mirror of
https://github.com/sartography/cr-connect-workflow.git
synced 2025-02-20 11:48:16 +00:00
Merge branch 'dev' into cr-workflow-108
This commit is contained in:
Kelly McDonald
commit
2b0f1acb72
5
Pipfile
5
Pipfile
@ -38,13 +38,14 @@ recommonmark = "*"
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requests = "*"
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sentry-sdk = {extras = ["flask"],version = "==0.14.4"}
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||||
sphinx = "*"
|
||||
spiffworkflow = {editable = true,git = "https://github.com/sartography/SpiffWorkflow.git",ref = "master"}
|
||||
#spiffworkflow = {editable = true,path="/home/kelly/sartography/SpiffWorkflow/"}
|
||||
swagger-ui-bundle = "*"
|
||||
spiffworkflow = {editable = true, git = "https://github.com/sartography/SpiffWorkflow.git", ref = "master"}
|
||||
webtest = "*"
|
||||
werkzeug = "*"
|
||||
xlrd = "*"
|
||||
xlsxwriter = "*"
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pygithub = "*"
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python-box = "*"
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[requires]
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python_version = "3.7"
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406
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generated
406
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@ -1,7 +1,7 @@
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@ -32,10 +32,11 @@
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@ -56,6 +58,7 @@
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|
||||
"sha256:64c4f340338c68c463f1b56e3f2f0423f7b17ba6c3febae80b81f0e093077f59",
|
||||
"sha256:675192fca634f0df69af3493a48224f211f8db4e84452b08d5fcebb9167adb01",
|
||||
"sha256:700997b77cfab016533b3e7dbc03b71d33ee4df1d79f2463a318ca0263fc29dd",
|
||||
"sha256:8505e614c983834239f865da2dd336dcf9d72776b951d5dfa5ac36b987726e1b",
|
||||
"sha256:962c44070c281d86398aeb8f64e1bf37816a4dfc6f4c0f114756b14fc575621d",
|
||||
"sha256:9e536783a5acee79a9b308be97d3952b662748c4037b6a24cbb339dc7ed8eb89",
|
||||
"sha256:9ea749fd447ce7fb1ac71f7616371f04054d969d412d37611716721931e36efd",
|
||||
"sha256:a34cb28e0747ea15e82d13e14de606747e9e484fb28d63c999483f5d5188e89b",
|
||||
"sha256:a3ee9c793ffefe2944d3a2bd928a0e436cd0ac2d9e3723152d6fd5398838ce7d",
|
||||
"sha256:aab75d99f3f2874733946a7648ce87a50019eb90baef931698f96b76b6769a46",
|
||||
"sha256:b1ed2bdb27b4c9fc87058a1cb751c4df8752002143ed393899edb82b131e0546",
|
||||
"sha256:b360d8fd88d2bad01cb953d81fd2edd4be539df7bfec41e8753fe9f4456a5082",
|
||||
"sha256:b8f58c7db64d8f27078cbf2a4391af6aa4e4767cc08b37555c4ae064b8558d9b",
|
||||
"sha256:c1bbb628ed5192124889b51204de27c575b3ffc05a5a91307e7640eff1d48da4",
|
||||
"sha256:c2ff24df02a125b7b346c4c9078c8936da06964cc2d276292c357d64378158f8",
|
||||
"sha256:c890728a93fffd0407d7d37c1e6083ff3f9f211c83b4316fae3778417eab9811",
|
||||
"sha256:c96472b8ca5dc135fb0aa62f79b033f02aa434fb03a8b190600a5ae4102df1fd",
|
||||
"sha256:ce7866f29d3025b5b34c2e944e66ebef0d92e4a4f2463f7266daa03a1332a651",
|
||||
"sha256:e26c993bd4b220429d4ec8c1468eca445a4064a61c74ca08da7429af9bc53bb0"
|
||||
],
|
||||
"index": "pypi",
|
||||
"version": "==5.2"
|
||||
"version": "==5.2.1"
|
||||
},
|
||||
"deprecated": {
|
||||
"hashes": [
|
||||
"sha256:525ba66fb5f90b07169fdd48b6373c18f1ee12728ca277ca44567a367d9d7f74",
|
||||
"sha256:a766c1dccb30c5f6eb2b203f87edd1d8588847709c78589e1521d769addc8218"
|
||||
],
|
||||
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
|
||||
"version": "==1.2.10"
|
||||
},
|
||||
"docutils": {
|
||||
"hashes": [
|
||||
"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": "==0.16"
|
||||
},
|
||||
"docxtpl": {
|
||||
@ -322,12 +338,14 @@
|
||||
"sha256:05b31d2034dd3f2a685cbbae4cfc4ed906b2a733cff7964ada450fd5e462b84e",
|
||||
"sha256:bfc7150eaf809b1c283879302f04c42791136060c6eeb12c0c6674fb1291fae5"
|
||||
],
|
||||
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
|
||||
"version": "==2.4.4"
|
||||
},
|
||||
"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"
|
||||
},
|
||||
"gunicorn": {
|
||||
@ -350,6 +368,7 @@
|
||||
"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": {
|
||||
@ -357,21 +376,15 @@
|
||||
"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"
|
||||
},
|
||||
"importlib-metadata": {
|
||||
"hashes": [
|
||||
"sha256:90bb658cdbbf6d1735b6341ce708fc7024a3e14e99ffdc5783edea9f9b077f83",
|
||||
"sha256:dc15b2969b4ce36305c51eebe62d418ac7791e9a157911d58bfb1f9ccd8e2070"
|
||||
],
|
||||
"markers": "python_version < '3.8'",
|
||||
"version": "==1.7.0"
|
||||
},
|
||||
"inflection": {
|
||||
"hashes": [
|
||||
"sha256:88b101b2668a1d81d6d72d4c2018e53bc6c7fc544c987849da1c7f77545c3bc9",
|
||||
"sha256:f576e85132d34f5bf7df5183c2c6f94cfb32e528f53065345cf71329ba0b8924"
|
||||
],
|
||||
"markers": "python_version >= '3.5'",
|
||||
"version": "==0.5.0"
|
||||
},
|
||||
"itsdangerous": {
|
||||
@ -379,6 +392,7 @@
|
||||
"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"
|
||||
},
|
||||
"jdcal": {
|
||||
@ -393,6 +407,7 @@
|
||||
"sha256:89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0",
|
||||
"sha256:f0a4641d3cf955324a89c04f3d94663aa4d638abe8f733ecd3582848e1c37035"
|
||||
],
|
||||
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
|
||||
"version": "==2.11.2"
|
||||
},
|
||||
"jsonschema": {
|
||||
@ -407,11 +422,16 @@
|
||||
"sha256:be48cdffb54a2194d93ad6533d73f69408486483d189fe9f5990ee24255b0e0a",
|
||||
"sha256:ca1b45faac8c0b18493d02a8571792f3c40291cf2bcf1f55afed3d8f3aa7ba74"
|
||||
],
|
||||
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
|
||||
"version": "==4.6.11"
|
||||
},
|
||||
"ldap3": {
|
||||
"hashes": [
|
||||
"sha256:17f04298b70bf7ecaa5db8a7d8622b5a962ef7fc2b245b2eea705ac1c24338c0",
|
||||
"sha256:298769ab0232b3a3efa1e84881096c24526fe37911c83a11285f222fe4975efd",
|
||||
"sha256:4fd2db72d0412cc16ee86be01332095e86e361329c3579b314231eb2e56c7871",
|
||||
"sha256:52ab557b3c4908db4a90bea16731aa714b1b54e039b54fd4c4b83994c6c48c0c",
|
||||
"sha256:53aaae5bf14f3827c69600ddf4d61b88f49c055bb93060e9702c5bafd206c744",
|
||||
"sha256:81df4ac8b6df10fb1f05b17c18d0cb8c4c344d5a03083c382824960ed959cf5b"
|
||||
],
|
||||
"index": "pypi",
|
||||
@ -459,6 +479,7 @@
|
||||
"sha256:8195c8c1400ceb53496064314c6736719c6f25e7479cd24c77be3d9361cddc27",
|
||||
"sha256:93729a258e4ff0747c876bd9e20df1b9758028946e976324ccd2d68245c7b6a9"
|
||||
],
|
||||
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
|
||||
"version": "==1.1.3"
|
||||
},
|
||||
"markdown": {
|
||||
@ -505,6 +526,7 @@
|
||||
"sha256:e249096428b3ae81b08327a63a485ad0878de3fb939049038579ac0ef61e17e7",
|
||||
"sha256:e8313f01ba26fbbe36c7be1966a7b7424942f670f38e666995b88d012765b9be"
|
||||
],
|
||||
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
|
||||
"version": "==1.1.1"
|
||||
},
|
||||
"marshmallow": {
|
||||
@ -560,15 +582,16 @@
|
||||
"sha256:ed8a311493cf5480a2ebc597d1e177231984c818a86875126cfd004241a73c3e",
|
||||
"sha256:ef71a1d4fd4858596ae80ad1ec76404ad29701f8ca7cdcebc50300178db14dfc"
|
||||
],
|
||||
"markers": "python_version >= '3.6'",
|
||||
"version": "==1.19.1"
|
||||
},
|
||||
"openapi-spec-validator": {
|
||||
"hashes": [
|
||||
"sha256:0caacd9829e9e3051e830165367bf58d436d9487b29a09220fa7edb9f47ff81b",
|
||||
"sha256:d4da8aef72bf5be40cf0df444abd20009a41baf9048a8e03750c07a934f1bdd8",
|
||||
"sha256:e489c7a273284bc78277ac22791482e8058d323b4a265015e9fcddf6a8045bcd"
|
||||
"sha256:6dd75e50c94f1bb454d0e374a56418e7e06a07affb2c7f1df88564c5d728dac3",
|
||||
"sha256:79381a69b33423ee400ae1624a461dae7725e450e2e306e32f2dd8d16a4d85cb",
|
||||
"sha256:ec1b01a00e20955a527358886991ae34b4b791b253027ee9f7df5f84b59d91c7"
|
||||
],
|
||||
"version": "==0.2.8"
|
||||
"version": "==0.2.9"
|
||||
},
|
||||
"openpyxl": {
|
||||
"hashes": [
|
||||
@ -583,29 +606,30 @@
|
||||
"sha256:4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8",
|
||||
"sha256:998416ba6962ae7fbd6596850b80e17859a5753ba17c32284f67bfff33784181"
|
||||
],
|
||||
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
|
||||
"version": "==20.4"
|
||||
},
|
||||
"pandas": {
|
||||
"hashes": [
|
||||
"sha256:02f1e8f71cd994ed7fcb9a35b6ddddeb4314822a0e09a9c5b2d278f8cb5d4096",
|
||||
"sha256:13f75fb18486759da3ff40f5345d9dd20e7d78f2a39c5884d013456cec9876f0",
|
||||
"sha256:35b670b0abcfed7cad76f2834041dcf7ae47fd9b22b63622d67cdc933d79f453",
|
||||
"sha256:4c73f373b0800eb3062ffd13d4a7a2a6d522792fa6eb204d67a4fad0a40f03dc",
|
||||
"sha256:5759edf0b686b6f25a5d4a447ea588983a33afc8a0081a0954184a4a87fd0dd7",
|
||||
"sha256:5a7cf6044467c1356b2b49ef69e50bf4d231e773c3ca0558807cdba56b76820b",
|
||||
"sha256:69c5d920a0b2a9838e677f78f4dde506b95ea8e4d30da25859db6469ded84fa8",
|
||||
"sha256:8778a5cc5a8437a561e3276b85367412e10ae9fff07db1eed986e427d9a674f8",
|
||||
"sha256:9871ef5ee17f388f1cb35f76dc6106d40cb8165c562d573470672f4cdefa59ef",
|
||||
"sha256:9c31d52f1a7dd2bb4681d9f62646c7aa554f19e8e9addc17e8b1b20011d7522d",
|
||||
"sha256:ab8173a8efe5418bbe50e43f321994ac6673afc5c7c4839014cf6401bbdd0705",
|
||||
"sha256:ae961f1f0e270f1e4e2273f6a539b2ea33248e0e3a11ffb479d757918a5e03a9",
|
||||
"sha256:b3c4f93fcb6e97d993bf87cdd917883b7dab7d20c627699f360a8fb49e9e0b91",
|
||||
"sha256:c9410ce8a3dee77653bc0684cfa1535a7f9c291663bd7ad79e39f5ab58f67ab3",
|
||||
"sha256:f69e0f7b7c09f1f612b1f8f59e2df72faa8a6b41c5a436dde5b615aaf948f107",
|
||||
"sha256:faa42a78d1350b02a7d2f0dbe3c80791cf785663d6997891549d0f86dc49125e"
|
||||
"sha256:0210f8fe19c2667a3817adb6de2c4fd92b1b78e1975ca60c0efa908e0985cbdb",
|
||||
"sha256:0227e3a6e3a22c0e283a5041f1e3064d78fbde811217668bb966ed05386d8a7e",
|
||||
"sha256:0bc440493cf9dc5b36d5d46bbd5508f6547ba68b02a28234cd8e81fdce42744d",
|
||||
"sha256:16504f915f1ae424052f1e9b7cd2d01786f098fbb00fa4e0f69d42b22952d798",
|
||||
"sha256:182a5aeae319df391c3df4740bb17d5300dcd78034b17732c12e62e6dd79e4a4",
|
||||
"sha256:35db623487f00d9392d8af44a24516d6cb9f274afaf73cfcfe180b9c54e007d2",
|
||||
"sha256:40ec0a7f611a3d00d3c666c4cceb9aa3f5bf9fbd81392948a93663064f527203",
|
||||
"sha256:47a03bfef80d6812c91ed6fae43f04f2fa80a4e1b82b35aa4d9002e39529e0b8",
|
||||
"sha256:4b21d46728f8a6be537716035b445e7ef3a75dbd30bd31aa1b251323219d853e",
|
||||
"sha256:4d1a806252001c5db7caecbe1a26e49a6c23421d85a700960f6ba093112f54a1",
|
||||
"sha256:60e20a4ab4d4fec253557d0fc9a4e4095c37b664f78c72af24860c8adcd07088",
|
||||
"sha256:9f61cca5262840ff46ef857d4f5f65679b82188709d0e5e086a9123791f721c8",
|
||||
"sha256:a15835c8409d5edc50b4af93be3377b5dd3eb53517e7f785060df1f06f6da0e2",
|
||||
"sha256:b39508562ad0bb3f384b0db24da7d68a2608b9ddc85b1d931ccaaa92d5e45273",
|
||||
"sha256:ed60848caadeacecefd0b1de81b91beff23960032cded0ac1449242b506a3b3f",
|
||||
"sha256:fc714895b6de6803ac9f661abb316853d0cd657f5d23985222255ad76ccedc25"
|
||||
],
|
||||
"index": "pypi",
|
||||
"version": "==1.0.5"
|
||||
"version": "==1.1.0"
|
||||
},
|
||||
"psycopg2-binary": {
|
||||
"hashes": [
|
||||
@ -645,8 +669,19 @@
|
||||
},
|
||||
"pyasn1": {
|
||||
"hashes": [
|
||||
"sha256:014c0e9976956a08139dc0712ae195324a75e142284d5f87f1a87ee1b068a359",
|
||||
"sha256:03840c999ba71680a131cfaee6fab142e1ed9bbd9c693e285cc6aca0d555e576",
|
||||
"sha256:0458773cfe65b153891ac249bcf1b5f8f320b7c2ce462151f8fa74de8934becf",
|
||||
"sha256:08c3c53b75eaa48d71cf8c710312316392ed40899cb34710d092e96745a358b7",
|
||||
"sha256:39c7e2ec30515947ff4e87fb6f456dfc6e84857d34be479c9d4a4ba4bf46aa5d",
|
||||
"sha256:aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba"
|
||||
"sha256:5c9414dcfede6e441f7e8f81b43b34e834731003427e5b09e4e00e3172a10f00",
|
||||
"sha256:6e7545f1a61025a4e58bb336952c5061697da694db1cae97b116e9c46abcf7c8",
|
||||
"sha256:78fa6da68ed2727915c4767bb386ab32cdba863caa7dbe473eaae45f9959da86",
|
||||
"sha256:7ab8a544af125fb704feadb008c99a88805126fb525280b2270bb25cc1d78a12",
|
||||
"sha256:99fcc3c8d804d1bc6d9a099921e39d827026409a58f2a720dcdb89374ea0c776",
|
||||
"sha256:aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba",
|
||||
"sha256:e89bf84b5437b532b0803ba5c9a5e054d21fec423a89952a74f87fa2c9b7bce2",
|
||||
"sha256:fec3e9d8e36808a28efb59b489e4528c10ad0f480e57dcc32b4de5c9d8c9fdf3"
|
||||
],
|
||||
"version": "==0.4.8"
|
||||
},
|
||||
@ -655,13 +690,23 @@
|
||||
"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": [
|
||||
"sha256:8375a058ec651cc0774244a3bc7395cf93617298735934cdd59e5bcd9a1df96e",
|
||||
"sha256:d2d17d1e3f4474e070353f201164685a95b5a92f5ee0897442504e399c7bc249"
|
||||
],
|
||||
"index": "pypi",
|
||||
"version": "==1.51"
|
||||
},
|
||||
"pygments": {
|
||||
"hashes": [
|
||||
"sha256:647344a061c249a3b74e230c739f434d7ea4d8b1d5f3721bc0f3558049b38f44",
|
||||
"sha256:ff7a40b4860b727ab48fad6360eb351cc1b33cbf9b15a0f689ca5353e9463324"
|
||||
],
|
||||
"markers": "python_version >= '3.5'",
|
||||
"version": "==2.6.1"
|
||||
},
|
||||
"pyjwt": {
|
||||
@ -677,6 +722,7 @@
|
||||
"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": {
|
||||
@ -687,10 +733,11 @@
|
||||
},
|
||||
"python-box": {
|
||||
"hashes": [
|
||||
"sha256:2df0d0e0769b6d6e7daed8d5e0b10a38e0b5486ee75914c30f2a927f7a374111",
|
||||
"sha256:ddea019b4ee53fe3f822407b0b26ec54ff6233042c68b54244d3503ae4d6218f"
|
||||
"sha256:bcb057e8960f4d888a4caf8f668eeca3c5c61ad349d8d81c4339414984fa9454",
|
||||
"sha256:f02e059a299cac0515687aafec7543d401b12759d6578e53fae74154e0cbaa79"
|
||||
],
|
||||
"version": "==5.0.1"
|
||||
"index": "pypi",
|
||||
"version": "==5.1.0"
|
||||
},
|
||||
"python-dateutil": {
|
||||
"hashes": [
|
||||
@ -710,7 +757,9 @@
|
||||
"hashes": [
|
||||
"sha256:1bf6e860a8ad52a14c3ee1252d5dc25b2030618ed80c022598f00176adc8367d",
|
||||
"sha256:51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b",
|
||||
"sha256:5f98b069316ea1c2ed3f67e7f5df6c0d8f10b689964a4a811ff64f0106819ec8"
|
||||
"sha256:5f98b069316ea1c2ed3f67e7f5df6c0d8f10b689964a4a811ff64f0106819ec8",
|
||||
"sha256:c3da2053dbab6b29c94e43c486ff67206eafbe7eb52dbec7390b5e2fb05aac77",
|
||||
"sha256:ea87e17f6ec459e780e4221f295411462e0d0810858e055fc514684350a2f522"
|
||||
],
|
||||
"version": "==1.0.4"
|
||||
},
|
||||
@ -824,6 +873,7 @@
|
||||
"sha256:30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259",
|
||||
"sha256:8b74bedcbbbaca38ff6d7491d76f2b06b3592611af620f8426e82dddb04a5ced"
|
||||
],
|
||||
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
|
||||
"version": "==1.15.0"
|
||||
},
|
||||
"snowballstemmer": {
|
||||
@ -838,6 +888,7 @@
|
||||
"sha256:1634eea42ab371d3d346309b93df7870a88610f0725d47528be902a0d95ecc55",
|
||||
"sha256:a59dc181727e95d25f781f0eb4fd1825ff45590ec8ff49eadfd7f1a537cc0232"
|
||||
],
|
||||
"markers": "python_version >= '3.5'",
|
||||
"version": "==2.0.1"
|
||||
},
|
||||
"sphinx": {
|
||||
@ -853,6 +904,7 @@
|
||||
"sha256:806111e5e962be97c29ec4c1e7fe277bfd19e9652fb1a4392105b43e01af885a",
|
||||
"sha256:a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58"
|
||||
],
|
||||
"markers": "python_version >= '3.5'",
|
||||
"version": "==1.0.2"
|
||||
},
|
||||
"sphinxcontrib-devhelp": {
|
||||
@ -860,6 +912,7 @@
|
||||
"sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e",
|
||||
"sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4"
|
||||
],
|
||||
"markers": "python_version >= '3.5'",
|
||||
"version": "==1.0.2"
|
||||
},
|
||||
"sphinxcontrib-htmlhelp": {
|
||||
@ -867,6 +920,7 @@
|
||||
"sha256:3c0bc24a2c41e340ac37c85ced6dafc879ab485c095b1d65d2461ac2f7cca86f",
|
||||
"sha256:e8f5bb7e31b2dbb25b9cc435c8ab7a79787ebf7f906155729338f3156d93659b"
|
||||
],
|
||||
"markers": "python_version >= '3.5'",
|
||||
"version": "==1.0.3"
|
||||
},
|
||||
"sphinxcontrib-jsmath": {
|
||||
@ -874,6 +928,7 @@
|
||||
"sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178",
|
||||
"sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"
|
||||
],
|
||||
"markers": "python_version >= '3.5'",
|
||||
"version": "==1.0.1"
|
||||
},
|
||||
"sphinxcontrib-qthelp": {
|
||||
@ -881,6 +936,7 @@
|
||||
"sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72",
|
||||
"sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"
|
||||
],
|
||||
"markers": "python_version >= '3.5'",
|
||||
"version": "==1.0.3"
|
||||
},
|
||||
"sphinxcontrib-serializinghtml": {
|
||||
@ -888,12 +944,13 @@
|
||||
"sha256:eaa0eccc86e982a9b939b2b82d12cc5d013385ba5eadcc7e4fed23f4405f77bc",
|
||||
"sha256:f242a81d423f59617a8e5cf16f5d4d74e28ee9a66f9e5b637a18082991db5a9a"
|
||||
],
|
||||
"markers": "python_version >= '3.5'",
|
||||
"version": "==1.1.4"
|
||||
},
|
||||
"spiffworkflow": {
|
||||
"editable": true,
|
||||
"git": "https://github.com/sartography/SpiffWorkflow.git",
|
||||
"ref": "74529738b4e16be5aadd846669a201560f81a6d4"
|
||||
"ref": "7c8d59e7b9a978795bc8d1f354002fdc89540672"
|
||||
},
|
||||
"sqlalchemy": {
|
||||
"hashes": [
|
||||
@ -926,6 +983,7 @@
|
||||
"sha256:f57be5673e12763dd400fea568608700a63ce1c6bd5bdbc3cc3a2c5fdb045274",
|
||||
"sha256:fc728ece3d5c772c196fd338a99798e7efac7a04f9cb6416299a3638ee9a94cd"
|
||||
],
|
||||
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
|
||||
"version": "==1.3.18"
|
||||
},
|
||||
"swagger-ui-bundle": {
|
||||
@ -938,16 +996,18 @@
|
||||
},
|
||||
"urllib3": {
|
||||
"hashes": [
|
||||
"sha256:3018294ebefce6572a474f0604c2021e33b3fd8006ecd11d62107a5d2a963527",
|
||||
"sha256:88206b0eb87e6d677d424843ac5209e3fb9d0190d0ee169599165ec25e9d9115"
|
||||
"sha256:91056c15fa70756691db97756772bb1eb9678fa585d9184f24534b100dc60f4a",
|
||||
"sha256:e7983572181f5e1522d9c98453462384ee92a0be7fac5f1413a1e35c56cc0461"
|
||||
],
|
||||
"version": "==1.25.9"
|
||||
"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": "==1.25.10"
|
||||
},
|
||||
"vine": {
|
||||
"hashes": [
|
||||
"sha256:133ee6d7a9016f177ddeaf191c1f58421a1dcc6ee9a42c58b34bed40e1d2cd87",
|
||||
"sha256:ea4947cc56d1fd6f2095c8d543ee25dad966f78692528e68b4fada11ba3f98af"
|
||||
],
|
||||
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
|
||||
"version": "==1.3.0"
|
||||
},
|
||||
"waitress": {
|
||||
@ -955,6 +1015,7 @@
|
||||
"sha256:1bb436508a7487ac6cb097ae7a7fe5413aefca610550baf58f0940e51ecfb261",
|
||||
"sha256:3d633e78149eb83b60a07dfabb35579c29aac2d24bb803c18b26fb2ab1a584db"
|
||||
],
|
||||
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
|
||||
"version": "==1.4.4"
|
||||
},
|
||||
"webob": {
|
||||
@ -962,6 +1023,7 @@
|
||||
"sha256:a3c89a8e9ba0aeb17382836cdb73c516d0ecf6630ec40ec28288f3ed459ce87b",
|
||||
"sha256:aa3a917ed752ba3e0b242234b2a373f9c4e2a75d35291dcbe977649bd21fd108"
|
||||
],
|
||||
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
|
||||
"version": "==1.8.6"
|
||||
},
|
||||
"webtest": {
|
||||
@ -980,12 +1042,18 @@
|
||||
"index": "pypi",
|
||||
"version": "==1.0.1"
|
||||
},
|
||||
"wrapt": {
|
||||
"hashes": [
|
||||
"sha256:b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7"
|
||||
],
|
||||
"version": "==1.12.1"
|
||||
},
|
||||
"wtforms": {
|
||||
"hashes": [
|
||||
"sha256:6ff8635f4caeed9f38641d48cfe019d0d3896f41910ab04494143fc027866e1b",
|
||||
"sha256:861a13b3ae521d6700dac3b2771970bd354a63ba7043ecc3a82b5288596a1972"
|
||||
"sha256:7b504fc724d0d1d4d5d5c114e778ec88c37ea53144683e084215eed5155ada4c",
|
||||
"sha256:81195de0ac94fbc8368abbaf9197b88c4f3ffd6c2719b5bf5fc9da744f3d829c"
|
||||
],
|
||||
"version": "==2.3.1"
|
||||
"version": "==2.3.3"
|
||||
},
|
||||
"xlrd": {
|
||||
"hashes": [
|
||||
@ -997,18 +1065,11 @@
|
||||
},
|
||||
"xlsxwriter": {
|
||||
"hashes": [
|
||||
"sha256:828b3285fc95105f5b1946a6a015b31cf388bd5378fdc6604e4d1b7839df2e77",
|
||||
"sha256:82a3b0e73e3913483da23791d1a25e4d2dbb3837d1be4129473526b9a270a5cc"
|
||||
"sha256:3015f707cf237d277cf1b2d7805f409f0387e32bc52f3c76db9f85098980e828",
|
||||
"sha256:ee3fc2f32890246aba44dd14d777d6b3135e3454f865d8cc669618e20152296b"
|
||||
],
|
||||
"index": "pypi",
|
||||
"version": "==1.2.9"
|
||||
},
|
||||
"zipp": {
|
||||
"hashes": [
|
||||
"sha256:aa36550ff0c0b7ef7fa639055d797116ee891440eac1a56f378e2d3179e0320b",
|
||||
"sha256:c599e4d75c98f6798c509911d08a22e6c021d074469042177c8c86fb92eefd96"
|
||||
],
|
||||
"version": "==3.1.0"
|
||||
"version": "==1.3.0"
|
||||
}
|
||||
},
|
||||
"develop": {
|
||||
@ -1017,61 +1078,62 @@
|
||||
"sha256:08a96c641c3a74e44eb59afb61a24f2cb9f4d7188748e76ba4bb5edfa3cb7d1c",
|
||||
"sha256:f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72"
|
||||
],
|
||||
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
|
||||
"version": "==19.3.0"
|
||||
},
|
||||
"coverage": {
|
||||
"hashes": [
|
||||
"sha256:0fc4e0d91350d6f43ef6a61f64a48e917637e1dcfcba4b4b7d543c628ef82c2d",
|
||||
"sha256:10f2a618a6e75adf64329f828a6a5b40244c1c50f5ef4ce4109e904e69c71bd2",
|
||||
"sha256:12eaccd86d9a373aea59869bc9cfa0ab6ba8b1477752110cb4c10d165474f703",
