31a04b5b6e72b846c"
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],
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"index": "pypi",
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"version": "==5.0"
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},
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"et-xmlfile": {
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"hashes": [
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@ -241,11 +279,11 @@
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},
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"importlib-metadata": {
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"hashes": [
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"sha256:b044f07694ef14a6683b097ba56bd081dbc7cdc7c7fe46011e499dfecc082f21",
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"sha256:e6ac600a142cf2db707b1998382cc7fc3b02befb7273876e01b8ad10b9652742"
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"sha256:073a852570f92da5f744a3472af1b61e28e9f78ccf0c9117658dc32b15de7b45",
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"sha256:d95141fbfa7ef2ec65cfd945e2af7e5a6ddbd7c8d9a25e66ff3be8e3daf9f60f"
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],
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"markers": "python_version < '3.8'",
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"version": "==1.1.0"
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"version": "==1.3.0"
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},
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"inflection": {
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"hashes": [
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@ -353,11 +391,11 @@
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},
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"marshmallow": {
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"hashes": [
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"sha256:1a358beb89c2b4d5555272065a9533591a3eb02f1b854f3c4002d88d8f2a1ddb",
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"sha256:eb97c42c5928b5720812c9268865fe863d4807bc1a8b48ddd7d5c9e1779a6af0"
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"sha256:0ba81b6da4ae69eb229b74b3c741ff13fe04fb899824377b1aff5aaa1a9fd46e",
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"sha256:3e53dd9e9358977a3929e45cdbe4a671f9eff53a7d6a23f33ed3eab8c1890d8f"
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],
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"index": "pypi",
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"version": "==3.2.2"
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"version": "==3.3.0"
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},
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"marshmallow-enum": {
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"hashes": [
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@ -369,18 +407,18 @@
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},
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"marshmallow-sqlalchemy": {
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"hashes": [
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"sha256:0878a01587a09dfa3088ac812522784944bdcfcab9a33fa4cc80ab0ab8ad7691",
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"sha256:50b4cce1387adf968928cf8b690664655d5caecb23acf2ec676cde91e93c514b"
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"sha256:0d72beaf777f8b420c4dc94684252ae0e0a79556ccc4128129d2588f9ff72888",
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"sha256:93fd8fad2b33d92a1ae58328eeb0f39ed174858d82f9e7084a174df7b41fd3a4"
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],
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"index": "pypi",
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"version": "==0.20.0"
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"version": "==0.21.0"
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},
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"more-itertools": {
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"hashes": [
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"sha256:53ff73f186307d9c8ef17a9600309154a6ae27f25579e80af4db8f047ba14bc2",
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"sha256:a0ea684c39bc4315ba7aae406596ef191fd84f873d2d2751f84d64e81a7a2d45"
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"sha256:b84b238cce0d9adad5ed87e745778d20a3f8487d0f0cb8b8a586816c7496458d",
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"sha256:c833ef592a0324bcc6a60e48440da07645063c453880c9477ceb22490aec1564"
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],
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"version": "==8.0.0"
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"version": "==8.0.2"
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},
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"openapi-spec-validator": {
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"hashes": [
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@ -484,9 +522,9 @@
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},
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"sqlalchemy": {
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"hashes": [
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"sha256:afa5541e9dea8ad0014251bc9d56171ca3d8b130c9627c6cb3681cff30be3f8a"
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"sha256:bfb8f464a5000b567ac1d350b9090cf081180ec1ab4aa87e7bca12dab25320ec"
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],
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"version": "==1.3.11"
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"version": "==1.3.12"
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},
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"swagger-ui-bundle": {
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"hashes": [
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@ -559,18 +597,18 @@
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},
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"importlib-metadata": {
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"hashes": [
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"sha256:b044f07694ef14a6683b097ba56bd081dbc7cdc7c7fe46011e499dfecc082f21",
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"sha256:e6ac600a142cf2db707b1998382cc7fc3b02befb7273876e01b8ad10b9652742"
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"sha256:073a852570f92da5f744a3472af1b61e28e9f78ccf0c9117658dc32b15de7b45",
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"sha256:d95141fbfa7ef2ec65cfd945e2af7e5a6ddbd7c8d9a25e66ff3be8e3daf9f60f"
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],
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"markers": "python_version < '3.8'",
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"version": "==1.1.0"
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"version": "==1.3.0"
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},
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"more-itertools": {
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"hashes": [
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"sha256:53ff73f186307d9c8ef17a9600309154a6ae27f25579e80af4db8f047ba14bc2",
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"sha256:a0ea684c39bc4315ba7aae406596ef191fd84f873d2d2751f84d64e81a7a2d45"
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"sha256:b84b238cce0d9adad5ed87e745778d20a3f8487d0f0cb8b8a586816c7496458d",
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"sha256:c833ef592a0324bcc6a60e48440da07645063c453880c9477ceb22490aec1564"
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],
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"version": "==8.0.0"
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"version": "==8.0.2"
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},
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"packaging": {
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"hashes": [
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@ -602,11 +640,11 @@
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},
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"pytest": {
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"hashes": [
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"sha256:63344a2e3bce2e4d522fd62b4fdebb647c019f1f9e4ca075debbd13219db4418",
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"sha256:f67403f33b2b1d25a6756184077394167fe5e2f9d8bdaab30707d19ccec35427"
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"sha256:6b571215b5a790f9b41f19f3531c53a45cf6bb8ef2988bc1ff9afb38270b25fa",
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"sha256:e41d489ff43948babd0fad7ad5e49b8735d5d55e26628a58673c39ff61d95de4"
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],
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"index": "pypi",
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"version": "==5.3.1"
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"version": "==5.3.2"
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},
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"six": {
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"hashes": [
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@ -1,11 +0,0 @@
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import logging
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import connexion
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from app.api import workflows
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logging.basicConfig(level=logging.INFO)
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connexion_app = connexion.FlaskApp(__name__)
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connexion_app.add_api('api.yml')
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app = connexion_app.app
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app.config.from_object('config.default')
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@ -1 +0,0 @@
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@ -1,25 +0,0 @@
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import datetime
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from typing import Tuple, Any, Union, Dict
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from connexion import NoContent
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workflows = {
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1: {
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'id': 1,
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'tag': 'expedited',
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'name': 'Full IRB Board Review',
