diff --git a/TESTING.md b/TESTING.md
index a6c1681716af0d211ad9f0fa8c24aba1433a1950..af53c2100fcd697ab3aaef8b4937fbdbb6282e22 100644
--- a/TESTING.md
+++ b/TESTING.md
@@ -13,7 +13,6 @@ All tests are executed by default. Subsets can be run using the filtering option
* To run linting, use `--lint` (`-l`)
* To run unit tests, use `--unit` (`-u`)
* To run integration tests, use `--integ` (`-i`)
-* To run abao tests, use `--abao` (`-a`)
* To pass any arguments to `py.test`, use `-- PYTEST_ARGS`
See [py.test usage](https://docs.pytest.org/en/latest/usage.html) for more.
@@ -34,11 +33,3 @@ Without rebuilding the image, run only integration tests matching `foo`, use the
```
**NOTE:** The mongodb version is pinned via the `MONGO_VERSION` variable in `tests/bin/run-tests-docker.sh`.
-
-### Tools
-- [abao](https://github.com/cybertk/abao/)
-
-### Testing API against RAML with Abao
-Abao is one of the testing tools run during our TravisCI build. It tests the API implementation against what鈥檚 defined in the RAML spec. Adding a new resource / url to the RAML spec will cause Abao to verify that resource during integration tests. Sometimes abao cannot properly test a resource (file field uploads) or a test may require chaining variable. Abao has before and after hooks for tests, written in javascript. These can be used to skip a test, inject variables into the request, or make extra assertions about the response. See tests/integration/abao in the repo for the hooks file. See [abao github readme](https://github.com/cybertk/abao/blob/master/README.md) for more information on how to use hooks.
-
-Abao tests can depend on specific resources (eg. group, project, session, etc.) pre-existing in the DB. That resource loading should be maintained within `tests/integration_tests/abao/load_fixture.py` and is executed automatically via the integration test scripts at `test/bin`.
diff --git a/api/config.py b/api/config.py
index 74657503d1b0904aa8660ff2c5cc8e094ec385b6..58b9eaba1c74a0ad74c9b41b5b87489da3c79f6e 100644
--- a/api/config.py
+++ b/api/config.py
@@ -157,7 +157,6 @@ expected_input_schemas = set([
'avatars.json',
'collection.json',
'collection-update.json',
- 'container.json',
'device.json',
'file.json',
'file-update.json',
@@ -182,8 +181,7 @@ expected_input_schemas = set([
'enginemetadata.json',
'labelupload.json',
'uidupload.json',
- 'uidmatchupload.json',
- 'search.json'
+ 'uidmatchupload.json'
])
mongo_schemas = set()
input_schemas = set()
diff --git a/raml/examples/input/acquisition-update.json b/raml/examples/input/acquisition-update.json
deleted file mode 100644
index bb0a63619ff34985c1316fc391622fb92c40cc64..0000000000000000000000000000000000000000
--- a/raml/examples/input/acquisition-update.json
+++ /dev/null
@@ -1,3 +0,0 @@
-{
- "label": "example-acquisition-new-label"
-}
diff --git a/raml/examples/input/acquisition.json b/raml/examples/input/acquisition.json
deleted file mode 100644
index 09d29718cefc38319f845f2d047e60945944cebc..0000000000000000000000000000000000000000
--- a/raml/examples/input/acquisition.json
+++ /dev/null
@@ -1,5 +0,0 @@
-{
- "label": "example-acquisition",
- "session": "57e45328466d8e000e33a85b",
- "public": false
-}
diff --git a/raml/examples/input/analysis-job.json b/raml/examples/input/analysis-job.json
deleted file mode 100644
index dcc0e303d77d95e2dbe75e1d0c413a3a5db17d26..0000000000000000000000000000000000000000
--- a/raml/examples/input/analysis-job.json
+++ /dev/null
@@ -1,16 +0,0 @@
-{
- "analysis": {
- "label": "Test Analysis 1"
- },
- "job" : {
- "gear": "dcm_convert",
- "inputs": {
- "dicom": {
- "type": "acquisition",
- "id": "57081d06b386a6dc79ca386b",
- "name" : "test_acquisition_dicom.zip"
- }
- },
- "tags": ["example"]
- }
-}
diff --git a/raml/examples/input/analysis.json b/raml/examples/input/analysis.json
index df5172f7f6dda6d1a27fe2e11bb8194cf2d33789..57a68f4fe6262f7acd3a9a1571f9f96cf4b4c2ac 100644
--- a/raml/examples/input/analysis.json
+++ b/raml/examples/input/analysis.json
@@ -43,5 +43,5 @@
"description": "This is an analysis description",
"job": "54759eb3c090d83494e2d804",
"label": "Analysis label",
- "user": "user_1"
-}
\ No newline at end of file
+ "user": "canakgun@flywheel.io"
+}
diff --git a/raml/examples/input/collection-update.json b/raml/examples/input/collection-update.json
deleted file mode 100644
index a5ba22e911c70a8648347309faec92282bb63b06..0000000000000000000000000000000000000000
--- a/raml/examples/input/collection-update.json
+++ /dev/null
@@ -1,9 +0,0 @@
-{
- "contents": {
- "operation": "add",
- "nodes": [{
- "level": "session",
- "_id": "57dc50b0931cefd8ac2a371e"
- }]
- }
-}
diff --git a/raml/examples/input/collection.json b/raml/examples/input/collection.json
deleted file mode 100644
index 3a3b621a34d20352d30ddd7ffbc8ce39c0b1d699..0000000000000000000000000000000000000000
--- a/raml/examples/input/collection.json
+++ /dev/null
@@ -1 +0,0 @@
-{"label":"control-group","description":"Control group collection"}
diff --git a/raml/examples/input/device.json b/raml/examples/input/device.json
deleted file mode 100644
index a3c4f9c39a9b357aea7cc9b07519a94275cd4540..0000000000000000000000000000000000000000
--- a/raml/examples/input/device.json
+++ /dev/null
@@ -1,9 +0,0 @@
-{
- "info": {
- "basic": "info"
- },
- "errors": [
- "An Error"
- ],
- "interval": 400
-}
diff --git a/raml/examples/input/group-new.json b/raml/examples/input/group-new.json
deleted file mode 100644
index 855d960bbb64d905f30f98bae0e9e66a55d6734a..0000000000000000000000000000000000000000
--- a/raml/examples/input/group-new.json
+++ /dev/null
@@ -1,4 +0,0 @@
-{
- "label": "Example Group",
- "_id": "example_group"
-}
diff --git a/raml/examples/input/group-update.json b/raml/examples/input/group-update.json
deleted file mode 100644
index ab1189cddb41b6dd83c1d11f3a109c4fc06095e0..0000000000000000000000000000000000000000
--- a/raml/examples/input/group-update.json
+++ /dev/null
@@ -1,3 +0,0 @@
-{
- "label":"New group label"
-}
diff --git a/raml/examples/input/note.json b/raml/examples/input/note.json
deleted file mode 100644
index a7083fe751b759d69868fd6d72f52953652354bd..0000000000000000000000000000000000000000
--- a/raml/examples/input/note.json
+++ /dev/null
@@ -1,3 +0,0 @@
-{
- "text":"Scitran core!"
-}
diff --git a/raml/examples/input/permission.json b/raml/examples/input/permission.json
deleted file mode 100644
index 7a6ecbf7a9fbb976cae976b172c74a1f82d5aae6..0000000000000000000000000000000000000000
--- a/raml/examples/input/permission.json
+++ /dev/null
@@ -1,4 +0,0 @@
-{
- "_id":"coltonlw@flywheel.io",
- "access":"admin"
-}
diff --git a/raml/examples/input/tag.json b/raml/examples/input/tag.json
deleted file mode 100644
index 64af535353a0a19503ee1be11adbcb4f58fb172a..0000000000000000000000000000000000000000
--- a/raml/examples/input/tag.json
+++ /dev/null
@@ -1,3 +0,0 @@
-{
- "value":"example-tag"
-}
diff --git a/raml/examples/input/user-new.json b/raml/examples/input/user-new.json
deleted file mode 100755
index c02daedf24d31afb0445c81b90405a068f76e47e..0000000000000000000000000000000000000000
--- a/raml/examples/input/user-new.json
+++ /dev/null
@@ -1,7 +0,0 @@
-{
- "_id": "jane.doe@gmail.com",
- "firstname": "Jane",
- "lastname": "Doe",
- "email": "jane.doe@gmail.com",
- "root": false
-}
diff --git a/raml/examples/input/user-update.json b/raml/examples/input/user-update.json
deleted file mode 100644
index 7b9da1c4eece71fa086e20513dd871c229b90f46..0000000000000000000000000000000000000000
--- a/raml/examples/input/user-update.json
+++ /dev/null
@@ -1,5 +0,0 @@
-{
- "firstname": "Jane",
- "lastname": "Smith",
- "email": "jane.smith@gmail.com"
-}
diff --git a/raml/examples/output/job-list.json b/raml/examples/output/job-list.json
index 5103e17118d9997d6427bd042b97371a977c6cf2..653ffd4d7e0739e62544824897ff39f9887a2311 100755
--- a/raml/examples/output/job-list.json
+++ b/raml/examples/output/job-list.json
@@ -1,13 +1,12 @@
[
{
- "inputs": [
- {
- "input": "dicom",
- "type": "acquisition",
- "id": "57d75ec38e4eb9699b3c245e",
- "name": "1_1_dicom.zip"
- }
- ],
+ "inputs": {
+ "dicom": {
+ "type": "acquisition",
+ "id": "57d75ec38e4eb9699b3c245e",
+ "name": "1_1_dicom.zip"
+ }
+ },
"attempt": 1,
"gear_id": "dcm-convert",
"tags": [
@@ -20,20 +19,19 @@
"modified": "2016-08-11T12:46:12.593000+00:00",
"created": "2016-08-11T12:46:12.593000+00:00",
"state": "pending",
- "_id": "57ac7394c700190017123fb8",
+ "id": "57ac7394c700190017123fb8",
"config":{
"speed":3
}
},
{
- "inputs": [
- {
- "input":"dicom",
+ "inputs": {
+ "dicom": {
"type": "acquisition",
"id": "57ac7394c700190017123fb7",
"name": "8403_4_1_t1_dicom.zip"
}
- ],
+ },
"attempt": 1,
"gear_id": "dcm_convert",
"tags": [
@@ -47,7 +45,7 @@
"modified": "2016-08-11T13:02:09.055000+00:00",
"created": "2016-08-11T13:02:09.055000+00:00",
"state": "pending",
- "_id": "57ac77515e325c0018cd17cf",
+ "id": "57ac77515e325c0018cd17cf",
"config":{
"speed":3
}
diff --git a/raml/examples/output/job-next.json b/raml/examples/output/job-next.json
deleted file mode 100755
index 42137ba411bf06119de50842697bdede15d3d274..0000000000000000000000000000000000000000
--- a/raml/examples/output/job-next.json
+++ /dev/null
@@ -1,44 +0,0 @@
-{
- "inputs": [{
- "input": "dicom",
- "type": "acquisition",
- "id": "57e45279a74e91000ed6898f",
- "name": "4784_1_1_localizer_dicom.zip"
- }],
- "attempt": 1,
- "gear_id": "dicom-mr-classifier",
- "tags": ["dicom-mr-classifier"],
- "destination": {
- "type": "acquisition",
- "id": "57e45279a74e91000ed6898f"
- },
- "request": {
- "inputs": [{
- "vu": "vu0:sha384:tXvdI2pspng-YH6lwa2UcLsww0yR6LfEKbLm89eIqEGicLRHW9d1V8bs7gXHTlZ3",
- "type": "http",
- "location": "/",
- "uri": "https://storage.googleapis.com/flywheel/gears/v1/scitran/dicom-mr-classifier/dicom-mr-classifier_latest_20160803T220847.856417Z.tar.gz"
- }, {
- "type": "scitran",
- "uri": "/acquisitions/57e45279a74e91000ed6898f/files/4784_1_1_localizer_dicom.zip",
- "location": "/flywheel/v0/input/dicom"
- }],
- "target": {
- "command": ["bash", "-c", "rm -rf output; mkdir -p output; ./run; echo \"Exit was $?\""],
- "env": {
- "PATH": "/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
- },
- "dir": "/flywheel/v0"
- },
- "outputs": [{
- "type": "scitran",