|
||||
"sha256:1874bdc943654ba46d28f179c1846f5710eda3aeb265ff029e0ac2b52daae404",
|
||||
"sha256:1dcebae667b73fd4aa69237e6afb39abc2f27520f2358590c1b13dd90e32abe7",
|
||||
"sha256:1e58fca3d9ec1a423f1b7f2aa34af4f733cbfa9020c8fe39ca451b6071237405",
|
||||
"sha256:214eb2110217f2636a9329bc766507ab71a3a06a8ea30cdeebb47c24dce5972d",
|
||||
"sha256:25fe74b5b2f1b4abb11e103bb7984daca8f8292683957d0738cd692f6a7cc64c",
|
||||
"sha256:32ecee61a43be509b91a526819717d5e5650e009a8d5eda8631a59c721d5f3b6",
|
||||
"sha256:3740b796015b889e46c260ff18b84683fa2e30f0f75a171fb10d2bf9fb91fc70",
|
||||
"sha256:3b2c34690f613525672697910894b60d15800ac7e779fbd0fccf532486c1ba40",
|
||||
"sha256:41d88736c42f4a22c494c32cc48a05828236e37c991bd9760f8923415e3169e4",
|
||||
"sha256:42fa45a29f1059eda4d3c7b509589cc0343cd6bbf083d6118216830cd1a51613",
|
||||
"sha256:4bb385a747e6ae8a65290b3df60d6c8a692a5599dc66c9fa3520e667886f2e10",
|
||||
"sha256:509294f3e76d3f26b35083973fbc952e01e1727656d979b11182f273f08aa80b",
|
||||
"sha256:5c74c5b6045969b07c9fb36b665c9cac84d6c174a809fc1b21bdc06c7836d9a0",
|
||||
"sha256:60a3d36297b65c7f78329b80120f72947140f45b5c7a017ea730f9112b40f2ec",
|
||||
"sha256:6f91b4492c5cde83bfe462f5b2b997cdf96a138f7c58b1140f05de5751623cf1",
|
||||
"sha256:7403675df5e27745571aba1c957c7da2dacb537c21e14007ec3a417bf31f7f3d",
|
||||
"sha256:87bdc8135b8ee739840eee19b184804e5d57f518578ffc797f5afa2c3c297913",
|
||||
"sha256:8a3decd12e7934d0254939e2bf434bf04a5890c5bf91a982685021786a08087e",
|
||||
"sha256:9702e2cb1c6dec01fb8e1a64c015817c0800a6eca287552c47a5ee0ebddccf62",
|
||||
"sha256:a4d511012beb967a39580ba7d2549edf1e6865a33e5fe51e4dce550522b3ac0e",
|
||||
"sha256:bbb387811f7a18bdc61a2ea3d102be0c7e239b0db9c83be7bfa50f095db5b92a",
|
||||
"sha256:bfcc811883699ed49afc58b1ed9f80428a18eb9166422bce3c31a53dba00fd1d",
|
||||
"sha256:c32aa13cc3fe86b0f744dfe35a7f879ee33ac0a560684fef0f3e1580352b818f",
|
||||
"sha256:ca63dae130a2e788f2b249200f01d7fa240f24da0596501d387a50e57aa7075e",
|
||||
"sha256:d54d7ea74cc00482a2410d63bf10aa34ebe1c49ac50779652106c867f9986d6b",
|
||||
"sha256:d67599521dff98ec8c34cd9652cbcfe16ed076a2209625fca9dc7419b6370e5c",
|
||||
"sha256:d82db1b9a92cb5c67661ca6616bdca6ff931deceebb98eecbd328812dab52032",
|
||||
"sha256:d9ad0a988ae20face62520785ec3595a5e64f35a21762a57d115dae0b8fb894a",
|
||||
"sha256:ebf2431b2d457ae5217f3a1179533c456f3272ded16f8ed0b32961a6d90e38ee",
|
||||
"sha256:ed9a21502e9223f563e071759f769c3d6a2e1ba5328c31e86830368e8d78bc9c",
|
||||
"sha256:f50632ef2d749f541ca8e6c07c9928a37f87505ce3a9f20c8446ad310f1aa87b"
|
||||
"sha256:098a703d913be6fbd146a8c50cc76513d726b022d170e5e98dc56d958fd592fb",
|
||||
"sha256:16042dc7f8e632e0dcd5206a5095ebd18cb1d005f4c89694f7f8aafd96dd43a3",
|
||||
"sha256:1adb6be0dcef0cf9434619d3b892772fdb48e793300f9d762e480e043bd8e716",
|
||||
"sha256:27ca5a2bc04d68f0776f2cdcb8bbd508bbe430a7bf9c02315cd05fb1d86d0034",
|
||||
"sha256:28f42dc5172ebdc32622a2c3f7ead1b836cdbf253569ae5673f499e35db0bac3",
|
||||
"sha256:2fcc8b58953d74d199a1a4d633df8146f0ac36c4e720b4a1997e9b6327af43a8",
|
||||
"sha256:304fbe451698373dc6653772c72c5d5e883a4aadaf20343592a7abb2e643dae0",
|
||||
"sha256:30bc103587e0d3df9e52cd9da1dd915265a22fad0b72afe54daf840c984b564f",
|
||||
"sha256:40f70f81be4d34f8d491e55936904db5c527b0711b2a46513641a5729783c2e4",
|
||||
"sha256:4186fc95c9febeab5681bc3248553d5ec8c2999b8424d4fc3a39c9cba5796962",
|
||||
"sha256:46794c815e56f1431c66d81943fa90721bb858375fb36e5903697d5eef88627d",
|
||||
"sha256:4869ab1c1ed33953bb2433ce7b894a28d724b7aa76c19b11e2878034a4e4680b",
|
||||
"sha256:4f6428b55d2916a69f8d6453e48a505c07b2245653b0aa9f0dee38785939f5e4",
|
||||
"sha256:52f185ffd3291196dc1aae506b42e178a592b0b60a8610b108e6ad892cfc1bb3",
|
||||
"sha256:538f2fd5eb64366f37c97fdb3077d665fa946d2b6d95447622292f38407f9258",
|
||||
"sha256:64c4f340338c68c463f1b56e3f2f0423f7b17ba6c3febae80b81f0e093077f59",
|
||||
"sha256:675192fca634f0df69af3493a48224f211f8db4e84452b08d5fcebb9167adb01",
|
||||
"sha256:700997b77cfab016533b3e7dbc03b71d33ee4df1d79f2463a318ca0263fc29dd",
|
||||
"sha256:8505e614c983834239f865da2dd336dcf9d72776b951d5dfa5ac36b987726e1b",
|
||||
"sha256:962c44070c281d86398aeb8f64e1bf37816a4dfc6f4c0f114756b14fc575621d",
|
||||
"sha256:9e536783a5acee79a9b308be97d3952b662748c4037b6a24cbb339dc7ed8eb89",
|
||||
"sha256:9ea749fd447ce7fb1ac71f7616371f04054d969d412d37611716721931e36efd",
|
||||
"sha256:a34cb28e0747ea15e82d13e14de606747e9e484fb28d63c999483f5d5188e89b",
|
||||
"sha256:a3ee9c793ffefe2944d3a2bd928a0e436cd0ac2d9e3723152d6fd5398838ce7d",
|
||||
"sha256:aab75d99f3f2874733946a7648ce87a50019eb90baef931698f96b76b6769a46",
|
||||
"sha256:b1ed2bdb27b4c9fc87058a1cb751c4df8752002143ed393899edb82b131e0546",
|
||||
"sha256:b360d8fd88d2bad01cb953d81fd2edd4be539df7bfec41e8753fe9f4456a5082",
|
||||
"sha256:b8f58c7db64d8f27078cbf2a4391af6aa4e4767cc08b37555c4ae064b8558d9b",
|
||||
"sha256:c1bbb628ed5192124889b51204de27c575b3ffc05a5a91307e7640eff1d48da4",
|
||||
"sha256:c2ff24df02a125b7b346c4c9078c8936da06964cc2d276292c357d64378158f8",
|
||||
"sha256:c890728a93fffd0407d7d37c1e6083ff3f9f211c83b4316fae3778417eab9811",
|
||||
"sha256:c96472b8ca5dc135fb0aa62f79b033f02aa434fb03a8b190600a5ae4102df1fd",
|
||||
"sha256:ce7866f29d3025b5b34c2e944e66ebef0d92e4a4f2463f7266daa03a1332a651",
|
||||
"sha256:e26c993bd4b220429d4ec8c1468eca445a4064a61c74ca08da7429af9bc53bb0"
|
||||
],
|
||||
"index": "pypi",
|
||||
"version": "==5.2"
|
||||
"version": "==5.2.1"
|
||||
},
|
||||
"importlib-metadata": {
|
||||
"iniconfig": {
|
||||
"hashes": [
|
||||
"sha256:90bb658cdbbf6d1735b6341ce708fc7024a3e14e99ffdc5783edea9f9b077f83",
|
||||
"sha256:dc15b2969b4ce36305c51eebe62d418ac7791e9a157911d58bfb1f9ccd8e2070"
|
||||
"sha256:80cf40c597eb564e86346103f609d74efce0f6b4d4f30ec8ce9e2c26411ba437",
|
||||
"sha256:e5f92f89355a67de0595932a6c6c02ab4afddc6fcdc0bfc5becd0d60884d3f69"
|
||||
],
|
||||
"markers": "python_version < '3.8'",
|
||||
"version": "==1.7.0"
|
||||
"version": "==1.0.1"
|
||||
},
|
||||
"more-itertools": {
|
||||
"hashes": [
|
||||
"sha256:68c70cc7167bdf5c7c9d8f6954a7837089c6a36bf565383919bb595efb8a17e5",
|
||||
"sha256:b78134b2063dd214000685165d81c154522c3ee0a1c0d4d113c80361c234c5a2"
|
||||
],
|
||||
"markers": "python_version >= '3.5'",
|
||||
"version": "==8.4.0"
|
||||
},
|
||||
"packaging": {
|
||||
@ -1079,6 +1141,7 @@
|
||||
"sha256:4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8",
|
||||
"sha256:998416ba6962ae7fbd6596850b80e17859a5753ba17c32284f67bfff33784181"
|
||||
],
|
||||
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
|
||||
"version": "==20.4"
|
||||
},
|
||||
"pbr": {
|
||||
@ -1094,6 +1157,7 @@
|
||||
"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": {
|
||||
@ -1101,6 +1165,7 @@
|
||||
"sha256:366389d1db726cd2fcfc79732e75410e5fe4d31db13692115529d34069a043c2",
|
||||
"sha256:9ca6883ce56b4e8da7e79ac18787889fa5206c79dcc67fb065376cd2fe03f342"
|
||||
],
|
||||
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
|
||||
"version": "==1.9.0"
|
||||
},
|
||||
"pyparsing": {
|
||||
@ -1108,36 +1173,31 @@
|
||||
"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": [
|
||||
"sha256:5c0db86b698e8f170ba4582a492248919255fcd4c79b1ee64ace34301fb589a1",
|
||||
"sha256:7979331bfcba207414f5e1263b5a0f8f521d0f457318836a7355531ed1a4c7d8"
|
||||
"sha256:85228d75db9f45e06e57ef9bf4429267f81ac7c0d742cc9ed63d09886a9fe6f4",
|
||||
"sha256:8b6007800c53fdacd5a5c192203f4e531eb2a1540ad9c752e052ec0f7143dbad"
|
||||
],
|
||||
"index": "pypi",
|
||||
"version": "==5.4.3"
|
||||
"version": "==6.0.1"
|
||||
},
|
||||
"six": {
|
||||
"hashes": [
|
||||
"sha256:30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259",
|
||||
"sha256:8b74bedcbbbaca38ff6d7491d76f2b06b3592611af620f8426e82dddb04a5ced"
|
||||
],
|
||||
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
|
||||
"version": "==1.15.0"
|
||||
},
|
||||
"wcwidth": {
|
||||
"toml": {
|
||||
"hashes": [
|
||||
"sha256:beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784",
|
||||
"sha256:c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83"
|
||||
"sha256:926b612be1e5ce0634a2ca03470f95169cf16f939018233a670519cb4ac58b0f",
|
||||
"sha256:bda89d5935c2eac546d648028b9901107a595863cb36bae0c73ac804a9b4ce88"
|
||||
],
|
||||
"version": "==0.2.5"
|
||||
},
|
||||
"zipp": {
|
||||
"hashes": [
|
||||
"sha256:aa36550ff0c0b7ef7fa639055d797116ee891440eac1a56f378e2d3179e0320b",
|
||||
"sha256:c599e4d75c98f6798c509911d08a22e6c021d074469042177c8c86fb92eefd96"
|
||||
],
|
||||
"version": "==3.1.0"
|
||||
"version": "==0.10.1"
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -18,6 +18,9 @@ Make sure all of the following are properly installed on your system:
|
||||
- [Install pipenv](https://pipenv-es.readthedocs.io/es/stable/)
|
||||
- [Add ${HOME}/.local/bin to your PATH](https://github.com/pypa/pipenv/issues/2122#issue-319600584)
|
||||
|
||||
### Running Postgres
|
||||
|
||||
|
||||
### Project Initialization
|
||||
1. Clone this repository.
|
||||
2. In PyCharm:
|
||||
|
||||
@ -46,6 +46,9 @@ PB_STUDY_DETAILS_URL = environ.get('PB_STUDY_DETAILS_URL', default=PB_BASE_URL +
|
||||
LDAP_URL = environ.get('LDAP_URL', default="ldap.virginia.edu").strip('/') # No trailing slash or http://
|
||||
LDAP_TIMEOUT_SEC = int(environ.get('LDAP_TIMEOUT_SEC', default=1))
|
||||
|
||||
# Github token
|
||||
GITHUB_TOKEN = environ.get('GITHUB_TOKEN', None)
|
||||
|
||||
# Email configuration
|
||||
DEFAULT_SENDER = 'askresearch@virginia.edu'
|
||||
FALLBACK_EMAILS = ['askresearch@virginia.edu', 'sartographysupport@googlegroups.com']
|
||||
|
||||
48
crc/api.yml
48
crc/api.yml
@ -31,6 +31,13 @@ paths:
|
||||
'304':
|
||||
description: Redirection to the hosted frontend with an auth_token header.
|
||||
/user:
|
||||
parameters:
|
||||
- name: admin_impersonate_uid
|
||||
in: query
|
||||
required: false
|
||||
description: For admins, the unique uid of an existing user to impersonate.
|
||||
schema:
|
||||
type: string
|
||||
get:
|
||||
operationId: crc.api.user.get_current_user
|
||||
summary: Returns the current user.
|
||||
@ -38,11 +45,27 @@ paths:
|
||||
- Users
|
||||
responses:
|
||||
'200':
|
||||
description: The currently authenticated user.
|
||||
description: The currently-authenticated user, or, if the current user is an admin and admin_impersonate_uid is provided, this will be the user with the given uid.
|
||||
content:
|
||||
application/json:
|
||||
schema:
|
||||
$ref: "#/components/schemas/User"
|
||||
/list_users:
|
||||
get:
|
||||
operationId: crc.api.user.get_all_users
|
||||
security:
|
||||
- auth_admin: ['secret']
|
||||
summary: Returns a list of all users in the database.
|
||||
tags:
|
||||
- Users
|
||||
responses:
|
||||
'200':
|
||||
description: All users in the database.
|
||||
content:
|
||||
application/json:
|
||||
schema:
|
||||
type: array
|
||||
$ref: "#/components/schemas/User"
|
||||
# /v1.0/study
|
||||
/study:
|
||||
get:
|
||||
@ -56,6 +79,7 @@ paths:
|
||||
content:
|
||||
application/json:
|
||||
schema:
|
||||
type: array
|
||||
$ref: "#/components/schemas/Study"
|
||||
post:
|
||||
operationId: crc.api.study.add_study
|
||||
@ -572,6 +596,18 @@ paths:
|
||||
description: The type of action the event documents, options include "ASSIGNMENT" for tasks that are waiting on you, "COMPLETE" for things have completed.
|
||||
schema:
|
||||
type: string
|
||||
- name: workflow
|
||||
in: query
|
||||
required: false
|
||||
description: Restrict results to the given workflow.
|
||||
schema:
|
||||
type: number
|
||||
- name: study
|
||||
in: query
|
||||
required: false
|
||||
description: Restrict results to the given study.
|
||||
schema:
|
||||
type: number
|
||||
get:
|
||||
operationId: crc.api.workflow.get_task_events
|
||||
summary: Returns a list of task events related to the current user. Can be filtered by type.
|
||||
@ -610,6 +646,12 @@ paths:
|
||||
description: Set this to true to reset the workflow
|
||||
schema:
|
||||
type: boolean
|
||||
- name: do_engine_steps
|
||||
in: query
|
||||
required: false
|
||||
description: Defaults to true, can be set to false if you are just looking at the workflow not completeing it.
|
||||
schema:
|
||||
type: boolean
|
||||
tags:
|
||||
- Workflows and Tasks
|
||||
responses:
|
||||
@ -1044,9 +1086,9 @@ components:
|
||||
user_uid:
|
||||
type: string
|
||||
example: dhf8r
|
||||
protocol_builder_status:
|
||||
status:
|
||||
type: string
|
||||
enum: [INCOMPLETE, ACTIVE, HOLD, OPEN, ABANDONED]
|
||||
enum: ['in_progress', 'hold', 'open_for_enrollment', 'abandoned']
|
||||
example: done
|
||||
sponsor:
|
||||
type: string
|
||||
|
||||
@ -3,19 +3,22 @@ import json
|
||||
|
||||
from flask import url_for
|
||||
from flask_admin import Admin
|
||||
from flask_admin.actions import action
|
||||
from flask_admin.contrib import sqla
|
||||
from flask_admin.contrib.sqla import ModelView
|
||||
from sqlalchemy import desc
|
||||
from werkzeug.utils import redirect
|
||||
from jinja2 import Markup
|
||||
|
||||
from crc import db, app
|
||||
from crc.api.user import verify_token, verify_token_admin
|
||||
from crc.models.approval import ApprovalModel
|
||||
from crc.models.file import FileModel
|
||||
from crc.models.file import FileModel, FileDataModel
|
||||
from crc.models.task_event import TaskEventModel
|
||||
from crc.models.study import StudyModel
|
||||
from crc.models.user import UserModel
|
||||
from crc.models.workflow import WorkflowModel
|
||||
from crc.services.file_service import FileService
|
||||
|
||||
|
||||
class AdminModelView(sqla.ModelView):
|
||||
@ -34,26 +37,40 @@ class AdminModelView(sqla.ModelView):
|
||||
# redirect to login page if user doesn't have access
|
||||
return redirect(url_for('home'))
|
||||
|
||||
|
||||
class UserView(AdminModelView):
|
||||
column_filters = ['uid']
|
||||
|
||||
|
||||
class StudyView(AdminModelView):
|
||||
column_filters = ['id', 'primary_investigator_id']
|
||||
column_searchable_list = ['title']
|
||||
|
||||
|
||||
class ApprovalView(AdminModelView):
|
||||
column_filters = ['study_id', 'approver_uid']
|
||||
|
||||
|
||||
class WorkflowView(AdminModelView):
|
||||
column_filters = ['study_id', 'id']
|
||||
|
||||
|
||||
class FileView(AdminModelView):
|
||||
column_filters = ['workflow_id']
|
||||
column_filters = ['workflow_id', 'type']
|
||||
|
||||
@action('publish', 'Publish', 'Are you sure you want to publish this file(s)?')
|
||||
def action_publish(self, ids):
|
||||
FileService.publish_to_github(ids)
|
||||
|
||||
@action('update', 'Update', 'Are you sure you want to update this file(s)?')
|
||||
def action_update(self, ids):
|
||||
FileService.update_from_github(ids)
|
||||
|
||||
|
||||
def json_formatter(view, context, model, name):
|
||||
value = getattr(model, name)
|
||||
json_value = json.dumps(value, ensure_ascii=False, indent=2)
|
||||
return Markup('<pre>{}</pre>'.format(json_value))
|
||||
return Markup(f'<pre>{json_value}</pre>')
|
||||
|
||||
class TaskEventView(AdminModelView):
|
||||
column_filters = ['workflow_id', 'action']
|
||||
@ -62,6 +79,7 @@ class TaskEventView(AdminModelView):
|
||||
'form_data': json_formatter,
|
||||
}
|
||||
|
||||
|
||||
admin = Admin(app)
|
||||
|
||||
admin.add_view(StudyView(StudyModel, db.session))
|
||||
|
||||
@ -1,5 +1,6 @@
|
||||
from SpiffWorkflow import WorkflowException
|
||||
from SpiffWorkflow.exceptions import WorkflowTaskExecException
|
||||
from flask import g
|
||||
|
||||
from crc import ma, app
|
||||
|
||||
@ -24,6 +25,11 @@ class ApiError(Exception):
|
||||
instance.task_id = task.task_spec.name or ""
|
||||
instance.task_name = task.task_spec.description or ""
|
||||
instance.file_name = task.workflow.spec.file or ""
|
||||
|
||||
# Fixme: spiffworkflow is doing something weird where task ends up referenced in the data in some cases.
|
||||
if "task" in task.data:
|
||||
task.data.pop("task")
|
||||
|
||||
instance.task_data = task.data
|
||||
app.logger.error(message, exc_info=True)
|
||||
return instance
|
||||
@ -60,3 +66,5 @@ class ApiErrorSchema(ma.Schema):
|
||||
def handle_invalid_usage(error):
|
||||
response = ApiErrorSchema().dump(error)
|
||||
return response, error.status_code
|
||||
|
||||
|
||||
|
||||
@ -6,8 +6,9 @@ from sqlalchemy.exc import IntegrityError
|
||||
from crc import session
|
||||
from crc.api.common import ApiError, ApiErrorSchema
|
||||
from crc.models.protocol_builder import ProtocolBuilderStatus
|
||||
from crc.models.study import StudySchema, StudyModel, Study
|
||||
from crc.models.study import Study, StudyModel, StudySchema, StudyStatus
|
||||
from crc.services.study_service import StudyService
|
||||
from crc.services.user_service import UserService
|
||||
|
||||
|
||||
def add_study(body):
|
||||
@ -17,11 +18,11 @@ def add_study(body):
|
||||
if 'title' not in body:
|
||||
raise ApiError("missing_title", "Can't create a new study without a title.")
|
||||
|
||||
study_model = StudyModel(user_uid=g.user.uid,
|
||||
study_model = StudyModel(user_uid=UserService.current_user().uid,
|
||||
title=body['title'],
|
||||
primary_investigator_id=body['primary_investigator_id'],
|
||||
last_updated=datetime.now(),
|
||||
protocol_builder_status=ProtocolBuilderStatus.ACTIVE)
|
||||
status=StudyStatus.in_progress)
|
||||
|
||||
session.add(study_model)
|
||||
errors = StudyService._add_all_workflow_specs_to_study(study_model)
|
||||
@ -65,8 +66,9 @@ def delete_study(study_id):
|
||||
|
||||
def user_studies():
|
||||
"""Returns all the studies associated with the current user. """
|
||||
StudyService.synch_with_protocol_builder_if_enabled(g.user)
|
||||
studies = StudyService.get_studies_for_user(g.user)
|
||||
user = UserService.current_user(allow_admin_impersonate=True)
|
||||
StudyService.synch_with_protocol_builder_if_enabled(user)
|
||||
studies = StudyService.get_studies_for_user(user)
|
||||
results = StudySchema(many=True).dump(studies)
|
||||
return results
|
||||
|
||||
|
||||
@ -1,10 +1,11 @@
|
||||
import flask
|
||||
from flask import g, request
|
||||
|
||||
from crc import app, db
|
||||
from crc import app, session
|
||||
from crc.api.common import ApiError
|
||||
from crc.models.user import UserModel, UserModelSchema
|
||||
from crc.services.ldap_service import LdapService, LdapModel
|
||||
from crc.services.user_service import UserService
|
||||
|
||||
"""
|
||||
.. module:: crc.api.user
|
||||
@ -31,14 +32,14 @@ def verify_token(token=None):
|
||||
failure_error = ApiError("invalid_token", "Unable to decode the token you provided. Please re-authenticate",
|
||||
status_code=403)
|
||||
|
||||
if not _is_production() and (token is None or 'user' not in g):
|
||||
g.user = UserModel.query.first()
|
||||
token = g.user.encode_auth_token()
|
||||
|
||||
if token:
|
||||
try:
|
||||
token_info = UserModel.decode_auth_token(token)
|
||||
g.user = UserModel.query.filter_by(uid=token_info['sub']).first()
|
||||
|
||||
# If the user is valid, store the token for this session
|
||||
if g.user:
|
||||
g.token = token
|
||||
except:
|
||||
raise failure_error
|
||||
if g.user is not None:
|
||||
@ -47,27 +48,37 @@ def verify_token(token=None):
|
||||
raise failure_error
|
||||
|
||||
# If there's no token and we're in production, get the user from the SSO headers and return their token
|
||||
if not token and _is_production():
|
||||
elif _is_production():
|
||||
uid = _get_request_uid(request)
|
||||
|
||||
if uid is not None:
|
||||
db_user = UserModel.query.filter_by(uid=uid).first()
|
||||
|
||||
# If the user is valid, store the user and token for this session
|
||||
if db_user is not None:
|
||||
g.user = db_user
|
||||
token = g.user.encode_auth_token().decode()
|
||||
g.token = token
|
||||
token_info = UserModel.decode_auth_token(token)
|
||||
return token_info
|
||||
|
||||
else:
|
||||
raise ApiError("no_user", "User not found. Please login via the frontend app before accessing this feature.",
|
||||
status_code=403)
|
||||
raise ApiError("no_user",
|
||||
"User not found. Please login via the frontend app before accessing this feature.",
|
||||
status_code=403)
|
||||
|
||||
else:
|
||||
# Fall back to a default user if this is not production.
|
||||
g.user = UserModel.query.first()
|
||||
token = g.user.encode_auth_token()
|
||||
token_info = UserModel.decode_auth_token(token)
|
||||
return token_info
|
||||
|
||||
|
||||
def verify_token_admin(token=None):
|
||||
"""
|
||||
Verifies the token for the user (if provided) in non-production environment. If in production environment,
|
||||
checks that the user is in the list of authorized admins
|
||||
Verifies the token for the user (if provided) in non-production environment.