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'last_updated': datetime.datetime.now(),
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}
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}
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def list_all(limit=100):
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# NOTE: we need to wrap it with list for Python 3 as dict_values is not JSON serializable
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return list(workflows.values())[0:limit]
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def get(workflow_id):
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id_ = int(workflow_id)
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if workflows.get(id_) is None:
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return NoContent, 404
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return workflows[id_]
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@ -1,85 +0,0 @@
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import datetime
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from connexion import NoContent
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workflow_tasks = [
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{
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'id': 1,
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'workflow_id': 1,
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'task_id': 1,
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'last_updated': datetime.datetime.now(),
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'status': 'Complete',
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},
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{
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'id': 2,
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'workflow_id': 1,
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'task_id': 2,
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'last_updated': datetime.datetime.now(),
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'status': 'Incomplete',
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},
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{
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'id': 3,
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'workflow_id': 1,
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'task_id': 3,
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'last_updated': datetime.datetime.now(),
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'status': 'Disabled',
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},
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{
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'id': 4,
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'workflow_id': 1,
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'task_id': 4,
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'last_updated': datetime.datetime.now(),
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'status': 'Incomplete',
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},
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]
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def start(workflow_id):
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# spec = TrainingWorkflowSpec()
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# wf = Workflow(spec)
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id_ = len(workflow_tasks)
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workflow_tasks.append({
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'id': id_,
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'workflow_id': workflow_id,
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'task_id': 1,
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'last_updated': datetime.datetime.now(),
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'status': 'Incomplete',
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})
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return workflow_tasks[id_]
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def get(workflow_id, task_id):
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i = _get_workflow_task_index(workflow_id, task_id)
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print(i)
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return workflow_tasks[i] if i is not None else NoContent, 404
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def post(workflow_id, task_id, body):
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i = _get_workflow_task_index(workflow_id, task_id)
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if i is not None:
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workflow_tasks[i]['last_updated'] = datetime.datetime.now()
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workflow_tasks[i]['status'] = body['status']
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return workflow_tasks[i]
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else:
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return NoContent, 404
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def delete(workflow_id, task_id):
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i = _get_workflow_task_index(workflow_id, task_id)
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if i is not None:
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del workflow_tasks[i]
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return NoContent, 204
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else:
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return NoContent, 404
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def _get_workflow_task_index(workflow_id, task_id):
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workflow_id = int(workflow_id)
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task_id = int(task_id)
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for i, wt in enumerate(workflow_tasks):
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if wt['workflow_id'] == workflow_id and wt['task_id'] == task_id:
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return i
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return None
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@ -1,6 +0,0 @@
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class Fact:
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types = ["cat", "buzzword", "norris"]
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type = "cat"
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details = "not yet set."
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@ -1,3 +1,7 @@
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import os
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basedir = os.path.abspath(os.path.dirname(__file__))
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NAME = "CR Connect Workflow"
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CORS_ENABLED = False
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DEVELOPMENT = True
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SQLALCHEMY_DATABASE_URI = "sqlite:////" + os.path.join(basedir, "cr_connect.db")
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@ -1,4 +1,8 @@
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import os
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basedir = os.path.abspath(os.path.dirname(__file__))
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NAME = "CR Connect Workflow"
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CORS_ENABLED = False
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DEVELOPMENT = True
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TESTING = True
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SQLALCHEMY_DATABASE_URI = "sqlite:////" + os.path.join(basedir, "test.db")
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|
|
@ -0,0 +1,33 @@
|
|||
import logging
|
||||
import os
|
||||
|
||||
import connexion
|
||||
from flask_marshmallow import Marshmallow
|
||||
from flask_sqlalchemy import SQLAlchemy
|
||||
from flask_migrate import Migrate
|
||||
|
||||
logging.basicConfig(level=logging.INFO)
|
||||
|
||||
connexion_app = connexion.FlaskApp(__name__)
|
||||
|
||||
app = connexion_app.app
|
||||
app.config.from_object('config.default')
|
||||
#app.config.from_pyfile('config.py')
|
||||
if "TESTING" in os.environ and os.environ["TESTING"] == "true":
|
||||
app.config.from_object('config.testing')
|
||||
app.config.from_pyfile('testing.py')
|
||||
|
||||
|
||||
db = SQLAlchemy(app)
|
||||
migrate = Migrate(app, db)
|
||||
ma = Marshmallow(app)
|
||||
|
||||
from crc import models
|
||||
|
||||
connexion_app.add_api('api.yml')
|
||||
|
||||
@app.cli.command()
|
||||
def load_example_data():
|
||||
"""Load example data into the database."""
|
||||
from study import ExampleDataLoader
|
||||
ExampleDataLoader().load_studies()
|
||||
|
|
@ -0,0 +1,72 @@
|
|||
from connexion import NoContent
|
||||
from flask_marshmallow import Schema
|
||||
|
||||
from crc import db, ma
|
||||
from crc.models import WorkflowModel, WorkflowSchema, StudySchema, StudyModel, WorkflowSpecSchema, WorkflowSpecModel
|
||||
from crc.workflow_processor import WorkflowProcessor
|
||||
|
||||
|
||||
class ApiError:
|
||||
def __init__(self, code, message):
|
||||
self.code = code
|
||||
self.message = message
|
||||
|
||||
|
||||
class ApiErrorSchema(ma.Schema):
|
||||
class Meta:
|
||||
fields = ("code", "message")
|
||||
|
||||
|
||||
def all_studies():
|
||||
#todo: Limit returned studies to a user
|
||||
schema = StudySchema(many=True)
|
||||
return schema.dump(db.session.query(StudyModel).all())
|
||||
|
||||
|
||||
def get_study(study_id):
|
||||
study = db.session.query(StudyModel).filter_by(id=study_id).first()
|
||||
schema = StudySchema()
|
||||
if study is None:
|
||||
return NoContent, 404
|
||||
return schema.dump(study)
|
||||
|
||||
|
||||
def all_specifications():
|
||||
schema = WorkflowSpecSchema(many=True)
|
||||
return schema.dump(db.session.query(WorkflowSpecModel).all())
|
||||
|
||||
|
||||
def post_update_study_from_protocol_builder(study_id):
|
||||
#todo: Actually get data from an external service here
|
||||
return NoContent, 304
|
||||
|
||||
|
||||
def get_study_workflows(study_id):
|
||||
workflows = db.session.query(WorkflowModel).filter_by(study_id=study_id).all()
|
||||
schema = WorkflowSchema(many=True)
|
||||
return schema.dump(workflows)
|
||||
|
||||
|
||||
def add_workflow_to_study(study_id, body):
|
||||
workflow_spec_model = db.session.query(WorkflowSpecModel).filter_by(id=body["id"]).first()
|
||||
if workflow_spec_model is None:
|
||||
error = ApiError('unknown_spec', 'The specification "' + body['id'] + '" is not recognized.')