- "uri": "/engine?level=acquisition&id=57e45279a74e91000ed6898f&job=57e45279a74e91000ed68991",
- "location": "/flywheel/v0/output"
- }]
- },
- "modified": "2016-09-28T16:11:36.260000+00:00",
- "created": "2016-09-22T21:51:53.174000+00:00",
- "state": "running",
- "_id": "57e45279a74e91000ed68991",
- "config": null
-}
diff --git a/raml/schemas/definitions/acquisition.json b/raml/schemas/definitions/acquisition.json
index ec7a8e5750d30615f8f6a6a8d2f249d0d10f8247..181bfb6da1d0244689a44c8eb836cb456aa979a5 100644
--- a/raml/schemas/definitions/acquisition.json
+++ b/raml/schemas/definitions/acquisition.json
@@ -2,11 +2,10 @@
"$schema": "http://json-schema.org/draft-04/schema#",
"definitions":{
"acquisition-input":{
- "x-gen-name": "acquisition",
"type": "object",
"properties": {
"public": {"$ref":"container.json#/definitions/public"},
- "label": {"$ref":"container.json#/definitions/label"},
+ "label": {"$ref":"common.json#/definitions/label"},
"info": {"$ref":"container.json#/definitions/info"},
"session": {"$ref":"common.json#/definitions/objectid"},
"uid": {"$ref":"container.json#/definitions/uid"},
@@ -15,13 +14,32 @@
},
"additionalProperties":false
},
+ "acquisition-metadata-input": {
+ "type": "object",
+ "x-note": "Are all of these fields still used/valid? Can this be reconciled with enginemetadata.json#/definitions/uid-upload-input?",
+ "properties": {
+ "public": {"type": ["boolean", "null"]},
+ "label": {"type": ["string", "null"]},
+ "info": {"type": ["object", "null"]},
+ "metadata": {"type": ["object", "null"]},
+ "measurement": {"type": ["string", "null"]},
+ "instrument": {"type": ["string", "null"]},
+ "uid": {"type": ["string", "null"]},
+ "timestamp": {"$ref":"container.json#/definitions/timestamp"},
+ "timezone": {"type": ["string", "null"]},
+ "files": {
+ "type": ["array", "null"],
+ "items": {"$ref": "file.json#/definitions/file-input"}
+ }
+ },
+ "additionalProperties": false
+ },
"acquisition-output":{
- "x-gen-name": "acquisition",
"type":"object",
"properties": {
"_id": {"$ref":"common.json#/definitions/objectid"},
"public": {"$ref":"container.json#/definitions/public"},
- "label": {"$ref":"container.json#/definitions/label"},
+ "label": {"$ref":"common.json#/definitions/label"},
"info": {"$ref":"container.json#/definitions/info"},
"session": {"$ref":"common.json#/definitions/objectid"},
"uid": {"$ref":"container.json#/definitions/uid"},
diff --git a/raml/schemas/definitions/analysis.json b/raml/schemas/definitions/analysis.json
index 271104f37a65b9be1131c07f2c9803aaf7f33a00..ea48fb875103e40a1e13b21ada614d6d3ad6e680 100644
--- a/raml/schemas/definitions/analysis.json
+++ b/raml/schemas/definitions/analysis.json
@@ -9,17 +9,16 @@
"type": ["array", "null"],
"items": {"$ref":"file.json#/definitions/file"}
},
- "user": {"type": "string"},
"analysis-input":{
"type":"object",
"properties":{
"inputs": {"$ref":"#/definitions/inputs"},
"outputs": {"$ref":"#/definitions/outputs"},
"notes": {"$ref":"note.json#/definitions/notes-list-output"},
- "description": {"type":"string"},
+ "description": {"$ref":"common.json#/definitions/description"},
"job": {"$ref":"common.json#/definitions/objectid"},
"label": {"$ref":"common.json#/definitions/label"},
- "user": {"$ref":"#/definitions/user"}
+ "user": {"$ref":"common.json#/definitions/user-id"}
},
"additionalProperties": false
},
@@ -45,13 +44,27 @@
]
},
"notes": {"$ref":"note.json#/definitions/notes-list-output"},
- "description": {"type":"string"},
+ "description": {"$ref":"common.json#/definitions/description"},
"label": {"$ref":"common.json#/definitions/label"},
"user": {"$ref":"common.json#/definitions/user-id"},
"created": {"$ref":"created-modified.json#/definitions/created"},
"modified": {"$ref":"created-modified.json#/definitions/modified"}
},
"required":["_id", "files", "label", "user", "created", "modified"]
+ },
+ "analysis-job": {
+ "type": "object",
+ "properties":{
+ "analysis":{
+ "type":"object",
+ "allOf":[{"$ref":"#/definitions/analysis-input"}],
+ "required":["label"]
+ }
+ },
+ "job":{
+ "type":"object",
+ "allOf":[{"$ref":"job.json#/definitions/job-input"}]
+ }
}
}
}
diff --git a/raml/schemas/definitions/collection.json b/raml/schemas/definitions/collection.json
index 2ab513a5bff871af2b97ae2b92c591a0baaefea4..bf3542b76662a789180c3a3f0ca2d528495ff948 100644
--- a/raml/schemas/definitions/collection.json
+++ b/raml/schemas/definitions/collection.json
@@ -1,59 +1,52 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"definitions":{
- "curator":{"$ref":"../definitions/user.json#/definitions/_id"},
- "description": {"type": "string"},
"collection-input":{
"type": "object",
"properties": {
- "public": {"$ref": "../definitions/container.json#/definitions/public"},
- "label": {"$ref": "../definitions/container.json#/definitions/label"},
- "info": {"$ref": "../definitions/container.json#/definitions/info"},
- "description": {"$ref": "../definitions/project.json#/definitions/description"}
+ "public": {"$ref": "container.json#/definitions/public"},
+ "label": {"$ref": "common.json#/definitions/label"},
+ "info": {"$ref": "container.json#/definitions/info"},
+ "description": {"$ref": "common.json#/definitions/description"}
},
"additionalProperties": false
},
"collection-input-with-contents":{
"type": "object",
"properties": {
- "public": {"$ref": "../definitions/container.json#/definitions/public"},
- "label": {"$ref": "../definitions/container.json#/definitions/label"},
- "info": {"$ref": "../definitions/container.json#/definitions/info"},
- "description": {"$ref": "../definitions/project.json#/definitions/description"},
- "contents": { "type": "object" }
+ "public": {"$ref": "container.json#/definitions/public"},
+ "label": {"$ref": "common.json#/definitions/label"},
+ "info": {"$ref": "container.json#/definitions/info"},
+ "description": {"$ref": "common.json#/definitions/description"},
+ "contents": { "type": "object" }
},
"additionalProperties": false
},
"collection-output":{
"type": "object",
"properties": {
- "_id":{"$ref":"../definitions/objectid.json#"},
- "public": {"$ref": "../definitions/container.json#/definitions/public"},
- "label": {"$ref": "../definitions/container.json#/definitions/label"},
- "description": {"$ref": "../definitions/collection.json#/definitions/description"},
- "info": {"$ref": "../definitions/container.json#/definitions/info"},
- "info_exists": {"$ref": "../definitions/container.json#/definitions/info_exists"},
- "curator": {"$ref":"#/definitions/curator"},
- "created":{"$ref":"../definitions/created-modified.json#/definitions/created"},
- "modified":{"$ref":"../definitions/created-modified.json#/definitions/modified"},
+ "_id": {"$ref":"common.json#/definitions/objectid"},
+ "public": {"$ref": "container.json#/definitions/public"},
+ "label": {"$ref": "common.json#/definitions/label"},
+ "description": {"$ref": "common.json#/definitions/description"},
+ "info": {"$ref": "container.json#/definitions/info"},
+ "info_exists": {"$ref": "container.json#/definitions/info_exists"},
+ "curator": {"$ref": "common.json#/definitions/user-id"},
+ "created": {"$ref": "created-modified.json#/definitions/created"},
+ "modified": {"$ref": "created-modified.json#/definitions/modified"},
"permissions":{
"type":"array",
- "items":{"$ref":"../definitions/permission.json#/definitions/permission-output-default-required"}
+ "items":{"$ref":"permission.json#/definitions/permission-output-default-required"}
},
"files":{
"type":"array",
- "items":{
- "allOf":[{"$ref":"../definitions/file.json#/definitions/file-output"}]
- }
+ "items":{"$ref":"file.json#/definitions/file-output"}
},
- "notes":{"allOf":[{"$ref":"../definitions/note.json#/definitions/notes-list-output"}]},
- "tags":{"allOf":[{"$ref":"../definitions/tag.json#/definitions/tag-output-list"}]},
+ "notes": {"$ref":"note.json#/definitions/notes-list-output"},
+ "tags": {"$ref":"tag.json#/definitions/tag-output-list"},
"analyses":{
"type":"array",
- "items":{
- "type":"object",
- "allOf":[{"$ref":"../definitions/analysis.json#/definitions/analysis-output"}]
- }
+ "items":{"$ref":"analysis.json#/definitions/analysis-output"}
}
},
"additionalProperties":false
diff --git a/raml/schemas/definitions/common.json b/raml/schemas/definitions/common.json
index 01db699dcaae9515cc4e872edf550ee03571118e..129a6bbe0d1c7baebf0b4f9e43ceede1c2f22749 100644
--- a/raml/schemas/definitions/common.json
+++ b/raml/schemas/definitions/common.json
@@ -6,6 +6,9 @@
"minLength": 1,
"maxLength": 256
},
+ "description": {
+ "type": "string"
+ },
"objectid": {
"type": "string",
"pattern": "^[a-fA-F0-9]{24}$"
@@ -19,6 +22,34 @@
"user-id": {
"type": "string",
"format": "email"
- }
+ },
+ "timestamp": {
+ "type": ["string", "null"],
+ "format": "date-time"
+ },
+ "deleted-count": {
+ "type":"object",
+ "properties": {
+ "deleted": {
+ "type": "integer"
+ }
+ }
+ },
+ "modified-count": {
+ "type": "object",
+ "properties": {
+ "modified": {
+ "type": "integer"
+ }
+ }
+ },
+ "object-created": {
+ "type": "object",
+ "properties": {
+ "_id": {
+ "type": "string"
+ }
+ }
+ }
}
}
\ No newline at end of file
diff --git a/raml/schemas/definitions/device.json b/raml/schemas/definitions/device.json
index 5f4608c2bb93a7065ea4f840b553040c5400bef4..7753d2e7a13bc8f9f16f14be80ed71b9beec471a 100644
--- a/raml/schemas/definitions/device.json
+++ b/raml/schemas/definitions/device.json
@@ -8,11 +8,24 @@
"type": "string"
}
},
- "name": {"type": "string"},
"interval": {"type": "integer"},
- "id": {"type": "string"},
- "method": {"type": "string"},
- "last_seen": {"type": ["string", "null"], "format": "date-time"},
+ "status-value": {
+ "type": "string",
+ "enum": ["ok", "missing", "error", "unknown"]
+ },
+ "device": {
+ "type": "object",
+ "properties": {
+ "_id": {"type":"string"},
+ "method": {"type":"string"},
+ "name": {"type":"string"},
+ "errors": {"$ref":"#/definitions/errors"},
+ "info": {"$ref":"#/definitions/info"},
+ "interval": {"$ref":"#/definitions/interval"},
+ "last_seen": {"$ref":"common.json#/definitions/timestamp"}
+ },
+ "additionalProperties": false
+ },
"device-input":{
"type": "object",
"properties": {
@@ -21,6 +34,25 @@
"info": {"$ref":"#/definitions/info"}
},
"additionalProperties": false
+ },
+ "device-output": {
+ "type": "object",