|
||||
If in production environment, checks that the user is in the list of authorized admins
|
||||
|
||||
Args:
|
||||
token: Optional[str]
|
||||
@ -75,21 +86,44 @@ def verify_token_admin(token=None):
|
||||
Returns:
|
||||
token: str
|
||||
"""
|
||||
|
||||
# If this is production, check that the user is in the list of admins
|
||||
if _is_production():
|
||||
uid = _get_request_uid(request)
|
||||
|
||||
if uid is not None and uid in app.config['ADMIN_UIDS']:
|
||||
return verify_token()
|
||||
|
||||
# If we're not in production, just use the normal verify_token method
|
||||
else:
|
||||
return verify_token(token)
|
||||
verify_token(token)
|
||||
if "user" in g and g.user.is_admin():
|
||||
token = g.user.encode_auth_token()
|
||||
token_info = UserModel.decode_auth_token(token)
|
||||
return token_info
|
||||
|
||||
|
||||
def get_current_user():
|
||||
return UserModelSchema().dump(g.user)
|
||||
def start_impersonating(uid):
|
||||
if uid is not None and UserService.user_is_admin():
|
||||
UserService.start_impersonating(uid)
|
||||
|
||||
user = UserService.current_user(allow_admin_impersonate=True)
|
||||
return UserModelSchema().dump(user)
|
||||
|
||||
|
||||
def stop_impersonating():
|
||||
if UserService.user_is_admin():
|
||||
UserService.stop_impersonating()
|
||||
|
||||
user = UserService.current_user(allow_admin_impersonate=False)
|
||||
return UserModelSchema().dump(user)
|
||||
|
||||
|
||||
def get_current_user(admin_impersonate_uid=None):
|
||||
if UserService.user_is_admin():
|
||||
if admin_impersonate_uid is not None:
|
||||
UserService.start_impersonating(admin_impersonate_uid)
|
||||
else:
|
||||
UserService.stop_impersonating()
|
||||
|
||||
user = UserService.current_user(UserService.user_is_admin() and UserService.admin_is_impersonating())
|
||||
return UserModelSchema().dump(user)
|
||||
|
||||
|
||||
def get_all_users():
|
||||
if "user" in g and g.user.is_admin():
|
||||
all_users = session.query(UserModel).all()
|
||||
return UserModelSchema(many=True).dump(all_users)
|
||||
|
||||
|
||||
def login(
|
||||
@ -132,7 +166,6 @@ def login(
|
||||
# X-Forwarded-Server: dev.crconnect.uvadcos.io
|
||||
# Connection: Keep-Alive
|
||||
|
||||
|
||||
# If we're in production, override any uid with the uid from the SSO request headers
|
||||
if _is_production():
|
||||
uid = _get_request_uid(request)
|
||||
@ -180,6 +213,8 @@ def _handle_login(user_info: LdapModel, redirect_url=None):
|
||||
|
||||
# Return the frontend auth callback URL, with auth token appended.
|
||||
auth_token = user.encode_auth_token().decode()
|
||||
g.token = auth_token
|
||||
|
||||
if redirect_url is not None:
|
||||
if redirect_url.find("http://") != 0 and redirect_url.find("https://") != 0:
|
||||
redirect_url = "http://" + redirect_url
|
||||
@ -192,13 +227,13 @@ def _handle_login(user_info: LdapModel, redirect_url=None):
|
||||
|
||||
|
||||
def _upsert_user(user_info):
|
||||
user = db.session.query(UserModel).filter(UserModel.uid == user_info.uid).first()
|
||||
user = session.query(UserModel).filter(UserModel.uid == user_info.uid).first()
|
||||
|
||||
if user is None:
|
||||
# Add new user
|
||||
user = UserModel()
|
||||
else:
|
||||
user = db.session.query(UserModel).filter(UserModel.uid == user_info.uid).with_for_update().first()
|
||||
user = session.query(UserModel).filter(UserModel.uid == user_info.uid).with_for_update().first()
|
||||
|
||||
user.uid = user_info.uid
|
||||
user.display_name = user_info.display_name
|
||||
@ -206,8 +241,8 @@ def _upsert_user(user_info):
|
||||
user.affiliation = user_info.affiliation
|
||||
user.title = user_info.title
|
||||
|
||||
db.session.add(user)
|
||||
db.session.commit()
|
||||
session.add(user)
|
||||
session.commit()
|
||||
return user
|
||||
|
||||
|
||||
|
||||
@ -13,6 +13,7 @@ from crc.models.workflow import WorkflowModel, WorkflowSpecModelSchema, Workflow
|
||||
from crc.services.file_service import FileService
|
||||
from crc.services.lookup_service import LookupService
|
||||
from crc.services.study_service import StudyService
|
||||
from crc.services.user_service import UserService
|
||||
from crc.services.workflow_processor import WorkflowProcessor
|
||||
from crc.services.workflow_service import WorkflowService
|
||||
|
||||
@ -95,19 +96,30 @@ def delete_workflow_specification(spec_id):
|
||||
session.commit()
|
||||
|
||||
|
||||
def get_workflow(workflow_id, soft_reset=False, hard_reset=False):
|
||||
def get_workflow(workflow_id, soft_reset=False, hard_reset=False, do_engine_steps=True):
|
||||
"""Soft reset will attempt to update to the latest spec without starting over,
|
||||
Hard reset will update to the latest spec and start from the beginning.
|
||||
Read Only will return the workflow in a read only state, without running any
|
||||
engine tasks or logging any events. """
|
||||
workflow_model: WorkflowModel = session.query(WorkflowModel).filter_by(id=workflow_id).first()
|
||||
processor = WorkflowProcessor(workflow_model, soft_reset=soft_reset, hard_reset=hard_reset)
|
||||
if do_engine_steps:
|
||||
processor.do_engine_steps()
|
||||
processor.save()
|
||||
WorkflowService.update_task_assignments(processor)
|
||||
workflow_api_model = WorkflowService.processor_to_workflow_api(processor)
|
||||
WorkflowService.update_task_assignments(processor)
|
||||
return WorkflowApiSchema().dump(workflow_api_model)
|
||||
|
||||
|
||||
def get_task_events(action):
|
||||
def get_task_events(action = None, workflow = None, study = None):
|
||||
"""Provides a way to see a history of what has happened, or get a list of tasks that need your attention."""
|
||||
query = session.query(TaskEventModel).filter(TaskEventModel.user_uid == g.user.uid)
|
||||
if action:
|
||||
query = query.filter(TaskEventModel.action == action)
|
||||
if workflow:
|
||||
query = query.filter(TaskEventModel.workflow_id == workflow)
|
||||
if study:
|
||||
query = query.filter(TaskEventModel.study_id == study)
|
||||
events = query.all()
|
||||
|
||||
# Turn the database records into something a little richer for the UI to use.
|
||||
@ -130,7 +142,7 @@ def set_current_task(workflow_id, task_id):
|
||||
task_id = uuid.UUID(task_id)
|
||||
spiff_task = processor.bpmn_workflow.get_task(task_id)
|
||||
_verify_user_and_role(processor, spiff_task)
|
||||
user_uid = g.user.uid
|
||||
user_uid = UserService.current_user(allow_admin_impersonate=True).uid
|
||||
if spiff_task.state != spiff_task.COMPLETED and spiff_task.state != spiff_task.READY:
|
||||
raise ApiError("invalid_state", "You may not move the token to a task who's state is not "
|
||||
"currently set to COMPLETE or READY.")
|
||||
@ -173,7 +185,8 @@ def update_task(workflow_id, task_id, body, terminate_loop=None):
|
||||
processor.save()
|
||||
|
||||
# Log the action, and any pending task assignments in the event of lanes in the workflow.
|
||||
WorkflowService.log_task_action(g.user.uid, processor, spiff_task, WorkflowService.TASK_ACTION_COMPLETE)
|
||||
user = UserService.current_user(allow_admin_impersonate=False) # Always log as the real user.
|
||||
WorkflowService.log_task_action(user.uid, processor, spiff_task, WorkflowService.TASK_ACTION_COMPLETE)
|
||||
WorkflowService.update_task_assignments(processor)
|
||||
|
||||
workflow_api_model = WorkflowService.processor_to_workflow_api(processor)
|
||||
@ -233,19 +246,11 @@ def lookup(workflow_id, field_id, query=None, value=None, limit=10):
|
||||
|
||||
def _verify_user_and_role(processor, spiff_task):
|
||||
"""Assures the currently logged in user can access the given workflow and task, or
|
||||
raises an error.
|
||||
Allow administrators to modify tasks, otherwise assure that the current user
|
||||
is allowed to edit or update the task. Will raise the appropriate error if user
|
||||
is not authorized. """
|
||||
|
||||
if 'user' not in g:
|
||||
raise ApiError("logged_out", "You are no longer logged in.", status_code=401)
|
||||
|
||||
if g.user.uid in app.config['ADMIN_UIDS']:
|
||||
return g.user.uid
|
||||
raises an error. """
|
||||
|
||||
user = UserService.current_user(allow_admin_impersonate=True)
|
||||
allowed_users = WorkflowService.get_users_assigned_to_task(processor, spiff_task)
|
||||
if g.user.uid not in allowed_users:
|
||||
if user.uid not in allowed_users:
|
||||
raise ApiError.from_task("permission_denied",
|
||||
f"This task must be completed by '{allowed_users}', "
|
||||
f"but you are {g.user.uid}", spiff_task)
|
||||
f"but you are {user.uid}", spiff_task)
|
||||
|
||||
@ -143,7 +143,8 @@ class NavigationItemSchema(ma.Schema):
|
||||
|
||||
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, title):
|
||||
spec_version, is_latest_spec, workflow_spec_id, total_tasks, completed_tasks,
|
||||
last_updated, title):
|
||||
self.id = id
|
||||
self.status = status
|
||||
self.next_task = next_task # The next task that requires user input.
|
||||
|
||||
@ -17,16 +17,17 @@ class ProtocolBuilderInvestigatorType(enum.Enum):
|
||||
SCI = "Scientific Contact"
|
||||
|
||||
|
||||
# Deprecated: Marked for removal
|
||||
class ProtocolBuilderStatus(enum.Enum):
|
||||
# • Active: found in PB and no HSR number and not hold
|
||||
# • Hold: store boolean value in CR Connect (add to Study Model)
|
||||
# • Open To Enrollment: has start date and HSR number?
|
||||
# • Abandoned: deleted in PB
|
||||
INCOMPLETE = 'incomplete' # Found in PB but not ready to start (not q_complete)
|
||||
ACTIVE = 'active', # found in PB, marked as "q_complete" and no HSR number and not hold
|
||||
HOLD = 'hold', # CR Connect side, if the Study ias marked as "hold".
|
||||
OPEN = 'open', # Open To Enrollment: has start date and HSR number?
|
||||
ABANDONED = 'Abandoned' # Not found in PB
|
||||
incomplete = 'incomplete' # Found in PB but not ready to start (not q_complete)
|
||||
active = 'active' # found in PB, marked as "q_complete" and no HSR number and not hold
|
||||
hold = 'hold' # CR Connect side, if the Study ias marked as "hold".
|
||||
open = 'open' # Open To Enrollment: has start date and HSR number?
|
||||
abandoned = 'abandoned' # Not found in PB
|
||||
|
||||
|
||||
#DRAFT = 'draft', # !Q_COMPLETE
|
||||
|
||||
@ -1,3 +1,7 @@
|
||||
import datetime
|
||||
import enum
|
||||
import json
|
||||
|
||||
import marshmallow
|
||||
from marshmallow import INCLUDE, fields
|
||||
from marshmallow_enum import EnumField
|
||||
@ -11,12 +15,26 @@ from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowState, Workfl
|
||||
WorkflowModel
|
||||
|
||||
|
||||
class StudyStatus(enum.Enum):
|
||||
in_progress = 'in_progress'
|
||||
hold = 'hold'
|
||||
open_for_enrollment = 'open_for_enrollment'
|
||||
abandoned = 'abandoned'
|
||||
|
||||
|
||||
class IrbStatus(enum.Enum):
|
||||
incomplete_in_protocol_builder = 'incomplete in protocol builder'
|
||||
completed_in_protocol_builder = 'completed in protocol builder'
|
||||
hsr_assigned = 'hsr number assigned'
|
||||
|
||||
|
||||
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))
|
||||
status = db.Column(db.Enum(StudyStatus))
|
||||
irb_status = db.Column(db.Enum(IrbStatus))
|
||||
primary_investigator_id = db.Column(db.String, nullable=True)
|
||||
sponsor = db.Column(db.String, nullable=True)
|
||||
hsr_number = db.Column(db.String, nullable=True)
|
||||
@ -25,6 +43,7 @@ class StudyModel(db.Model):
|
||||
investigator_uids = db.Column(db.ARRAY(db.String), nullable=True)
|
||||
requirements = db.Column(db.ARRAY(db.Integer), nullable=True)
|
||||
on_hold = db.Column(db.Boolean, default=False)
|
||||
enrollment_date = db.Column(db.DateTime(timezone=True), nullable=True)
|
||||
|
||||
def update_from_protocol_builder(self, pbs: ProtocolBuilderStudy):
|
||||
self.hsr_number = pbs.HSRNUMBER
|
||||
@ -32,22 +51,27 @@ class StudyModel(db.Model):
|
||||
self.user_uid = pbs.NETBADGEID
|
||||
self.last_updated = pbs.DATE_MODIFIED
|
||||
|
||||
self.protocol_builder_status = ProtocolBuilderStatus.ACTIVE
|
||||
self.irb_status = IrbStatus.incomplete_in_protocol_builder
|
||||
self.status = StudyStatus.in_progress
|
||||
if pbs.HSRNUMBER:
|
||||
self.protocol_builder_status = ProtocolBuilderStatus.OPEN
|
||||
self.irb_status = IrbStatus.hsr_assigned
|
||||
self.status = StudyStatus.open_for_enrollment
|
||||
if self.on_hold:
|
||||
self.protocol_builder_status = ProtocolBuilderStatus.HOLD
|
||||
self.status = StudyStatus.hold
|
||||
|
||||
|
||||
class WorkflowMetadata(object):
|
||||
def __init__(self, id, name, display_name, description, spec_version, category_id, state: WorkflowState, status: WorkflowStatus,
|
||||
total_tasks, completed_tasks, display_order):
|
||||
def __init__(self, id, name = None, display_name = None, description = None, spec_version = None,
|
||||
category_id = None, category_display_name = None, state: WorkflowState = None,
|
||||
status: WorkflowStatus = None, total_tasks = None, completed_tasks = None,
|
||||
display_order = None):
|
||||
self.id = id
|
||||
self.name = name
|
||||
self.display_name = display_name
|
||||
self.description = description
|
||||
self.spec_version = spec_version
|
||||
self.category_id = category_id
|
||||
self.category_display_name = category_display_name
|
||||
self.state = state
|
||||
self.status = status
|
||||
self.total_tasks = total_tasks
|
||||
@ -64,6 +88,7 @@ class WorkflowMetadata(object):
|
||||
description=workflow.workflow_spec.description,
|
||||
spec_version=workflow.spec_version(),
|
||||
category_id=workflow.workflow_spec.category_id,
|
||||
category_display_name=workflow.workflow_spec.category.display_name,
|
||||
state=WorkflowState.optional,
|
||||
status=workflow.status,
|
||||
total_tasks=workflow.total_tasks,
|
||||
@ -79,7 +104,8 @@ class WorkflowMetadataSchema(ma.Schema):
|
||||
class Meta:
|
||||
model = WorkflowMetadata
|
||||
additional = ["id", "name", "display_name", "description",
|
||||
"total_tasks", "completed_tasks", "display_order"]
|
||||
"total_tasks", "completed_tasks", "display_order",
|
||||
"category_id", "category_display_name"]
|
||||
unknown = INCLUDE
|
||||
|
||||
|
||||
@ -102,15 +128,15 @@ class CategorySchema(ma.Schema):
|
||||
class Study(object):
|
||||
|
||||
def __init__(self, title, last_updated, primary_investigator_id, user_uid,
|
||||
id=None,
|
||||
protocol_builder_status=None,
|
||||
id=None, status=None, irb_status=None,
|
||||
sponsor="", hsr_number="", ind_number="", categories=[],
|
||||
files=[], approvals=[], **argsv):
|
||||
files=[], approvals=[], enrollment_date=None, **argsv):
|
||||
self.id = id
|
||||
self.user_uid = user_uid
|
||||
self.title = title
|
||||
self.last_updated = last_updated
|
||||
self.protocol_builder_status = protocol_builder_status
|
||||
self.status = status
|
||||
self.irb_status = irb_status
|
||||
self.primary_investigator_id = primary_investigator_id
|
||||
self.sponsor = sponsor
|
||||
self.hsr_number = hsr_number
|
||||
@ -119,6 +145,7 @@ class Study(object):
|
||||
self.approvals = approvals
|
||||
self.warnings = []
|
||||
self.files = files
|
||||
self.enrollment_date = enrollment_date
|
||||
|
||||
@classmethod
|
||||
def from_model(cls, study_model: StudyModel):
|
||||
@ -128,9 +155,29 @@ class Study(object):
|
||||
return instance
|
||||
|
||||
def update_model(self, study_model: StudyModel):
|
||||
for k,v in self.__dict__.items():
|
||||
if not k.startswith('_'):
|
||||
study_model.__dict__[k] = v
|
||||
"""As the case for update was very reduced, it's mostly and specifically
|
||||
updating only the study status and generating a history record
|
||||
"""
|
||||
status = StudyStatus(self.status)
|
||||
study_model.last_updated = datetime.datetime.now()
|
||||
study_model.status = status
|
||||
|
||||
if status == StudyStatus.open_for_enrollment:
|
||||
study_model.enrollment_date = self.enrollment_date
|
||||
|
||||
# change = {
|
||||
# 'status': ProtocolBuilderStatus(self.protocol_builder_status).value,
|
||||
# 'comment': '' if not hasattr(self, 'comment') else self.comment,
|
||||
# 'date': str(datetime.datetime.now())
|
||||
# }
|
||||
|
||||
# if study_model.changes_history:
|
||||
# changes_history = json.loads(study_model.changes_history)
|
||||
# changes_history.append(change)
|
||||
# else:
|
||||
# changes_history = [change]
|
||||
# study_model.changes_history = json.dumps(changes_history)
|
||||
|
||||
|
||||
def model_args(self):
|
||||
"""Arguments that can be passed into the Study Model to update it."""
|
||||
@ -140,22 +187,44 @@ class Study(object):
|
||||
return self_dict
|
||||
|
||||
|
||||
class StudySchema(ma.Schema):
|
||||
class StudyForUpdateSchema(ma.Schema):
|
||||
|
||||
id = fields.Integer(required=False, allow_none=True)
|
||||
categories = fields.List(fields.Nested(CategorySchema), dump_only=True)
|
||||
warnings = fields.List(fields.Nested(ApiErrorSchema), dump_only=True)
|
||||
protocol_builder_status = EnumField(ProtocolBuilderStatus)
|
||||
status = EnumField(StudyStatus, by_value=True)
|
||||
hsr_number = fields.String(allow_none=True)
|
||||
sponsor = fields.String(allow_none=True)
|
||||
ind_number = fields.String(allow_none=True)
|
||||
files = fields.List(fields.Nested(FileSchema), dump_only=True)
|
||||
approvals = fields.List(fields.Nested('ApprovalSchema'), dump_only=True)
|
||||
enrollment_date = fields.DateTime(allow_none=True)
|
||||
comment = fields.String(allow_none=True)
|
||||
|
||||
class Meta:
|
||||
model = Study
|
||||
additional = ["id", "title", "last_updated", "primary_investigator_id", "user_uid",
|
||||
"sponsor", "ind_number", "approvals", "files"]
|
||||
unknown = INCLUDE
|
||||
|
||||
@marshmallow.post_load
|
||||
def make_study(self, data, **kwargs):
|
||||
"""Can load the basic study data for updates to the database, but categories are write only"""
|
||||
return Study(**data)
|
||||
|
||||
|
||||
class StudySchema(ma.Schema):
|
||||
|
||||
id = fields.Integer(required=False, allow_none=True)
|
||||
categories = fields.List(fields.Nested(CategorySchema), dump_only=True)
|
||||
warnings = fields.List(fields.Nested(ApiErrorSchema), dump_only=True)
|
||||
protocol_builder_status = EnumField(StudyStatus, by_value=True)
|
||||
status = EnumField(StudyStatus, by_value=True)
|
||||
hsr_number = fields.String(allow_none=True)
|
||||
sponsor = fields.String(allow_none=True)
|
||||
ind_number = fields.String(allow_none=True)
|
||||
files = fields.List(fields.Nested(FileSchema), dump_only=True)
|
||||
approvals = fields.List(fields.Nested('ApprovalSchema'), dump_only=True)
|
||||
enrollment_date = fields.Date(allow_none=True)
|
||||
|
||||
class Meta:
|
||||
model = Study
|
||||
additional = ["id", "title", "last_updated", "primary_investigator_id", "user_uid",
|
||||
"sponsor", "ind_number", "approvals", "files", "enrollment_date"]
|
||||
unknown = INCLUDE
|
||||
|
||||
@marshmallow.post_load
|
||||
|
||||
@ -50,15 +50,16 @@ class TaskEvent(object):
|
||||
self.task_type = model.task_type
|
||||
self.task_state = model.task_state
|
||||
self.task_lane = model.task_lane
|
||||
self.date = model.date
|
||||
|
||||
|
||||
class TaskEventSchema(ma.Schema):
|
||||
|
||||
study = fields.Nested(StudySchema, dump_only=True)
|
||||
workflow = fields.Nested(WorkflowMetadataSchema, dump_only=True)
|
||||
|
||||
task_lane = fields.String(allow_none=True, required=False)
|
||||
class Meta:
|
||||
model = TaskEvent
|
||||
additional = ["id", "user_uid", "action", "task_id", "task_title",
|
||||
"task_name", "task_type", "task_state", "task_lane"]
|
||||
"task_name", "task_type", "task_state", "task_lane", "date"]
|
||||
unknown = INCLUDE
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
import datetime
|
||||
|
||||
import jwt
|
||||
from marshmallow import fields
|
||||
from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
|
||||
|
||||
from crc import db, app
|
||||
@ -21,6 +22,10 @@ class UserModel(db.Model):
|
||||
|
||||
# TODO: Add Department and School
|
||||
|
||||
def is_admin(self):
|
||||
# Currently admin abilities are set in the configuration, but this
|
||||
# may change in the future.
|
||||
return self.uid in app.config['ADMIN_UIDS']
|
||||
|
||||
def encode_auth_token(self):
|
||||
"""
|
||||
@ -60,4 +65,14 @@ class UserModelSchema(SQLAlchemyAutoSchema):
|
||||
model = UserModel
|
||||
load_instance = True
|
||||
include_relationships = True
|
||||
is_admin = fields.Method('get_is_admin', dump_only=True)
|
||||
|
||||
def get_is_admin(self, obj):
|
||||
return obj.is_admin()
|
||||
|
||||
|
||||
class AdminSessionModel(db.Model):
|
||||
__tablename__ = 'admin_session'
|
||||
id = db.Column(db.Integer, primary_key=True)
|
||||
token = db.Column(db.String, unique=True)
|
||||
admin_impersonate_uid = db.Column(db.String)
|
||||
|
||||
@ -40,7 +40,7 @@ class FactService(Script):
|
||||
else:
|
||||
details = "unknown fact type."
|
||||
|
||||
self.add_data_to_task(task, details)
|
||||
#self.add_data_to_task(task, details)
|
||||
|
||||
print(details)
|
||||
return details
|
||||
|
||||
50
crc/scripts/ldap.py
Normal file
50
crc/scripts/ldap.py
Normal file
@ -0,0 +1,50 @@
|
||||
import copy
|
||||
|
||||
from crc import app
|
||||
from crc.api.common import ApiError
|
||||
from crc.scripts.script import Script
|
||||
from crc.services.ldap_service import LdapService
|
||||
|
||||
|
||||
class Ldap(Script):
|
||||
"""This Script allows to be introduced as part of a workflow and called from there, taking
|
||||
a UID (or several) as input and looking it up through LDAP to return the person's details """
|
||||
|
||||
def get_description(self):
|
||||
return """
|
||||
Attempts to create a dictionary with person details, using the
|
||||
provided argument (a UID) and look it up through LDAP.
|
||||
|
||||
Examples:
|
||||
supervisor_info = ldap(supervisor_uid) // Sets the supervisor information to ldap details for the given uid.
|
||||
"""
|
||||
|
||||
def do_task_validate_only(self, task, *args, **kwargs):
|
||||
return self.set_users_info_in_task(task, args)
|
||||
|
||||
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
|
||||
return self.set_users_info_in_task(task, args)
|
||||
|
||||
def set_users_info_in_task(self, task, args):
|
||||
if len(args) != 1:
|
||||
raise ApiError(code="missing_argument",
|
||||
message="Ldap takes a single argument, the "
|
||||
"UID for the person we want to look up")
|
||||
uid = args[0]
|
||||
user_info_dict = {}
|
||||
|
||||
user_info = LdapService.user_info(uid)
|
||||
user_info_dict = {
|
||||
"display_name": user_info.display_name,
|
||||
"given_name": user_info.given_name,
|
||||
"email_address": user_info.email_address,
|
||||
"telephone_number": user_info.telephone_number,
|
||||
"title": user_info.title,
|
||||
"department": user_info.department,
|
||||
"affiliation": user_info.affiliation,
|
||||
"sponsor_type": user_info.sponsor_type,
|
||||
"uid": user_info.uid,
|
||||
"proper_name": user_info.proper_name()
|
||||
}
|
||||
|
||||
return user_info_dict
|
||||
@ -11,7 +11,7 @@ class RequestApproval(Script):
|
||||
return """
|
||||
Creates an approval request on this workflow, by the given approver_uid(s),"
|
||||
Takes multiple arguments, which should point to data located in current task
|
||||
or be quoted strings. The order is important. Approvals will be processed
|
||||
or be quoted strings. The order is important. Approvals will be processed
|
||||
in this order.
|
||||
|
||||
Example:
|
||||
|
||||
@ -23,6 +23,53 @@ class Script(object):
|
||||
"This is an internal error. The script you are trying to execute '%s' " % self.__class__.__name__ +
|
||||
"does must provide a validate_only option that mimics the do_task, " +
|
||||
"but does not make external calls or database updates." )
|
||||
@staticmethod
|
||||
def generate_augmented_list(task, study_id,workflow_id):
|
||||
"""
|
||||
this makes a dictionary of lambda functions that are closed over the class instance that
|
||||
They represent. This is passed into PythonScriptParser as a list of helper functions that are
|
||||
available for running. In general, they maintain the do_task call structure that they had, but
|
||||
they always return a value rather than updating the task data.
|
||||
|
||||
We may be able to remove the task for each of these calls if we are not using it other than potentially
|
||||
updating the task data.
|
||||
"""
|
||||
def make_closure(subclass,task,study_id,workflow_id):
|
||||
instance = subclass()
|
||||
return lambda *a : subclass.do_task(instance,task,study_id,workflow_id,*a)
|
||||
execlist = {}
|
||||
subclasses = Script.get_all_subclasses()
|
||||
for x in range(len(subclasses)):
|
||||
subclass = subclasses[x]
|
||||
execlist[subclass.__module__.split('.')[-1]] = make_closure(subclass,task,study_id,
|
||||
workflow_id)
|
||||
return execlist
|
||||
|
||||
@staticmethod
|
||||
def generate_augmented_validate_list(task, study_id, workflow_id):
|
||||
"""
|
||||
this makes a dictionary of lambda functions that are closed over the class instance that
|
||||
They represent. This is passed into PythonScriptParser as a list of helper functions that are
|
||||
available for running. In general, they maintain the do_task call structure that they had, but
|
||||
they always return a value rather than updating the task data.
|
||||
|
||||
We may be able to remove the task for each of these calls if we are not using it other than potentially
|
||||
updating the task data.
|
||||
"""
|
||||
|
||||
def make_closure_validate(subclass,task,study_id,workflow_id):
|
||||
instance = subclass()
|
||||
return lambda *a : subclass.do_task_validate_only(instance,task,study_id,workflow_id,*a)
|
||||
execlist = {}
|
||||
subclasses = Script.get_all_subclasses()
|
||||
for x in range(len(subclasses)):
|
||||
subclass = subclasses[x]
|
||||
execlist[subclass.__module__.split('.')[-1]] = make_closure_validate(subclass,task,study_id,
|
||||
workflow_id)
|
||||
return execlist
|
||||
|
||||
|
||||
|
||||
|
||||
@staticmethod
|
||||
def get_all_subclasses():
|
||||
|
||||
@ -8,7 +8,7 @@ from crc.scripts.script import Script
|
||||
from crc.services.file_service import FileService
|
||||
from crc.services.protocol_builder import ProtocolBuilderService
|
||||
from crc.services.study_service import StudyService
|
||||
|
||||
from box import Box
|
||||
|
||||
class StudyInfo(Script):
|
||||
"""Please see the detailed description that is provided below. """
|
||||
@ -149,11 +149,11 @@ Returns information specific to the protocol.