|
||||
return ApiErrorSchema.dump(error), 404
|
||||
processor = WorkflowProcessor.create(workflow_spec_model.id)
|
||||
|
||||
|
||||
def get_workflow(workflow_id):
|
||||
return db.session.query(WorkflowModel).filter_by(id=workflow_id).first()
|
||||
|
||||
|
||||
def get_task(workflow_id, task_id):
|
||||
workflow = db.session.query(WorkflowModel).filter_by(id=workflow_id).first()
|
||||
return workflow.bpmn_workflow().get_task(task_id)
|
||||
|
||||
|
||||
def update_task(workflow_id, task_id, body):
|
||||
global bpmn_workflow
|
||||
for field in body["task"]["form"]:
|
||||
print("Setting " + field["id"] + " to " + field["value"])
|
||||
return body
|
||||
|
||||
|
|
@ -10,10 +10,10 @@ paths:
|
|||
# /v1.0/study
|
||||
/study:
|
||||
get:
|
||||
operationId: app.api.study.list_all
|
||||
operationId: crc.api.all_studies
|
||||
summary: Provides a list of studies related to the current user.
|
||||
tags:
|
||||
- Studies and Requirements
|
||||
- Studies
|
||||
responses:
|
||||
'200':
|
||||
description: An array of studies, ordered by the last modified date.
|
||||
|
|
@ -27,13 +27,12 @@ paths:
|
|||
application/json:
|
||||
schema:
|
||||
$ref: "#/components/schemas/Error"
|
||||
|
||||
/study/{study_id}/requirement:
|
||||
/study/{study_id}:
|
||||
get:
|
||||
operationId: app.api.requirements.list_all
|
||||
summary: Provides a list of requirements for the study.
|
||||
operationId: crc.api.get_study
|
||||
summary: Provides a single study
|
||||
tags:
|
||||
- Studies and Requirements
|
||||
- Studies
|
||||
parameters:
|
||||
- name: study_id
|
||||
in: path
|
||||
|
|
@ -44,65 +43,131 @@ paths:
|
|||
format: int32
|
||||
responses:
|
||||
'200':
|
||||
description: An array of requirements
|
||||
description: An Study Object
|
||||
content:
|
||||
application/json:
|
||||
schema:
|
||||
$ref: "#/components/schemas/Study"
|
||||
default:
|
||||
description: unexpected error
|
||||
content:
|
||||
application/json:
|
||||
schema:
|
||||
$ref: "#/components/schemas/Error"
|
||||
/study-update/{study_id}:
|
||||
post:
|
||||
operationId: crc.api.post_update_study_from_protocol_builder
|
||||
summary: If the study is up-to-date with Protocol Builder, returns a 304 Not Modified. If out of date, return a 202 Accepted and study state changes to updating.
|
||||
tags:
|
||||
- Study Status
|
||||
parameters:
|
||||
- name: study_id
|
||||
in: path
|
||||
required: true
|
||||
description: The id of the study that should be checked for updates.
|
||||
schema:
|
||||
type: integer
|
||||
format: int32
|
||||
responses:
|
||||
'304':
|
||||
description: Study is currently up to date and does not need to be reloaded from Protocol Builder
|
||||
'202':
|
||||
description: Request accepted, will preform an update. Study state set to "updating"
|
||||
default:
|
||||
description: unexpected error
|
||||
content:
|
||||
application/json:
|
||||
schema:
|
||||
$ref: "#/components/schemas/Error"
|
||||
|
||||
/study/{study_id}/workflows:
|
||||
get:
|
||||
operationId: crc.api.get_study_workflows
|
||||
summary: Provides a list of workflows to be completed for the given study.
|
||||
tags:
|
||||
- Studies
|
||||
parameters:
|
||||
- name: study_id
|
||||
in: path
|
||||
required: true
|
||||
description: The id of the study for which workflows should be returned.
|
||||
schema:
|
||||
type: integer
|
||||
format: int32
|
||||
responses:
|
||||
'200':
|
||||
description: An array of workflows
|
||||
content:
|
||||
application/json:
|
||||
schema:
|
||||
type: array
|
||||
items:
|
||||
$ref: "#/components/schemas/Requirement"
|
||||
$ref: "#/components/schemas/Workflow"
|
||||
default:
|
||||
description: unexpected error
|
||||
content:
|
||||
application/json:
|
||||
schema:
|
||||
$ref: "#/components/schemas/Error"
|
||||
/study/{study_id}/requirement/{requirement_id}:
|
||||
post:
|
||||
operationId: app.api.study.create_workflow
|
||||
summary: Generate a new instance of a workflow, based on a requirement.
|
||||
operationId: crc.api.add_workflow_to_study
|
||||
summary: Starts a new workflow for the given study using the provided spec. This is atypical, and should be left to the protocol builder.
|
||||
tags:
|
||||
- Studies and Requirements
|
||||
- Studies
|
||||
parameters:
|
||||
- in: body
|
||||
name: workflow_spec
|
||||
schema:
|
||||
$ref: '#/components/schemas/WorkflowSpec'
|
||||
- name: study_id
|
||||
in: path
|
||||
required: true
|
||||
description: The id of the study for which workflows should be returned.
|
||||
schema:
|
||||
type: integer
|
||||
format: int32
|
||||
- name: requirement_id
|
||||
in: path
|
||||
required: true
|
||||
description: The id of the requirement for which to generate or start a new workflow.
|
||||
description: The id of the study for which a workflow should start
|
||||
schema:
|
||||
type: integer
|
||||
format: int32
|
||||
responses:
|
||||
'200':
|
||||
description: Returns a new workflow instance on which to work.
|
||||
description: An array of workflows
|
||||
content:
|
||||
application/json:
|
||||
schema:
|
||||
type: array
|
||||
items:
|
||||
$ref: "#/components/schemas/Workflow"
|
||||
'412':
|
||||
description: You already have a workflow underway to complete this requirement.
|
||||
content:
|
||||
application/json:
|
||||
schema:
|
||||
$ref: "#/components/schemas/Error"
|
||||
default:
|
||||
description: unexpected error
|
||||
content:
|
||||
application/json:
|
||||
schema:
|
||||
$ref: "#/components/schemas/Error"
|
||||
|
||||
# /v1.0/workflow/0
|
||||
/workflow-specification:
|
||||
get:
|
||||
operationId: crc.api.all_specifications
|
||||
summary: Provides a list of workflows specifications that can be added to a study manually. Please note that Protocol Builder will handle this most of the time.