+ "allOf": [{"$ref":"#/definitions/device"}],
+ "required": ["_id", "name", "method", "last_seen"]
+ },
+ "device-status": {
+ "type":"object",
+ "patternProperties": {
+ "^[0-9a-z.@_-]*$":{
+ "properties":{
+ "errors": {"$ref":"#/definitions/errors"},
+ "last_seen": {"$ref":"common.json#/definitions/timestamp"},
+ "status": {"$ref":"#/definitions/status-value"}
+ },
+ "additionalProperties":false,
+ "required": ["last_seen", "status"]
+ }
+ }
}
}
}
diff --git a/raml/schemas/definitions/download.json b/raml/schemas/definitions/download.json
new file mode 100644
index 0000000000000000000000000000000000000000..6fa32a24ddebc335f4d2baac6cf741ed683df56c
--- /dev/null
+++ b/raml/schemas/definitions/download.json
@@ -0,0 +1,70 @@
+{
+ "$schema": "http://json-schema.org/draft-04/schema#",
+ "definitions": {
+ "filter-definition": {
+ "type": "object",
+ "properties": {
+ "+": {"$ref": "#/definitions/filter-items"},
+ "plus": {"$ref": "#definitions/filterItems"},
+ "-": {"$ref": "#/definitions/filter-items"},
+ "minus": {"$ref": "#definitions/filterItems"}
+ },
+ "additionalProperties": false
+ },
+ "filter-items": { "type": "array",
+ "minItems": 1,
+ "items": {
+ "type": "string"
+ }
+ },
+ "download-node": {
+ "type": "object",
+ "properties": {
+ "level": {
+ "type": "string",
+ "enum": ["project", "session", "acquisition", "analysis"]
+ },
+ "_id": {
+ "type": "string",
+ "pattern": "^[0-9a-f]{24}$"
+ }
+ },
+ "required": ["level", "_id"],
+ "additionalProperties": false
+ },
+ "download-filter": {
+ "type": "object",
+ "properties": {
+ "tags": {"$ref": "#/definitions/filter-definition"},
+ "types": {"$ref": "#/definitions/filter-definition"}
+ }
+ },
+ "download-input": {
+ "title": "Download",
+ "type": "object",
+ "properties": {
+ "optional": { "type": "boolean" },
+ "nodes": {
+ "type": "array",
+ "minItems": 1,
+ "items": {"$ref": "#/definitions/download-node"}
+ },
+ "filters": {
+ "type": "array",
+ "minItems": 1,
+ "items": {"$ref": "#/definitions/download-filter"}
+ }
+ },
+ "required": ["optional", "nodes"],
+ "additionalProperties": false
+ },
+ "download-ticket": {
+ "type":"object",
+ "properties":{
+ "ticket":{"type":"string"}
+ },
+ "additionalProperties":false,
+ "required":["ticket"]
+ }
+ }
+}
diff --git a/raml/schemas/definitions/enginemetadata.json b/raml/schemas/definitions/enginemetadata.json
new file mode 100644
index 0000000000000000000000000000000000000000..be2c0036cd53bc7348fca11ce35cd5f526362c57
--- /dev/null
+++ b/raml/schemas/definitions/enginemetadata.json
@@ -0,0 +1,103 @@
+{
+ "$schema": "http://json-schema.org/draft-04/schema#",
+ "definitions": {
+ "upload-acquisition-metadata-input": {
+ "type": "object",
+ "properties": {
+ "public": {"type": ["boolean", "null"]},
+ "label": {"type": ["string", "null"]},
+ "info": {"type": ["object", "null"]},
+ "uid": {"type": ["string", "null"]},
+ "timestamp": {"$ref":"container.json#/definitions/timestamp"},
+ "timezone": {"type": ["string", "null"]},
+ "files": {
+ "type": ["array", "null"],
+ "items": {"$ref": "file.json#/definitions/file-input"}
+ }
+ },
+ "additionalProperties": false
+ },
+
+ "engine-upload-input": {
+ "type": "object",
+ "properties": {
+ "project": {"$ref": "project.json#/definitions/project-metadata-input"},
+ "session": {"$ref": "session.json#/definitions/session-metadata-input"},
+ "acquisition": {"$ref": "acquisition.json#/definitions/acquisition-metadata-input"}
+ },
+ "additionalProperties": false
+ },
+ "label-upload-input": {
+ "type": "object",
+ "properties": {
+ "group": {
+ "type": "object",
+ "allOf": [{"$ref":"group.json#/definitions/group-metadata-input"}],
+ "required": ["_id"]
+ },
+ "project": {
+ "type": "object",
+ "allOf": [{"$ref":"project.json#/definitions/project-metadata-input"}],
+ "required": ["label"]
+ },
+ "session": {
+ "type": "object",
+ "allOf": [{"$ref":"session.json#/definitions/session-metadata-input"}],
+ "required": ["label"]
+ },
+ "acquisition": {
+ "type": "object",
+ "allOf": [{"$ref":"#/definitions/upload-acquisition-metadata-input"}],
+ "required": ["label"]
+ }
+ },
+ "required": ["group", "project"],
+ "additionalProperties": false
+ },
+ "uid-upload-input": {
+ "type": "object",
+ "properties": {
+ "group": {
+ "type": "object",
+ "allOf": [{"$ref":"group.json#/definitions/group-metadata-input"}],
+ "required": ["_id"]
+ },
+ "project": {
+ "type": "object",
+ "allOf": [{"$ref":"project.json#/definitions/project-metadata-input"}],
+ "required": ["label"]
+ },
+ "session": {
+ "type": "object",
+ "allOf": [{"$ref":"session.json#/definitions/session-metadata-input"}],
+ "required": ["uid"]
+ },
+ "acquisition": {
+ "type": "object",
+ "allOf": [{"$ref":"#/definitions/upload-acquisition-metadata-input"}],
+ "required": ["uid"]
+ }
+ },
+ "required": ["acquisition", "group", "project", "session"],
+ "additionalProperties": false
+ },
+ "uid-match-upload-input": {
+ "type": "object",
+ "properties": {
+ "project": {"$ref": "project.json#/definitions/project-metadata-input"},
+ "session": {
+ "type": "object",
+ "allOf": [{"$ref":"session.json#/definitions/session-metadata-input"}],
+ "required": ["uid"]
+ },
+ "acquisition": {
+ "type": "object",
+ "allOf": [{"$ref":"#/definitions/upload-acquisition-metadata-input"}],
+ "required": ["uid"]
+ }
+ },
+ "required": ["acquisition", "session"],
+ "additionalProperties": false
+ }
+ }
+}
\ No newline at end of file
diff --git a/raml/schemas/definitions/file.json b/raml/schemas/definitions/file.json
index 9e3578b132d48b78db71dc2835181d3dc0c83032..a3be0aa7673a3abc562b51464f5efbd2fd9bc88a 100644
--- a/raml/schemas/definitions/file.json
+++ b/raml/schemas/definitions/file.json
@@ -52,16 +52,16 @@
]
},
"measurements": {"$ref":"#/definitions/measurements"},
- "tags": {"$ref":"#/definitions/tags"},
- "info": {"$ref":"#/definitions/info"},
- "origin":{"$ref":"#/definitions/origin"},
- "hash":{"$ref":"#/definitions/hash"},
- "created":{"$ref":"../definitions/created-modified.json#/definitions/created"},
- "modified":{"$ref":"../definitions/created-modified.json#/definitions/modified"},
- "size":{"$ref":"#/definitions/size"},
+ "tags": {"$ref":"#/definitions/tags"},
+ "info": {"$ref":"#/definitions/info"},
+ "origin": {"$ref":"#/definitions/origin"},
+ "hash": {"$ref":"#/definitions/hash"},
+ "created": {"$ref":"created-modified.json#/definitions/created"},
+ "modified": {"$ref":"created-modified.json#/definitions/modified"},
+ "size": {"$ref":"#/definitions/size"},
"info_exists": {"type": "boolean"},
- "input": {"type":"boolean"},
- "output": {"type":"boolean"}
+ "input": {"type":"boolean"},
+ "output": {"type":"boolean"}
},
"additionalProperties": false
},
@@ -73,8 +73,8 @@
"mimetype": {"$ref":"#/definitions/mimetype"},
"modality": {"$ref":"#/definitions/modality"},
"measurements": {"$ref":"#/definitions/measurements"},
- "tags": {"$ref":"#/definitions/tags"},
- "info": {"$ref":"#/definitions/info"}
+ "tags": {"$ref":"#/definitions/tags"},
+ "info": {"$ref":"#/definitions/info"}
},
"additionalProperties": false
},
diff --git a/raml/schemas/definitions/group.json b/raml/schemas/definitions/group.json
index a3d75631804a5364da821c15b666483cbc6b1ff9..e03a5e73c1dc7dfc982d18e50542168eb60a3796 100644
--- a/raml/schemas/definitions/group.json
+++ b/raml/schemas/definitions/group.json
@@ -1,7 +1,6 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"definitions":{
- "_id":{"$ref":"../definitions/string-id.json#"},
"label": {
"maxLength": 64,
"minLength": 1,
@@ -9,57 +8,50 @@
"title": "label",
"type": "string"
},
+ "group": {
+ "type": "object",
+ "properties": {
+ "_id":{"$ref":"common.json#/definitions/string-id"},
+ "label": {"$ref": "#/definitions/label"},
+ "permissions": {"$ref": "permission.json#/definitions/permission-output-list"},
+ "created": {"$ref":"created-modified.json#/definitions/created"},
+ "modified": {"$ref":"created-modified.json#/definitions/modified"}
+ },
+ "additionalProperties":false
+ },
"group-input":{
"type": "object",
"properties": {
- "_id":{"$ref":"#/definitions/_id"},
- "label": {"$ref": "../definitions/container.json#/definitions/label"}
+ "_id":{"$ref":"common.json#/definitions/string-id"},
+ "label": {"$ref": "#/definitions/label"}
},
"additionalProperties": false
},
- "group-output":{
+ "group-metadata-input": {
"type": "object",
"properties": {
- "_id":{"$ref":"#/definitions/_id"},
- "label": {"$ref": "../definitions/container.json#/definitions/label"},
- "permissions": {
- "type": "array",
- "items": {"$ref": "../definitions/permission.json#/definitions/permission-output-default-required"},
- "uniqueItems": true
- },
- "created": {"$ref":"../definitions/created-modified.json#/definitions/created"},
- "modified": {"$ref":"../definitions/created-modified.json#/definitions/modified"}
+ "_id":{"type":"string"}
},
- "additionalProperties":false,
+ "additionalProperties": false
+ },
+ "group-output":{
+ "type": "object",
+ "allOf": [{"$ref":"#/definitions/group"}],
"required": ["permissions", "created","modified","_id"]
},
"group-output-list":{
"type":"array",
- "items":{
- "allOf":[{"$ref":"#/definitions/group-output"}]
- }
+ "items":{"$ref":"#/definitions/group-output"}
},
"project-group-output":{
"type": "object",
- "properties": {
- "_id":{"$ref":"#/definitions/_id"},
- "label": {"$ref": "../definitions/container.json#/definitions/label"},
- "permissions": {
- "type": "array",
- "items": {"$ref": "../definitions/permission.json#/definitions/permission-output-default-required"},
- "uniqueItems": true
- },
- "created": {"$ref":"../definitions/created-modified.json#/definitions/created"},
- "modified": {"$ref":"../definitions/created-modified.json#/definitions/modified"}
- },
- "additionalProperties":false,
+ "allOf": [{"$ref":"#/definitions/group"}],
"required": ["_id"]
},
"project-group-output-list":{
"type":"array",
- "items":{
- "allOf":[{"$ref":"#/definitions/project-group-output"}]
- }
+ "items":{"$ref":"#/definitions/project-group-output"}
}
}
}
+
diff --git a/raml/schemas/definitions/info.json b/raml/schemas/definitions/info.json
new file mode 100644
index 0000000000000000000000000000000000000000..fc4d65558c4296fd7d685731fadb73f509e209d7
--- /dev/null
+++ b/raml/schemas/definitions/info.json