|
||||
|
||||
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
|
||||
"""For validation only, pretend no results come back from pb"""
|
||||
self.check_args(args)
|
||||
self.check_args(args,2)
|
||||
# Assure the reference file exists (a bit hacky, but we want to raise this error early, and cleanly.)
|
||||
FileService.get_reference_file_data(FileService.DOCUMENT_LIST)
|
||||
FileService.get_reference_file_data(FileService.INVESTIGATOR_LIST)
|
||||
data = {
|
||||
data = Box({
|
||||
"study":{
|
||||
"info": {
|
||||
"id": 12,
|
||||
@ -195,38 +195,50 @@ Returns information specific to the protocol.
|
||||
'id': 0,
|
||||
}
|
||||
}
|
||||
}
|
||||
self.add_data_to_task(task=task, data=data["study"])
|
||||
self.add_data_to_task(task, {"documents": StudyService().get_documents_status(study_id)})
|
||||
})
|
||||
if args[0]=='documents':
|
||||
return StudyService().get_documents_status(study_id)
|
||||
return data['study'][args[0]]
|
||||
#self.add_data_to_task(task=task, data=data["study"])
|
||||
#self.add_data_to_task(task, {"documents": StudyService().get_documents_status(study_id)})
|
||||
|
||||
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
|
||||
self.check_args(args)
|
||||
|
||||
self.check_args(args,2)
|
||||
prefix = None
|
||||
if len(args) > 1:
|
||||
prefix = args[1]
|
||||
cmd = args[0]
|
||||
study_info = {}
|
||||
if self.__class__.__name__ in task.data:
|
||||
study_info = task.data[self.__class__.__name__]
|
||||
|
||||
# study_info = {}
|
||||
# if self.__class__.__name__ in task.data:
|
||||
# study_info = task.data[self.__class__.__name__]
|
||||
retval = None
|
||||
if cmd == 'info':
|
||||
study = session.query(StudyModel).filter_by(id=study_id).first()
|
||||
schema = StudySchema()
|
||||
self.add_data_to_task(task, {cmd: schema.dump(study)})
|
||||
retval = schema.dump(study)
|
||||
if cmd == 'investigators':
|
||||
self.add_data_to_task(task, {cmd: StudyService().get_investigators(study_id)})
|
||||
retval = StudyService().get_investigators(study_id)
|
||||
if cmd == 'roles':
|
||||
self.add_data_to_task(task, {cmd: StudyService().get_investigators(study_id, all=True)})
|
||||
retval = StudyService().get_investigators(study_id, all=True)
|
||||
if cmd == 'details':
|
||||
self.add_data_to_task(task, {cmd: self.pb.get_study_details(study_id)})
|
||||
retval = self.pb.get_study_details(study_id)
|
||||
if cmd == 'approvals':
|
||||
self.add_data_to_task(task, {cmd: StudyService().get_approvals(study_id)})
|
||||
retval = StudyService().get_approvals(study_id)
|
||||
if cmd == 'documents':
|
||||
self.add_data_to_task(task, {cmd: StudyService().get_documents_status(study_id)})
|
||||
retval = StudyService().get_documents_status(study_id)
|
||||
if cmd == 'protocol':
|
||||
self.add_data_to_task(task, {cmd: StudyService().get_protocol(study_id)})
|
||||
retval = StudyService().get_protocol(study_id)
|
||||
if isinstance(retval,dict) and prefix is not None:
|
||||
return Box({x:retval[x] for x in retval.keys() if x[:len(prefix)] == prefix})
|
||||
elif isinstance(retval,dict):
|
||||
return Box(retval)
|
||||
else:
|
||||
return retval
|
||||
|
||||
|
||||
def check_args(self, args):
|
||||
if len(args) != 1 or (args[0] not in StudyInfo.type_options):
|
||||
|
||||
def check_args(self, args, maxlen=1):
|
||||
if len(args) < 1 or len(args) > maxlen or (args[0] not in StudyInfo.type_options):
|
||||
raise ApiError(code="missing_argument",
|
||||
message="The StudyInfo script requires a single argument which must be "
|
||||
"one of %s" % ",".join(StudyInfo.type_options))
|
||||
|
||||
@ -2,6 +2,7 @@ import hashlib
|
||||
import json
|
||||
import os
|
||||
from datetime import datetime
|
||||
from github import Github, UnknownObjectException
|
||||
from uuid import UUID
|
||||
from lxml import etree
|
||||
|
||||
@ -78,7 +79,8 @@ class FileService(object):
|
||||
""" Opens a reference file (assumes that it is xls file) and returns the data as a
|
||||
dictionary, each row keyed on the given index_column name. If there are columns
|
||||
that should be represented as integers, pass these as an array of int_columns, lest
|
||||
you get '1.0' rather than '1' """
|
||||
you get '1.0' rather than '1'
|
||||
fixme: This is stupid stupid slow. Place it in the database and just check if it is up to date."""
|
||||
data_model = FileService.get_reference_file_data(reference_file_name)
|
||||
xls = ExcelFile(data_model.data)
|
||||
df = xls.parse(xls.sheet_names[0])
|
||||
@ -332,3 +334,51 @@ class FileService(object):
|
||||
file_model.archived = True
|
||||
session.commit()
|
||||
app.logger.info("Failed to delete file, so archiving it instead. %i, due to %s" % (file_id, str(ie)))
|
||||
|
||||
@staticmethod
|
||||
def update_from_github(file_ids):
|
||||
gh_token = app.config['GITHUB_TOKEN']
|
||||
_github = Github(gh_token)
|
||||
repo = _github.get_user().get_repo('crispy-fiesta')
|
||||
|
||||
for file_id in file_ids:
|
||||
file_data_model = FileDataModel.query.filter_by(
|
||||
file_model_id=file_id
|
||||
).order_by(
|
||||
desc(FileDataModel.version)
|
||||
).first()
|
||||
try:
|
||||
repo_file = repo.get_contents(file_data_model.file_model.name)
|
||||
except UnknownObjectException:
|
||||
# TODO: Add message indicating file is not in the repo
|
||||
pass
|
||||
else:
|
||||
file_data_model.data = repo_file.decoded_content
|
||||
session.add(file_data_model)
|
||||
session.commit()
|
||||
|
||||
@staticmethod
|
||||
def publish_to_github(file_ids):
|
||||
gh_token = app.config['GITHUB_TOKEN']
|
||||
_github = Github(gh_token)
|
||||
repo = _github.get_user().get_repo('crispy-fiesta')
|
||||
|
||||
for file_id in file_ids:
|
||||
file_data_model = FileDataModel.query.filter_by(file_model_id=file_id).first()
|
||||
try:
|
||||
repo_file = repo.get_contents(file_data_model.file_model.name)
|
||||
except UnknownObjectException:
|
||||
repo.create_file(
|
||||
path=file_data_model.file_model.name,
|
||||
message=f'Creating {file_data_model.file_model.name}',
|
||||
content=file_data_model.data
|
||||
)
|
||||
return {'created': True}
|
||||
else:
|
||||
updated = repo.update_file(
|
||||
path=repo_file.path,
|
||||
message=f'Updating {file_data_model.file_model.name}',
|
||||
content=file_data_model.data,
|
||||
sha=repo_file.sha
|
||||
)
|
||||
return {'updated': True}
|
||||
|
||||
@ -1,6 +1,5 @@
|
||||
from copy import copy
|
||||
from datetime import datetime
|
||||
import json
|
||||
from typing import List
|
||||
|
||||
import requests
|
||||
@ -13,16 +12,15 @@ from crc.api.common import ApiError
|
||||
from crc.models.file import FileModel, FileModelSchema, File
|
||||
from crc.models.ldap import LdapSchema
|
||||
from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStatus
|
||||
from crc.models.task_event import TaskEventModel
|
||||
from crc.models.study import StudyModel, Study, Category, WorkflowMetadata
|
||||
from crc.models.study import StudyModel, Study, StudyStatus, Category, WorkflowMetadata
|
||||
from crc.models.task_event import TaskEventModel, TaskEvent
|
||||
from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowModel, WorkflowSpecModel, WorkflowState, \
|
||||
WorkflowStatus
|
||||
from crc.services.approval_service import ApprovalService
|
||||
from crc.services.file_service import FileService
|
||||
from crc.services.ldap_service import LdapService
|
||||
from crc.services.protocol_builder import ProtocolBuilderService
|
||||
from crc.services.workflow_processor import WorkflowProcessor
|
||||
from crc.services.approval_service import ApprovalService
|
||||
from crc.models.approval import Approval
|
||||
|
||||
|
||||
class StudyService(object):
|
||||
@ -63,11 +61,10 @@ class StudyService(object):
|
||||
files = (File.from_models(model, FileService.get_file_data(model.id),
|
||||
FileService.get_doc_dictionary()) for model in files)
|
||||
study.files = list(files)
|
||||
|
||||
# Calling this line repeatedly is very very slow. It creates the
|
||||
# master spec and runs it. Don't execute this for Abandoned studies, as
|
||||
# we don't have the information to process them.
|
||||
if study.protocol_builder_status != ProtocolBuilderStatus.ABANDONED:
|
||||
if study.status != StudyStatus.abandoned:
|
||||
status = StudyService.__get_study_status(study_model)
|
||||
study.warnings = StudyService.__update_status_of_workflow_meta(workflow_metas, status)
|
||||
|
||||
@ -268,7 +265,7 @@ class StudyService(object):
|
||||
for study in db_studies:
|
||||
pb_study = next((pbs for pbs in pb_studies if pbs.STUDYID == study.id), None)
|
||||
if not pb_study:
|
||||
study.protocol_builder_status = ProtocolBuilderStatus.ABANDONED
|
||||
study.status = StudyStatus.abandoned
|
||||
|
||||
db.session.commit()
|
||||
|
||||
|
||||
117
crc/services/user_service.py
Normal file
117
crc/services/user_service.py
Normal file
@ -0,0 +1,117 @@
|
||||
from flask import g
|
||||
|
||||
from crc import session
|
||||
from crc.api.common import ApiError
|
||||
from crc.models.user import UserModel, AdminSessionModel
|
||||
|
||||
|
||||
class UserService(object):
|
||||
"""Provides common tools for working with users"""
|
||||
|
||||
# Returns true if the current user is logged in.
|
||||
@staticmethod
|
||||
def has_user():
|
||||
return 'token' in g and \
|
||||
bool(g.token) and \
|
||||
'user' in g and \
|
||||
bool(g.user)
|
||||
|
||||
# Returns true if the current user is an admin.
|
||||
@staticmethod
|
||||
def user_is_admin():
|
||||
return UserService.has_user() and g.user.is_admin()
|
||||
|
||||
# Returns true if the current admin user is impersonating another user.
|
||||
@staticmethod
|
||||
def admin_is_impersonating():
|
||||
if UserService.user_is_admin():
|
||||
adminSession: AdminSessionModel = UserService.get_admin_session()
|
||||
return adminSession is not None
|
||||
|
||||
else:
|
||||
raise ApiError("unauthorized", "You do not have permissions to do this.", status_code=403)
|
||||
|
||||
# Returns true if the given user uid is different from the current user's uid.
|
||||
@staticmethod
|
||||
def is_different_user(uid):
|
||||
return UserService.has_user() and uid is not None and uid is not g.user.uid
|
||||
|
||||
@staticmethod
|
||||
def current_user(allow_admin_impersonate=False) -> UserModel:
|
||||
if not UserService.has_user():
|
||||
raise ApiError("logged_out", "You are no longer logged in.", status_code=401)
|
||||
|
||||
# Admins can pretend to be different users and act on a user's behalf in
|
||||
# some circumstances.
|
||||
if UserService.user_is_admin() and allow_admin_impersonate and UserService.admin_is_impersonating():
|
||||
return UserService.get_admin_session_user()
|
||||
else:
|
||||
return g.user
|
||||
|
||||
# Admins can pretend to be different users and act on a user's behalf in some circumstances.
|
||||
# This method allows an admin user to start impersonating another user with the given uid.
|
||||
# Stops impersonating if the uid is None or invalid.
|
||||
@staticmethod
|
||||
def start_impersonating(uid=None):
|
||||
if not UserService.has_user():
|
||||
raise ApiError("logged_out", "You are no longer logged in.", status_code=401)
|
||||
|
||||
if not UserService.user_is_admin():
|
||||
raise ApiError("unauthorized", "You do not have permissions to do this.", status_code=403)
|
||||
|
||||
if uid is None:
|
||||
raise ApiError("invalid_uid", "Please provide a valid user uid.")
|
||||
|
||||
if not UserService.admin_is_impersonating() and UserService.is_different_user(uid):
|
||||
# Impersonate the user if the given uid is valid.
|
||||
impersonate_user = session.query(UserModel).filter(UserModel.uid == uid).first()
|
||||
|
||||
if impersonate_user is not None:
|
||||
g.impersonate_user = impersonate_user
|
||||
|
||||
# Store the uid and user session token.
|
||||
session.add(AdminSessionModel(token=g.token, admin_impersonate_uid=uid))
|
||||
session.commit()
|
||||
else:
|
||||
raise ApiError("invalid_uid", "The uid provided is not valid.")
|
||||
|
||||
@staticmethod
|
||||
def stop_impersonating():
|
||||
if not UserService.has_user():
|
||||
raise ApiError("logged_out", "You are no longer logged in.", status_code=401)
|
||||
|
||||
# Clear out the current impersonating user.
|
||||
if 'impersonate_user' in g:
|
||||
del g.impersonate_user
|
||||
|
||||
admin_session: AdminSessionModel = UserService.get_admin_session()
|
||||
if admin_session:
|
||||
session.delete(admin_session)
|
||||
session.commit()
|
||||
|
||||
@staticmethod
|
||||
def in_list(uids, allow_admin_impersonate=False):
|
||||
"""Returns true if the current user's id is in the given list of ids. False if there
|
||||
is no user, or the user is not in the list."""
|
||||
if UserService.has_user(): # If someone is logged in, lock tasks that don't belong to them.
|
||||
user = UserService.current_user(allow_admin_impersonate)
|
||||
if user.uid in uids:
|
||||
return True
|
||||
return False
|
||||
|
||||
@staticmethod
|
||||
def get_admin_session() -> AdminSessionModel:
|
||||
if UserService.user_is_admin():
|
||||
return session.query(AdminSessionModel).filter(AdminSessionModel.token == g.token).first()
|
||||
else:
|
||||
raise ApiError("unauthorized", "You do not have permissions to do this.", status_code=403)
|
||||
|
||||
@staticmethod
|
||||
def get_admin_session_user() -> UserModel:
|
||||
if UserService.user_is_admin():
|
||||
admin_session = UserService.get_admin_session()
|
||||
|
||||
if admin_session is not None:
|
||||
return session.query(UserModel).filter(UserModel.uid == admin_session.admin_impersonate_uid).first()
|
||||
else:
|
||||
raise ApiError("unauthorized", "You do not have permissions to do this.", status_code=403)
|
||||
@ -17,6 +17,7 @@ from SpiffWorkflow.dmn.parser.BpmnDmnParser import BpmnDmnParser
|
||||
from SpiffWorkflow.exceptions import WorkflowTaskExecException
|
||||
from SpiffWorkflow.specs import WorkflowSpec
|
||||
|
||||
import crc
|
||||
from crc import session, app
|
||||
from crc.api.common import ApiError
|
||||
from crc.models.file import FileDataModel, FileModel, FileType
|
||||
@ -28,64 +29,71 @@ from crc import app
|
||||
|
||||
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. """
|
||||
It will execute python code read in from the bpmn. It will also make any scripts in the
|
||||
scripts directory available for execution. """
|
||||
|
||||
def execute(self, task: SpiffTask, script, data):
|
||||
"""
|
||||
Functions in two modes.
|
||||
1. If the command is proceeded by #! then this is assumed to be a python script, and will
|
||||
attempt to load that python module and execute the do_task method on that script. Scripts
|
||||
must be located in the scripts package and they must extend the script.py class.
|
||||
2. If not proceeded by the #! this will attempt to execute the script directly and assumes it is
|
||||
valid Python.
|
||||
"""
|
||||
# Shlex splits the whole string while respecting double quoted strings within
|
||||
if not script.startswith('#!'):
|
||||
try:
|
||||
super().execute(task, script, data)
|
||||
except SyntaxError as e:
|
||||
raise ApiError.from_task('syntax_error',
|
||||
f'If you are running a pre-defined script, please'
|
||||
f' proceed the script with "#!", otherwise this is assumed to be'
|
||||
f' pure python: {script}, {e.msg}', task=task)
|
||||
else:
|
||||
self.run_predefined_script(task, script[2:], data) # strip off the first two characters.
|
||||
|
||||
def run_predefined_script(self, task: SpiffTask, script, data):
|
||||
commands = shlex.split(script)
|
||||
path_and_command = commands[0].rsplit(".", 1)
|
||||
if len(path_and_command) == 1:
|
||||
module_name = "crc.scripts." + self.camel_to_snake(path_and_command[0])
|
||||
class_name = path_and_command[0]
|
||||
study_id = task.workflow.data[WorkflowProcessor.STUDY_ID_KEY]
|
||||
if WorkflowProcessor.WORKFLOW_ID_KEY in task.workflow.data:
|
||||
workflow_id = task.workflow.data[WorkflowProcessor.WORKFLOW_ID_KEY]
|
||||
else:
|
||||
module_name = "crc.scripts." + path_and_command[0] + "." + self.camel_to_snake(path_and_command[1])
|
||||
class_name = path_and_command[1]
|
||||
workflow_id = None
|
||||
|
||||
try:
|
||||
mod = __import__(module_name, fromlist=[class_name])
|
||||
klass = getattr(mod, class_name)
|
||||
study_id = task.workflow.data[WorkflowProcessor.STUDY_ID_KEY]
|
||||
if WorkflowProcessor.WORKFLOW_ID_KEY in task.workflow.data:
|
||||
workflow_id = task.workflow.data[WorkflowProcessor.WORKFLOW_ID_KEY]
|
||||
else:
|
||||
workflow_id = None
|
||||
|
||||
if not isinstance(klass(), Script):
|
||||
raise ApiError.from_task("invalid_script",
|
||||
"This is an internal error. The script '%s:%s' you called " %
|
||||
(module_name, class_name) +
|
||||
"does not properly implement the CRC Script class.",
|
||||
task=task)
|
||||
if task.workflow.data[WorkflowProcessor.VALIDATION_PROCESS_KEY]:
|
||||
"""If this is running a validation, and not a normal process, then we want to
|
||||
mimic running the script, but not make any external calls or database changes."""
|
||||
klass().do_task_validate_only(task, study_id, workflow_id, *commands[1:])
|
||||
augmentMethods = Script.generate_augmented_validate_list(task, study_id, workflow_id)
|
||||
else:
|
||||
klass().do_task(task, study_id, workflow_id, *commands[1:])
|
||||
except ModuleNotFoundError:
|
||||
raise ApiError.from_task("invalid_script",
|
||||
"Unable to locate Script: '%s:%s'" % (module_name, class_name),
|
||||
task=task)
|
||||
augmentMethods = Script.generate_augmented_list(task, study_id, workflow_id)
|
||||
|
||||
super().execute(task, script, data, externalMethods=augmentMethods)
|
||||
except SyntaxError as e:
|
||||
raise ApiError('syntax_error',
|
||||
f'Something is wrong with your python script '
|
||||
f'please correct the following:'
|
||||
f' {script}, {e.msg}')
|
||||
except NameError as e:
|
||||
raise ApiError('name_error',
|
||||
f'something you are referencing does not exist:'
|
||||
f' {script}, {e.name}')
|
||||
|
||||
# else:
|
||||
# self.run_predefined_script(task, script[2:], data) # strip off the first two characters.
|
||||
|
||||
# def run_predefined_script(self, task: SpiffTask, script, data):
|
||||
# commands = shlex.split(script)
|
||||
# path_and_command = commands[0].rsplit(".", 1)
|
||||
# if len(path_and_command) == 1:
|
||||
# module_name = "crc.scripts." + self.camel_to_snake(path_and_command[0])
|
||||
# class_name = path_and_command[0]
|
||||
# else:
|
||||
# module_name = "crc.scripts." + path_and_command[0] + "." + self.camel_to_snake(path_and_command[1])
|
||||
# class_name = path_and_command[1]
|
||||
# try:
|
||||
# mod = __import__(module_name, fromlist=[class_name])
|
||||
# klass = getattr(mod, class_name)
|
||||
# study_id = task.workflow.data[WorkflowProcessor.STUDY_ID_KEY]
|
||||
# if WorkflowProcessor.WORKFLOW_ID_KEY in task.workflow.data:
|
||||
# workflow_id = task.workflow.data[WorkflowProcessor.WORKFLOW_ID_KEY]
|
||||
# else:
|
||||
# workflow_id = None
|
||||
#
|
||||
# if not isinstance(klass(), Script):
|
||||
# raise ApiError.from_task("invalid_script",
|
||||
# "This is an internal error. The script '%s:%s' you called " %
|
||||
# (module_name, class_name) +
|
||||
# "does not properly implement the CRC Script class.",
|
||||
# task=task)
|
||||
# if task.workflow.data[WorkflowProcessor.VALIDATION_PROCESS_KEY]:
|
||||
# """If this is running a validation, and not a normal process, then we want to
|
||||
# mimic running the script, but not make any external calls or database changes."""
|
||||
# klass().do_task_validate_only(task, study_id, workflow_id, *commands[1:])
|
||||
# else:
|
||||
# klass().do_task(task, study_id, workflow_id, *commands[1:])
|
||||
# except ModuleNotFoundError:
|
||||
# raise ApiError.from_task("invalid_script",
|
||||
# "Unable to locate Script: '%s:%s'" % (module_name, class_name),
|
||||
# task=task)
|
||||
|
||||
def evaluate_expression(self, task, expression):
|
||||
"""
|
||||
@ -117,7 +125,8 @@ class WorkflowProcessor(object):
|
||||
STUDY_ID_KEY = "study_id"
|
||||
VALIDATION_PROCESS_KEY = "validate_only"
|
||||
|
||||
def __init__(self, workflow_model: WorkflowModel, soft_reset=False, hard_reset=False, validate_only=False):
|
||||
def __init__(self, workflow_model: WorkflowModel,
|
||||
soft_reset=False, hard_reset=False, validate_only=False):
|
||||
"""Create a Workflow Processor based on the serialized information available in the workflow model.
|
||||
If soft_reset is set to true, it will try to use the latest version of the workflow specification
|
||||
without resetting to the beginning of the workflow. This will work for some minor changes to the spec.
|
||||
@ -180,10 +189,10 @@ class WorkflowProcessor(object):
|
||||
bpmn_workflow = BpmnWorkflow(spec, script_engine=self._script_engine)
|
||||
bpmn_workflow.data[WorkflowProcessor.STUDY_ID_KEY] = workflow_model.study_id
|
||||
bpmn_workflow.data[WorkflowProcessor.VALIDATION_PROCESS_KEY] = validate_only
|
||||
try:
|
||||
bpmn_workflow.do_engine_steps()
|
||||
except WorkflowException as we:
|
||||
raise ApiError.from_task_spec("error_loading_workflow", str(we), we.sender)
|
||||
# try:
|
||||
# bpmn_workflow.do_engine_steps()
|
||||
# except WorkflowException as we:
|
||||
# raise ApiError.from_task_spec("error_loading_workflow", str(we), we.sender)
|
||||
return bpmn_workflow
|
||||
|
||||
def save(self):
|
||||
|
||||
@ -30,6 +30,7 @@ from crc.models.workflow import WorkflowModel, WorkflowStatus, WorkflowSpecModel
|
||||
from crc.services.file_service import FileService
|
||||
from crc.services.lookup_service import LookupService
|
||||
from crc.services.study_service import StudyService
|
||||
from crc.services.user_service import UserService
|
||||
from crc.services.workflow_processor import WorkflowProcessor
|
||||
|
||||
|
||||
@ -154,10 +155,9 @@ class WorkflowService(object):
|
||||
if len(field.options) > 0:
|
||||
random_choice = random.choice(field.options)
|
||||
if isinstance(random_choice, dict):
|
||||
choice = random.choice(field.options)
|
||||
return {
|
||||
'value': choice['id'],
|
||||
'label': choice['name']
|
||||
'value': random_choice['id'],
|
||||
'label': random_choice['name']
|
||||
}
|
||||
else:
|
||||
# fixme: why it is sometimes an EnumFormFieldOption, and other times not?
|
||||
@ -239,7 +239,7 @@ class WorkflowService(object):
|
||||
nav_item['title'] = nav_item['task'].title # Prefer the task title.