|
||||
tags:
|
||||
- Workflow Specifications
|
||||
responses:
|
||||
'200':
|
||||
description: An array of workflow specifications
|
||||
content:
|
||||
application/json:
|
||||
schema:
|
||||
type: array
|
||||
items:
|
||||
$ref: "#/components/schemas/WorkflowSpec"
|
||||
default:
|
||||
description: unexpected error
|
||||
content:
|
||||
application/json:
|
||||
schema:
|
||||
$ref: "#/components/schemas/Error"
|
||||
# /v1.0/workflow/0
|
||||
/workflow/{workflow_id}:
|
||||
get:
|
||||
operationId: app.api.workflows.getWorkflow
|
||||
summary: Status info for a specific workflow instance
|
||||
operationId: crc.api.get_workflow
|
||||
summary: Detailed information for a specific workflow instance
|
||||
tags:
|
||||
- Workflows and Tasks
|
||||
parameters:
|
||||
|
|
@ -127,11 +192,11 @@ paths:
|
|||
schema:
|
||||
$ref: "#/components/schemas/Error"
|
||||
|
||||
# /v1.0/workflow/0/tasks/0
|
||||
/workflow/{workflow_id}/tasks/{task_id}:
|
||||
# /v1.0/workflow/0/task/0
|
||||
/workflow/{workflow_id}/task/{task_id}:
|
||||
get:
|
||||
operationId: app.api.workflows_tasks.get
|
||||
summary: Get status of specific task in specific workflow instance
|
||||
operationId: crc.api.get_task
|
||||
summary: Get details of specific task in specific workflow instance
|
||||
tags:
|
||||
- Workflows and Tasks
|
||||
parameters:
|
||||
|
|
@ -147,8 +212,7 @@ paths:
|
|||
required: true
|
||||
description: The id of the task
|
||||
schema:
|
||||
type: integer
|
||||
format: int32
|
||||
type: string
|
||||
responses:
|
||||
'200':
|
||||
description: Expected response to a valid request
|
||||
|
|
@ -163,12 +227,16 @@ paths:
|
|||
schema:
|
||||
$ref: "#/components/schemas/Error"
|
||||
|
||||
post:
|
||||
operationId: app.api.workflows_tasks.post
|
||||
put:
|
||||
operationId: crc.api.update_task
|
||||
summary: Update, attempt to complete a workflow task
|
||||
tags:
|
||||
- Workflows and Tasks
|
||||
parameters:
|
||||
- in: body
|
||||
name: task
|
||||
schema:
|
||||
$ref: '#/components/schemas/Task'
|
||||
- name: workflow_id
|
||||
in: path
|
||||
required: true
|
||||
|
|
@ -181,14 +249,7 @@ paths:
|
|||
required: true
|
||||
description: The id of the task
|
||||
schema:
|
||||
type: integer
|
||||
format: int32
|
||||
requestBody:
|
||||
description: Task status to update
|
||||
content:
|
||||
application/json:
|
||||
schema:
|
||||
$ref: "#/components/schemas/Task"
|
||||
type: string
|
||||
responses:
|
||||
'201':
|
||||
description: Null response
|
||||
|
|
@ -236,69 +297,55 @@ components:
|
|||
ind_number:
|
||||
type: string
|
||||
example: "27b-6-42"
|
||||
Requirement:
|
||||
required:
|
||||
- id
|
||||
- name
|
||||
- type
|
||||
- status
|
||||
- description
|
||||
WorkflowSpec:
|
||||
properties:
|
||||
id:
|
||||
type: string
|
||||
name:
|
||||
display_name:
|
||||
type: string
|
||||
type:
|
||||
type: string
|
||||
enum: [workflow, non-functional]
|
||||
status:
|
||||
type: string
|
||||
enum: [new, in-process, complete]
|
||||
description:
|
||||
type: string
|
||||
workflow:
|
||||
type: integer
|
||||
example:
|
||||
id: ids_submission
|
||||
name: Investigational Drug Services
|
||||
type: workflow
|
||||
status: in-process
|
||||
description: This workflow will help determine what application needs be provided to IDS, create the template, and submit it for approval.
|
||||
workflow_id: 21
|
||||
bpmn_url:
|
||||
type: string
|
||||
svg_url:
|
||||
type: string
|
||||
Workflow:
|
||||
required:
|
||||
- id
|
||||
- messages
|
||||
- current_status
|
||||
- current_task_id
|
||||
properties:
|
||||
id:
|
||||
readOnly: true
|
||||
type: integer
|
||||
format: int64
|
||||
name:
|
||||
type: string
|
||||
current_status:
|
||||
status:
|
||||
type: enum
|
||||
enum: ['user_input_required','waiting','complete']
|
||||
$ref: "#/components/schemas/Task"
|
||||
current_task_id:
|
||||
readOnly: true,
|
||||
type: string
|
||||
study_id:
|
||||
readOnly: true
|
||||
type: integer
|
||||
workflow_spec:
|
||||
$ref: "#/components/schemas/WorkflowSpec"
|
||||
current_task_ids:
|
||||
type: array
|
||||
items:
|
||||
type: String
|
||||
messages:
|
||||
type: array
|
||||
items:
|
||||
type: String
|
||||
example:
|
||||
id: 291234
|
||||
requirement_id: ids_submission
|
||||
workflow_status: 'user_input_required'
|
||||
current_task_id: study_identification
|
||||
status: 'user_input_required'
|
||||
current_task_ids: ['study_identification','Detailed Reports']
|
||||
workflow_spec:
|
||||
id: 'prot_def'
|
||||
display_name: 'Protocol Definition'
|
||||
description: 'Collect some additional information about your protocol to complete forms and processes.'
|
||||
bpmn_url: 'https://crconnect.viriginia.edu/prot_def.bpmn'
|
||||
svg_url: 'https://crconnect.viriginia.edu/prot_def.svg'
|
||||
messages: [
|
||||
"Protocol Builder reports that the protocol process is complete for this study.",
|
||||
"IDS Submission Template was generated successfully."