@@ -0,0 +1,33 @@
+{
+ "$schema": "http://json-schema.org/draft-04/schema#",
+ "definitions": {
+ "info-add-remove": {
+ "properties": {
+ "set": {"type": "object", "minProperties": 1},
+ "delete": {
+ "type": "array",
+ "uniqueItems": true,
+ "minItems": 1,
+ "items": {
+ "type": "string"
+ }
+ }
+ },
+ "additionalProperties": false
+ },
+ "info-replace": {
+ "properties": {
+ "replace": {"type": "object"}
+ },
+ "additionalProperties": false
+ },
+ "info-update-input": {
+ "description": "Helper endpoint for editing an object's info key",
+ "type": "object",
+ "oneOf": [
+ {"$ref":"#/definitions/info-add-remove"},
+ {"$ref":"#/definitions/info-replace"}
+ ]
+ }
+ }
+}
diff --git a/raml/schemas/definitions/job.json b/raml/schemas/definitions/job.json
index bd4742d01534e4feabc50915cecc1231dca58e59..e2a3acfce477c972a56da5d772a81f53c1d222b6 100644
--- a/raml/schemas/definitions/job.json
+++ b/raml/schemas/definitions/job.json
@@ -1,15 +1,17 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"definitions": {
- "_id": {"$ref":"../definitions/objectid.json#"},
+
"gear_id": {"type":"string"},
"previous_job_id": {"type":"string"},
+
"inputs-property-type":{"type":"string"},
"inputs-property-id":{"type":"string"},
"inputs-property-name":{"type":"string"},
+
"inputs-object": {
"type": "object",
- "additionalProperties": {
+ "properties": {
"type": "object",
"properties": {
"type": {"$ref":"#/definitions/inputs-property-type"},
@@ -117,6 +119,47 @@
"target":{"type":"object"},
"outputs":{"type":"array"}
}
+ },
+ "job": {
+ "type":"object",
+ "properties":{
+ "id":{"$ref":"common.json#/definitions/objectid"},
+ "origin":{"$ref":"#/definitions/origin"},
+ "gear_id":{"$ref":"#/definitions/gear_id"},
+ "previous_job_id":{"type":"string"},
+ "inputs":{"$ref":"#/definitions/inputs-object"},
+ "destination":{"$ref":"#/definitions/destination"},
+ "tags":{"$ref":"#/definitions/tags"},
+ "state":{"$ref":"#/definitions/state"},
+ "attempt":{"$ref":"#/definitions/attempt"},
+ "created":{"$ref":"created-modified.json#/definitions/created"},
+ "modified":{"$ref":"created-modified.json#/definitions/modified"},
+ "config":{"$ref":"#/definitions/config"},
+ "request":{"$ref":"#/definitions/request"},
+ "saved_files":{"$ref":"#/definitions/saved_files"},
+ "produced_metadata":{"$ref":"#/definitions/produced_metadata"}
+ },
+ "additionalProperties":false
+ },
+ "job-input": {
+ "type":"object",
+ "properties": {
+ "gear_id":{"$ref":"#/definitions/gear_id"},
+ "inputs":{"$ref":"#/definitions/inputs-object"},
+ "destination":{"$ref":"#/definitions/destination"},
+ "tags":{"$ref":"#/definitions/tags"},
+ "config":{"$ref":"#/definitions/config"}
+ },
+ "required": ["gear_id"],
+ "additionalProperties":false
+ },
+ "job-output": {
+ "type": "object",
+ "allOf": [{"$ref":"#/definitions/job"}],
+ "required": [
+ "id", "gear_id", "inputs", "config",
+ "destination", "tags", "state", "attempt"
+ ]
}
}
}
diff --git a/raml/schemas/definitions/note.json b/raml/schemas/definitions/note.json
index 2e033431678f98e225d9220738c41bdd3a4376ff..58298f1a373a93d4b07057d669a0476584dde544 100644
--- a/raml/schemas/definitions/note.json
+++ b/raml/schemas/definitions/note.json
@@ -16,11 +16,11 @@
"note-output":{
"type":"object",
"properties":{
- "_id":{"$ref":"../definitions/objectid.json"},
+ "_id":{"$ref":"common.json#/definitions/objectid"},
"text":{"$ref":"#/definitions/text"},
- "created":{"$ref":"../definitions/created-modified.json#/definitions/created"},
- "modified":{"$ref":"../definitions/created-modified.json#/definitions/modified"},
- "user":{"$ref":"../definitions/user.json#/definitions/_id"}
+ "created":{"$ref":"created-modified.json#/definitions/created"},
+ "modified":{"$ref":"created-modified.json#/definitions/modified"},
+ "user":{"$ref":"common.json#/definitions/user-id"}
},
"additionalProperties": false,
"required":["_id", "text", "created", "modified", "user"]
diff --git a/raml/schemas/definitions/packfile.json b/raml/schemas/definitions/packfile.json
new file mode 100644
index 0000000000000000000000000000000000000000..d40dcffd21742962cec0a838de584827db4d821d
--- /dev/null
+++ b/raml/schemas/definitions/packfile.json
@@ -0,0 +1,59 @@
+{
+ "$schema": "http://json-schema.org/draft-04/schema#",
+ "definitions": {
+ "packfile-project-input": {
+ "type": "object",
+ "properties": {
+ "_id": {"type": "string"}
+ },
+ "additionalProperties": false,
+ "required": ["_id"]
+ },
+ "packfile-session-input": {
+ "type": "object",
+ "properties": {
+ "label": {"type": "string"},
+ "subject": {"$ref": "subject.json#/definitions/subject-input"}
+ },
+ "additionalProperties": false,
+ "required": ["label"]
+ },
+ "packfile-acquisition-input": {
+ "type": "object",
+ "properties": {
+ "label": {"type": "string"},
+ "timestamp": {"type": ["string", "null"], "format": "date-time"},
+ "timezone": {"type": "string"}
+ },
+ "additionalProperties": false,
+ "required": ["label"]
+ },
+ "packfile-packfile-input": {
+ "type": "object",
+ "properties": {
+ "type": {"type": "string"}
+ },
+ "additionalProperties": false,
+ "required": ["type"]
+ },
+
+ "packfile-input": {
+ "title": "Packfile",
+ "type": "object",
+ "properties": {
+ "project": {"$ref":"#/definitions/packfile-project-input"},
+ "session": {"$ref":"#/definitions/packfile-session-input"},
+ "acquisition": {"$ref":"#/definitions/packfile-acquisition-input"},
+ "packfile": {"$ref":"#/definitions/packfile-packfile-input"}
+ },
+ "required": ["project", "session", "acquisition", "packfile"],
+ "additionalProperties": false
+ },
+ "packfile-start": {
+ "type":"object",
+ "properties":{
+ "token":{"$ref":"common.json#/definitions/objectid"}
+ }
+ }
+ }
+}
diff --git a/raml/schemas/definitions/permission.json b/raml/schemas/definitions/permission.json
index bd4e63db4787387abed78bcb816f69d69de59966..03a48fd55d930e2413008dcdcf9320c79f3cfc44 100644
--- a/raml/schemas/definitions/permission.json
+++ b/raml/schemas/definitions/permission.json
@@ -1,12 +1,11 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"definitions": {
- "_id": { "type": "string" },
"access": { "enum": ["ro", "rw", "admin"] },
"permission":{
"type":"object",
"properties":{
- "_id":{"$ref":"#/definitions/_id"},
+ "_id":{"$ref":"common.json#/definitions/user-id"},
"access":{"$ref":"#/definitions/access"}
},
"additionalProperties": false
@@ -14,6 +13,11 @@
"permission-output-default-required":{
"allOf":[{"$ref":"#/definitions/permission"}],
"required":["_id", "access"]
+ },
+ "permission-output-list": {
+ "type": "array",
+ "items": {"$ref": "#/definitions/permission-output-default-required"},
+ "uniqueItems": true
}
}
}
diff --git a/raml/schemas/definitions/project.json b/raml/schemas/definitions/project.json
index ee77eab1818c976dbda75b1a33dbe610d3d0e9c4..6cb7dc156b1481fe769d92fee2b66a42cbf8eccc 100644
--- a/raml/schemas/definitions/project.json
+++ b/raml/schemas/definitions/project.json
@@ -1,49 +1,55 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"definitions":{
- "description": {"type": "string"},
"project-input":{
"type": "object",
"properties": {
- "public": {"$ref": "../definitions/container.json#/definitions/public"},
- "label": {"$ref": "../definitions/container.json#/definitions/label"},
- "info": {"$ref": "../definitions/container.json#/definitions/info"},
- "description": {"$ref": "../definitions/project.json#/definitions/description"},
- "group":{"$ref":"../definitions/group.json#/definitions/_id"}
+ "public": {"$ref":"container.json#/definitions/public"},
+ "label": {"$ref":"common.json#/definitions/label"},
+ "info": {"$ref":"container.json#/definitions/info"},
+ "description": {"$ref":"common.json#/definitions/description"},
+ "group": {"$ref":"common.json#/definitions/string-id"}
+ },
+ "additionalProperties": false
+ },
+ "project-metadata-input": {
+ "type": "object",
+ "properties": {
+ "public": {"type": ["boolean", "null"]},
+ "label": {"type": ["string", "null"]},
+ "info": {"type": ["object", "null"]},
+ "files": {
+ "type": ["array", "null"],
+ "items": {"$ref": "file.json#/definitions/file-input"}
+ }
},
"additionalProperties": false
},
"project-output":{
"type": "object",
"properties": {
- "_id": {"$ref":"../definitions/objectid.json#"},
- "public": {"$ref": "../definitions/container.json#/definitions/public"},
- "label": {"$ref": "../definitions/container.json#/definitions/label"},
- "info": {"$ref": "../definitions/container.json#/definitions/info"},
- "info_exists": {"$ref": "../definitions/container.json#/definitions/info_exists"},
- "description": {"$ref": "../definitions/project.json#/definitions/description"},
- "group":{"$ref":"../definitions/group.json#/definitions/_id"},
- "created":{"$ref":"../definitions/created-modified.json#/definitions/created"},
- "modified":{"$ref":"../definitions/created-modified.json#/definitions/modified"},
- "template":{"type":"object"},
- "permissions":{
- "type":"array",
- "items":{"$ref":"../definitions/permission.json#/definitions/permission-output-default-required"}
- },
+ "_id": {"$ref":"common.json#/definitions/objectid"},
+ "public": {"$ref":"container.json#/definitions/public"},
+ "label": {"$ref":"common.json#/definitions/label"},
+ "info": {"$ref":"container.json#/definitions/info"},
+ "info_exists": {"$ref":"container.json#/definitions/info_exists"},
+ "description": {"$ref":"common.json#/definitions/description"},
+ "group": {"$ref":"common.json#/definitions/string-id"},
+ "created": {"$ref":"created-modified.json#/definitions/created"},
+ "modified": {"$ref":"created-modified.json#/definitions/modified"},
+ "template": {"type":"object"},
+ "permissions": {"$ref":"permission.json#/definitions/permission-output-list"},
"files":{
"type":"array",
"items":{
- "allOf":[{"$ref":"../definitions/file.json#/definitions/file-output"}]
+ "allOf":[{"$ref":"file.json#/definitions/file-output"}]
}
},
- "notes":{"allOf":[{"$ref":"../definitions/note.json#/definitions/notes-list-output"}]},
- "tags":{"allOf":[{"$ref":"../definitions/tag.json#/definitions/tag-output-list"}]},
+ "notes": {"$ref":"note.json#/definitions/notes-list-output"},
+ "tags": {"$ref":"tag.json#/definitions/tag-output-list"},
"analyses":{
"type":"array",
- "items":{
- "type":"object",