|
||||
|
||||
user_uids = WorkflowService.get_users_assigned_to_task(processor, spiff_task)
|
||||
if 'user' not in g or not g.user or g.user.uid not in user_uids:
|
||||
if not UserService.in_list(user_uids, allow_admin_impersonate=True):
|
||||
nav_item['state'] = WorkflowService.TASK_STATE_LOCKED
|
||||
|
||||
else:
|
||||
@ -272,7 +272,7 @@ class WorkflowService(object):
|
||||
workflow_api.next_task = WorkflowService.spiff_task_to_api_task(next_task, add_docs_and_forms=True)
|
||||
# Update the state of the task to locked if the current user does not own the task.
|
||||
user_uids = WorkflowService.get_users_assigned_to_task(processor, next_task)
|
||||
if 'user' not in g or not g.user or g.user.uid not in user_uids:
|
||||
if not UserService.in_list(user_uids, allow_admin_impersonate=True):
|
||||
workflow_api.next_task.state = WorkflowService.TASK_STATE_LOCKED
|
||||
return workflow_api
|
||||
|
||||
@ -471,6 +471,7 @@ class WorkflowService(object):
|
||||
db.session.query(TaskEventModel). \
|
||||
filter(TaskEventModel.workflow_id == processor.workflow_model.id). \
|
||||
filter(TaskEventModel.action == WorkflowService.TASK_ACTION_ASSIGNMENT).delete()
|
||||
db.session.commit()
|
||||
|
||||
for task in processor.get_current_user_tasks():
|
||||
user_ids = WorkflowService.get_users_assigned_to_task(processor, task)
|
||||
|
||||
@ -212,7 +212,8 @@
|
||||
<bpmn:scriptTask id="Activity_10nxpt2" name="Load Study Details">
|
||||
<bpmn:incoming>SequenceFlow_1r3yrhy</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_09h1imz</bpmn:outgoing>
|
||||
<bpmn:script>#! StudyInfo details</bpmn:script>
|
||||
<bpmn:script>StudyInfo = {}
|
||||
StudyInfo['details'] = study_info('details')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:businessRuleTask id="Activity_PBMultiSiteCheckQ12" name="PB Multi-Site Check Q12" camunda:decisionRef="Decision_core_info_multi_site_q12">
|
||||
<bpmn:incoming>Flow_09h1imz</bpmn:incoming>
|
||||
|
||||
@ -453,7 +453,7 @@ Indicate all the possible formats in which you will transmit your data outside o
|
||||
<bpmn:incoming>SequenceFlow_0k2r83n</bpmn:incoming>
|
||||
<bpmn:incoming>SequenceFlow_0t6xl9i</bpmn:incoming>
|
||||
<bpmn:outgoing>SequenceFlow_16kyite</bpmn:outgoing>
|
||||
<bpmn:script>#! CompleteTemplate NEW_DSP_template.docx Study_DataSecurityPlan</bpmn:script>
|
||||
<bpmn:script>complete_template('NEW_DSP_template.docx','Study_DataSecurityPlan')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:manualTask id="Task_0q6ir2l" name="View Instructions">
|
||||
<bpmn:documentation>##### Instructions
|
||||
|
||||
@ -44,7 +44,7 @@
|
||||
{% endif %}{% endfor %}</bpmn:documentation>
|
||||
<bpmn:extensionElements>
|
||||
<camunda:properties>
|
||||
<camunda:property name="display_name" value="Documents and Approvals" />
|
||||
<camunda:property name="display_name" value="'Documents and Approvals'" />
|
||||
</camunda:properties>
|
||||
</bpmn:extensionElements>
|
||||
<bpmn:incoming>Flow_142jtxs</bpmn:incoming>
|
||||
@ -53,12 +53,13 @@
|
||||
<bpmn:scriptTask id="Activity_0a14x7j" name="Load Approvals">
|
||||
<bpmn:incoming>Flow_0c7ryff</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_142jtxs</bpmn:outgoing>
|
||||
<bpmn:script>#! StudyInfo approvals</bpmn:script>
|
||||
<bpmn:script>StudyInfo['approvals'] = study_info('approvals')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:scriptTask id="Activity_1aju60t" name="Load Documents">
|
||||
<bpmn:incoming>Flow_1k3su2q</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_0c7ryff</bpmn:outgoing>
|
||||
<bpmn:script>#! StudyInfo documents</bpmn:script>
|
||||
<bpmn:script>StudyInfo = {}
|
||||
StudyInfo['documents'] = study_info('documents')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:sequenceFlow id="Flow_142jtxs" sourceRef="Activity_0a14x7j" targetRef="Activity_DisplayDocsAndApprovals" />
|
||||
<bpmn:sequenceFlow id="Flow_0c7ryff" sourceRef="Activity_1aju60t" targetRef="Activity_0a14x7j" />
|
||||
|
||||
@ -36,7 +36,8 @@
|
||||
<bpmn:scriptTask id="ScriptTask_1fn00ox" name="Load IRB Details">
|
||||
<bpmn:incoming>SequenceFlow_1dhb8f4</bpmn:incoming>
|
||||
<bpmn:outgoing>SequenceFlow_1uzcl1f</bpmn:outgoing>
|
||||
<bpmn:script>#! StudyInfo details</bpmn:script>
|
||||
<bpmn:script>StudyInfo = {}
|
||||
StudyInfo['details'] = study_info('details')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:sequenceFlow id="SequenceFlow_1uzcl1f" sourceRef="ScriptTask_1fn00ox" targetRef="Task_SupplementIDE" />
|
||||
<bpmn:exclusiveGateway id="ExclusiveGateway_1fib89p" name="IS_IDE = True and Number Provided? ">
|
||||
|
||||
@ -217,7 +217,8 @@ Protocol Owner: **(need to insert value here)**</bpmn:documentation>
|
||||
<bpmn:scriptTask id="Activity_LoadDocuments" name="Load Documents">
|
||||
<bpmn:incoming>SequenceFlow_1dexemq</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_1x9d2mo</bpmn:outgoing>
|
||||
<bpmn:script>#! StudyInfo documents</bpmn:script>
|
||||
<bpmn:script>StudyInfo = {}
|
||||
StudyInfo['documents'] = study_info('documents')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
</bpmn:process>
|
||||
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
|
||||
|
||||
@ -12,7 +12,8 @@
|
||||
<bpmn:scriptTask id="ScriptTask_LoadIRBDetails" name="Load IRB Details">
|
||||
<bpmn:incoming>SequenceFlow_1dhb8f4</bpmn:incoming>
|
||||
<bpmn:outgoing>SequenceFlow_1uzcl1f</bpmn:outgoing>
|
||||
<bpmn:script>#! StudyInfo details</bpmn:script>
|
||||
<bpmn:script>StudyInfo = {}
|
||||
StudyInfo['details'] = study_info('details')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:sequenceFlow id="SequenceFlow_1uzcl1f" sourceRef="ScriptTask_LoadIRBDetails" targetRef="Task_SupplementIDE" />
|
||||
<bpmn:businessRuleTask id="Task_SupplementIDE" name="Current IND Status" camunda:decisionRef="decision_ind_check">
|
||||
|
||||
@ -8,7 +8,8 @@
|
||||
<bpmn:scriptTask id="ScriptTask_02924vs" name="Load IRB Details">
|
||||
<bpmn:incoming>SequenceFlow_1fmyo77</bpmn:incoming>
|
||||
<bpmn:outgoing>SequenceFlow_18nr0gf</bpmn:outgoing>
|
||||
<bpmn:script>#! StudyInfo details</bpmn:script>
|
||||
<bpmn:script>StudyInfo = {}
|
||||
StudyInfo['details'] = study_info('details')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:sequenceFlow id="SequenceFlow_1fmyo77" sourceRef="StartEvent_1" targetRef="ScriptTask_02924vs" />
|
||||
<bpmn:sequenceFlow id="SequenceFlow_18nr0gf" sourceRef="ScriptTask_02924vs" targetRef="Activity_FromIRB-API" />
|
||||
|
||||
@ -7,7 +7,8 @@
|
||||
<bpmn:scriptTask id="ScriptTask_LoadPersonnel" name="Load IRB Personnel">
|
||||
<bpmn:incoming>Flow_0kcrx5l</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_1dcsioh</bpmn:outgoing>
|
||||
<bpmn:script>#! StudyInfo investigators</bpmn:script>
|
||||
<bpmn:script>StudyInfo = {}
|
||||
StudyInfo['investigators'] = study_info('investigators')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:endEvent id="EndEvent_1qor16n">
|
||||
<bpmn:documentation>## The following information was gathered:
|
||||
|
||||
@ -1,33 +1,116 @@
|
||||
<?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:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_300b2c3" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.0.0-dev">
|
||||
<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:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_300b2c3" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="4.0.0">
|
||||
<bpmn:collaboration id="Collaboration_163c7c8">
|
||||
<bpmn:participant id="Participant_1mnua71" name="team" processRef="Process_cd666f3" />
|
||||
</bpmn:collaboration>
|
||||
<bpmn:process id="Process_cd666f3" isExecutable="true">
|
||||
<bpmn:laneSet id="LaneSet_0ucxzw3">
|
||||
<bpmn:lane id="Lane_16ml9fk">
|
||||
<bpmn:flowNodeRef>StartEvent_1</bpmn:flowNodeRef>
|
||||
<bpmn:flowNodeRef>Activity_1qpy9ra</bpmn:flowNodeRef>
|
||||
<bpmn:flowNodeRef>Event_1m9fnmv</bpmn:flowNodeRef>
|
||||
<bpmn:flowNodeRef>Activity_0c5drp3</bpmn:flowNodeRef>
|
||||
</bpmn:lane>
|
||||
<bpmn:lane id="Lane_1jw70kl" name="supervisor">
|
||||
<bpmn:flowNodeRef>Gateway_0ved0t9</bpmn:flowNodeRef>
|
||||
<bpmn:flowNodeRef>Activity_107ojvq</bpmn:flowNodeRef>
|
||||
</bpmn:lane>
|
||||
</bpmn:laneSet>
|
||||
<bpmn:startEvent id="StartEvent_1">
|
||||
<bpmn:outgoing>Flow_0q51aiq</bpmn:outgoing>
|
||||
</bpmn:startEvent>
|
||||
<bpmn:sequenceFlow id="Flow_0q51aiq" sourceRef="StartEvent_1" targetRef="Activity_1qpy9ra" />
|
||||
<bpmn:userTask id="Activity_1qpy9ra" name="Placeholder" camunda:formKey="Formkey_placeholder">
|
||||
<bpmn:userTask id="Activity_1qpy9ra" name="Assign Approver" camunda:formKey="form_assign_approver">
|
||||
<bpmn:extensionElements>
|
||||
<camunda:formData>
|
||||
<camunda:formField id="FormField_2t2220o" label="Will this be updated later" type="boolean" />
|
||||
<camunda:formField id="supervisor" label="Approver UID" type="string" defaultValue="dhf8r">
|
||||
<camunda:validation>
|
||||
<camunda:constraint name="required" config="true" />
|
||||
</camunda:validation>
|
||||
</camunda:formField>
|
||||
</camunda:formData>
|
||||
</bpmn:extensionElements>
|
||||
<bpmn:incoming>Flow_0q51aiq</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_0ai4j1x</bpmn:outgoing>
|
||||
<bpmn:incoming>Flow_1ugh4wn</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_0d2snmk</bpmn:outgoing>
|
||||
</bpmn:userTask>
|
||||
<bpmn:sequenceFlow id="Flow_0q51aiq" sourceRef="StartEvent_1" targetRef="Activity_1qpy9ra" />
|
||||
<bpmn:sequenceFlow id="Flow_0d2snmk" sourceRef="Activity_1qpy9ra" targetRef="Activity_107ojvq" />
|
||||
<bpmn:exclusiveGateway id="Gateway_0ved0t9" name="Approved?">
|
||||
<bpmn:incoming>Flow_0apr3nj</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_0mhtlkt</bpmn:outgoing>
|
||||
<bpmn:outgoing>Flow_11tnx3n</bpmn:outgoing>
|
||||
</bpmn:exclusiveGateway>
|
||||
<bpmn:sequenceFlow id="Flow_0apr3nj" sourceRef="Activity_107ojvq" targetRef="Gateway_0ved0t9" />
|
||||
<bpmn:sequenceFlow id="Flow_0mhtlkt" name="Yes" sourceRef="Gateway_0ved0t9" targetRef="Event_1m9fnmv">
|
||||
<bpmn:conditionExpression xsi:type="bpmn:tFormalExpression">is_study_approved == True</bpmn:conditionExpression>
|
||||
</bpmn:sequenceFlow>
|
||||
<bpmn:endEvent id="Event_1m9fnmv">
|
||||
<bpmn:incoming>Flow_0ai4j1x</bpmn:incoming>
|
||||
<bpmn:incoming>Flow_0mhtlkt</bpmn:incoming>
|
||||
</bpmn:endEvent>
|
||||
<bpmn:sequenceFlow id="Flow_0ai4j1x" sourceRef="Activity_1qpy9ra" targetRef="Event_1m9fnmv" />
|
||||
<bpmn:sequenceFlow id="Flow_11tnx3n" name="No" sourceRef="Gateway_0ved0t9" targetRef="Activity_0c5drp3">
|
||||
<bpmn:conditionExpression xsi:type="bpmn:tFormalExpression">is_study_approved == False</bpmn:conditionExpression>
|
||||
</bpmn:sequenceFlow>
|
||||
<bpmn:userTask id="Activity_107ojvq" name="Approve Study" camunda:formKey="form_approve_study">
|
||||
<bpmn:extensionElements>
|
||||
<camunda:formData>
|
||||
<camunda:formField id="is_study_approved" label="Approve this study?" type="boolean">
|
||||
<camunda:validation>
|
||||
<camunda:constraint name="required" config="true" />
|
||||
</camunda:validation>
|
||||
</camunda:formField>
|
||||
</camunda:formData>
|
||||
</bpmn:extensionElements>
|
||||
<bpmn:incoming>Flow_0d2snmk</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_0apr3nj</bpmn:outgoing>
|
||||
</bpmn:userTask>
|
||||
<bpmn:sequenceFlow id="Flow_1ugh4wn" sourceRef="Activity_0c5drp3" targetRef="Activity_1qpy9ra" />
|
||||
<bpmn:manualTask id="Activity_0c5drp3" name="Review Feedback">
|
||||
<bpmn:documentation>Your request was not approved. Try again.</bpmn:documentation>
|
||||
<bpmn:incoming>Flow_11tnx3n</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_1ugh4wn</bpmn:outgoing>
|
||||
</bpmn:manualTask>
|
||||
</bpmn:process>
|
||||
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
|
||||
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_cd666f3">
|
||||
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Collaboration_163c7c8">
|
||||
<bpmndi:BPMNShape id="Participant_1mnua71_di" bpmnElement="Participant_1mnua71" isHorizontal="true">
|
||||
<dc:Bounds x="129" y="117" width="600" height="250" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNShape id="Lane_1jw70kl_di" bpmnElement="Lane_1jw70kl" isHorizontal="true">
|
||||
<dc:Bounds x="159" y="242" width="570" height="125" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNShape id="Lane_16ml9fk_di" bpmnElement="Lane_16ml9fk" isHorizontal="true">
|
||||
<dc:Bounds x="159" y="117" width="570" height="125" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNEdge id="Flow_11tnx3n_di" bpmnElement="Flow_11tnx3n">
|
||||
<di:waypoint x="460" y="275" />
|
||||
<di:waypoint x="460" y="217" />
|
||||
<bpmndi:BPMNLabel>
|
||||
<dc:Bounds x="468" y="241" width="15" height="14" />
|
||||
</bpmndi:BPMNLabel>
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNEdge id="Flow_0mhtlkt_di" bpmnElement="Flow_0mhtlkt">
|
||||
<di:waypoint x="485" y="300" />
|
||||
<di:waypoint x="660" y="300" />
|
||||
<di:waypoint x="660" y="195" />
|
||||
<bpmndi:BPMNLabel>
|
||||
<dc:Bounds x="563" y="282" width="19" height="14" />
|
||||
</bpmndi:BPMNLabel>
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNEdge id="Flow_0apr3nj_di" bpmnElement="Flow_0apr3nj">
|
||||
<di:waypoint x="370" y="300" />
|
||||
<di:waypoint x="435" y="300" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNEdge id="Flow_0d2snmk_di" bpmnElement="Flow_0d2snmk">
|
||||
<di:waypoint x="320" y="217" />
|
||||
<di:waypoint x="320" y="260" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNEdge id="Flow_0q51aiq_di" bpmnElement="Flow_0q51aiq">
|
||||
<di:waypoint x="215" y="177" />
|
||||
<di:waypoint x="270" y="177" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNEdge id="Flow_0ai4j1x_di" bpmnElement="Flow_0ai4j1x">
|
||||
<bpmndi:BPMNEdge id="Flow_1ugh4wn_di" bpmnElement="Flow_1ugh4wn">
|
||||
<di:waypoint x="400" y="177" />
|
||||
<di:waypoint x="370" y="177" />
|
||||
<di:waypoint x="432" y="177" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
|
||||
<dc:Bounds x="179" y="159" width="36" height="36" />
|
||||
@ -35,8 +118,20 @@
|
||||
<bpmndi:BPMNShape id="Activity_14cpuv6_di" bpmnElement="Activity_1qpy9ra">
|
||||
<dc:Bounds x="270" y="137" width="100" height="80" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNShape id="Gateway_0ved0t9_di" bpmnElement="Gateway_0ved0t9" isMarkerVisible="true">
|
||||
<dc:Bounds x="435" y="275" width="50" height="50" />
|
||||
<bpmndi:BPMNLabel>
|
||||
<dc:Bounds x="435" y="332" width="54" height="14" />
|
||||
</bpmndi:BPMNLabel>
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNShape id="Event_1m9fnmv_di" bpmnElement="Event_1m9fnmv">
|
||||
<dc:Bounds x="432" y="159" width="36" height="36" />
|
||||
<dc:Bounds x="642" y="159" width="36" height="36" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNShape id="Activity_1ps6jft_di" bpmnElement="Activity_107ojvq">
|
||||
<dc:Bounds x="270" y="260" width="100" height="80" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNShape id="Activity_1al86eb_di" bpmnElement="Activity_0c5drp3">
|
||||
<dc:Bounds x="400" y="137" width="100" height="80" />
|
||||
</bpmndi:BPMNShape>
|
||||
</bpmndi:BPMNPlane>
|
||||
</bpmndi:BPMNDiagram>
|
||||
|
||||
@ -598,7 +598,7 @@ Use the EHS [Lab Safety Plan During COVID 19 template](https://www.google.com/ur
|
||||
This step is internal to the system and do not require and user interaction</bpmn:documentation>
|
||||
<bpmn:incoming>Flow_11uqavk</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_0aqgwvu</bpmn:outgoing>
|
||||
<bpmn:script>#! CompleteTemplate ResearchRampUpPlan.docx RESEARCH_RAMPUP</bpmn:script>
|
||||
<bpmn:script>complete_template('ResearchRampUpPlan.docx','RESEARCH_RAMPUP')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:sequenceFlow id="Flow_0aqgwvu" sourceRef="Activity_GenerateRRP" targetRef="Activity_AcknowledgePlanReview" />
|
||||
<bpmn:sequenceFlow id="Flow_0j4rs82" sourceRef="Activity_SubmitPlan" targetRef="Activity_0absozl" />
|
||||
@ -755,7 +755,7 @@ Notify the Area Monitor for
|
||||
This step is internal to the system and do not require and user interaction</bpmn:documentation>
|
||||
<bpmn:incoming>Flow_0j4rs82</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_07ge8uf</bpmn:outgoing>
|
||||
<bpmn:script>#!RequestApproval ApprvlApprvr1 ApprvlApprvr2</bpmn:script>
|
||||
<bpmn:script>request_approval('ApprvlApprvr1','ApprvlApprvr2')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:scriptTask id="Activity_1u58hox" name="Update Request">
|
||||
<bpmn:documentation>#### Script Task
|
||||
@ -764,7 +764,7 @@ This step is internal to the system and do not require and user interaction</bpm
|
||||
This step is internal to the system and do not require and user interaction</bpmn:documentation>
|
||||
<bpmn:incoming>Flow_16y8glw</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_0uc4o6c</bpmn:outgoing>
|
||||
<bpmn:script>#! UpdateStudy title:PIComputingID.label pi:PIComputingID.value</bpmn:script>
|
||||
<bpmn:script>update_study('title:PIComputingID.label','pi:PIComputingID.value')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:userTask id="PersonnelSchedule" name="Upload Weekly Personnel Schedule(s)" camunda:formKey="Personnel Weekly Schedule">
|
||||
<bpmn:documentation>#### Weekly Personnel Schedule(s)
|
||||
|
||||
@ -116,7 +116,7 @@
|
||||
</camunda:formField>
|
||||
</camunda:formData>
|
||||
<camunda:properties>
|
||||
<camunda:property name="display_name" value="Select Template Type" />
|
||||
<camunda:property name="display_name" value="'Select Template Type'" />
|
||||
</camunda:properties>
|
||||
</bpmn:extensionElements>
|
||||
<bpmn:incoming>SequenceFlow_0schnpa</bpmn:incoming>
|
||||
|
||||
@ -11,7 +11,8 @@
|
||||
<bpmn:scriptTask id="Task_Load_Requirements" name="Load Documents From PB">
|
||||
<bpmn:incoming>SequenceFlow_1ees8ka</bpmn:incoming>
|
||||
<bpmn:outgoing>SequenceFlow_17ct47v</bpmn:outgoing>
|
||||
<bpmn:script>#! StudyInfo documents</bpmn:script>
|
||||
<bpmn:script>StudyInfo = {}
|
||||
StudyInfo['documents'] = study_info('documents')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:businessRuleTask id="Activity_1yqy50i" name="Enter Core Info " camunda:decisionRef="enter_core_info">
|
||||
<bpmn:incoming>Flow_1m8285h</bpmn:incoming>
|
||||
@ -29,7 +30,7 @@
|
||||
<bpmn:parallelGateway id="Gateway_1nta7st" name="Some Name">
|
||||
<bpmn:extensionElements>
|
||||
<camunda:properties>
|
||||
<camunda:property name="display_name" value="Some Name" />
|
||||
<camunda:property name="display_name" value="'Some Name'" />
|
||||
</camunda:properties>
|
||||
</bpmn:extensionElements>
|
||||
<bpmn:incoming>SequenceFlow_17ct47v</bpmn:incoming>
|
||||
@ -62,7 +63,8 @@
|
||||
<bpmn:scriptTask id="Activity_0f295la" name="Load Details from PB">
|
||||
<bpmn:incoming>Flow_0pwtiqm</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_0eq6px2</bpmn:outgoing>
|
||||
<bpmn:script>#! StudyInfo details</bpmn:script>
|
||||
<bpmn:script>StudyInfo = {}
|
||||
StudyInfo['details'] = study_info('details')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:businessRuleTask id="Activity_0ahlc3u" name="IDE Supplement" camunda:decisionRef="decision_ide_menu_check">
|
||||
<bpmn:incoming>Flow_14ce1d7</bpmn:incoming>
|
||||
@ -91,7 +93,8 @@
|
||||
<bpmn:scriptTask id="Activity_0g3qa1c" name="Load Personnel from PB">
|
||||
<bpmn:incoming>Flow_1qyrmzn</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_0vo6ul1</bpmn:outgoing>
|
||||
<bpmn:script>#! StudyInfo investigators</bpmn:script>
|
||||
<bpmn:script>StudyInfo = {}
|
||||
StudyInfo['investigators'] = study_info('investigators')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:sequenceFlow id="Flow_1ybicki" sourceRef="Activity_13ep6ar" targetRef="Event_135x8jg" />
|
||||
<bpmn:businessRuleTask id="Activity_13ep6ar" name="Personnel" camunda:decisionRef="personnel">
|
||||
|
||||
@ -251,7 +251,6 @@ class ExampleDataLoader:
|
||||
master_spec=False,
|
||||
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):
|
||||
"""Assumes that a directory exists in static/bpmn with the same name as the given id.
|
||||
|
||||
36
migrations/versions/1c3f88dbccc3_.py
Normal file
36
migrations/versions/1c3f88dbccc3_.py
Normal file
@ -0,0 +1,36 @@
|
||||
"""empty message
|
||||
|
||||
Revision ID: 1c3f88dbccc3
|
||||
Revises: 2e7b377cbc7b
|
||||
Create Date: 2020-07-30 18:51:01.816284
|
||||
|
||||
"""
|
||||
from alembic import op
|
||||
import sqlalchemy as sa
|
||||
from sqlalchemy.dialects import postgresql
|
||||
|
||||
# revision identifiers, used by Alembic.
|
||||
revision = '1c3f88dbccc3'
|
||||
down_revision = 'ab06a94e5d4c'
|
||||
branch_labels = None
|
||||
depends_on = None
|
||||
|
||||
|
||||
def upgrade():
|
||||
op.execute("CREATE TYPE irbstatus AS ENUM('incomplete_in_protocol_builder', 'completed_in_protocol_builder', 'hsr_assigned')")
|
||||
op.execute("CREATE TYPE studystatus AS ENUM('in_progress', 'hold', 'open_for_enrollment', 'abandoned')")
|
||||
# ### commands auto generated by Alembic - please adjust! ###
|
||||
op.add_column('study', sa.Column('irb_status', sa.Enum('incomplete_in_protocol_builder', 'completed_in_protocol_builder', 'hsr_assigned', name='irbstatus'), nullable=True))
|
||||
op.add_column('study', sa.Column('status', sa.Enum('in_progress', 'hold', 'open_for_enrollment', 'abandoned', name='studystatus'), nullable=True))
|
||||
op.drop_column('study', 'protocol_builder_status')
|
||||
# ### end Alembic commands ###
|
||||
|
||||
|
||||
def downgrade():
|
||||
# ### commands auto generated by Alembic - please adjust! ###
|
||||
op.add_column('study', sa.Column('protocol_builder_status', postgresql.ENUM('incomplete', 'active', 'hold', 'open', 'abandoned', name='protocolbuilderstatus'), autoincrement=False, nullable=True))
|
||||
op.drop_column('study', 'status')
|
||||
op.drop_column('study', 'irb_status')
|
||||
# ### end Alembic commands ###
|
||||
op.execute('DROP TYPE studystatus')
|
||||
op.execute('DROP TYPE irbstatus')
|
||||
32
migrations/versions/2e7b377cbc7b_.py
Normal file
32
migrations/versions/2e7b377cbc7b_.py
Normal file
@ -0,0 +1,32 @@
|
||||
"""empty message
|
||||
|
||||
Revision ID: 2e7b377cbc7b
|
||||
Revises: c4ddb69e7ef4
|
||||
Create Date: 2020-07-28 17:03:23.586828
|
||||
|
||||
"""
|
||||
from alembic import op
|
||||
import sqlalchemy as sa
|
||||
|
||||
|
||||
# revision identifiers, used by Alembic.
|
||||
revision = '2e7b377cbc7b'
|
||||
down_revision = 'c4ddb69e7ef4'
|
||||
branch_labels = None
|
||||
depends_on = None
|
||||
|
||||
|
||||
def upgrade():
|
||||
op.execute('update study set protocol_builder_status = NULL;')
|
||||
op.execute('ALTER TYPE protocolbuilderstatus RENAME TO pbs_old;')
|
||||
op.execute("CREATE TYPE protocolbuilderstatus AS ENUM('incomplete', 'active', 'hold', 'open', 'abandoned')")
|
||||
op.execute("ALTER TABLE study ALTER COLUMN protocol_builder_status TYPE protocolbuilderstatus USING protocol_builder_status::text::protocolbuilderstatus;")
|
||||
op.execute('DROP TYPE pbs_old;')
|
||||
op.execute("update study set protocol_builder_status = 'incomplete';")
|
||||
|
||||
def downgrade():
|
||||
op.execute('update study set protocol_builder_status = NULL;')
|
||||
op.execute('ALTER TYPE protocolbuilderstatus RENAME TO pbs_old;')
|
||||
op.execute("CREATE TYPE protocolbuilderstatus AS ENUM('INCOMPLETE', 'ACTIVE', 'HOLD', 'OPEN', 'ABANDONED')")
|
||||
op.execute("ALTER TABLE study ALTER COLUMN protocol_builder_status TYPE protocolbuilderstatus USING protocol_builder_status::text::protocolbuilderstatus;")
|
||||
op.execute('DROP TYPE pbs_old;')
|
||||
34
migrations/versions/ab06a94e5d4c_.py
Normal file
34
migrations/versions/ab06a94e5d4c_.py
Normal file
@ -0,0 +1,34 @@
|
||||
"""empty message
|
||||
|
||||
Revision ID: ab06a94e5d4c
|
||||
Revises: 2e7b377cbc7b
|
||||
Create Date: 2020-07-30 11:23:46.601338
|
||||
|
||||
"""
|
||||
from alembic import op
|
||||
import sqlalchemy as sa
|
||||
|
||||
|
||||
# revision identifiers, used by Alembic.
|
||||
revision = 'ab06a94e5d4c'
|
||||
down_revision = '2e7b377cbc7b'
|
||||
branch_labels = None
|
||||
depends_on = None
|
||||
|
||||
|
||||
def upgrade():
|
||||
# ### commands auto generated by Alembic - please adjust! ###
|
||||
op.create_table('admin_session',
|
||||
sa.Column('id', sa.Integer(), nullable=False),
|
||||
sa.Column('token', sa.String(), nullable=True),
|
||||
sa.Column('admin_impersonate_uid', sa.String(), nullable=True),
|
||||
sa.PrimaryKeyConstraint('id'),
|
||||
sa.UniqueConstraint('token')
|
||||
)
|
||||
# ### end Alembic commands ###
|
||||
|
||||
|
||||
def downgrade():
|
||||
# ### commands auto generated by Alembic - please adjust! ###
|
||||
op.drop_table('admin_session')
|
||||
# ### end Alembic commands ###
|
||||
28
migrations/versions/c4ddb69e7ef4_.py
Normal file
28
migrations/versions/c4ddb69e7ef4_.py
Normal file
@ -0,0 +1,28 @@
|
||||
"""empty message
|
||||
|
||||
Revision ID: c4ddb69e7ef4
|
||||
Revises: ffef4661a37d
|
||||
Create Date: 2020-07-22 09:04:09.769239
|
||||
|
||||
"""
|
||||
from alembic import op
|
||||
import sqlalchemy as sa
|
||||
|
||||
|
||||
# revision identifiers, used by Alembic.
|
||||
revision = 'c4ddb69e7ef4'
|
||||
down_revision = 'ffef4661a37d'
|
||||
branch_labels = None
|
||||
depends_on = None
|
||||
|
||||
|
||||
def upgrade():
|
||||
# ### commands auto generated by Alembic - please adjust! ###
|
||||
op.add_column('study', sa.Column('enrollment_date', sa.DateTime(timezone=True), nullable=True))
|
||||
# ### end Alembic commands ###
|
||||
|
||||
|
||||
def downgrade():
|
||||
# ### commands auto generated by Alembic - please adjust! ###
|
||||
op.drop_column('study', 'enrollment_date')
|
||||
# ### end Alembic commands ###
|
||||
2
setup.py
2
setup.py
@ -1,3 +1,3 @@
|
||||
from setuptools import setup
|
||||
|
||||
setup(setup_requires=["pbr"], pbr=True)
|
||||
setup(setup_requires=["pbr"], pbr=True, install_requires=['box'])
|
||||
|
||||
@ -15,18 +15,19 @@ from crc import app, db, session
|
||||
from crc.models.api_models import WorkflowApiSchema, MultiInstanceType
|
||||
from crc.models.approval import ApprovalModel, ApprovalStatus
|
||||
from crc.models.file import FileModel, FileDataModel, CONTENT_TYPES
|
||||
from crc.models.protocol_builder import ProtocolBuilderStatus
|
||||
from crc.models.task_event import TaskEventModel
|
||||
from crc.models.study import StudyModel
|
||||
from crc.models.study import StudyModel, StudyStatus
|
||||
from crc.models.user import UserModel
|
||||
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel
|
||||
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecCategoryModel
|
||||
from crc.services.file_service import FileService
|
||||
from crc.services.study_service import StudyService
|
||||
from crc.services.user_service import UserService
|
||||
from crc.services.workflow_service import WorkflowService
|
||||
from example_data import ExampleDataLoader
|
||||
|
||||
#UNCOMMENT THIS FOR DEBUGGING SQL ALCHEMY QUERIES
|
||||
# UNCOMMENT THIS FOR DEBUGGING SQL ALCHEMY QUERIES
|
||||
import logging
|
||||
|
||||
logging.basicConfig()
|
||||
|
||||
|
||||
@ -37,22 +38,32 @@ class BaseTest(unittest.TestCase):
|
||||
|
||||
if not app.config['TESTING']:
|
||||
raise (Exception("INVALID TEST CONFIGURATION. This is almost always in import order issue."