|
||||
]
|
||||
Task:
|
||||
required:
|
||||
- id
|
||||
- name
|
||||
- type
|
||||
properties:
|
||||
id:
|
||||
readOnly: true
|
||||
|
|
@ -309,7 +356,7 @@ components:
|
|||
type:
|
||||
type: string
|
||||
form:
|
||||
$ref: "#/components/schemas/Task"
|
||||
$ref: "#/components/schemas/Form"
|
||||
example:
|
||||
{
|
||||
id: study_identification,
|
||||
|
|
@ -325,6 +372,31 @@ components:
|
|||
}
|
||||
}
|
||||
}
|
||||
Form:
|
||||
properties:
|
||||
fields:
|
||||
type: array
|
||||
items:
|
||||
$ref: "#/components/schemas/Field"
|
||||
Field:
|
||||
properties:
|
||||
id:
|
||||
type: string
|
||||
readOnly: true
|
||||
label:
|
||||
type: string
|
||||
readOnly: true
|
||||
type:
|
||||
type: enum
|
||||
enum: ['text','number', 'enum']
|
||||
readOnly: true
|
||||
options:
|
||||
type: array
|
||||
items:
|
||||
type: string
|
||||
readOnly: true
|
||||
value:
|
||||
type: string
|
||||
Error:
|
||||
required:
|
||||
- code
|
||||
|
|
@ -0,0 +1,66 @@
|
|||
import enum
|
||||
|
||||
from flask_marshmallow.sqla import ModelSchema
|
||||
from marshmallow_enum import EnumField
|
||||
from sqlalchemy import func
|
||||
|
||||
from crc import db
|
||||
|
||||
|
||||
class ProtocolBuilderStatus(enum.Enum):
|
||||
out_of_date = "out_of_date"
|
||||
in_process = "in_process"
|
||||
complete = "complete"
|
||||
updating = "updating"
|
||||
|
||||
|
||||
class StudyModel(db.Model):
|
||||
__tablename__ = 'study'
|
||||
id = db.Column(db.Integer, primary_key=True)
|
||||
title = db.Column(db.String)
|
||||
last_updated = db.Column(db.DateTime(timezone=True), default=func.now())
|
||||
protocol_builder_status = db.Column(db.Enum(ProtocolBuilderStatus))
|
||||
primary_investigator_id = db.Column(db.String)
|
||||
sponsor = db.Column(db.String)
|
||||
ind_number = db.Column(db.String)
|
||||
|
||||
|
||||
class StudySchema(ModelSchema):
|
||||
class Meta:
|
||||
model = StudyModel
|
||||
protocol_builder_status = EnumField(ProtocolBuilderStatus)
|
||||
|
||||
|
||||
class WorkflowSpecModel(db.Model):
|
||||
__tablename__ = 'workflow_spec'
|
||||
id = db.Column(db.String, primary_key=True)
|
||||
display_name = db.Column(db.String)
|
||||
description = db.Column(db.Text)
|
||||
|
||||
class WorkflowSpecSchema(ModelSchema):
|
||||
class Meta:
|
||||
model = WorkflowSpecModel
|
||||
|
||||
class WorkflowStatus(enum.Enum):
|
||||
new = "new"
|
||||
user_input_required = "user_input_required"
|
||||
waiting = "waiting"
|
||||
complete = "complete"
|
||||
|
||||
|
||||
class WorkflowModel(db.Model):
|
||||
__tablename__ = 'workflow'
|
||||
id = db.Column(db.Integer, primary_key=True)
|
||||
bpmn_workflow_json = db.Column(db.TEXT)
|
||||
status = db.Column(db.Enum(WorkflowStatus))
|
||||
study_id = db.Column(db.Integer, db.ForeignKey('study.id'))
|
||||
workflow_spec_id = db.Column(db.Integer, db.ForeignKey('workflow_spec.id'))
|
||||
messages: db.Column
|
||||
|
||||
class WorkflowSchema(ModelSchema):
|
||||
class Meta:
|
||||
model = WorkflowModel
|
||||
status = EnumField(WorkflowStatus)
|
||||
|
||||
|
||||
|
||||
|
|
@ -30,4 +30,4 @@ class FactService:
|
|||
details = self.get_buzzword()
|
||||
else:
|
||||
details = "unknown fact type."
|
||||
print("The fact is : " + details)
|
||||
data['details'] = details
|
||||
|
|
@ -19,7 +19,7 @@
|
|||
</camunda:properties>
|
||||
</bpmn:extensionElements>
|
||||
<bpmn:incoming>SequenceFlow_0ik56h0</bpmn:incoming>
|
||||
<bpmn:outgoing>SequenceFlow_1wl4cli</bpmn:outgoing>
|
||||
<bpmn:outgoing>SequenceFlow_1291h6i</bpmn:outgoing>
|
||||
</bpmn:userTask>
|
||||
<bpmn:scriptTask id="Task_Get_Fact_From_API" name="Display Fact">
|
||||
<bpmn:extensionElements>
|
||||
|
|
@ -27,15 +27,15 @@
|
|||
<camunda:inputParameter name="Fact.type" />
|
||||
</camunda:inputOutput>
|
||||
</bpmn:extensionElements>
|
||||
<bpmn:incoming>SequenceFlow_1wl4cli</bpmn:incoming>
|
||||
<bpmn:incoming>SequenceFlow_1291h6i</bpmn:incoming>
|
||||
<bpmn:outgoing>SequenceFlow_0am07in</bpmn:outgoing>
|
||||
<bpmn:script>scripts.FactService</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:sequenceFlow id="SequenceFlow_1wl4cli" sourceRef="Task_User_Select_Type" targetRef="Task_Get_Fact_From_API" />
|
||||
<bpmn:endEvent id="EndEvent_0u1cgrf">
|
||||
<bpmn:incoming>SequenceFlow_0am07in</bpmn:incoming>
|
||||
</bpmn:endEvent>
|
||||
<bpmn:sequenceFlow id="SequenceFlow_0am07in" sourceRef="Task_Get_Fact_From_API" targetRef="EndEvent_0u1cgrf" />
|
||||
<bpmn:sequenceFlow id="SequenceFlow_1291h6i" sourceRef="Task_User_Select_Type" targetRef="Task_Get_Fact_From_API" />
|
||||
<bpmn:textAnnotation id="TextAnnotation_09fq7kh">
|
||||
<bpmn:text>User sets the Fact.type to cat, norris, or buzzword</bpmn:text>
|
||||
</bpmn:textAnnotation>
|
||||
|
|
@ -60,10 +60,6 @@
|
|||
<bpmndi:BPMNShape id="ScriptTask_10keafb_di" bpmnElement="Task_Get_Fact_From_API">
|
||||
<dc:Bounds x="480" y="210" width="100" height="80" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNEdge id="SequenceFlow_1wl4cli_di" bpmnElement="SequenceFlow_1wl4cli">
|
||||
<di:waypoint x="370" y="250" />
|
||||
<di:waypoint x="480" y="250" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNShape id="TextAnnotation_09fq7kh_di" bpmnElement="TextAnnotation_09fq7kh">
|
||||
<dc:Bounds x="330" y="116" width="99.99202297383536" height="68.28334396936822" />
|
||||
</bpmndi:BPMNShape>
|
||||
|
|
@ -85,6 +81,10 @@
|
|||
<di:waypoint x="580" y="250" />
|
||||
<di:waypoint x="692" y="250" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNEdge id="SequenceFlow_1291h6i_di" bpmnElement="SequenceFlow_1291h6i">
|
||||
<di:waypoint x="370" y="250" />
|
||||
<di:waypoint x="480" y="250" />
|
||||
</bpmndi:BPMNEdge>
|
||||
</bpmndi:BPMNPlane>
|
||||
</bpmndi:BPMNDiagram>
|
||||
</bpmn:definitions>
|
||||
|
|
@ -0,0 +1,79 @@
|
|||
import os
|
||||
|
||||
from SpiffWorkflow.bpmn.BpmnScriptEngine import BpmnScriptEngine
|
||||
from SpiffWorkflow.bpmn.serializer.BpmnSerializer import BpmnSerializer
|
||||
from SpiffWorkflow.bpmn.serializer.CompactWorkflowSerializer import CompactWorkflowSerializer
|
||||
from SpiffWorkflow.bpmn.workflow import BpmnWorkflow
|
||||
from SpiffWorkflow.camunda.serializer.CamundaSerializer import CamundaSerializer
|
||||
from SpiffWorkflow.serializer.json import JSONSerializer
|
||||
|
||||
from crc import app
|
||||
from crc.models import WorkflowModel, WorkflowStatus, WorkflowSpecModel
|
||||
|
||||
|
||||
class CustomBpmnScriptEngine(BpmnScriptEngine):
|
||||
"""This is a custom script processor that can be easily injected into Spiff Workflow.