- "allOf":[{"$ref":"../definitions/analysis.json#/definitions/analysis-output"}]
- }
+ "items":{"$ref":"analysis.json#/definitions/analysis-output"}
}
},
"additionalProperties": false
diff --git a/raml/schemas/definitions/report.json b/raml/schemas/definitions/report.json
new file mode 100644
index 0000000000000000000000000000000000000000..ca8af0d424afd3e183c6ce87fd7befe58ceff2a8
--- /dev/null
+++ b/raml/schemas/definitions/report.json
@@ -0,0 +1,113 @@
+{
+ "$schema": "http://json-schema.org/draft-04/schema#",
+ "type":"object",
+ "definitions":{
+ "gender_count":{
+ "type":"object",
+ "properties":{
+ "Male": {"type":"integer"},
+ "Unknown or Not Reported":{"type":"integer"},
+ "Female":{"type":"integer"}
+ },
+ "additionalProperties":false,
+ "required":["Male", "Female", "Unknown or Not Reported"]
+ },
+ "ethnicity_grid":{
+ "type":"object",
+ "properties":{
+ "Not Hispanic or Latino":{
+ "allOf":[{"$ref":"#/definitions/gender_count"}]
+ },
+ "Hispanic or Latino":{
+ "allOf":[{"$ref":"#/definitions/gender_count"}]
+ },
+ "Unknown or Not Reported":{
+ "allOf":[{"$ref":"#/definitions/gender_count"}]
+ },
+ "Total":{"type":"integer"}
+ }
+ },
+ "demographics_grid": {
+ "type":"object",
+ "properties":{
+ "Black or African American":{
+ "allOf":[{"$ref":"#/definitions/ethnicity_grid"}]
+ },
+ "Unknown or Not Reported":{
+ "allOf":[{"$ref":"#/definitions/ethnicity_grid"}]
+ },
+ "American Indian or Alaska Native":{
+ "allOf":[{"$ref":"#/definitions/ethnicity_grid"}]
+ },
+ "Asian":{
+ "allOf":[{"$ref":"#/definitions/ethnicity_grid"}]
+ },
+ "White":{
+ "allOf":[{"$ref":"#/definitions/ethnicity_grid"}]
+ },
+ "Total":{
+ "allOf":[{"$ref":"#/definitions/ethnicity_grid"}]
+ },
+ "Native Hawaiian or Other Pacific Islander":{
+ "allOf":[{"$ref":"#/definitions/ethnicity_grid"}]
+ },
+ "More Than One Race":{
+ "allOf":[{"$ref":"#/definitions/ethnicity_grid"}]
+ },
+ "male_count": {"type":"integer"},
+ "group_label": {"$ref":"common.json#/definitions/label"},
+ "over_18_count": {"type":"integer"},
+ "under_18_count": {"type":"integer"},
+ "female_count": {"type":"integer"},
+ "subjects_count": {"type":"integer"},
+ "other_count": {"type":"integer"},
+ "name": {"$ref":"common.json#/definitions/label"},
+ "session_count": {"type":"integer"},
+ "admins": {
+ "type":"array",
+ "items":{
+ "type":"string"
+ }
+ },
+ "demographics_total": {"type":"integer"}
+ }
+ },
+ "group-report": {
+ "type":"object",
+ "properties":{
+ "project_count":{"type":"integer"},
+ "label":{
+ "oneOf":[
+ {"$ref":"group.json#/definitions/label"},
+ {"type":"null"}
+ ]
+ },
+ "session_count":{"type":"integer"}
+ },
+ "additionalProperties":false,
+ "required":["project_count", "label", "session_count"]
+ },
+
+ "report-project": {
+ "type":"object",
+ "properties":{
+ "projects":{
+ "type":"array",
+ "items":{"$ref":"#/definitions/demographics_grid"}
+ }
+ }
+ },
+ "report-site": {
+ "type":"object",
+ "properties":{
+ "group_count":{"type":"integer"},
+ "groups":{
+ "type":"array",
+ "items":{"$ref":"#/definitions/group-report"}
+ }
+ },
+ "additionalProperties":false,
+ "required":["group_count", "groups"]
+ }
+ }
+}
diff --git a/raml/schemas/definitions/session.json b/raml/schemas/definitions/session.json
index 920b7f07479126cfcb70a699db78b610520c8734..9c1c9775b2dd385282df95b6341973d605926f09 100644
--- a/raml/schemas/definitions/session.json
+++ b/raml/schemas/definitions/session.json
@@ -8,63 +8,98 @@
"session-input":{
"type": "object",
"properties": {
- "operator": {"$ref": "#/definitions/operator"},
- "public": {"$ref": "../definitions/container.json#/definitions/public"},
- "label": {"$ref": "../definitions/container.json#/definitions/label"},
- "info": {"$ref": "../definitions/container.json#/definitions/info"},
+ "operator": {"$ref":"#/definitions/operator"},
+ "public": {"$ref":"container.json#/definitions/public"},
+ "label": {"$ref":"common.json#/definitions/label"},
+ "info": {"$ref":"container.json#/definitions/info"},
"project": {"$ref":"#/definitions/project"},
- "uid": {"$ref":"../definitions/container.json#/definitions/uid"},
- "timestamp": {"$ref":"../definitions/container.json#/definitions/timestamp"},
- "timezone": {"$ref":"../definitions/container.json#/definitions/timezone"},
- "subject": {
- "allOf":[{"$ref": "../definitions/subject.json#/definitions/subject-input"}]
- }
+ "uid": {"$ref":"container.json#/definitions/uid"},
+ "timestamp": {"$ref":"container.json#/definitions/timestamp"},
+ "timezone": {"$ref":"container.json#/definitions/timezone"},
+ "subject": {"$ref": "subject.json#/definitions/subject-input"}
},
"additionalProperties": false
},
+ "session-metadata-input": {
+ "type": "object",
+ "properties": {
+ "public": {"type": ["boolean", "null"]},
+ "label": {"type": ["string", "null"]},
+ "info": {"type": ["object", "null"]},
+ "operator": {"type": ["string", "null"]},
+ "uid": {"type": ["string", "null"]},
+ "timestamp": {"type": ["string", "null"], "format": "date-time"},
+ "timezone": {"type": ["string", "null"]},
+ "subject": {"$ref": "subject.json#/definitions/subject-input"},
+ "files": {
+ "type": ["array", "null"],
+ "items": {"$ref": "file.json#/definitions/file-input"}
+ }
+ },
+ "additionalProperties": false
+ },
"session-output":{
"type": "object",
"properties": {
- "_id": {"$ref":"../definitions/objectid.json#"},
- "public": {"$ref": "../definitions/container.json#/definitions/public"},
- "label": {"$ref": "../definitions/container.json#/definitions/label"},
- "info": {"$ref": "../definitions/container.json#/definitions/info"},
- "info_exists": {"$ref": "../definitions/container.json#/definitions/info_exists"},
- "operator": {"$ref": "#/definitions/operator"},
+ "_id": {"$ref":"common.json#/definitions/objectid"},
+ "public": {"$ref":"container.json#/definitions/public"},
+ "label": {"$ref":"common.json#/definitions/label"},
+ "info": {"$ref":"container.json#/definitions/info"},
+ "info_exists": {"$ref":"container.json#/definitions/info_exists"},
+ "operator": {"$ref":"#/definitions/operator"},
"project": {"$ref":"#/definitions/project"},
- "uid": {"$ref":"../definitions/container.json#/definitions/uid"},
- "timestamp": {"$ref":"../definitions/container.json#/definitions/timestamp"},
- "timezone": {"$ref":"../definitions/container.json#/definitions/timezone"},
- "subject": {
- "type":"object",
- "allOf":[{"$ref": "../definitions/subject.json#/definitions/subject-output-default-required"}]
- },
- "created":{"$ref":"../definitions/created-modified.json#/definitions/created"},
- "modified":{"$ref":"../definitions/created-modified.json#/definitions/modified"},
- "permissions":{
- "type":"array",
- "items":{"$ref":"../definitions/permission.json#/definitions/permission-output-default-required"}
- },
- "group":{"$ref":"../definitions/group.json#/definitions/_id"},
- "project_has_template":{"$ref":"#/definitions/project_has_template"},
- "satisfies_template":{"$ref":"#/definitions/satisfies_template"},
+ "uid": {"$ref":"container.json#/definitions/uid"},
+ "timestamp": {"$ref":"container.json#/definitions/timestamp"},
+ "timezone": {"$ref":"container.json#/definitions/timezone"},
+ "subject": {"$ref":"subject.json#/definitions/subject-output-default-required"},
+ "created": {"$ref":"created-modified.json#/definitions/created"},
+ "modified": {"$ref":"created-modified.json#/definitions/modified"},
+ "permissions": {"$ref":"permission.json#/definitions/permission-output-list"},
+ "group": {"$ref":"common.json#/definitions/string-id"},
+ "project_has_template": {"$ref":"#/definitions/project_has_template"},
+ "satisfies_template": {"$ref":"#/definitions/satisfies_template"},
"files":{
"type":"array",
- "items":{
- "allOf":[{"$ref":"../definitions/file.json#/definitions/file-output"}]
- }
+ "items":{"$ref":"file.json#/definitions/file-output"}
},
- "notes":{"allOf":[{"$ref":"../definitions/note.json#/definitions/notes-list-output"}]},
- "tags":{"allOf":[{"$ref":"../definitions/tag.json#/definitions/tag-output-list"}]},
+ "notes": {"$ref":"note.json#/definitions/notes-list-output"},
+ "tags": {"$ref":"tag.json#/definitions/tag-output-list"},
"analyses":{
+ "type":"array",
+ "items":{"$ref":"analysis.json#/definitions/analysis-output"}
+ }
+ },
+ "additionalProperties": false
+ },
+ "session-jobs-output": {
+ "type": "object",
+ "properties":{
+ "jobs":{
+ "type":"array",
+ "items":{"$ref": "job.json#/definitions/job-output"}
+ },
+ "containers":{
+ "patternProperties": {
+ "^[a-fA-F0-9]{24}$":{
+ "type": "object"
+ }
+ }
+ }
+ },
+ "additionalProperties":false
+ },
+ "session-template-recalc-output": {
+ "type": "object",
+ "properties":{
+ "sessions_changed":{
"type":"array",
"items":{
- "type":"object",
- "allOf":[{"$ref":"../definitions/analysis.json#/definitions/analysis-output"}]
+ "allOf":[{"$ref":"common.json#/definitions/objectid"}]
}
}
},
- "additionalProperties": false
+ "additionalProperties":false,
+ "required":["sessions_changed"]
}
}
}
diff --git a/raml/schemas/definitions/subject.json b/raml/schemas/definitions/subject.json
index 4b0a0aa3b50fc3b14748520e804b12f8f4490a65..1e5e00c58156fb8f1255356cc87e17c154b12520 100644
--- a/raml/schemas/definitions/subject.json
+++ b/raml/schemas/definitions/subject.json
@@ -1,7 +1,7 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"definitions":{
- "_id": {"$ref":"../definitions/objectid.json#"},
+ "_id": {"$ref":"common.json#/definitions/objectid"},
"firstname": { "type": "string", "maxLength": 64 },
"lastname": { "type": "string", "maxLength": 64 },
"age": { "type": ["integer", "null"] },
@@ -29,9 +29,7 @@
"info": {"$ref":"#/definitions/info"},
"files":{
"type":"array",
- "items":{
- "allOf":[{"$ref":"../definitions/file.json#/definitions/file-input"}]
- }
+ "items":{"$ref":"file.json#/definitions/file-input"}
}
},
"additionalProperties": false
@@ -54,9 +52,7 @@
"info_exists": {"$ref": "../definitions/container.json#/definitions/info_exists"},
"files":{
"type":"array",
- "items":{
- "allOf":[{"$ref":"../definitions/file.json#/definitions/file-output"}]
- }
+ "items":{"$ref":"file.json#/definitions/file-output"}
}
},
"additionalProperties": false
diff --git a/raml/schemas/definitions/user.json b/raml/schemas/definitions/user.json
index 4478bad02680ea97f3669885193b8ab911988a88..71a68f5f11ed78faccf7d76e92ed0aeea93d20fd 100644