|
||||
"The first class to import in each test should be the base_test.py file."))
|
||||
"The first class to import in each test should be the base_test.py file."))
|
||||
|
||||
auths = {}
|
||||
test_uid = "dhf8r"
|
||||
|
||||
users = [
|
||||
{
|
||||
'uid':'dhf8r',
|
||||
'email_address':'dhf8r@virginia.EDU',
|
||||
'display_name':'Daniel Harold Funk',
|
||||
'affiliation':'staff@virginia.edu;member@virginia.edu',
|
||||
'eppn':'dhf8r@virginia.edu',
|
||||
'first_name':'Daniel',
|
||||
'last_name':'Funk',
|
||||
'title':'SOFTWARE ENGINEER V'
|
||||
}
|
||||
'uid': 'dhf8r',
|
||||
'email_address': 'dhf8r@virginia.EDU',
|
||||
'display_name': 'Daniel Harold Funk',
|
||||
'affiliation': 'staff@virginia.edu;member@virginia.edu',
|
||||
'eppn': 'dhf8r@virginia.edu',
|
||||
'first_name': 'Daniel',
|
||||
'last_name': 'Funk',
|
||||
'title': 'SOFTWARE ENGINEER V'
|
||||
},
|
||||
{
|
||||
'uid': 'lbd3p',
|
||||
'email_address': 'lbd3p@virginia.EDU',
|
||||
'display_name': 'Laura Barnes',
|
||||
'affiliation': 'staff@virginia.edu;member@virginia.edu',
|
||||
'eppn': 'lbd3p@virginia.edu',
|
||||
'first_name': 'Laura',
|
||||
'last_name': 'Barnes',
|
||||
'title': 'Associate Professor of Systems and Information Engineering'
|
||||
},
|
||||
]
|
||||
|
||||
studies = [
|
||||
@ -60,7 +71,7 @@ class BaseTest(unittest.TestCase):
|
||||
'id':0,
|
||||
'title':'The impact of fried pickles on beer consumption in bipedal software developers.',
|
||||
'last_updated':datetime.datetime.now(),
|
||||
'protocol_builder_status':ProtocolBuilderStatus.ACTIVE,
|
||||
'status':StudyStatus.in_progress,
|
||||
'primary_investigator_id':'dhf8r',
|
||||
'sponsor':'Sartography Pharmaceuticals',
|
||||
'ind_number':'1234',
|
||||
@ -70,7 +81,7 @@ class BaseTest(unittest.TestCase):
|
||||
'id':1,
|
||||
'title':'Requirement of hippocampal neurogenesis for the behavioral effects of soft pretzels',
|
||||
'last_updated':datetime.datetime.now(),
|
||||
'protocol_builder_status':ProtocolBuilderStatus.ACTIVE,
|
||||
'status':StudyStatus.in_progress,
|
||||
'primary_investigator_id':'dhf8r',
|
||||
'sponsor':'Makerspace & Co.',
|
||||
'ind_number':'5678',
|
||||
@ -78,7 +89,6 @@ class BaseTest(unittest.TestCase):
|
||||
}
|
||||
]
|
||||
|
||||
|
||||
@classmethod
|
||||
def setUpClass(cls):
|
||||
app.config.from_object('config.testing')
|
||||
@ -98,7 +108,7 @@ class BaseTest(unittest.TestCase):
|
||||
|
||||
def tearDown(self):
|
||||
ExampleDataLoader.clean_db()
|
||||
g.user = None
|
||||
self.logout()
|
||||
self.auths = {}
|
||||
|
||||
def logged_in_headers(self, user=None, redirect_url='http://some/frontend/url'):
|
||||
@ -118,7 +128,8 @@ class BaseTest(unittest.TestCase):
|
||||
self.assertIsNotNone(user_model.display_name)
|
||||
self.assertEqual(user_model.uid, uid)
|
||||
self.assertTrue('user' in g, 'User should be in Flask globals')
|
||||
self.assertEqual(uid, g.user.uid, 'Logged in user should match given user uid')
|
||||
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())
|
||||
|
||||
@ -135,16 +146,21 @@ class BaseTest(unittest.TestCase):
|
||||
else:
|
||||
ExampleDataLoader().load_test_data()
|
||||
|
||||
for user_json in self.users:
|
||||
db.session.add(UserModel(**user_json))
|
||||
db.session.commit()
|
||||
# If in production mode, only add the first user.
|
||||
if app.config['PRODUCTION']:
|
||||
session.add(UserModel(**self.users[0]))
|
||||
else:
|
||||
for user_json in self.users:
|
||||
session.add(UserModel(**user_json))
|
||||
|
||||
session.commit()
|
||||
for study_json in self.studies:
|
||||
study_model = StudyModel(**study_json)
|
||||
db.session.add(study_model)
|
||||
session.add(study_model)
|
||||
StudyService._add_all_workflow_specs_to_study(study_model)
|
||||
db.session.execute(Sequence(StudyModel.__tablename__ + '_id_seq'))
|
||||
db.session.commit()
|
||||
db.session.flush()
|
||||
session.execute(Sequence(StudyModel.__tablename__ + '_id_seq'))
|
||||
session.commit()
|
||||
session.flush()
|
||||
|
||||
specs = session.query(WorkflowSpecModel).all()
|
||||
self.assertIsNotNone(specs)
|
||||
@ -164,14 +180,21 @@ class BaseTest(unittest.TestCase):
|
||||
self.assertGreater(len(file_data), 0)
|
||||
|
||||
@staticmethod
|
||||
def load_test_spec(dir_name, master_spec=False, category_id=None):
|
||||
def load_test_spec(dir_name, display_name=None, master_spec=False, category_id=None):
|
||||
"""Loads a spec into the database based on a directory in /tests/data"""
|
||||
if category_id is None:
|
||||
category = WorkflowSpecCategoryModel(name="test", display_name="Test Workflows", display_order=0)
|
||||
session.add(category)
|
||||
session.commit()
|
||||
category_id = category.id
|
||||
|
||||
if session.query(WorkflowSpecModel).filter_by(id=dir_name).count() > 0:
|
||||
return session.query(WorkflowSpecModel).filter_by(id=dir_name).first()
|
||||
filepath = os.path.join(app.root_path, '..', 'tests', 'data', dir_name, "*")
|
||||
if display_name is None:
|
||||
display_name = dir_name
|
||||
return ExampleDataLoader().create_spec(id=dir_name, name=dir_name, filepath=filepath, master_spec=master_spec,
|
||||
category_id=category_id)
|
||||
display_name=display_name, category_id=category_id)
|
||||
|
||||
@staticmethod
|
||||
def protocol_builder_response(file_name):
|
||||
@ -210,14 +233,13 @@ class BaseTest(unittest.TestCase):
|
||||
|
||||
return '?%s' % '&'.join(query_string_list)
|
||||
|
||||
|
||||
def replace_file(self, name, file_path):
|
||||
"""Replaces a stored file with the given name with the contents of the file at the given path."""
|
||||
file_service = FileService()
|
||||
file = open(file_path, "rb")
|
||||
data = file.read()
|
||||
|
||||
file_model = db.session.query(FileModel).filter(FileModel.name == name).first()
|
||||
file_model = session.query(FileModel).filter(FileModel.name == name).first()
|
||||
noise, file_extension = os.path.splitext(file_path)
|
||||
content_type = CONTENT_TYPES[file_extension[1:]]
|
||||
file_service.update_file(file_model, data, content_type)
|
||||
@ -226,18 +248,19 @@ class BaseTest(unittest.TestCase):
|
||||
user = session.query(UserModel).filter(UserModel.uid == uid).first()
|
||||
if user is None:
|
||||
user = UserModel(uid=uid, email_address=email, display_name=display_name)
|
||||
db.session.add(user)
|
||||
db.session.commit()
|
||||
session.add(user)
|
||||
session.commit()
|
||||
return user
|
||||
|
||||
def create_study(self, uid="dhf8r", title="Beer consumption in the bipedal software engineer", primary_investigator_id="lb3dp"):
|
||||
def create_study(self, uid="dhf8r", title="Beer consumption in the bipedal software engineer",
|
||||
primary_investigator_id="lb3dp"):
|
||||
study = session.query(StudyModel).filter_by(user_uid=uid).filter_by(title=title).first()
|
||||
if study is None:
|
||||
user = self.create_user(uid=uid)
|
||||
study = StudyModel(title=title, protocol_builder_status=ProtocolBuilderStatus.ACTIVE,
|
||||
study = StudyModel(title=title, status=StudyStatus.in_progress,
|
||||
user_uid=user.uid, primary_investigator_id=primary_investigator_id)
|
||||
db.session.add(study)
|
||||
db.session.commit()
|
||||
session.add(study)
|
||||
session.commit()
|
||||
return study
|
||||
|
||||
def _create_study_workflow_approvals(self, user_uid, title, primary_investigator_id, approver_uids, statuses,
|
||||
@ -263,11 +286,13 @@ class BaseTest(unittest.TestCase):
|
||||
|
||||
return full_study
|
||||
|
||||
def create_workflow(self, workflow_name, study=None, category_id=None, as_user="dhf8r"):
|
||||
db.session.flush()
|
||||
spec = db.session.query(WorkflowSpecModel).filter(WorkflowSpecModel.name == workflow_name).first()
|
||||
def create_workflow(self, workflow_name, display_name=None, study=None, category_id=None, as_user="dhf8r"):
|
||||
session.flush()
|
||||
spec = session.query(WorkflowSpecModel).filter(WorkflowSpecModel.name == workflow_name).first()
|
||||
if spec is None:
|
||||
spec = self.load_test_spec(workflow_name, category_id=category_id)
|
||||
if display_name is None:
|
||||
display_name = workflow_name
|
||||
spec = self.load_test_spec(workflow_name, display_name, category_id=category_id)
|
||||
if study is None:
|
||||
study = self.create_study(uid=as_user)
|
||||
workflow_model = StudyService._create_workflow_model(study, spec)
|
||||
@ -282,29 +307,31 @@ class BaseTest(unittest.TestCase):
|
||||
file.close()
|
||||
|
||||
def create_approval(
|
||||
self,
|
||||
study=None,
|
||||
workflow=None,
|
||||
approver_uid=None,
|
||||
status=None,
|
||||
version=None,
|
||||
self,
|
||||
study=None,
|
||||
workflow=None,
|
||||
approver_uid=None,
|
||||
status=None,
|
||||
version=None,
|
||||
):
|
||||
study = study or self.create_study()
|
||||
workflow = workflow or self.create_workflow()
|
||||
approver_uid = approver_uid or self.test_uid
|
||||
status = status or ApprovalStatus.PENDING.value
|
||||
version = version or 1
|
||||
approval = ApprovalModel(study=study, workflow=workflow, approver_uid=approver_uid, status=status, version=version)
|
||||
db.session.add(approval)
|
||||
db.session.commit()
|
||||
approval = ApprovalModel(study=study, workflow=workflow, approver_uid=approver_uid, status=status,
|
||||
version=version)
|
||||
session.add(approval)
|
||||
session.commit()
|
||||
return approval
|
||||
|
||||
def get_workflow_api(self, workflow, soft_reset=False, hard_reset=False, user_uid="dhf8r"):
|
||||
def get_workflow_api(self, workflow, soft_reset=False, hard_reset=False, do_engine_steps=True, user_uid="dhf8r"):
|
||||
user = session.query(UserModel).filter_by(uid=user_uid).first()
|
||||
self.assertIsNotNone(user)
|
||||
|
||||
rv = self.app.get('/v1.0/workflow/%i?soft_reset=%s&hard_reset=%s' %
|
||||
(workflow.id, str(soft_reset), str(hard_reset)),
|
||||
rv = self.app.get(f'/v1.0/workflow/{workflow.id}'
|
||||
f'?soft_reset={str(soft_reset)}'
|
||||
f'&hard_reset={str(hard_reset)}'
|
||||
f'&do_engine_steps={str(do_engine_steps)}',
|
||||
headers=self.logged_in_headers(user),
|
||||
content_type="application/json")
|
||||
self.assert_success(rv)
|
||||
@ -313,7 +340,6 @@ class BaseTest(unittest.TestCase):
|
||||
self.assertEqual(workflow.workflow_spec_id, workflow_api.workflow_spec_id)
|
||||
return workflow_api
|
||||
|
||||
|
||||
def complete_form(self, workflow_in, task_in, dict_data, error_code=None, terminate_loop=None, user_uid="dhf8r"):
|
||||
prev_completed_task_count = workflow_in.completed_tasks
|
||||
if isinstance(task_in, dict):
|
||||
@ -378,12 +404,18 @@ class BaseTest(unittest.TestCase):
|
||||
|
||||
self.assertEqual(task_in.multi_instance_count, event.mi_count)
|
||||
if task_in.multi_instance_type == 'looping' and not terminate_loop:
|
||||
self.assertEqual(task_in.multi_instance_index+1, event.mi_index)
|
||||
self.assertEqual(task_in.multi_instance_index + 1, event.mi_index)
|
||||
else:
|
||||
self.assertEqual(task_in.multi_instance_index, event.mi_index)
|
||||
self.assertEqual(task_in.process_name, event.process_name)
|
||||
self.assertIsNotNone(event.date)
|
||||
|
||||
|
||||
workflow = WorkflowApiSchema().load(json_data)
|
||||
return workflow
|
||||
|
||||
def logout(self):
|
||||
if 'user' in g:
|
||||
del g.user
|
||||
|
||||
if 'impersonate_user' in g:
|
||||
del g.impersonate_user
|
||||
|
||||
@ -27,7 +27,7 @@
|
||||
</bpmn:extensionElements>
|
||||
<bpmn:incoming>SequenceFlow_1i7hk1a</bpmn:incoming>
|
||||
<bpmn:outgoing>SequenceFlow_11c35oq</bpmn:outgoing>
|
||||
<bpmn:script>#! CompleteTemplate Letter.docx AD_CoCApp</bpmn:script>
|
||||
<bpmn:script>complete_template('Letter.docx','AD_CoCApp')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:endEvent id="EndEvent_0evb22x">
|
||||
<bpmn:incoming>SequenceFlow_11c35oq</bpmn:incoming>
|
||||
|
||||
@ -20,7 +20,7 @@ Email content to be delivered to {{ ApprvlApprvr1 }}
|
||||
---</bpmn:documentation>
|
||||
<bpmn:incoming>Flow_08n2npe</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_1xlrgne</bpmn:outgoing>
|
||||
<bpmn:script>#! Email "Camunda Email Subject" ApprvlApprvr1 PIComputingID</bpmn:script>
|
||||
<bpmn:script>email("Camunda Email Subject",'ApprvlApprvr1','PIComputingID')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:sequenceFlow id="Flow_1synsig" sourceRef="StartEvent_1" targetRef="Activity_1l9vih3" />
|
||||
<bpmn:sequenceFlow id="Flow_1xlrgne" sourceRef="Activity_0s5v97n" targetRef="Event_0izrcj4" />
|
||||
|
||||
@ -11,7 +11,7 @@
|
||||
<bpmn:scriptTask id="Invalid_Script_Task" name="An Invalid Script Reference">
|
||||
<bpmn:incoming>SequenceFlow_1pnq3kg</bpmn:incoming>
|
||||
<bpmn:outgoing>SequenceFlow_12pf6um</bpmn:outgoing>
|
||||
<bpmn:script>#! NoSuchScript withArg1</bpmn:script>
|
||||
<bpmn:script>no_such_script('withArg1')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:sequenceFlow id="SequenceFlow_12pf6um" sourceRef="Invalid_Script_Task" targetRef="EndEvent_063bpg6" />
|
||||
</bpmn:process>
|
||||
|
||||
70
tests/data/ldap_replace/ldap_replace.bpmn
Normal file
70
tests/data/ldap_replace/ldap_replace.bpmn
Normal file
@ -0,0 +1,70 @@
|
||||
<?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:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_0y2dq4f" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
|
||||
<bpmn:process id="Process_0tad5ma" name="Set Recipients" isExecutable="true">
|
||||
<bpmn:startEvent id="StartEvent_1">
|
||||
<bpmn:outgoing>Flow_1synsig</bpmn:outgoing>
|
||||
</bpmn:startEvent>
|
||||
<bpmn:endEvent id="Event_0izrcj4">
|
||||
<bpmn:incoming>Flow_11e7jgz</bpmn:incoming>
|
||||
</bpmn:endEvent>
|
||||
<bpmn:scriptTask id="Activity_0s5v97n" name="Ldap Replace">
|
||||
<bpmn:incoming>Flow_08n2npe</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_1xlrgne</bpmn:outgoing>
|
||||
<bpmn:script>Supervisor = ldap(Supervisor)
|
||||
Investigator = ldap(Investigator)</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:sequenceFlow id="Flow_1synsig" sourceRef="StartEvent_1" targetRef="Activity_1l9vih3" />
|
||||
<bpmn:sequenceFlow id="Flow_1xlrgne" sourceRef="Activity_0s5v97n" targetRef="Activity_0f78ek5" />
|
||||
<bpmn:sequenceFlow id="Flow_08n2npe" sourceRef="Activity_1l9vih3" targetRef="Activity_0s5v97n" />
|
||||
<bpmn:userTask id="Activity_1l9vih3" name="Set UIDs">
|
||||
<bpmn:extensionElements>
|
||||
<camunda:formData>
|
||||
<camunda:formField id="Supervisor" label="Approver" type="string" />
|
||||
<camunda:formField id="Investigator" label="Primary Investigator" type="string" />
|
||||
</camunda:formData>
|
||||
</bpmn:extensionElements>
|
||||
<bpmn:incoming>Flow_1synsig</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_08n2npe</bpmn:outgoing>
|
||||
</bpmn:userTask>
|
||||
<bpmn:sequenceFlow id="Flow_11e7jgz" sourceRef="Activity_0f78ek5" targetRef="Event_0izrcj4" />
|
||||
<bpmn:userTask id="Activity_0f78ek5" name="Read UIDs">
|
||||
<bpmn:incoming>Flow_1xlrgne</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_11e7jgz</bpmn:outgoing>
|
||||
</bpmn:userTask>
|
||||
</bpmn:process>
|
||||
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
|
||||
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_0tad5ma">
|
||||
<bpmndi:BPMNEdge id="Flow_11e7jgz_di" bpmnElement="Flow_11e7jgz">
|
||||
<di:waypoint x="720" y="117" />
|
||||
<di:waypoint x="802" y="117" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNEdge id="Flow_08n2npe_di" bpmnElement="Flow_08n2npe">
|
||||
<di:waypoint x="370" y="117" />
|
||||
<di:waypoint x="450" y="117" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNEdge id="Flow_1xlrgne_di" bpmnElement="Flow_1xlrgne">
|
||||
<di:waypoint x="550" y="117" />
|
||||
<di:waypoint x="620" y="117" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNEdge id="Flow_1synsig_di" bpmnElement="Flow_1synsig">
|
||||
<di:waypoint x="215" y="117" />
|
||||
<di:waypoint x="270" y="117" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
|
||||
<dc:Bounds x="179" y="99" width="36" height="36" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNShape id="Event_0izrcj4_di" bpmnElement="Event_0izrcj4">
|
||||
<dc:Bounds x="802" y="99" width="36" height="36" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNShape id="Activity_04imfm6_di" bpmnElement="Activity_0s5v97n">
|
||||
<dc:Bounds x="450" y="77" width="100" height="80" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNShape id="Activity_0xugr62_di" bpmnElement="Activity_1l9vih3">
|
||||
<dc:Bounds x="270" y="77" width="100" height="80" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNShape id="Activity_17h05g6_di" bpmnElement="Activity_0f78ek5">
|
||||
<dc:Bounds x="620" y="77" width="100" height="80" />
|
||||
</bpmndi:BPMNShape>
|
||||
</bpmndi:BPMNPlane>
|
||||
</bpmndi:BPMNDiagram>
|
||||
</bpmn:definitions>
|
||||
@ -1,5 +1,5 @@
|
||||
<?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:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" id="Definitions_17fwemw" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
|
||||
<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:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" id="Definitions_17fwemw" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
|
||||
<bpmn:process id="MultiInstance" isExecutable="true">
|
||||
<bpmn:startEvent id="StartEvent_1" name="StartEvent_1">
|
||||
<bpmn:outgoing>Flow_0t6p1sb</bpmn:outgoing>
|
||||
@ -29,7 +29,8 @@
|
||||
<bpmn:scriptTask id="Task_1v0e2zu" name="Load Personnel">
|
||||
<bpmn:incoming>Flow_0t6p1sb</bpmn:incoming>
|
||||
<bpmn:outgoing>SequenceFlow_1p568pp</bpmn:outgoing>
|
||||
<bpmn:script>#! StudyInfo investigators</bpmn:script>
|
||||
<bpmn:script>StudyInfo = {}
|
||||
StudyInfo['investigators'] = study_info('investigators')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
</bpmn:process>
|
||||
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
|
||||
|
||||
@ -11,7 +11,7 @@
|
||||
<bpmn:sequenceFlow id="Flow_0ugjw69" sourceRef="MultiInstanceTask" targetRef="Event_End" />
|
||||
<bpmn:userTask id="MultiInstanceTask" name="Gather more information" camunda:formKey="GetEmail">
|
||||
<bpmn:documentation># Please provide addtional information about:
|
||||
## Investigator ID: {{investigator.user_id}}
|
||||
## Investigator ID: {{investigator.user_id}}
|
||||
## Role: {{investigator.type_full}}</bpmn:documentation>
|
||||
<bpmn:extensionElements>
|
||||
<camunda:formData>
|
||||
@ -29,7 +29,8 @@
|
||||
<bpmn:scriptTask id="Task_1v0e2zu" name="Load Personnel">
|
||||
<bpmn:incoming>Flow_0t6p1sb</bpmn:incoming>
|
||||
<bpmn:outgoing>SequenceFlow_1p568pp</bpmn:outgoing>
|
||||
<bpmn:script>#! StudyInfo investigators</bpmn:script>
|
||||
<bpmn:script>StudyInfo = {}
|
||||
StudyInfo['investigators'] = study_info('investigators')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
</bpmn:process>
|
||||
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
|
||||
|
||||
@ -132,7 +132,7 @@ Autoconverted link https://github.com/nodeca/pica (enable linkify to see)
|
||||
</bpmn:extensionElements>
|
||||
<bpmn:incoming>SequenceFlow_0641sh6</bpmn:incoming>
|
||||
<bpmn:outgoing>SequenceFlow_0t29gjo</bpmn:outgoing>
|
||||
<bpmn:script>#! FactService</bpmn:script>
|
||||
<bpmn:script>FactService = fact_service()</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:endEvent id="EndEvent_0u1cgrf">
|
||||
<bpmn:documentation># Great Job!
|
||||
|
||||
@ -8,12 +8,19 @@
|
||||
<bpmn:scriptTask id="Task_Script_Load_Study_Details" name="Load Study Info">
|
||||
<bpmn:incoming>SequenceFlow_1nfe5m9</bpmn:incoming>
|
||||
<bpmn:outgoing>SequenceFlow_1bqiin0</bpmn:outgoing>
|
||||
<bpmn:script>#! StudyInfo info</bpmn:script>
|
||||
<bpmn:script>StudyInfo = {}
|
||||
StudyInfo['info'] = study_info('info')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:sequenceFlow id="SequenceFlow_1bqiin0" sourceRef="Task_Script_Load_Study_Details" targetRef="EndEvent_171dj09" />
|
||||
<bpmn:sequenceFlow id="SequenceFlow_1bqiin0" sourceRef="Task_Script_Load_Study_Details" targetRef="Activity_0w91u9s" />
|
||||
<bpmn:endEvent id="EndEvent_171dj09">
|
||||
<bpmn:incoming>SequenceFlow_1bqiin0</bpmn:incoming>
|
||||
<bpmn:incoming>Flow_0ochvmi</bpmn:incoming>
|
||||
</bpmn:endEvent>
|
||||
<bpmn:sequenceFlow id="Flow_0ochvmi" sourceRef="Activity_0w91u9s" targetRef="EndEvent_171dj09" />
|
||||
<bpmn:scriptTask id="Activity_0w91u9s" name="StudyInfo as Script">
|
||||
<bpmn:incoming>SequenceFlow_1bqiin0</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_0ochvmi</bpmn:outgoing>
|
||||
<bpmn:script>study = study_info('info','p')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
</bpmn:process>
|
||||
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
|
||||
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_0exnnpv">
|
||||
@ -29,10 +36,17 @@
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNEdge id="SequenceFlow_1bqiin0_di" bpmnElement="SequenceFlow_1bqiin0">
|
||||
<di:waypoint x="370" y="117" />
|
||||
<di:waypoint x="402" y="117" />
|
||||
<di:waypoint x="430" y="117" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNShape id="EndEvent_171dj09_di" bpmnElement="EndEvent_171dj09">
|
||||
<dc:Bounds x="402" y="99" width="36" height="36" />
|
||||
<dc:Bounds x="622" y="99" width="36" height="36" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNEdge id="Flow_0ochvmi_di" bpmnElement="Flow_0ochvmi">
|
||||
<di:waypoint x="530" y="117" />
|
||||
<di:waypoint x="622" y="117" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNShape id="Activity_1wtk4bb_di" bpmnElement="Activity_0w91u9s">
|
||||
<dc:Bounds x="430" y="77" width="100" height="80" />
|
||||
</bpmndi:BPMNShape>
|
||||
</bpmndi:BPMNPlane>
|
||||
</bpmndi:BPMNDiagram>
|
||||
|
||||
@ -11,7 +11,8 @@
|
||||
<bpmn:scriptTask id="Task_Load_Requirements" name="Load Required Documents From PM">
|
||||
<bpmn:incoming>SequenceFlow_1ees8ka</bpmn:incoming>
|
||||
<bpmn:outgoing>SequenceFlow_17ct47v</bpmn:outgoing>
|
||||
<bpmn:script>#! StudyInfo documents</bpmn:script>
|
||||
<bpmn:script>StudyInfo = {}
|
||||
StudyInfo['documents'] = study_info('documents')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:businessRuleTask id="Activity_1yqy50i" name="Enter Core Info " camunda:decisionRef="enter_core_info">
|
||||
<bpmn:incoming>Flow_1m8285h</bpmn:incoming>
|
||||
|
||||
@ -1,9 +1,45 @@
|
||||
from github import UnknownObjectException
|
||||
from sqlalchemy import desc
|
||||
from tests.base_test import BaseTest
|
||||
from unittest.mock import patch, Mock
|
||||
|
||||
from crc import db
|
||||
from crc.models.file import FileDataModel
|
||||
from crc.services.file_service import FileService
|
||||
from crc.services.workflow_processor import WorkflowProcessor
|
||||
|
||||
|
||||
class FakeGithubCreates(Mock):
|
||||
def get_user(var):
|
||||
class FakeUser(Mock):
|
||||
def get_repo(var, name):
|
||||
class FakeRepo(Mock):
|
||||
def get_contents(var, filename):
|
||||
raise UnknownObjectException(status='Failure', data='Failed data')
|
||||
def update_file(var, path, message, content, sha):
|
||||
pass
|
||||
return FakeRepo()
|
||||
return FakeUser()
|
||||
|
||||
|
||||
class FakeGithub(Mock):
|
||||
def get_user(var):
|
||||
class FakeUser(Mock):
|
||||
def get_repo(var, name):
|
||||
class FakeRepo(Mock):
|
||||
def get_contents(var, filename):
|
||||
fake_file = Mock()
|
||||
fake_file.decoded_content = b'Some bytes'
|
||||
fake_file.path = '/el/path/'
|
||||
fake_file.data = 'Serious data'
|
||||
fake_file.sha = 'Sha'
|
||||
return fake_file
|
||||
def update_file(var, path, message, content, sha):
|
||||
pass
|
||||
return FakeRepo()
|
||||
return FakeUser()
|
||||
|
||||
|
||||
class TestFileService(BaseTest):
|
||||
"""Largely tested via the test_file_api, and time is tight, but adding new tests here."""