|
||||
Rather than execute arbitrary code, this assumes the script references a fully qualified python class
|
||||
such as myapp.RandomFact. """
|
||||
|
||||
def execute(self, task, script, **kwargs):
|
||||
"""
|
||||
Assume that the script read in from the BPMN file is a fully qualified python class. Instantiate
|
||||
that class, pass in any data available to the current task so that it might act on it.
|
||||
Assume that the class implements the "do_task" method.
|
||||
|
||||
This allows us to reference custom code from the BPMN diagram.
|
||||
"""
|
||||
module_name = "crc." + script
|
||||
class_name = module_name.split(".")[-1]
|
||||
mod = __import__(module_name, fromlist=[class_name])
|
||||
klass = getattr(mod, class_name)
|
||||
klass().do_task(task.data)
|
||||
|
||||
|
||||
class WorkflowProcessor:
|
||||
|
||||
script_engine = CustomBpmnScriptEngine()
|
||||
serializer = CompactWorkflowSerializer()
|
||||
|
||||
def __init__(self, workflow_spec_id, bpmn_json):
|
||||
self.bpmn_workflow = self.serializer.deserialize_workflow(bpmn_json, self.get_spec(workflow_spec_id))
|
||||
self.bpmn_workflow.script_engine = self.script_engine
|
||||
|
||||
@staticmethod
|
||||
def get_spec(workflow_spec_id):
|
||||
filename = os.path.join(app.root_path, 'static', 'bpmn', workflow_spec_id)
|
||||
return CamundaSerializer().deserialize_workflow_spec(filename)
|
||||
|
||||
@classmethod
|
||||
def create(cls, workflow_spec_id):
|
||||
spec = cls.get_spec(workflow_spec_id)
|
||||
bpmn_workflow = BpmnWorkflow(spec, script_engine=cls.script_engine)
|
||||
bpmn_workflow.do_engine_steps()
|
||||
json = cls.serializer.serialize_workflow(bpmn_workflow)
|
||||
processor = cls(workflow_spec_id, json)
|
||||
return processor
|
||||
|
||||
def get_status(self):
|
||||
if self.bpmn_workflow.is_completed():
|
||||
return WorkflowStatus.complete
|
||||
user_tasks = self.bpmn_workflow.get_ready_user_tasks()
|
||||
if len(user_tasks) > 0:
|
||||
return WorkflowStatus.user_input_required
|
||||
else:
|
||||
return WorkflowStatus.waiting
|
||||
|
||||
def do_engine_steps(self):
|
||||
self.bpmn_workflow.do_engine_steps()
|
||||
|
||||
def serialize(self):
|
||||
return self.bpmn_workflow.serialize(JSONSerializer())
|
||||
|
||||
def next_user_tasks(self):
|
||||
return self.bpmn_workflow.get_ready_user_tasks()
|
||||
|
||||
def complete_task(self, task):
|
||||
self.bpmn_workflow.complete_task_from_id(task.id)
|
||||
|
||||
def get_data(self):
|
||||
return self.bpmn_workflow.data
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
import datetime
|
||||
|
||||
from crc import db
|
||||
from crc.models import StudyModel, WorkflowSpecModel
|
||||
|
||||
|
||||
class ExampleDataLoader:
|
||||
studies = [StudyModel(id=1,
|
||||
title='The impact of fried pickles on beer consumption in bipedal software developers.',
|
||||
last_updated=datetime.datetime.now(),
|
||||
protocol_builder_status='in_process',
|
||||
primary_investigator_id='dhf8r',
|
||||
sponsor='Sartography Pharmaceuticals',
|
||||
ind_number='1234')]
|
||||
|
||||
workflow_specs = [WorkflowSpecModel(
|
||||
id="random_fact",
|
||||
display_name="Random Fact Generator",
|
||||
description='Displays a random fact about a topic of your choosing.',
|
||||
)]
|
||||
|
||||
def load_all(self):
|
||||
db.session.bulk_save_objects(ExampleDataLoader.studies)
|
||||
db.session.bulk_save_objects(ExampleDataLoader.workflow_specs)
|
||||
db.session.commit()
|
||||
|
|
@ -0,0 +1 @@
|
|||
Generic single-database configuration.
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
# A generic, single database configuration.
|
||||
|
||||
[alembic]
|
||||
# template used to generate migration files
|
||||
# file_template = %%(rev)s_%%(slug)s
|
||||
|
||||
# set to 'true' to run the environment during
|
||||
# the 'revision' command, regardless of autogenerate
|
||||
# revision_environment = false
|
||||
|
||||
|
||||
# Logging configuration
|
||||
[loggers]
|
||||
keys = root,sqlalchemy,alembic
|
||||
|
||||
[handlers]
|
||||
keys = console
|
||||
|
||||
[formatters]
|
||||
keys = generic
|
||||
|
||||
[logger_root]
|
||||
level = WARN
|
||||
handlers = console
|
||||
qualname =
|
||||
|
||||
[logger_sqlalchemy]
|
||||
level = WARN
|
||||
handlers =
|
||||
qualname = sqlalchemy.engine
|
||||
|
||||
[logger_alembic]
|
||||
level = INFO
|
||||
handlers =
|
||||
qualname = alembic
|
||||
|
||||
[handler_console]
|
||||
class = StreamHandler
|
||||
args = (sys.stderr,)
|
||||
level = NOTSET
|
||||
formatter = generic
|
||||
|
||||
[formatter_generic]