--- a/raml/schemas/definitions/user.json
+++ b/raml/schemas/definitions/user.json
@@ -1,11 +1,6 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"definitions": {
- "_id": {
- "format": "email",
- "title": "ID",
- "type": "string"
- },
"firstname": {
"maxLength": 64,
"minLength": 1,
@@ -42,7 +37,7 @@
"type":"object",
"properties":{
"key": {"type": "string"},
- "created": {"$ref":"../definitions/created-modified.json#/definitions/created"},
+ "created": {"$ref":"created-modified.json#/definitions/created"},
"last_used": {}
},
"additionalProperties":false
@@ -50,7 +45,7 @@
"user-input":{
"type":"object",
"properties":{
- "_id":{"$ref":"#/definitions/_id"},
+ "_id":{"$ref":"common.json#/definitions/user-id"},
"firstname":{"$ref":"#/definitions/firstname"},
"lastname":{"$ref":"#/definitions/lastname"},
"email":{"$ref":"#/definitions/email"},
@@ -68,7 +63,7 @@
"user-output":{
"type":"object",
"properties":{
- "_id":{"$ref":"#/definitions/_id"},
+ "_id":{"$ref":"common.json#/definitions/user-id"},
"firstname":{"$ref":"#/definitions/firstname"},
"lastname":{"$ref":"#/definitions/lastname"},
"email":{"$ref":"#/definitions/email"},
@@ -80,10 +75,35 @@
"wechat":{"$ref":"#/definitions/wechat"},
"firstlogin":{"$ref":"#/definitions/firstlogin"},
"lastlogin":{"$ref":"#/definitions/lastlogin"},
- "created":{"$ref":"../definitions/created-modified.json#/definitions/created"},
- "modified":{"$ref":"../definitions/created-modified.json#/definitions/modified"}
+ "created":{"$ref":"created-modified.json#/definitions/created"},
+ "modified":{"$ref":"created-modified.json#/definitions/modified"}
},
"additionalProperties":false
+ },
+ "user-output-api-key": {
+ "type":"object",
+ "properties":{
+ "_id":{"$ref":"common.json#/definitions/user-id"},
+ "api_key":{"$ref":"#/definitions/api_key"},
+ "firstname":{"$ref":"#/definitions/firstname"},
+ "lastname":{"$ref":"#/definitions/lastname"},
+ "email":{"$ref":"#/definitions/email"},
+ "avatar":{"$ref":"#/definitions/avatar"},
+ "avatars":{"$ref":"#/definitions/avatars"},
+ "root":{"$ref":"#/definitions/root"},
+ "disabled":{"$ref":"#/definitions/disabled"},
+ "preferences":{"$ref":"#/definitions/preferences"},
+ "wechat":{"$ref":"#/definitions/wechat"},
+ "firstlogin":{"$ref":"#/definitions/firstlogin"},
+ "lastlogin":{"$ref":"#/definitions/lastlogin"},
+ "created":{"$ref":"created-modified.json#/definitions/created"},
+ "modified":{"$ref":"created-modified.json#/definitions/modified"}
+ },
+ "additionalProperties":false,
+ "required":[
+ "_id", "firstname", "lastname",
+ "root", "email", "created", "modified"
+ ]
}
}
}
diff --git a/raml/schemas/definitions/version.json b/raml/schemas/definitions/version.json
new file mode 100644
index 0000000000000000000000000000000000000000..b819ec7ed466fab5fbe079a98e7827d1fcb09b4a
--- /dev/null
+++ b/raml/schemas/definitions/version.json
@@ -0,0 +1,20 @@
+{
+ "$schema": "http://json-schema.org/draft-04/schema#",
+ "definitions": {
+ "version-output": {
+ "type": "object",
+ "properties": {
+ "_id": {
+ "type": "string"
+ },
+ "database": {
+ "type": "integer"
+ }
+ },
+ "required": [
+ "_id",
+ "database"
+ ]
+ }
+ }
+}
diff --git a/raml/schemas/input/acquisition-update.json b/raml/schemas/input/acquisition-update.json
index 0475b21448bb18fb5f20b90fc15c718d468ce3dc..df6a087fdeec84ebed16982dcbe77552b8e044c1 100644
--- a/raml/schemas/input/acquisition-update.json
+++ b/raml/schemas/input/acquisition-update.json
@@ -2,5 +2,8 @@
"$schema": "http://json-schema.org/draft-04/schema#",
"title": "Acquisition",
"type": "object",
- "allOf": [{"$ref": "../definitions/acquisition.json#/definitions/acquisition-input"}]
+ "allOf": [{"$ref": "../definitions/acquisition.json#/definitions/acquisition-input"}],
+ "example": {
+ "label": "example-acquisition-new-label"
+ }
}
diff --git a/raml/schemas/input/acquisition.json b/raml/schemas/input/acquisition.json
index 572c9606373c744be6d3628a0e3ee498397690db..eeb6f83acca045313156792d4834cc8a4395134a 100644
--- a/raml/schemas/input/acquisition.json
+++ b/raml/schemas/input/acquisition.json
@@ -3,5 +3,10 @@
"title": "Acquisition",
"type": "object",
"allOf": [{"$ref": "../definitions/acquisition.json#/definitions/acquisition-input"}],
- "required": ["label", "session"]
+ "required": ["label", "session"],
+ "example": {
+ "label": "example-acquisition",
+ "session": "57e45328466d8e000e33a85b",
+ "public": false
+ }
}
diff --git a/raml/schemas/input/analysis-job.json b/raml/schemas/input/analysis-job.json
index 8de987c371c824da5da976cabcee8c7f3a80599f..ff780505924e50d0eb6165f0f14a16868ecd41a8 100644
--- a/raml/schemas/input/analysis-job.json
+++ b/raml/schemas/input/analysis-job.json
@@ -1,14 +1,21 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "object",
- "properties":{
- "analysis":{
- "type":"object",
- "allOf":[{"$ref":"../definitions/analysis.json#/definitions/analysis-input"}],
- "required":["label"]
+ "allOf": [{"$ref":"../definitions/analysis.json#/definitions/analysis-job"}],
+ "example": {
+ "analysis": {
+ "label": "Test Analysis 1"
},
- "job":{
- "type":"object"
+ "job" : {
+ "gear_id": "dcm_convert",
+ "inputs": {
+ "dicom": {
+ "type": "acquisition",
+ "id": "57081d06b386a6dc79ca386b",
+ "name" : "test_acquisition_dicom.zip"
+ }
+ },
+ "tags": ["example"]
}
}
}
diff --git a/raml/schemas/input/collection-update.json b/raml/schemas/input/collection-update.json
index 0548ea23a41968440cef93e352ee50657346397d..8f295d9b10b54e98b2ff6986a4d1fcddd4de7728 100644
--- a/raml/schemas/input/collection-update.json
+++ b/raml/schemas/input/collection-update.json
@@ -4,6 +4,12 @@
"type": "object",
"allOf": [{"$ref": "../definitions/collection.json#/definitions/collection-input-with-contents"}],
"example": {
- "$ref": "../../examples/input/collection-update.json"
- }
+ "contents": {
+ "operation": "add",
+ "nodes": [{
+ "level": "session",
+ "_id": "57dc50b0931cefd8ac2a371e"
+ }]
+ }
+ }
}
diff --git a/raml/schemas/input/collection.json b/raml/schemas/input/collection.json
index bd52b275a9a5657840f13ae6204b73f54537f1c8..05a952ab5ce0b99a3417ea945ffd60600b7338c7 100644
--- a/raml/schemas/input/collection.json
+++ b/raml/schemas/input/collection.json
@@ -5,6 +5,7 @@
"allOf": [{"$ref": "../definitions/collection.json#/definitions/collection-input"}],
"required": ["label"],
"example": {
- "$ref": "../../examples/input/collection.json"
+ "label":"control-group",
+ "description":"Control group collection"
}
}
diff --git a/raml/schemas/input/device.json b/raml/schemas/input/device.json
index ea54fede5bc43678d2e1d7c8dc30c72aeb39db13..2e9a433c5ee2bfb1527a0ea443e5800b29f8844e 100644
--- a/raml/schemas/input/device.json
+++ b/raml/schemas/input/device.json
@@ -2,6 +2,12 @@
"$schema": "http://json-schema.org/draft-04/schema#",
"allOf":[{"$ref":"../definitions/device.json#/definitions/device-input"}],
"example": {
- "$ref": "../../examples/input/device.json"
- }
+ "info": {
+ "basic": "info"
+ },
+ "errors": [
+ "An Error"
+ ],
+ "interval": 400
+ }
}
diff --git a/raml/schemas/input/download.json b/raml/schemas/input/download.json
index fc5141878216d414d87c1998cd59b916479cfd69..ce1541d04c1a0019c644334b7bf95bbafb346c87 100644
--- a/raml/schemas/input/download.json
+++ b/raml/schemas/input/download.json
@@ -1,64 +1,8 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "definitions": {
- "filterDefinition": {
- "type": "object",
- "properties": {
- "+": {"$ref": "#/definitions/filterItems"},
- "plus": {"$ref": "#definitions/filterItems"},
- "-": {"$ref": "#/definitions/filterItems"},
- "minus": {"$ref": "#definitions/filterItems"}
- },
- "additionalProperties": false
- },
- "filterItems": {
- "type": "array",
- "minItems": 1,
- "items": {
- "type": "string"
- }
- }
- },
- "title": "Download",
- "type": "object",
+ "$ref": "../definitions/download.json#/definitions/download-input",
+
"example": {
"$ref": "../../examples/create_download_incomplete_and_dicom.json"
- },
- "properties": {
- "optional": {
- "type": "boolean"
- },
- "nodes": {
- "type": "array",
- "minItems": 1,
- "items": {
- "type": "object",
- "properties": {
- "level": {
- "type": "string",
- "enum": ["project", "session", "acquisition", "analysis"]
- },
- "_id": {
- "type": "string",
- "pattern": "^[0-9a-f]{24}$"
- }
- },
- "required": ["level", "_id"],
- "additionalProperties": false
- }
- },
- "filters": {
- "type": "array",
- "minItems": 1,
- "items": {
- "type": "object",
- "properties": {
- "tags": {"$ref": "#/definitions/filterDefinition"},
- "types": {"$ref": "#/definitions/filterDefinition"}
- }
- }
- }
- },
- "required": ["optional", "nodes"],
- "additionalProperties": false
+ }
}
diff --git a/raml/schemas/input/enginemetadata.json b/raml/schemas/input/enginemetadata.json
index 7a50879d393281acd926f8b0228b5202e57c19d2..928435559e0ff3613597411fa255f9f491d8dc66 100644
--- a/raml/schemas/input/enginemetadata.json
+++ b/raml/schemas/input/enginemetadata.json
@@ -1,58 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "title": "EngineMetadata",
- "type": "object",
- "properties": {
- "project": {
- "type": "object",
- "properties": {
- "public": {"type": ["boolean", "null"]},
- "label": {"type": ["string", "null"]},
- "info": {"type": ["object", "null"]},
- "files": {
- "type": ["array", "null"],
- "items": {"$ref": "file.json"}
- }
- },
- "additionalProperties": false
- },
- "session": {
- "type": "object",
- "properties": {
- "public": {"type": ["boolean", "null"]},
- "label": {"type": ["string", "null"]},
- "info": {"type": ["object", "null"]},
- "operator": {"type": ["string", "null"]},
- "uid": {"type": ["string", "null"]},
- "timestamp": {"type": ["string", "null"], "format": "date-time"},
- "timezone": {"type": ["string", "null"]},
- "subject": {"$ref": "subject.json"},
- "files": {
- "type": ["array", "null"],
- "items": {"$ref": "file.json"}
- }
- },
- "additionalProperties": false
- },
- "acquisition": {
- "type": "object",
- "properties": {
- "public": {"type": ["boolean", "null"]},
- "label": {"type": ["string", "null"]},
- "info": {"type": ["object", "null"]},
- "metadata": {"type": ["object", "null"]},
- "measurement": {"type": ["string", "null"]},
- "instrument": {"type": ["string", "null"]},