|
||||
|
||||
@ -103,3 +139,62 @@ class TestFileService(BaseTest):
|
||||
binary_data=b'5678')
|
||||
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
|
||||
self.assertEqual(2, len(file_models))
|
||||
|
||||
@patch('crc.services.file_service.Github')
|
||||
def test_update_from_github(self, mock_github):
|
||||
mock_github.return_value = FakeGithub()
|
||||
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow('file_upload_form')
|
||||
processor = WorkflowProcessor(workflow)
|
||||
task = processor.next_task()
|
||||
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
|
||||
file_model = FileService.add_workflow_file(workflow_id=workflow.id,
|
||||
irb_doc_code=irb_code,
|
||||
name="anything.png", content_type="text",
|
||||
binary_data=b'1234')
|
||||
FileService.update_from_github([file_model.id])
|
||||
|
||||
file_model_data = FileDataModel.query.filter_by(
|
||||
file_model_id=file_model.id
|
||||
).order_by(
|
||||
desc(FileDataModel.version)
|
||||
).first()
|
||||
self.assertEqual(file_model_data.data, b'Some bytes')
|
||||
|
||||
@patch('crc.services.file_service.Github')
|
||||
def test_publish_to_github_creates(self, mock_github):
|
||||
mock_github.return_value = FakeGithubCreates()
|
||||
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow('file_upload_form')
|
||||
processor = WorkflowProcessor(workflow)
|
||||
task = processor.next_task()
|
||||
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
|
||||
file_model = FileService.add_workflow_file(workflow_id=workflow.id,
|
||||
irb_doc_code=irb_code,
|
||||
name="anything.png", content_type="text",
|
||||
binary_data=b'1234')
|
||||
result = FileService.publish_to_github([file_model.id])
|
||||
|
||||
self.assertEqual(result['created'], True)
|
||||
|
||||
@patch('crc.services.file_service.Github')
|
||||
def test_publish_to_github_updates(self, mock_github):
|
||||
mock_github.return_value = FakeGithub()
|
||||
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow('file_upload_form')
|
||||
processor = WorkflowProcessor(workflow)
|
||||
task = processor.next_task()
|
||||
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
|
||||
file_model = FileService.add_workflow_file(workflow_id=workflow.id,
|
||||
irb_doc_code=irb_code,
|
||||
name="anything.png", content_type="text",
|
||||
binary_data=b'1234')
|
||||
result = FileService.publish_to_github([file_model.id])
|
||||
|
||||
self.assertEqual(result['updated'], True)
|
||||
|
||||
@ -72,10 +72,10 @@ class TestFilesApi(BaseTest):
|
||||
self.assertEqual(file, file2)
|
||||
|
||||
def test_add_file_from_task_and_form_errors_on_invalid_form_field_name(self):
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow('file_upload_form')
|
||||
processor = WorkflowProcessor(workflow)
|
||||
processor.do_engine_steps()
|
||||
task = processor.next_task()
|
||||
data = {'file': (io.BytesIO(b"abcdef"), 'random_fact.svg')}
|
||||
correct_name = task.task_spec.form.fields[0].id
|
||||
@ -96,6 +96,7 @@ class TestFilesApi(BaseTest):
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow('file_upload_form')
|
||||
processor = WorkflowProcessor(workflow)
|
||||
processor.do_engine_steps()
|
||||
task = processor.next_task()
|
||||
data = {'file': (io.BytesIO(b"abcdef"), 'random_fact.svg')}
|
||||
correct_name = task.task_spec.form.fields[0].id
|
||||
|
||||
70
tests/ldap/test_ldap_lookup_script.py
Normal file
70
tests/ldap/test_ldap_lookup_script.py
Normal file
@ -0,0 +1,70 @@
|
||||
from tests.base_test import BaseTest
|
||||
|
||||
from crc.services.workflow_processor import WorkflowProcessor
|
||||
from crc.scripts.ldap import Ldap
|
||||
from crc.api.common import ApiError
|
||||
from crc import db, mail
|
||||
|
||||
|
||||
class TestLdapLookupScript(BaseTest):
|
||||
|
||||
def test_get_existing_user_details(self):
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow('empty_workflow')
|
||||
processor = WorkflowProcessor(workflow)
|
||||
task = processor.next_task()
|
||||
|
||||
script = Ldap()
|
||||
user_details = script.do_task(task, workflow.study_id, workflow.id, "dhf8r")
|
||||
|
||||
self.assertEqual(user_details['display_name'], 'Dan Funk')
|
||||
self.assertEqual(user_details['given_name'], 'Dan')
|
||||
self.assertEqual(user_details['email_address'], 'dhf8r@virginia.edu')
|
||||
self.assertEqual(user_details['telephone_number'], '+1 (434) 924-1723')
|
||||
self.assertEqual(user_details['title'], 'E42:He\'s a hoopy frood')
|
||||
self.assertEqual(user_details['department'], 'E0:EN-Eng Study of Parallel Universes')
|
||||
self.assertEqual(user_details['affiliation'], 'faculty')
|
||||
self.assertEqual(user_details['sponsor_type'], 'Staff')
|
||||
self.assertEqual(user_details['uid'], 'dhf8r')
|
||||
self.assertEqual(user_details['proper_name'], 'Dan Funk - (dhf8r)')
|
||||
|
||||
def test_get_invalid_user_details(self):
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow('empty_workflow')
|
||||
processor = WorkflowProcessor(workflow)
|
||||
task = processor.next_task()
|
||||
|
||||
task.data = {
|
||||
'PIComputingID': 'rec3z'
|
||||
}
|
||||
|
||||
script = Ldap()
|
||||
with(self.assertRaises(ApiError)):
|
||||
user_details = script.do_task(task, workflow.study_id, workflow.id, "PIComputingID")
|
||||
|
||||
|
||||
def test_bpmn_task_receives_user_details(self):
|
||||
workflow = self.create_workflow('ldap_replace')
|
||||
|
||||
task_data = {
|
||||
'Supervisor': 'dhf8r',
|
||||
'Investigator': 'lb3dp'
|
||||
}
|
||||
task = self.get_workflow_api(workflow).next_task
|
||||
|
||||
self.complete_form(workflow, task, task_data)
|
||||
|
||||
task = self.get_workflow_api(workflow).next_task
|
||||
|
||||
self.assertEqual(task.data['Supervisor']['display_name'], 'Dan Funk')
|
||||
self.assertEqual(task.data['Supervisor']['given_name'], 'Dan')
|
||||
self.assertEqual(task.data['Supervisor']['email_address'], 'dhf8r@virginia.edu')
|
||||
self.assertEqual(task.data['Supervisor']['telephone_number'], '+1 (434) 924-1723')
|
||||
self.assertEqual(task.data['Supervisor']['title'], 'E42:He\'s a hoopy frood')
|
||||
self.assertEqual(task.data['Supervisor']['department'], 'E0:EN-Eng Study of Parallel Universes')
|
||||
self.assertEqual(task.data['Supervisor']['affiliation'], 'faculty')
|
||||
self.assertEqual(task.data['Supervisor']['sponsor_type'], 'Staff')
|
||||
self.assertEqual(task.data['Supervisor']['uid'], 'dhf8r')
|
||||
self.assertEqual(task.data['Supervisor']['proper_name'], 'Dan Funk - (dhf8r)')
|
||||
@ -1,4 +1,6 @@
|
||||
import json
|
||||
from profile import Profile
|
||||
|
||||
from tests.base_test import BaseTest
|
||||
|
||||
from datetime import datetime, timezone
|
||||
@ -9,10 +11,11 @@ from crc.models.protocol_builder import ProtocolBuilderStatus, \
|
||||
ProtocolBuilderStudySchema
|
||||
from crc.models.approval import ApprovalStatus
|
||||
from crc.models.task_event import TaskEventModel
|
||||
from crc.models.study import StudyModel, StudySchema
|
||||
from crc.models.study import StudyModel, StudySchema, StudyStatus
|
||||
from crc.models.workflow import WorkflowSpecModel, WorkflowModel
|
||||
from crc.services.file_service import FileService
|
||||
from crc.services.workflow_processor import WorkflowProcessor
|
||||
from crc.services.workflow_service import WorkflowService
|
||||
|
||||
|
||||
class TestStudyApi(BaseTest):
|
||||
@ -21,16 +24,17 @@ class TestStudyApi(BaseTest):
|
||||
"title": "Phase III Trial of Genuine People Personalities (GPP) Autonomous Intelligent Emotional Agents "
|
||||
"for Interstellar Spacecraft",
|
||||
"last_updated": datetime.now(tz=timezone.utc),
|
||||
"protocol_builder_status": ProtocolBuilderStatus.ACTIVE,
|
||||
"primary_investigator_id": "tmm2x",
|
||||
"user_uid": "dhf8r",
|
||||
}
|
||||
|
||||
def add_test_study(self):
|
||||
study_schema = StudySchema().dump(self.TEST_STUDY)
|
||||
study_schema['status'] = StudyStatus.in_progress.value
|
||||
rv = self.app.post('/v1.0/study',
|
||||
content_type="application/json",
|
||||
headers=self.logged_in_headers(),
|
||||
data=json.dumps(StudySchema().dump(self.TEST_STUDY)))
|
||||
data=json.dumps(study_schema))
|
||||
self.assert_success(rv)
|
||||
return json.loads(rv.get_data(as_text=True))
|
||||
|
||||
@ -132,15 +136,16 @@ class TestStudyApi(BaseTest):
|
||||
self.load_example_data()
|
||||
study: StudyModel = session.query(StudyModel).first()
|
||||
study.title = "Pilot Study of Fjord Placement for Single Fraction Outcomes to Cortisol Susceptibility"
|
||||
study.protocol_builder_status = ProtocolBuilderStatus.ACTIVE
|
||||
study_schema = StudySchema().dump(study)
|
||||
study_schema['status'] = StudyStatus.in_progress.value
|
||||
rv = self.app.put('/v1.0/study/%i' % study.id,
|
||||
content_type="application/json",
|
||||
headers=self.logged_in_headers(),
|
||||
data=json.dumps(StudySchema().dump(study)))
|
||||
data=json.dumps(study_schema))
|
||||
self.assert_success(rv)
|
||||
json_data = json.loads(rv.get_data(as_text=True))
|
||||
self.assertEqual(study.title, json_data['title'])
|
||||
self.assertEqual(study.protocol_builder_status.name, json_data['protocol_builder_status'])
|
||||
self.assertEqual(study.status.value, json_data['status'])
|
||||
|
||||
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # mock_studies
|
||||
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
|
||||
@ -178,15 +183,15 @@ class TestStudyApi(BaseTest):
|
||||
|
||||
num_incomplete = 0
|
||||
num_abandoned = 0
|
||||
num_active = 0
|
||||
num_in_progress = 0
|
||||
num_open = 0
|
||||
|
||||
for study in json_data:
|
||||
if study['protocol_builder_status'] == 'ABANDONED': # One study does not exist in user_studies.json
|
||||
if study['status'] == 'abandoned': # One study does not exist in user_studies.json
|
||||
num_abandoned += 1
|
||||
if study['protocol_builder_status'] == 'ACTIVE': # One study is marked complete without HSR Number
|
||||
num_active += 1
|
||||
if study['protocol_builder_status'] == 'OPEN': # One study is marked complete and has an HSR Number
|
||||
if study['status'] == 'in_progress': # One study is marked complete without HSR Number
|
||||
num_in_progress += 1
|
||||
if study['status'] == 'open_for_enrollment': # One study is marked complete and has an HSR Number
|
||||
num_open += 1
|
||||
|
||||
db_studies_after = session.query(StudyModel).all()
|
||||
@ -194,10 +199,10 @@ class TestStudyApi(BaseTest):
|
||||
self.assertGreater(num_db_studies_after, num_db_studies_before)
|
||||
self.assertEqual(num_abandoned, 1)
|
||||
self.assertEqual(num_open, 1)
|
||||
self.assertEqual(num_active, 2)
|
||||
self.assertEqual(num_in_progress, 2)
|
||||
self.assertEqual(num_incomplete, 0)
|
||||
self.assertEqual(len(json_data), num_db_studies_after)
|
||||
self.assertEqual(num_open + num_active + num_incomplete + num_abandoned, num_db_studies_after)
|
||||
self.assertEqual(num_open + num_in_progress + num_incomplete + num_abandoned, num_db_studies_after)
|
||||
|
||||
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # mock_studies
|
||||
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
|
||||
@ -225,7 +230,7 @@ class TestStudyApi(BaseTest):
|
||||
json_data = json.loads(rv.get_data(as_text=True))
|
||||
self.assertEqual(study.id, json_data['id'])
|
||||
self.assertEqual(study.title, json_data['title'])
|
||||
self.assertEqual(study.protocol_builder_status.name, json_data['protocol_builder_status'])
|
||||
self.assertEqual(study.status.value, json_data['status'])
|
||||
self.assertEqual(study.primary_investigator_id, json_data['primary_investigator_id'])
|
||||
self.assertEqual(study.sponsor, json_data['sponsor'])
|
||||
self.assertEqual(study.ind_number, json_data['ind_number'])
|
||||
|
||||
@ -6,7 +6,7 @@ from tests.base_test import BaseTest
|
||||
|
||||
from crc import db, app
|
||||
from crc.models.protocol_builder import ProtocolBuilderStatus
|
||||
from crc.models.study import StudyModel
|
||||
from crc.models.study import StudyModel, StudyStatus
|
||||
from crc.models.user import UserModel
|
||||
from crc.models.workflow import WorkflowModel, WorkflowStatus, \
|
||||
WorkflowSpecCategoryModel
|
||||
@ -27,7 +27,10 @@ class TestStudyService(BaseTest):
|
||||
|
||||
# Assure some basic models are in place, This is a damn mess. Our database models need an overhaul to make
|
||||
# this easier - better relationship modeling is now critical.
|
||||
self.load_test_spec("top_level_workflow", master_spec=True)
|
||||
cat = WorkflowSpecCategoryModel(name="approvals", display_name="Approvals", display_order=0)
|
||||
db.session.add(cat)
|
||||
db.session.commit()
|
||||
self.load_test_spec("top_level_workflow", master_spec=True, category_id=cat.id)
|
||||
user = db.session.query(UserModel).filter(UserModel.uid == "dhf8r").first()
|
||||
if not user:
|
||||
user = UserModel(uid="dhf8r", email_address="whatever@stuff.com", display_name="Stayathome Smellalots")
|
||||
@ -37,13 +40,9 @@ class TestStudyService(BaseTest):
|
||||
for study in db.session.query(StudyModel).all():
|
||||
StudyService().delete_study(study.id)
|
||||
|
||||
study = StudyModel(title="My title", protocol_builder_status=ProtocolBuilderStatus.ACTIVE, user_uid=user.uid)
|
||||
study = StudyModel(title="My title", status=StudyStatus.in_progress, user_uid=user.uid)
|
||||
db.session.add(study)
|
||||
cat = WorkflowSpecCategoryModel(name="approvals", display_name="Approvals", display_order=0)
|
||||
db.session.add(cat)
|
||||
db.session.commit()
|
||||
|
||||
self.assertIsNotNone(cat.id)
|
||||
self.load_test_spec("random_fact", category_id=cat.id)
|
||||
|
||||
self.assertIsNotNone(study.id)
|
||||
@ -80,6 +79,7 @@ class TestStudyService(BaseTest):
|
||||
# Initialize the Workflow with the workflow processor.
|
||||
workflow_model = db.session.query(WorkflowModel).filter(WorkflowModel.id == workflow.id).first()
|
||||
processor = WorkflowProcessor(workflow_model)
|
||||
processor.do_engine_steps()
|
||||
|
||||
# Assure the workflow is now started, and knows the total and completed tasks.
|
||||
studies = StudyService.get_studies_for_user(user)
|
||||
|
||||
@ -5,14 +5,16 @@ from datetime import timezone, datetime, timedelta
|
||||
import jwt
|
||||
|
||||
from tests.base_test import BaseTest
|
||||
from crc import db, app
|
||||
from crc import app, session
|
||||
from crc.api.common import ApiError
|
||||
from crc.models.protocol_builder import ProtocolBuilderStatus
|
||||
from crc.models.study import StudySchema, StudyModel
|
||||
from crc.models.study import StudySchema, StudyModel, StudyStatus
|
||||
from crc.models.user import UserModel
|
||||
|
||||
|
||||
class TestAuthentication(BaseTest):
|
||||
admin_uid = 'dhf8r'
|
||||
non_admin_uid = 'lb3dp'
|
||||
|
||||
def tearDown(self):
|
||||
# Assure we set the production flag back to false.
|
||||
@ -58,9 +60,9 @@ class TestAuthentication(BaseTest):
|
||||
self.assertTrue(expected_exp_3 - 1000 <= actual_exp_3 <= expected_exp_3 + 1000)
|
||||
|
||||
def test_non_production_auth_creates_user(self):
|
||||
new_uid = 'lb3dp' ## Assure this user id is in the fake responses from ldap.
|
||||
new_uid = self.non_admin_uid ## Assure this user id is in the fake responses from ldap.
|
||||
self.load_example_data()
|
||||
user = db.session.query(UserModel).filter(UserModel.uid == new_uid).first()
|
||||
user = session.query(UserModel).filter(UserModel.uid == new_uid).first()
|
||||
self.assertIsNone(user)
|
||||
|
||||
user_info = {'uid': new_uid, 'first_name': 'Cordi', 'last_name': 'Nator',
|
||||
@ -72,7 +74,7 @@ class TestAuthentication(BaseTest):
|
||||
self.assertTrue(rv_1.status_code == 302)
|
||||
self.assertTrue(str.startswith(rv_1.location, redirect_url))
|
||||
|
||||
user = db.session.query(UserModel).filter(UserModel.uid == new_uid).first()
|
||||
user = session.query(UserModel).filter(UserModel.uid == new_uid).first()
|
||||
self.assertIsNotNone(user)
|
||||
self.assertIsNotNone(user.display_name)
|
||||
self.assertIsNotNone(user.email_address)
|
||||
@ -88,21 +90,20 @@ class TestAuthentication(BaseTest):
|
||||
|
||||
self.load_example_data()
|
||||
|
||||
new_uid = 'lb3dp' # This user is in the test ldap system.
|
||||
user = db.session.query(UserModel).filter_by(uid=new_uid).first()
|
||||
# User should not be in the system yet.
|
||||
user = session.query(UserModel).filter(UserModel.uid == self.non_admin_uid).first()
|
||||
self.assertIsNone(user)
|
||||
redirect_url = 'http://worlds.best.website/admin'
|
||||
headers = dict(Uid=new_uid)
|
||||
db.session.flush()
|
||||
rv = self.app.get('v1.0/login', follow_redirects=False, headers=headers)
|
||||
|
||||
self.assert_success(rv)
|
||||
user = db.session.query(UserModel).filter_by(uid=new_uid).first()
|
||||
self.assertIsNotNone(user)
|
||||
self.assertEqual(new_uid, user.uid)
|
||||
self.assertEqual("Laura Barnes", user.display_name)
|
||||
self.assertEqual("lb3dp@virginia.edu", user.email_address)
|
||||
self.assertEqual("E0:Associate Professor of Systems and Information Engineering", user.title)
|
||||
# Log in
|
||||
non_admin_user = self._login_as_non_admin()
|
||||
|
||||
# User should be in the system now.
|
||||
redirect_url = 'http://worlds.best.website/admin'
|
||||
rv_user = self.app.get('/v1.0/user', headers=self.logged_in_headers(non_admin_user, redirect_url=redirect_url))
|
||||
self.assert_success(rv_user)
|
||||
user_data = json.loads(rv_user.get_data(as_text=True))
|
||||
self.assertEqual(self.non_admin_uid, user_data['uid'])
|
||||
self.assertFalse(user_data['is_admin'])
|
||||
|
||||
# Switch production mode back off
|
||||
app.config['PRODUCTION'] = False
|
||||
@ -119,6 +120,8 @@ class TestAuthentication(BaseTest):
|
||||
user = UserModel(uid="dhf8r", first_name='Dan', last_name='Funk', email_address='dhf8r@virginia.edu')
|
||||
rv = self.app.get('/v1.0/user', headers=self.logged_in_headers(user, redirect_url='http://omg.edu/lolwut'))
|
||||
self.assert_success(rv)
|
||||
user_data = json.loads(rv.get_data(as_text=True))
|
||||
self.assertTrue(user_data['is_admin'])
|
||||
|
||||
def test_admin_can_access_admin_only_endpoints(self):
|
||||
# Switch production mode on
|
||||
@ -126,21 +129,8 @@ class TestAuthentication(BaseTest):
|
||||
|
||||
self.load_example_data()
|
||||
|
||||
admin_uids = app.config['ADMIN_UIDS']
|
||||
self.assertGreater(len(admin_uids), 0)
|
||||
admin_uid = admin_uids[0]
|
||||
self.assertEqual(admin_uid, 'dhf8r') # This user is in the test ldap system.
|
||||
admin_headers = dict(Uid=admin_uid)
|
||||
|
||||
rv = self.app.get('v1.0/login', follow_redirects=False, headers=admin_headers)
|
||||
self.assert_success(rv)
|
||||
|
||||
admin_user = db.session.query(UserModel).filter(UserModel.uid == admin_uid).first()
|
||||
self.assertIsNotNone(admin_user)
|
||||
self.assertEqual(admin_uid, admin_user.uid)
|
||||
|
||||
admin_study = self._make_fake_study(admin_uid)
|
||||
|
||||
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())
|
||||
|
||||
rv_add_study = self.app.post(
|
||||
@ -153,7 +143,7 @@ class TestAuthentication(BaseTest):
|
||||
self.assert_success(rv_add_study, 'Admin user should be able to add a study')
|
||||
|
||||
new_admin_study = json.loads(rv_add_study.get_data(as_text=True))
|
||||
db_admin_study = db.session.query(StudyModel).filter_by(id=new_admin_study['id']).first()
|
||||
db_admin_study = session.query(StudyModel).filter_by(id=new_admin_study['id']).first()
|
||||
self.assertIsNotNone(db_admin_study)
|
||||
|
||||
rv_del_study = self.app.delete(
|
||||
@ -173,26 +163,9 @@ class TestAuthentication(BaseTest):
|
||||
self.load_example_data()
|
||||
|
||||
# Non-admin user should not be able to delete a study
|
||||
non_admin_uid = 'lb3dp'
|
||||
admin_uids = app.config['ADMIN_UIDS']
|
||||
self.assertGreater(len(admin_uids), 0)
|
||||
self.assertNotIn(non_admin_uid, admin_uids)
|
||||
|
||||
non_admin_headers = dict(Uid=non_admin_uid)
|
||||
|
||||
rv = self.app.get(
|
||||
'v1.0/login',
|
||||
follow_redirects=False,
|
||||
headers=non_admin_headers
|
||||
)
|
||||
self.assert_success(rv)
|
||||
|
||||
non_admin_user = db.session.query(UserModel).filter_by(uid=non_admin_uid).first()
|
||||
self.assertIsNotNone(non_admin_user)
|
||||
|
||||
non_admin_user = self._login_as_non_admin()
|
||||
non_admin_token_headers = dict(Authorization='Bearer ' + non_admin_user.encode_auth_token().decode())
|
||||
|
||||
non_admin_study = self._make_fake_study(non_admin_uid)
|
||||
non_admin_study = self._make_fake_study(non_admin_user.uid)
|
||||
|
||||
rv_add_study = self.app.post(
|
||||
'/v1.0/study',
|
||||
@ -203,7 +176,7 @@ class TestAuthentication(BaseTest):
|
||||
self.assert_success(rv_add_study, 'Non-admin user should be able to add a study')
|
||||
|
||||
new_non_admin_study = json.loads(rv_add_study.get_data(as_text=True))
|
||||
db_non_admin_study = db.session.query(StudyModel).filter_by(id=new_non_admin_study['id']).first()
|
||||
db_non_admin_study = session.query(StudyModel).filter_by(id=new_non_admin_study['id']).first()
|
||||
self.assertIsNotNone(db_non_admin_study)
|
||||
|
||||
rv_non_admin_del_study = self.app.delete(
|
||||
@ -216,11 +189,131 @@ class TestAuthentication(BaseTest):
|
||||
# Switch production mode back off
|
||||
app.config['PRODUCTION'] = False
|
||||
|
||||
def test_list_all_users(self):
|
||||
self.load_example_data()
|
||||
rv = self.app.get('/v1.0/user')
|
||||
self.assert_failure(rv, 401)
|
||||
|
||||
rv = self.app.get('/v1.0/user', headers=self.logged_in_headers())
|
||||
self.assert_success(rv)
|
||||
|
||||
all_users = session.query(UserModel).all()
|
||||
|
||||
rv = self.app.get('/v1.0/list_users', headers=self.logged_in_headers())
|
||||
self.assert_success(rv)
|
||||
user_data = json.loads(rv.get_data(as_text=True))
|
||||
self.assertEqual(len(user_data), len(all_users))
|
||||
|
||||
def test_admin_can_impersonate_another_user(self):
|
||||
# Switch production mode on
|
||||
app.config['PRODUCTION'] = True
|
||||
|
||||
self.load_example_data()
|
||||
|
||||
admin_user = self._login_as_admin()
|
||||
admin_token_headers = dict(Authorization='Bearer ' + admin_user.encode_auth_token().decode())