|
||||
format = %(levelname)-5.5s [%(name)s] %(message)s
|
||||
datefmt = %H:%M:%S
|
||||
|
|
@ -0,0 +1,96 @@
|
|||
from __future__ import with_statement
|
||||
|
||||
import logging
|
||||
from logging.config import fileConfig
|
||||
|
||||
from sqlalchemy import engine_from_config
|
||||
from sqlalchemy import pool
|
||||
|
||||
from alembic import context
|
||||
|
||||
# this is the Alembic Config object, which provides
|
||||
# access to the values within the .ini file in use.
|
||||
config = context.config
|
||||
|
||||
# Interpret the config file for Python logging.
|
||||
# This line sets up loggers basically.
|
||||
fileConfig(config.config_file_name)
|
||||
logger = logging.getLogger('alembic.env')
|
||||
|
||||
# add your model's MetaData object here
|
||||
# for 'autogenerate' support
|
||||
# from myapp import mymodel
|
||||
# target_metadata = mymodel.Base.metadata
|
||||
from flask import current_app
|
||||
config.set_main_option(
|
||||
'sqlalchemy.url', current_app.config.get(
|
||||
'SQLALCHEMY_DATABASE_URI').replace('%', '%%'))
|
||||
target_metadata = current_app.extensions['migrate'].db.metadata
|
||||
|
||||
# other values from the config, defined by the needs of env.py,
|
||||
# can be acquired:
|
||||
# my_important_option = config.get_main_option("my_important_option")
|
||||
# ... etc.
|
||||
|
||||
|
||||
def run_migrations_offline():
|
||||
"""Run migrations in 'offline' mode.
|
||||
|
||||
This configures the context with just a URL
|
||||
and not an Engine, though an Engine is acceptable
|
||||
here as well. By skipping the Engine creation
|
||||
we don't even need a DBAPI to be available.
|
||||
|
||||
Calls to context.execute() here emit the given string to the
|
||||
script output.
|
||||
|
||||
"""
|
||||
url = config.get_main_option("sqlalchemy.url")
|
||||
context.configure(
|
||||
url=url, target_metadata=target_metadata, literal_binds=True
|
||||
)
|
||||
|
||||
with context.begin_transaction():
|
||||
context.run_migrations()
|
||||
|
||||
|
||||
def run_migrations_online():
|
||||
"""Run migrations in 'online' mode.
|
||||
|
||||
In this scenario we need to create an Engine
|
||||
and associate a connection with the context.
|
||||
|
||||
"""
|
||||
|
||||
# this callback is used to prevent an auto-migration from being generated
|
||||
# when there are no changes to the schema
|
||||
# reference: http://alembic.zzzcomputing.com/en/latest/cookbook.html
|
||||
def process_revision_directives(context, revision, directives):
|
||||
if getattr(config.cmd_opts, 'autogenerate', False):
|
||||
script = directives[0]
|
||||
if script.upgrade_ops.is_empty():
|
||||
directives[:] = []
|
||||
logger.info('No changes in schema detected.')
|
||||
|
||||
connectable = engine_from_config(
|
||||
config.get_section(config.config_ini_section),
|
||||
prefix='sqlalchemy.',
|
||||
poolclass=pool.NullPool,
|
||||
)
|
||||
|
||||
with connectable.connect() as connection:
|
||||
context.configure(
|
||||
connection=connection,
|
||||
target_metadata=target_metadata,
|
||||
process_revision_directives=process_revision_directives,
|
||||
**current_app.extensions['migrate'].configure_args
|
||||
)
|
||||
|
||||
with context.begin_transaction():
|
||||
context.run_migrations()
|
||||
|
||||
|
||||
if context.is_offline_mode():
|
||||
run_migrations_offline()
|
||||
else:
|
||||
run_migrations_online()
|
||||
|
|
@ -0,0 +1,24 @@
|
|||
"""${message}
|
||||
|
||||
Revision ID: ${up_revision}
|
||||
Revises: ${down_revision | comma,n}
|
||||
Create Date: ${create_date}
|
||||
|
||||
"""
|
||||
from alembic import op
|
||||
import sqlalchemy as sa
|
||||
${imports if imports else ""}
|
||||
|
||||
# revision identifiers, used by Alembic.
|
||||
revision = ${repr(up_revision)}
|
||||
down_revision = ${repr(down_revision)}
|
||||
branch_labels = ${repr(branch_labels)}
|
||||
depends_on = ${repr(depends_on)}
|
||||
|
||||
|
||||
def upgrade():
|
||||
${upgrades if upgrades else "pass"}
|
||||
|
||||
|
||||
def downgrade():
|
||||
${downgrades if downgrades else "pass"}
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
"""empty message
|
||||
|
||||
Revision ID: 4363c8bb8f1b
|
||||
Revises:
|
||||
Create Date: 2019-12-16 11:25:16.540952
|
||||
|
||||
"""
|
||||
from alembic import op
|
||||
import sqlalchemy as sa
|
||||
|
||||
|
||||
# revision identifiers, used by Alembic.
|
||||
revision = '4363c8bb8f1b'
|
||||
down_revision = None
|
||||
branch_labels = None
|
||||
depends_on = None
|
||||
|
||||
|
||||
def upgrade():
|
||||
# ### commands auto generated by Alembic - please adjust! ###
|
||||
op.create_table('requirement',
|
||||
sa.Column('id', sa.Integer(), nullable=False),
|
||||
sa.PrimaryKeyConstraint('id')
|
||||
)
|
||||
op.create_table('study',
|
||||
sa.Column('id', sa.Integer(), nullable=False),
|
||||
sa.Column('title', sa.String(), nullable=True),
|
||||
sa.Column('last_updated', sa.DateTime(timezone=True), nullable=True),
|
||||
sa.Column('protocol_builder_status', sa.String(), nullable=True),
|
||||
sa.Column('primary_investigator_id', sa.String(), nullable=True),
|
||||
sa.Column('sponsor', sa.String(), nullable=True),
|
||||
sa.Column('ind_number', sa.String(), nullable=True),
|
||||
sa.PrimaryKeyConstraint('id')
|
||||
)
|
||||
op.create_table('user',
|
||||
sa.Column('id', sa.String(), nullable=False),
|
||||
sa.PrimaryKeyConstraint('id')
|
||||
)
|
||||
op.create_table('workflow',
|
||||
sa.Column('id', sa.Integer(), nullable=False),
|
||||
sa.Column('requirement', sa.String(), nullable=True),
|
||||
sa.Column('bpmn_workflow_json', sa.TEXT(), nullable=True),
|
||||
sa.PrimaryKeyConstraint('id')
|
||||
)
|
||||
# ### end Alembic commands ###
|
||||
|
||||
|
||||
def downgrade():
|
||||
# ### commands auto generated by Alembic - please adjust! ###
|
||||
op.drop_table('workflow')
|
||||
op.drop_table('user')
|
||||
op.drop_table('study')
|
||||
op.drop_table('requirement')