- "uid": {"type": ["string", "null"]},
- "timestamp": {"type": ["string", "null"], "format": "date-time"},
- "timezone": {"type": ["string", "null"]},
- "files": {
- "type": ["array", "null"],
- "items": {"$ref": "file.json"}
- }
- },
- "additionalProperties": false
- }
- },
- "additionalProperties": false
+ "$ref": "../definitions/enginemetadata.json#/definitions/engine-upload-input"
}
diff --git a/raml/schemas/input/group-new.json b/raml/schemas/input/group-new.json
index a91eeab7b0c1993a37370397e76cb476e1e162d8..09a7e2be6abed5193e5cd2019b7a522c15e65793 100644
--- a/raml/schemas/input/group-new.json
+++ b/raml/schemas/input/group-new.json
@@ -5,6 +5,7 @@
],
"required": ["_id"],
"example": {
- "$ref": "../../examples/input/group-new.json"
- }
+ "label": "Example Group",
+ "_id": "example_group"
+ }
}
diff --git a/raml/schemas/input/group-update.json b/raml/schemas/input/group-update.json
index ca78a1358dc28f14e2b28ae2766faaf73e1503e4..7a1ee81e54d37fe8a096c9d8925f7150a2c058b0 100644
--- a/raml/schemas/input/group-update.json
+++ b/raml/schemas/input/group-update.json
@@ -2,6 +2,6 @@
"$schema": "http://json-schema.org/draft-04/schema#",
"allOf":[{"$ref":"../definitions/group.json#/definitions/group-input"}],
"example": {
- "$ref": "../../examples/input/group-update.json"
- }
+ "label":"New group label"
+ }
}
diff --git a/raml/schemas/input/info_update.json b/raml/schemas/input/info_update.json
index 353780b0d9bc20c45245163c8ed2031038eed05b..d483672a2654e1df3d717236da7726d2e3f92b1c 100644
--- a/raml/schemas/input/info_update.json
+++ b/raml/schemas/input/info_update.json
@@ -1,25 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "description": "Helper endpoint for editing an object's info key",
- "type": "object",
- "oneOf": [
- {
- "properties": {
- "set": {"type": "object", "minProperties": 1},
- "delete": {
- "type": "array",
- "uniqueItems": true,
- "minItems": 1,
- "items": {
- "type": "string"
- }
- }
- }, "additionalProperties": false
- },
- {
- "properties": {
- "replace": {"type": "object"}
- }, "additionalProperties": false
- }
- ]
+ "$ref": "../definitions/info.json#/definitions/info-update-input"
}
diff --git a/raml/schemas/input/labelupload.json b/raml/schemas/input/labelupload.json
index da6bde93d5fedf337a26e8fc8b780e1bf977cd47..a981784ef25a863e87ea176f19e5cc8d3e7d5850 100644
--- a/raml/schemas/input/labelupload.json
+++ b/raml/schemas/input/labelupload.json
@@ -1,67 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "title": "EngineMetadata",
- "type": "object",
- "properties": {
- "group": {
- "type": "object",
- "properties": {
- "_id": {"type": "string"}
- },
- "additionalProperties": false,
- "required": ["_id"]
- },
- "project": {
- "type": "object",
- "properties": {
- "public": {"type": ["boolean", "null"]},
- "label": {"type": "string"},
- "info": {"type": ["object", "null"]},
- "files": {
- "type": ["array", "null"],
- "items": {"$ref": "file.json"}
- }
- },
- "additionalProperties": false,
- "required": ["label"]
- },
- "session": {
- "type": "object",
- "properties": {
- "public": {"type": ["boolean", "null"]},
- "label": {"type": "string"},
- "info": {"type": ["object", "null"]},
- "operator": {"type": ["string", "null"]},
- "uid": {"type": ["string", "null"]},
- "timestamp": {"type": ["string", "null"], "format": "date-time"},
- "timezone": {"type": ["string", "null"]},
- "subject": {"$ref": "subject.json"},
- "files": {
- "type": ["array", "null"],
- "items": {"$ref": "file.json"}
- }
- },
- "additionalProperties": false,
- "required": ["label"]
- },
- "acquisition": {
- "type": "object",
- "properties": {
- "public": {"type": ["boolean", "null"]},
- "label": {"type": "string"},
- "info": {"type": ["object", "null"]},
- "uid": {"type": ["string", "null"]},
- "timestamp": {"type": ["string", "null"], "format": "date-time"},
- "timezone": {"type": ["string", "null"]},
- "files": {
- "type": ["array", "null"],
- "items": {"$ref": "file.json"}
- }
- },
- "additionalProperties": false,
- "required": ["label"]
- }
- },
- "required": ["group", "project"],
- "additionalProperties": false
+ "$ref": "../definitions/enginemetadata.json#/definitions/label-upload-input"
}
diff --git a/raml/schemas/input/note.json b/raml/schemas/input/note.json
index abca18417c4c481368b6f5c07c9fc2a8cedfe7b1..372193eedc09367a5d8efbbecd4cde1187351c12 100644
--- a/raml/schemas/input/note.json
+++ b/raml/schemas/input/note.json
@@ -4,6 +4,6 @@
"allOf":[{"$ref":"../definitions/note.json#/definitions/note-input"}],
"required": ["text"],
"example": {
- "$ref": "../../examples/input/note.json"
- }
+ "text":"Scitran core!"
+ }
}
diff --git a/raml/schemas/input/packfile.json b/raml/schemas/input/packfile.json
index c82d2999d2f9905fa97399bbabc3c7797e20fd22..7bc27ec0ad4ade00315e282882da9dae203a9b98 100644
--- a/raml/schemas/input/packfile.json
+++ b/raml/schemas/input/packfile.json
@@ -1,44 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "title": "Packfile",
- "type": "object",
- "properties": {
- "project": {
- "type": "object",
- "properties": {
- "_id": {"type": "string"}
- },
- "additionalProperties": false,
- "required": ["_id"]
- },
- "session": {
- "type": "object",
- "properties": {
- "label": {"type": "string"},
- "subject": {"$ref": "subject.json"}
- },
- "additionalProperties": false,
- "required": ["label"]
- },
- "acquisition": {
- "type": "object",
- "properties": {
- "label": {"type": "string"},
- "timestamp": {"type": ["string", "null"], "format": "date-time"},
- "timezone": {"type": "string"}
- },
- "additionalProperties": false,
- "required": ["label"]
- },
- "packfile": {
- "type": "object",
- "properties": {
- "type": {"type": "string"}
- },
- "additionalProperties": false,
- "required": ["type"]
- }
- },
- "required": ["project", "session", "acquisition", "packfile"],
- "additionalProperties": false
+ "$ref": "../definitions/packfile.json#/definitions/packfile-input"
}
diff --git a/raml/schemas/input/permission.json b/raml/schemas/input/permission.json
index 0a609c4498d68ac149c7e7393884b40c87b3df30..b773ec8176832941cf3ba40e0cebf03bf5eb770b 100644
--- a/raml/schemas/input/permission.json
+++ b/raml/schemas/input/permission.json
@@ -5,6 +5,7 @@
"key_fields": ["_id"],
"required": ["_id", "access"],
"example": {
- "$ref": "../../examples/input/permission.json"
- }
+ "_id":"coltonlw@flywheel.io",
+ "access":"admin"
+ }
}
diff --git a/raml/schemas/input/search.json b/raml/schemas/input/search.json
deleted file mode 100644
index 9cb5be0dcd90830f9fb72c6839d4266404d0f845..0000000000000000000000000000000000000000
--- a/raml/schemas/input/search.json
+++ /dev/null
@@ -1,21 +0,0 @@
-{
- "$schema": "http://json-schema.org/draft-04/schema#",
- "type": "object",
- "properties": {
- "node_type": {
- "type": "string",
- "enum": ["project", "session", "acquisition", "file", "note"]
- },
- "rel_type": {
- "type": "string",
- "enum": ["target", "parent", "child"]
- },
- "query": {"type": "object"},
- "relations": {
- "type": "array",
- "items": {"$ref": "#"}
- }
- },
- "additionalProperties": false,
- "required": ["node_type", "rel_type", "query", "relations"]
-}
diff --git a/raml/schemas/input/tag.json b/raml/schemas/input/tag.json
index b540ddbc0ef934632bcacb8a1cee8c790171b2f1..d47d9bab7ecd4f7037585d2221a57baafaa43143 100644
--- a/raml/schemas/input/tag.json
+++ b/raml/schemas/input/tag.json
@@ -2,6 +2,6 @@
"$schema": "http://json-schema.org/draft-04/schema#",
"allOf":[{"$ref":"../definitions/tag.json#/definitions/tag"}],
"example": {
- "$ref": "../../examples/input/tag.json"
- }
+ "value":"example-tag"
+ }
}
diff --git a/raml/schemas/input/uidmatchupload.json b/raml/schemas/input/uidmatchupload.json
index ee4fe89f429eef554d4c5868a8d49d239ba71029..bfbe7b5640fdec422d821fa53bbbc9354441c617 100644
--- a/raml/schemas/input/uidmatchupload.json
+++ b/raml/schemas/input/uidmatchupload.json
@@ -1,58 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "title": "EngineMetadata",
- "type": "object",
- "properties": {
- "project": {
- "type": "object",
- "properties": {
- "public": {"type": ["boolean", "null"]},
- "label": {"type": "string"},
- "info": {"type": ["object", "null"]},
- "files": {
- "type": ["array", "null"],
- "items": {"$ref": "file.json"}
- }
- },
- "additionalProperties": false
- },
- "session": {
- "type": "object",
- "properties": {
- "public": {"type": ["boolean", "null"]},
- "label": {"type": ["string", "null"]},
- "info": {"type": ["object", "null"]},
- "operator": {"type": ["string", "null"]},
- "uid": {"type": "string"},
- "timestamp": {"type": ["string", "null"], "format": "date-time"},
- "timezone": {"type": ["string", "null"]},
- "subject": {"$ref": "subject.json"},
- "files": {
- "type": ["array", "null"],
- "items": {"$ref": "file.json"}
- }
- },
- "additionalProperties": false,
- "required": ["uid"]
- },
- "acquisition": {
- "type": "object",
- "properties": {
- "public": {"type": ["boolean", "null"]},
- "label": {"type": ["string", "null"]},
- "info": {"type": ["object", "null"]},
- "uid": {"type": "string"},
- "timestamp": {"type": ["string", "null"], "format": "date-time"},
- "timezone": {"type": ["string", "null"]},
- "files": {
- "type": ["array", "null"],
- "items": {"$ref": "file.json"}
- }
- },
- "additionalProperties": false,
- "required": ["uid"]
- }
- },
- "required": ["acquisition", "session"],
- "additionalProperties": false
+ "$ref": "../definitions/enginemetadata.json#/definitions/uid-match-upload-input"
}
diff --git a/raml/schemas/input/uidupload.json b/raml/schemas/input/uidupload.json
index deb84256fdd9a8af64dd4b5ac51e4134ecb6d383..319cbddf40939c3f8e82acaed711333a7bb4eacd 100644
--- a/raml/schemas/input/uidupload.json
+++ b/raml/schemas/input/uidupload.json
@@ -1,67 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "title": "EngineMetadata",
- "type": "object",
- "properties": {
- "group": {
- "type": "object",
- "properties": {
- "_id": {"type": "string"}
- },
- "additionalProperties": false,
- "required": ["_id"]
- },
- "project": {
- "type": "object",
- "properties": {
- "public": {"type": ["boolean", "null"]},
- "label": {"type": "string"},
- "info": {"type": ["object", "null"]},
- "files": {
- "type": ["array", "null"],
- "items": {"$ref": "file.json"}
- }
- },
- "additionalProperties": false,