|
||||
|
||||
# User should not be in the system yet.
|
||||
non_admin_user = session.query(UserModel).filter(UserModel.uid == self.non_admin_uid).first()
|
||||
self.assertIsNone(non_admin_user)
|
||||
|
||||
# Admin should not be able to impersonate non-existent user
|
||||
rv_1 = self.app.get(
|
||||
'/v1.0/user?admin_impersonate_uid=' + self.non_admin_uid,
|
||||
content_type="application/json",
|
||||
headers=admin_token_headers,
|
||||
follow_redirects=False
|
||||
)
|
||||
self.assert_failure(rv_1, 400)
|
||||
|
||||
# Add the non-admin user now
|
||||
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())
|
||||
|
||||
# Add a study for the non-admin user
|
||||
non_admin_study = self._make_fake_study(self.non_admin_uid)
|
||||
rv_add_study = self.app.post(
|
||||
'/v1.0/study',
|
||||
content_type="application/json",
|
||||
headers=non_admin_token_headers,
|
||||
data=json.dumps(StudySchema().dump(non_admin_study))
|
||||
)
|
||||
self.assert_success(rv_add_study, 'Non-admin user should be able to add a study')
|
||||
self.logout()
|
||||
|
||||
# Admin should be able to impersonate user now
|
||||
admin_user = self._login_as_admin()
|
||||
rv_2 = self.app.get(
|
||||
'/v1.0/user?admin_impersonate_uid=' + self.non_admin_uid,
|
||||
content_type="application/json",
|
||||
headers=admin_token_headers,
|
||||
follow_redirects=False
|
||||
)
|
||||
self.assert_success(rv_2)
|
||||
user_data_2 = json.loads(rv_2.get_data(as_text=True))
|
||||
self.assertEqual(user_data_2['uid'], self.non_admin_uid, 'Admin user should impersonate non-admin user')
|
||||
|
||||
# Study endpoint should return non-admin user's studies
|
||||
rv_study = self.app.get(
|
||||
'/v1.0/study',
|
||||
content_type="application/json",
|
||||
headers=admin_token_headers,
|
||||
follow_redirects=False
|
||||
)
|
||||
self.assert_success(rv_study, 'Admin user should be able to get impersonated user studies')
|
||||
study_data = json.loads(rv_study.get_data(as_text=True))
|
||||
self.assertGreaterEqual(len(study_data), 1)
|
||||
self.assertEqual(study_data[0]['user_uid'], self.non_admin_uid)
|
||||
|
||||
# Switch production mode back off
|
||||
app.config['PRODUCTION'] = False
|
||||
|
||||
def _make_fake_study(self, uid):
|
||||
return {
|
||||
"title": "blah",
|
||||
"last_updated": datetime.now(tz=timezone.utc),
|
||||
"protocol_builder_status": ProtocolBuilderStatus.ACTIVE,
|
||||
"status": StudyStatus.in_progress,
|
||||
"primary_investigator_id": uid,
|
||||
"user_uid": uid,
|
||||
}
|
||||
|
||||
def _login_as_admin(self):
|
||||
admin_uids = app.config['ADMIN_UIDS']
|
||||
self.assertGreater(len(admin_uids), 0)
|
||||
self.assertIn(self.admin_uid, admin_uids)
|
||||
admin_headers = dict(Uid=self.admin_uid)
|
||||
|
||||
rv = self.app.get('v1.0/login', follow_redirects=False, headers=admin_headers)
|
||||
self.assert_success(rv)
|
||||
|
||||
admin_user = session.query(UserModel).filter(UserModel.uid == self.admin_uid).first()
|
||||
self.assertIsNotNone(admin_user)
|
||||
self.assertEqual(self.admin_uid, admin_user.uid)
|
||||
self.assertTrue(admin_user.is_admin())
|
||||
return admin_user
|
||||
|
||||
def _login_as_non_admin(self):
|
||||
admin_uids = app.config['ADMIN_UIDS']
|
||||
self.assertGreater(len(admin_uids), 0)
|
||||
self.assertNotIn(self.non_admin_uid, admin_uids)
|
||||
|
||||
non_admin_headers = dict(Uid=self.non_admin_uid)
|
||||
|
||||
rv = self.app.get(
|
||||
'v1.0/login?uid=' + self.non_admin_uid,
|
||||
follow_redirects=False,
|
||||
headers=non_admin_headers
|
||||
)
|
||||
self.assert_success(rv)
|
||||
|
||||
user = session.query(UserModel).filter(UserModel.uid == self.non_admin_uid).first()
|
||||
self.assertIsNotNone(user)
|
||||
self.assertFalse(user.is_admin())
|
||||
self.assertIsNotNone(user)
|
||||
self.assertEqual(self.non_admin_uid, user.uid)
|
||||
self.assertEqual("Laura Barnes", user.display_name)
|
||||
self.assertEqual("lb3dp@virginia.edu", user.email_address)
|
||||
self.assertEqual("E0:Associate Professor of Systems and Information Engineering", user.title)
|
||||
return user
|
||||
|
||||
43
tests/test_events.py
Normal file
43
tests/test_events.py
Normal file
@ -0,0 +1,43 @@
|
||||
import json
|
||||
|
||||
from tests.base_test import BaseTest
|
||||
from crc.models.workflow import WorkflowStatus
|
||||
from crc import db
|
||||
from crc.api.common import ApiError
|
||||
from crc.models.task_event import TaskEventModel, TaskEventSchema
|
||||
from crc.services.workflow_service import WorkflowService
|
||||
|
||||
|
||||
class TestEvents(BaseTest):
|
||||
|
||||
|
||||
def test_list_events_by_workflow(self):
|
||||
workflow_one = self.create_workflow('exclusive_gateway')
|
||||
|
||||
# Start a the workflow.
|
||||
first_task = self.get_workflow_api(workflow_one).next_task
|
||||
self.complete_form(workflow_one, first_task, {"has_bananas": True})
|
||||
workflow_one = self.get_workflow_api(workflow_one)
|
||||
self.assertEqual('Task_Num_Bananas', workflow_one.next_task.name)
|
||||
|
||||
# Start a second workflow
|
||||
workflow_two = self.create_workflow('subprocess')
|
||||
workflow_api_two = self.get_workflow_api(workflow_two)
|
||||
|
||||
# Get all action events across workflows
|
||||
rv = self.app.get('/v1.0/task_events?action=ASSIGNMENT',
|
||||
headers=self.logged_in_headers(),
|
||||
content_type="application/json")
|
||||
self.assert_success(rv)
|
||||
json_data = json.loads(rv.get_data(as_text=True))
|
||||
tasks = TaskEventSchema(many=True).load(json_data)
|
||||
self.assertEqual(2, len(tasks))
|
||||
|
||||
# Get action events for a single workflow
|
||||
rv = self.app.get(f'/v1.0/task_events?action=ASSIGNMENT&workflow={workflow_one.id}',
|
||||
headers=self.logged_in_headers(),
|
||||
content_type="application/json")
|
||||
self.assert_success(rv)
|
||||
json_data = json.loads(rv.get_data(as_text=True))
|
||||
tasks = TaskEventSchema(many=True).load(json_data)
|
||||
self.assertEqual(1, len(tasks))
|
||||
@ -30,4 +30,4 @@ class TestLdapService(BaseTest):
|
||||
user_info = LdapService.user_info("nosuch")
|
||||
self.assertFalse(True, "An API error should be raised.")
|
||||
except ApiError as ae:
|
||||
self.assertEqual("missing_ldap_record", ae.code)
|
||||
self.assertEqual("missing_ldap_record", ae.code)
|
||||
|
||||
@ -9,6 +9,7 @@ from crc import session, app
|
||||
from crc.models.api_models import WorkflowApiSchema, MultiInstanceType, TaskSchema
|
||||
from crc.models.file import FileModelSchema
|
||||
from crc.models.workflow import WorkflowStatus
|
||||
from crc.models.task_event import TaskEventModel
|
||||
|
||||
|
||||
class TestTasksApi(BaseTest):
|
||||
@ -42,6 +43,24 @@ class TestTasksApi(BaseTest):
|
||||
"""
|
||||
self.assertTrue(str.startswith(task.documentation, expected_docs))
|
||||
|
||||
def test_get_workflow_without_running_engine_steps(self):
|
||||
# Set up a new workflow
|
||||
workflow = self.create_workflow('two_forms')
|
||||
# get the first form in the two form workflow.
|
||||
workflow_api = self.get_workflow_api(workflow, do_engine_steps=False)
|
||||
|
||||
# There should be no task event logs related to the workflow at this point.
|
||||
task_events = session.query(TaskEventModel).filter(TaskEventModel.workflow_id == workflow.id).all()
|
||||
self.assertEqual(0, len(task_events))
|
||||
|
||||
# Since the workflow was not started, the call to read-only should not execute any engine steps the
|
||||
# current task should be the start event.
|
||||
self.assertEqual("Start", workflow_api.next_task.name)
|
||||
|
||||
def test_get_form_for_previously_completed_task(self):
|
||||
"""Assure we can look at previously completed steps without moving the token for the workflow."""
|
||||
|
||||
|
||||
def test_two_forms_task(self):
|
||||
# Set up a new workflow
|
||||
self.load_example_data()
|
||||
@ -69,7 +88,6 @@ class TestTasksApi(BaseTest):
|
||||
self.assertIsNotNone(val)
|
||||
|
||||
def test_error_message_on_bad_gateway_expression(self):
|
||||
self.load_example_data()
|
||||
workflow = self.create_workflow('exclusive_gateway')
|
||||
|
||||
# get the first form in the two form workflow.
|
||||
@ -77,7 +95,6 @@ class TestTasksApi(BaseTest):
|
||||
self.complete_form(workflow, task, {"has_bananas": True})
|
||||
|
||||
def test_workflow_with_parallel_forms(self):
|
||||
self.load_example_data()
|
||||
workflow = self.create_workflow('exclusive_gateway')
|
||||
|
||||
# get the first form in the two form workflow.
|
||||
@ -89,7 +106,6 @@ class TestTasksApi(BaseTest):
|
||||
self.assertEqual("Task_Num_Bananas", workflow_api.next_task.name)
|
||||
|
||||
def test_navigation_with_parallel_forms(self):
|
||||
self.load_example_data()
|
||||
workflow = self.create_workflow('exclusive_gateway')
|
||||
|
||||
# get the first form in the two form workflow.
|
||||
@ -107,7 +123,6 @@ class TestTasksApi(BaseTest):
|
||||
self.assertEqual("NOOP", nav[3]['state'])
|
||||
|
||||
def test_navigation_with_exclusive_gateway(self):
|
||||
self.load_example_data()
|
||||
workflow = self.create_workflow('exclusive_gateway_2')
|
||||
|
||||
# get the first form in the two form workflow.
|
||||
@ -124,7 +139,6 @@ class TestTasksApi(BaseTest):
|
||||
self.assertEqual("Task 3", nav[6]['title'])
|
||||
|
||||
def test_document_added_to_workflow_shows_up_in_file_list(self):
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
workflow = self.create_workflow('docx')
|
||||
|
||||
@ -153,7 +167,6 @@ class TestTasksApi(BaseTest):
|
||||
|
||||
|
||||
def test_get_documentation_populated_in_end(self):
|
||||
self.load_example_data()
|
||||
workflow = self.create_workflow('random_fact')
|
||||
workflow_api = self.get_workflow_api(workflow)
|
||||
task = workflow_api.next_task
|
||||
@ -167,9 +180,7 @@ class TestTasksApi(BaseTest):
|
||||
self.assertTrue("norris" in workflow_api.next_task.documentation)
|
||||
|
||||
def test_load_workflow_from_outdated_spec(self):
|
||||
|
||||
# Start the basic two_forms workflow and complete a task.
|
||||
self.load_example_data()
|
||||
workflow = self.create_workflow('two_forms')
|
||||
workflow_api = self.get_workflow_api(workflow)
|
||||
self.complete_form(workflow, workflow_api.next_task, {"color": "blue"})
|
||||
@ -194,9 +205,7 @@ class TestTasksApi(BaseTest):
|
||||
self.assertTrue(workflow_api.is_latest_spec)
|
||||
|
||||
def test_soft_reset_errors_out_and_next_result_is_on_original_version(self):
|
||||
|
||||
# Start the basic two_forms workflow and complete a task.
|
||||
self.load_example_data()
|
||||
workflow = self.create_workflow('two_forms')
|
||||
workflow_api = self.get_workflow_api(workflow)
|
||||
self.complete_form(workflow, workflow_api.next_task, {"color": "blue"})
|
||||
@ -221,7 +230,6 @@ class TestTasksApi(BaseTest):
|
||||
|
||||
|
||||
def test_manual_task_with_external_documentation(self):
|
||||
self.load_example_data()
|
||||
workflow = self.create_workflow('manual_task_with_external_documentation')
|
||||
|
||||
# get the first form in the two form workflow.
|
||||
@ -235,7 +243,6 @@ class TestTasksApi(BaseTest):
|
||||
self.assertTrue('Dan' in workflow_api.next_task.documentation)
|
||||
|
||||
def test_bpmn_extension_properties_are_populated(self):
|
||||
self.load_example_data()
|
||||
workflow = self.create_workflow('manual_task_with_external_documentation')
|
||||
|
||||
# get the first form in the two form workflow.
|
||||
@ -268,9 +275,7 @@ class TestTasksApi(BaseTest):
|
||||
# Assure that the names for each task are properly updated, so they aren't all the same.
|
||||
self.assertEqual("Primary Investigator", workflow.next_task.properties['display_name'])
|
||||
|
||||
|
||||
def test_lookup_endpoint_for_task_field_enumerations(self):
|
||||
self.load_example_data()
|
||||
workflow = self.create_workflow('enum_options_with_search')
|
||||
# get the first form in the two form workflow.
|
||||
workflow = self.get_workflow_api(workflow)
|
||||
@ -286,7 +291,6 @@ class TestTasksApi(BaseTest):
|
||||
self.assert_options_populated(results, ['CUSTOMER_NUMBER', 'CUSTOMER_NAME', 'CUSTOMER_CLASS_MEANING'])
|
||||
|
||||
def test_lookup_endpoint_for_task_field_using_lookup_entry_id(self):
|
||||
self.load_example_data()
|
||||
workflow = self.create_workflow('enum_options_with_search')
|
||||
# get the first form in the two form workflow.
|
||||
workflow = self.get_workflow_api(workflow)
|
||||
@ -316,7 +320,6 @@ class TestTasksApi(BaseTest):
|
||||
# the key/values from the spreadsheet are added directly to the form and it shows up as
|
||||
# a dropdown. This tests the case of wanting to get additional data when a user selects
|
||||
# something from a dropdown.
|
||||
self.load_example_data()
|
||||
workflow = self.create_workflow('enum_options_from_file')
|
||||
# get the first form in the two form workflow.
|
||||
workflow = self.get_workflow_api(workflow)
|
||||
@ -334,7 +337,6 @@ class TestTasksApi(BaseTest):
|
||||
self.assertIsInstance(results[0]['data'], dict)
|
||||
|
||||
def test_enum_from_task_data(self):
|
||||
self.load_example_data()
|
||||
workflow = self.create_workflow('enum_options_from_task_data')
|
||||
# get the first form in the two form workflow.
|
||||
workflow_api = self.get_workflow_api(workflow)
|
||||
@ -359,7 +361,6 @@ class TestTasksApi(BaseTest):
|
||||
self.assertEqual('Chesterfield', options[2]['data']['first_name'])
|
||||
|
||||
def test_lookup_endpoint_for_task_ldap_field_lookup(self):
|
||||
self.load_example_data()
|
||||
workflow = self.create_workflow('ldap_lookup')
|
||||
# get the first form
|
||||
workflow = self.get_workflow_api(workflow)
|
||||
@ -378,7 +379,6 @@ class TestTasksApi(BaseTest):
|
||||
self.assertEqual(1, len(results))
|
||||
|
||||
def test_sub_process(self):
|
||||
self.load_example_data()
|
||||
workflow = self.create_workflow('subprocess')
|
||||
|
||||
workflow_api = self.get_workflow_api(workflow)
|
||||
@ -399,7 +399,6 @@ class TestTasksApi(BaseTest):
|
||||
self.assertEqual(WorkflowStatus.complete, workflow_api.status)
|
||||
|
||||
def test_update_task_resets_token(self):
|
||||
self.load_example_data()
|
||||
workflow = self.create_workflow('exclusive_gateway')
|
||||
|
||||
# Start the workflow.
|
||||
@ -477,3 +476,5 @@ class TestTasksApi(BaseTest):
|
||||
workflow = self.get_workflow_api(workflow)
|
||||
self.assertEqual(WorkflowStatus.complete, workflow.status)
|
||||
|
||||
|
||||
|
||||
|
||||
@ -68,7 +68,7 @@ class TestTasksApi(BaseTest):
|
||||
def test_get_outstanding_tasks_awaiting_current_user(self):
|
||||
submitter = self.create_user(uid='lje5u')
|
||||
supervisor = self.create_user(uid='lb3dp')
|
||||
workflow = self.create_workflow('roles', as_user=submitter.uid)
|
||||
workflow = self.create_workflow('roles', display_name="Roles", as_user=submitter.uid)
|
||||
workflow_api = self.get_workflow_api(workflow, user_uid=submitter.uid)
|
||||
|
||||
# User lje5u can complete the first task, and set her supervisor
|
||||
@ -94,6 +94,7 @@ class TestTasksApi(BaseTest):
|
||||
self.assertEquals(1, len(tasks))
|
||||
self.assertEquals(workflow.id, tasks[0]['workflow']['id'])
|
||||
self.assertEquals(workflow.study.id, tasks[0]['study']['id'])
|
||||
self.assertEquals("Test Workflows", tasks[0]['workflow']['category_display_name'])
|
||||
|
||||
# Assure we can say something sensible like:
|
||||
# You have a task called "Approval" to be completed in the "Supervisor Approval" workflow
|
||||
@ -110,6 +111,7 @@ class TestTasksApi(BaseTest):
|
||||
data['approval'] = True
|
||||
self.complete_form(workflow, workflow_api.next_task, data, user_uid=supervisor.uid)
|
||||
|
||||
|
||||
def test_navigation_and_current_task_updates_through_workflow(self):
|
||||
|
||||
submitter = self.create_user(uid='lje5u')
|
||||
@ -178,7 +180,7 @@ class TestTasksApi(BaseTest):
|
||||
workflow_api = self.complete_form(workflow, workflow_api.next_task, data, user_uid=submitter.uid)
|
||||
nav = workflow_api.navigation
|
||||
self.assertEquals(5, len(nav))
|
||||
self.assertEquals('COMPLETED', nav[0]['state']) # We still have some issues here, the navigation will be off when looping back.
|
||||
self.assertEquals('READY', nav[0]['state']) # When you loop back the task is again in the ready state.
|
||||
self.assertEquals('LOCKED', nav[1]['state']) # Second item is locked, it is the review and doesn't belong to this user.
|
||||
self.assertEquals('LOCKED', nav[2]['state']) # third item is a gateway belonging to the supervisor, and is locked.
|
||||
self.assertEquals('READY', workflow_api.next_task.state)
|
||||
@ -199,4 +201,67 @@ class TestTasksApi(BaseTest):
|
||||
workflow_api = self.get_workflow_api(workflow, user_uid=submitter.uid)
|
||||
self.assertEquals('COMPLETED', workflow_api.next_task.state)
|
||||
self.assertEquals('EndEvent', workflow_api.next_task.type) # Are are at the end.
|
||||
self.assertEquals(WorkflowStatus.complete, workflow_api.status)
|
||||
self.assertEquals(WorkflowStatus.complete, workflow_api.status)
|
||||
|
||||
def get_assignment_task_events(self, uid):
|
||||
return db.session.query(TaskEventModel). \
|
||||
filter(TaskEventModel.user_uid == uid). \
|
||||
filter(TaskEventModel.action == WorkflowService.TASK_ACTION_ASSIGNMENT).all()
|
||||
|
||||
def test_workflow_reset_correctly_resets_the_task_events(self):
|
||||
|
||||
submitter = self.create_user(uid='lje5u')
|
||||
supervisor = self.create_user(uid='lb3dp')
|
||||
workflow = self.create_workflow('roles', display_name="Roles", as_user=submitter.uid)
|
||||
workflow_api = self.get_workflow_api(workflow, user_uid=submitter.uid)
|
||||
|
||||
# User lje5u can complete the first task, and set her supervisor
|
||||
data = workflow_api.next_task.data
|
||||
data['supervisor'] = supervisor.uid
|
||||
workflow_api = self.complete_form(workflow, workflow_api.next_task, data, user_uid=submitter.uid)
|
||||
|
||||
# At this point there should be a task_log with an action of ASSIGNMENT on it for
|
||||
# the supervisor.
|
||||
self.assertEquals(1, len(self.get_assignment_task_events(supervisor.uid)))
|
||||
|
||||
# Resetting the workflow at this point should clear the event log.
|
||||
workflow_api = self.get_workflow_api(workflow, hard_reset=True, user_uid=submitter.uid)
|
||||
self.assertEquals(0, len(self.get_assignment_task_events(supervisor.uid)))
|
||||
|
||||
# Re-complete first task, and awaiting tasks should shift to 0 for for submitter, and 1 for supervisor
|
||||
workflow_api = self.complete_form(workflow, workflow_api.next_task, data, user_uid=submitter.uid)
|
||||
self.assertEquals(0, len(self.get_assignment_task_events(submitter.uid)))
|
||||
self.assertEquals(1, len(self.get_assignment_task_events(supervisor.uid)))
|
||||
|
||||
# Complete the supervisor task with rejected approval, and the assignments should switch.
|
||||
workflow_api = self.get_workflow_api(workflow, user_uid=supervisor.uid)
|
||||
data = workflow_api.next_task.data
|
||||
data["approval"] = False
|
||||
workflow_api = self.complete_form(workflow, workflow_api.next_task, data, user_uid=supervisor.uid)
|
||||
self.assertEquals(1, len(self.get_assignment_task_events(submitter.uid)))
|
||||
self.assertEquals(0, len(self.get_assignment_task_events(supervisor.uid)))
|
||||
|
||||
# Mark the return form review page as complete, and then recomplete the form, and assignments switch yet again.
|
||||
workflow_api = self.get_workflow_api(workflow, user_uid=submitter.uid)
|
||||
workflow_api = self.complete_form(workflow, workflow_api.next_task, data, user_uid=submitter.uid)
|
||||
workflow_api = self.complete_form(workflow, workflow_api.next_task, data, user_uid=submitter.uid)
|
||||
self.assertEquals(0, len(self.get_assignment_task_events(submitter.uid)))
|
||||
self.assertEquals(1, len(self.get_assignment_task_events(supervisor.uid)))
|
||||
|
||||
# Complete the supervisor task, accepting the approval, and the workflow is completed.
|
||||
# When it is all done, there should be no outstanding assignments.
|
||||
workflow_api = self.get_workflow_api(workflow, user_uid=supervisor.uid)
|
||||
data = workflow_api.next_task.data
|
||||
data["approval"] = True
|
||||
workflow_api = self.complete_form(workflow, workflow_api.next_task, data, user_uid=supervisor.uid)
|
||||
self.assertEquals(WorkflowStatus.complete, workflow_api.status)
|
||||
self.assertEquals('EndEvent', workflow_api.next_task.type) # Are are at the end.
|
||||
self.assertEquals(0, len(self.get_assignment_task_events(submitter.uid)))
|
||||
self.assertEquals(0, len(self.get_assignment_task_events(supervisor.uid)))
|
||||
|
||||
# Sending any subsequent complete forms does not result in a new task event
|
||||
with self.assertRaises(AssertionError) as _api_error:
|
||||
workflow_api = self.complete_form(workflow, workflow_api.next_task, data, user_uid=submitter.uid)
|
||||
|
||||
self.assertEquals(0, len(self.get_assignment_task_events(submitter.uid)))
|
||||
self.assertEquals(0, len(self.get_assignment_task_events(supervisor.uid)))
|
||||
|
||||
@ -36,6 +36,7 @@ class TestWorkflowProcessor(BaseTest):
|
||||
workflow_spec_model = self.load_test_spec("random_fact")
|
||||
study = session.query(StudyModel).first()
|
||||
processor = self.get_processor(study, workflow_spec_model)
|
||||
processor.do_engine_steps()
|
||||
self.assertEqual(study.id, processor.bpmn_workflow.data[WorkflowProcessor.STUDY_ID_KEY])
|
||||
self.assertIsNotNone(processor)
|
||||
self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
|
||||
@ -62,6 +63,7 @@ class TestWorkflowProcessor(BaseTest):
|
||||
files = session.query(FileModel).filter_by(workflow_spec_id='decision_table').all()
|
||||
self.assertEqual(2, len(files))
|
||||
processor = self.get_processor(study, workflow_spec_model)
|
||||
processor.do_engine_steps()
|
||||
self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
|
||||
next_user_tasks = processor.next_user_tasks()
|
||||
self.assertEqual(1, len(next_user_tasks))
|
||||
@ -86,6 +88,7 @@ class TestWorkflowProcessor(BaseTest):
|
||||
workflow_spec_model = self.load_test_spec("parallel_tasks")
|
||||
study = session.query(StudyModel).first()
|
||||
processor = self.get_processor(study, workflow_spec_model)
|
||||
processor.do_engine_steps()
|
||||
self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
|
||||
|
||||
# Complete the first steps of the 4 parallel tasks
|
||||
@ -127,6 +130,7 @@ class TestWorkflowProcessor(BaseTest):
|
||||
study = session.query(StudyModel).first()
|
||||
workflow_spec_model = self.load_test_spec("parallel_tasks")
|
||||
processor = self.get_processor(study, workflow_spec_model)
|
||||
processor.do_engine_steps()
|
||||
self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
|
||||
next_user_tasks = processor.next_user_tasks()
|
||||
self.assertEqual(4, len(next_user_tasks))
|
||||
@ -215,6 +219,7 @@ class TestWorkflowProcessor(BaseTest):
|
||||
self.assertEqual(2, len(files))
|
||||
workflow_spec_model = session.query(WorkflowSpecModel).filter_by(id="docx").first()
|
||||
processor = self.get_processor(study, workflow_spec_model)
|
||||
processor.do_engine_steps()
|
||||
self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
|
||||
next_user_tasks = processor.next_user_tasks()
|
||||
self.assertEqual(1, len(next_user_tasks))
|
||||
@ -278,6 +283,7 @@ class TestWorkflowProcessor(BaseTest):
|
||||
study = session.query(StudyModel).first()
|
||||
workflow_spec_model = self.load_test_spec("two_forms")
|
||||
processor = self.get_processor(study, workflow_spec_model)
|
||||
processor.do_engine_steps()
|
||||
self.assertEqual(processor.workflow_model.workflow_spec_id, workflow_spec_model.id)
|
||||
task = processor.next_task()
|
||||
task.data = {"color": "blue"}
|
||||
|
||||
@ -47,6 +47,7 @@ class TestWorkflowProcessorMultiInstance(BaseTest):
|
||||
workflow_spec_model = self.load_test_spec("multi_instance")
|
||||
study = session.query(StudyModel).first()
|
||||
processor = self.get_processor(study, workflow_spec_model)
|
||||
processor.bpmn_workflow.do_engine_steps()
|
||||
self.assertEqual(study.id, processor.bpmn_workflow.data[WorkflowProcessor.STUDY_ID_KEY])
|
||||
self.assertIsNotNone(processor)
|
||||
self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
|
||||
|
||||
@ -89,8 +89,8 @@ class TestWorkflowSpecValidation(BaseTest):
|
||||
self.load_example_data()
|
||||
errors = self.validate_workflow("invalid_script")
|
||||
self.assertEqual(2, len(errors))
|
||||
self.assertEqual("error_loading_workflow", errors[0]['code'])
|
||||
self.assertTrue("NoSuchScript" in errors[0]['message'])
|
||||
self.assertEqual("workflow_validation_exception", errors[0]['code'])
|
||||
#self.assertTrue("NoSuchScript" in errors[0]['message'])
|
||||
self.assertEqual("Invalid_Script_Task", errors[0]['task_id'])
|
||||
self.assertEqual("An Invalid Script Reference", errors[0]['task_name'])
|
||||
self.assertEqual("invalid_script.bpmn", errors[0]['file_name'])
|
||||
@ -99,7 +99,7 @@ class TestWorkflowSpecValidation(BaseTest):
|
||||
self.load_example_data()
|
||||
errors = self.validate_workflow("invalid_script2")
|
||||
self.assertEqual(2, len(errors))
|
||||
self.assertEqual("error_loading_workflow", errors[0]['code'])
|
||||
self.assertEqual("workflow_validation_exception", errors[0]['code'])
|
||||
self.assertEqual("Invalid_Script_Task", errors[0]['task_id'])
|
||||
self.assertEqual("An Invalid Script Reference", errors[0]['task_name'])
|
||||
self.assertEqual("invalid_script2.bpmn", errors[0]['file_name'])
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user