|
||||
# ### end Alembic commands ###
|
||||
|
|
@ -1,4 +1,17 @@
|
|||
from app import app
|
||||
# Set environment variable to testing before loading.
|
||||
# IMPORTANT - Environment must be loaded before app, models, etc....
|
||||
import json
|
||||
import os
|
||||
os.environ["TESTING"] = "true"
|
||||
|
||||
from crc import app, db
|
||||
|
||||
|
||||
def clean_db():
|
||||
for table in reversed(db.metadata.sorted_tables):
|
||||
db.session.execute(table.delete())
|
||||
db.session.flush()
|
||||
|
||||
|
||||
# Great class to inherit from, as it sets up and tears down
|
||||
# classes efficiently when we have a database in place.
|
||||
|
|
@ -11,27 +24,33 @@ class BaseTest:
|
|||
app.config.from_object('config.testing')
|
||||
cls.ctx = app.test_request_context()
|
||||
cls.app = app.test_client()
|
||||
# Great place to do a db.create_all()
|
||||
db.create_all()
|
||||
|
||||
@classmethod
|
||||
def tearDownClass(cls):
|
||||
# Create place to clear everything out ...
|
||||
# db.drop_all()
|
||||
# db.session.remove()
|
||||
# elastic_index.clear()
|
||||
db.drop_all()
|
||||
db.session.remove()
|
||||
pass
|
||||
|
||||
def setUp(self):
|
||||
self.ctx.push()
|
||||
|
||||
def tearDown(self):
|
||||
# db.session.rollback()
|
||||
# Most efficient thing here is to delete all rows from
|
||||
# the database with a clear db method like this one:
|
||||
# def clean_db(db):
|
||||
# for table in reversed(db.metadata.sorted_tables):
|
||||
# db.session.execute(table.delete())
|
||||
# clean_db(db)
|
||||
clean_db() # This does not seem to work, some colision of sessions.
|
||||
self.ctx.pop()
|
||||
self.auths = {}
|
||||
|
||||
def load_example_data(self):
|
||||
clean_db()
|
||||
from example_data import ExampleDataLoader
|
||||
ExampleDataLoader().load_all()
|
||||
|
||||
def assert_success(self, rv, msg=""):
|
||||
try:
|
||||
data = json.loads(rv.get_data(as_text=True))
|
||||
self.assertTrue(rv.status_code >= 200 and rv.status_code < 300,
|
||||
"BAD Response: %i. \n %s" %
|
||||
(rv.status_code, json.dumps(data)) + ". " + msg)
|
||||
except:
|
||||
self.assertTrue(rv.status_code >= 200 and rv.status_code < 300,
|
||||
"BAD Response: %i." % rv.status_code + ". " + msg)
|
||||
|
|
|
|||
|
|
@ -0,0 +1,54 @@
|
|||
import json
|
||||
import unittest
|
||||
from crc import db
|
||||
from crc.models import StudyModel, StudySchema, WorkflowSpecModel, WorkflowSpecSchema
|
||||
from tests.base_test import BaseTest
|
||||
|
||||
|
||||
class TestStudy(BaseTest, unittest.TestCase):
|
||||
|
||||
def test_study_basics(self):
|
||||
self.load_example_data()
|
||||
study = db.session.query(StudyModel).first()
|
||||
self.assertIsNotNone(study)
|
||||
|
||||
def test_study_api_get_single_study(self):
|
||||
self.load_example_data()
|
||||
study = db.session.query(StudyModel).first()
|
||||
rv = self.app.get('/v1.0/study/%i' % study.id,
|
||||
follow_redirects=True,
|
||||
content_type="application/json")
|
||||
self.assert_success(rv)
|
||||
json_data = json.loads(rv.get_data(as_text=True))
|
||||
study2 = StudySchema().load(json_data, session=db.session)
|
||||
self.assertEqual(study, study2)
|
||||
self.assertEqual(study.id, study2.id)
|
||||
self.assertEqual(study.title, study2.title)
|
||||
self.assertEqual(study.last_updated, study2.last_updated)
|
||||
self.assertEqual(study.protocol_builder_status, study2.protocol_builder_status)
|
||||
self.assertEqual(study.primary_investigator_id, study2.primary_investigator_id)
|
||||
self.assertEqual(study.sponsor, study2.sponsor)
|
||||
self.assertEqual(study.ind_number, study2.ind_number)
|
||||
|
||||
def test_list_workflow_specifications(self):
|
||||
self.load_example_data()
|
||||
spec = db.session.query(WorkflowSpecModel).first()
|
||||
rv = self.app.get('/v1.0/workflow-specification',
|
||||
follow_redirects=True,
|
||||
content_type="application/json")
|
||||
self.assert_success(rv)
|
||||
json_data = json.loads(rv.get_data(as_text=True))
|
||||
specs = WorkflowSpecSchema(many=True).load(json_data, session=db.session)
|
||||
spec2 = specs[0]
|
||||
self.assertEqual(spec.id, spec2.id)
|
||||
self.assertEqual(spec.display_name, spec2.display_name)
|
||||
self.assertEqual(spec.description, spec2.description)
|
||||
|
||||
def test_add_workflow_to_study(self):
|
||||
self.load_example_data()
|
||||
study = db.session.query(StudyModel).first()
|
||||
spec = db.session.query(WorkflowSpecModel).first()
|
||||
rv = self.app.post('/v1.0/study/%i/workflows' % study.id, data=WorkflowSpecSchema().dump(spec))
|
||||
self.assert_success(rv)
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,32 @@
|
|||
import json
|
||||
import unittest
|
||||
|
||||
from crc import db
|
||||
from crc.workflow_processor import WorkflowProcessor
|
||||
from crc.models import StudyModel, WorkflowModel, WorkflowSpecModel, WorkflowStatus
|
||||
from tests.base_test import BaseTest
|
||||
|
||||
|
||||
class TestWorkflowProcessor(BaseTest, unittest.TestCase):
|
||||
|
||||
def test_create_and_complete_workflow(self):
|
||||
self.load_example_data()
|
||||
workflow_spec_model = db.session.query(WorkflowSpecModel).filter_by(id="random_fact").first()
|
||||
processor = WorkflowProcessor.create(workflow_spec_model.id)
|
||||
self.assertIsNotNone(processor)
|
||||
self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
|
||||
next_user_tasks = processor.next_user_tasks()
|
||||
self.assertEqual(1, len(next_user_tasks))
|
||||
task = next_user_tasks[0]
|
||||
self.assertEqual("Task_User_Select_Type", task.get_name())
|
||||
model = {"Fact.type": "cat"}
|
||||
if task.data is None:
|
||||
task.data = {}
|
||||
task.data.update(model)
|
||||
processor.complete_task(task)
|
||||
self.assertEqual(WorkflowStatus.waiting, processor.get_status())
|
||||
processor.do_engine_steps()
|
||||
self.assertEqual(WorkflowStatus.complete, processor.get_status())
|
||||
data = processor.get_data()
|
||||
self.assertIsNotNone(data)
|
||||
self.assertIn("details", data)
|
||||
Loading…
Reference in New Issue