- "required": ["label"]
- },
- "session": {
- "type": "object",
- "properties": {
- "public": {"type": ["boolean", "null"]},
- "label": {"type": ["string", "null"]},
- "info": {"type": ["object", "null"]},
- "operator": {"type": ["string", "null"]},
- "uid": {"type": "string"},
- "timestamp": {"type": ["string", "null"], "format": "date-time"},
- "timezone": {"type": ["string", "null"]},
- "subject": {"$ref": "subject.json"},
- "files": {
- "type": ["array", "null"],
- "items": {"$ref": "file.json"}
- }
- },
- "additionalProperties": false,
- "required": ["uid"]
- },
- "acquisition": {
- "type": "object",
- "properties": {
- "public": {"type": ["boolean", "null"]},
- "label": {"type": ["string", "null"]},
- "info": {"type": ["object", "null"]},
- "uid": {"type": "string"},
- "timestamp": {"type": ["string", "null"], "format": "date-time"},
- "timezone": {"type": ["string", "null"]},
- "files": {
- "type": ["array", "null"],
- "items": {"$ref": "file.json"}
- }
- },
- "additionalProperties": false,
- "required": ["uid"]
- }
- },
- "required": ["acquisition", "group", "project", "session"],
- "additionalProperties": false
+ "$ref": "../definitions/enginemetadata.json#/definitions/uid-upload-input"
}
diff --git a/raml/schemas/input/user-new.json b/raml/schemas/input/user-new.json
index 7e8d50cf76ba9cb62548fb066b9f7b3a714ae306..0043b064ab8c528bc2e9b703911d293dbd37ba20 100644
--- a/raml/schemas/input/user-new.json
+++ b/raml/schemas/input/user-new.json
@@ -4,6 +4,10 @@
"allOf":[{"$ref":"../definitions/user.json#/definitions/user-input"}],
"required":["_id", "firstname", "lastname"],
"example": {
- "$ref": "../../examples/input/user-new.json"
- }
+ "_id": "jane.doe@gmail.com",
+ "firstname": "Jane",
+ "lastname": "Doe",
+ "email": "jane.doe@gmail.com",
+ "root": false
+ }
}
diff --git a/raml/schemas/input/user-update.json b/raml/schemas/input/user-update.json
index 1a9ca4a648024848af80eae499a51fa9eba2d1b8..2f401f23e3c3a9909aab5c9b730175c1e0857d6a 100644
--- a/raml/schemas/input/user-update.json
+++ b/raml/schemas/input/user-update.json
@@ -6,6 +6,8 @@
{"$ref":"../definitions/user.json#/definitions/user-input"}
],
"example": {
- "$ref": "../../examples/input/user-update.json"
- }
+ "firstname": "Jane",
+ "lastname": "Smith",
+ "email": "jane.smith@gmail.com"
+ }
}
diff --git a/raml/schemas/output/collection-curators-list.json b/raml/schemas/output/collection-curators-list.json
index 0775505e85cde5e5aea77a2d352e26397ebe6ce5..302206059378ba8014afe877512773c2aa6ea1b4 100644
--- a/raml/schemas/output/collection-curators-list.json
+++ b/raml/schemas/output/collection-curators-list.json
@@ -5,7 +5,7 @@
"properties":{
"firstname":{"$ref":"../definitions/user.json#/definitions/firstname"},
"lastname":{"$ref":"../definitions/user.json#/definitions/lastname"},
- "_id":{"$ref":"../definitions/user.json#/definitions/_id"}
+ "_id":{"$ref":"../definitions/common.json#/definitions/user-id"}
}
}
}
diff --git a/raml/schemas/output/device-list.json b/raml/schemas/output/device-list.json
index c65170b95356b528e9fc654f5de0496b110f237e..d137fddad79ab51c2a232b83f135c955b70e5004 100644
--- a/raml/schemas/output/device-list.json
+++ b/raml/schemas/output/device-list.json
@@ -1,20 +1,5 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "array",
- "items": {
- "type":"object",
- "properties":{
- "_id":{"$ref":"../definitions/device.json#/definitions/id"},
- "method":{"$ref":"../definitions/device.json#/definitions/method"},
- "name":{"$ref":"../definitions/device.json#/definitions/name"},
- "errors":{"$ref":"../definitions/device.json#/definitions/errors"},
- "info":{"$ref":"../definitions/device.json#/definitions/info"},
- "interval":{"$ref":"../definitions/device.json#/definitions/interval"},
- "last_seen":{"$ref":"../definitions/device.json#/definitions/last_seen"}
- },
- "additionalProperties":false,
- "required":[
- "_id", "name", "method", "last_seen"
- ]
- }
+ "items": { "$ref":"../definitions/device.json#/definitions/device-output" }
}
diff --git a/raml/schemas/output/device-status.json b/raml/schemas/output/device-status.json
index 6b1999ca6759cbe0eb5cbe316c90d36ec32d25ee..d4c85724b389d0b667b9127ed753576e05c63a23 100644
--- a/raml/schemas/output/device-status.json
+++ b/raml/schemas/output/device-status.json
@@ -1,17 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "type":"object",
- "patternProperties": {
- "^[0-9a-z.@_-]*$":{
- "properties":{
- "errors":{"$ref":"../definitions/device.json#/definitions/errors"},
- "last_seen":{"$ref":"../definitions/device.json#/definitions/last_seen"},
- "status": { "enum": ["ok", "missing", "error", "unknown"] }
- },
- "additionalProperties":false,
- "required":[
- "last_seen", "status"
- ]
- }
- }
+ "allOf": [{"$ref":"../definitions/device.json#/definitions/device-status"}]
}
diff --git a/raml/schemas/output/device.json b/raml/schemas/output/device.json
index 8f270db7b70fb8eb8e7d9a9983969be662567aa0..cb79c43788aea1e60fe84d4bdae59777355bdc96 100644
--- a/raml/schemas/output/device.json
+++ b/raml/schemas/output/device.json
@@ -1,17 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "type":"object",
- "properties":{
- "_id":{"$ref":"../definitions/device.json#/definitions/id"},
- "method":{"$ref":"../definitions/device.json#/definitions/method"},
- "name":{"$ref":"../definitions/device.json#/definitions/name"},
- "errors":{"$ref":"../definitions/device.json#/definitions/errors"},
- "info":{"$ref":"../definitions/device.json#/definitions/info"},
- "interval":{"$ref":"../definitions/device.json#/definitions/interval"},
- "last_seen":{"$ref":"../definitions/device.json#/definitions/last_seen"}
- },
- "additionalProperties":false,
- "required":[
- "_id", "name", "method", "last_seen"
- ]
+ "allOf":[{"$ref":"../definitions/device.json#/definitions/device-output"}]
}
diff --git a/raml/schemas/output/file-download.json b/raml/schemas/output/file-download.json
index 3c7592e29aa1be072cf0232f6c10eea9837360f2..8cd7a7f05ead309888996a2473cfe17cd257ea0d 100644
--- a/raml/schemas/output/file-download.json
+++ b/raml/schemas/output/file-download.json
@@ -1,9 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "type":"object",
- "properties":{
- "ticket":{"type":"string"}
- },
- "additionalProperties":false,
- "required":["ticket"]
+ "$ref": "../definitions/download.json#/definitions/download-ticket"
}
diff --git a/raml/schemas/output/gears-list.json b/raml/schemas/output/gears-list.json
deleted file mode 100644
index e10eaf826b3f7020b1e9cd051e70c2ae8b67f635..0000000000000000000000000000000000000000
--- a/raml/schemas/output/gears-list.json
+++ /dev/null
@@ -1,15 +0,0 @@
-{
- "$schema": "http://json-schema.org/draft-04/schema#",
- "type": "array",
- "items": {
- "type": "object",
- "properties": {
- "name": {
- "type": "string"
- }
- },
- "required": [
- "name"
- ]
- }
-}
diff --git a/raml/schemas/output/group-delete.json b/raml/schemas/output/group-delete.json
index 300c991e4f1547ed8e41856281ae7cb85a9349c5..12e4a66089b694f7d02d9caa54cc14a5d2af1f55 100644
--- a/raml/schemas/output/group-delete.json
+++ b/raml/schemas/output/group-delete.json
@@ -1,9 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "type":"object",
- "properties":{
- "deleted":{
- "type":"number"
- }
- }
+ "$ref": "../definitions/common.json#/definitions/deleted-count"
}
diff --git a/raml/schemas/output/job-list.json b/raml/schemas/output/job-list.json
index 7dcaf6d09153ea4ed47cd03cd36c7fba9149bc36..a7d1ac7b68d0ec31469ff0b2abbacfe1ee0b1715 100644
--- a/raml/schemas/output/job-list.json
+++ b/raml/schemas/output/job-list.json
@@ -1,29 +1,5 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "array",
- "items": {
- "type":"object",
- "properties":{
- "_id":{"$ref":"../definitions/job.json#/definitions/_id"},
- "origin":{"$ref":"../definitions/job.json#/definitions/origin"},
- "gear_id":{"$ref":"../definitions/job.json#/definitions/gear_id"},
- "previous_job_id":{"$ref":"../definitions/job.json#/definitions/previous_job_id"},
- "inputs":{"$ref":"../definitions/job.json#/definitions/inputs-array"},
- "destination":{"$ref":"../definitions/job.json#/definitions/destination"},
- "tags":{"$ref":"../definitions/job.json#/definitions/tags"},
- "state":{"$ref":"../definitions/job.json#/definitions/state"},
- "attempt":{"$ref":"../definitions/job.json#/definitions/attempt"},
- "created":{"$ref":"../definitions/created-modified.json#/definitions/created"},
- "modified":{"$ref":"../definitions/created-modified.json#/definitions/modified"},
- "config":{"$ref":"../definitions/job.json#/definitions/config"},
- "request":{"$ref":"../definitions/job.json#/definitions/request"},
- "saved_files":{"$ref":"../definitions/job.json#/definitions/saved_files"},
- "produced_metadata":{"$ref":"../definitions/job.json#/definitions/produced_metadata"}
- },
- "additionalProperties":false,
- "required":[
- "_id", "gear_id", "inputs",
- "destination", "tags", "state", "attempt"
- ]
- }
+ "items": {"$ref": "../definitions/job.json#/definitions/job-output"}
}
diff --git a/raml/schemas/output/job-new.json b/raml/schemas/output/job-new.json
index f4cb59603fb44101bb4397b9c7e7489b9218b9ac..f153b501ed410139871f63d07f51f6c5c3fd4ee6 100644
--- a/raml/schemas/output/job-new.json
+++ b/raml/schemas/output/job-new.json
@@ -1,12 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "type": "object",
- "properties": {
- "_id": {
- "type": "string"
- }
- },
- "required": [
- "_id"
- ]
+ "$ref": "../definitions/common.json#/definitions/object-created"
}
diff --git a/raml/schemas/output/job-next.json b/raml/schemas/output/job-next.json
deleted file mode 100644
index 98cc5684e051efd997bf7b9cb7f0e67a234d8116..0000000000000000000000000000000000000000
--- a/raml/schemas/output/job-next.json
+++ /dev/null
@@ -1,26 +0,0 @@
-{
- "$schema": "http://json-schema.org/draft-04/schema#",
- "type":"object",
- "properties":{
- "_id":{"$ref":"../definitions/job.json#/definitions/_id"},
- "origin":{"$ref":"../definitions/job.json#/definitions/origin"},
- "gear_id":{"$ref":"../definitions/job.json#/definitions/gear_id"},
- "previous_job_id":{"$ref":"../definitions/job.json#/definitions/previous_job_id"},
- "inputs":{"$ref":"../definitions/job.json#/definitions/inputs-array"},
- "destination":{"$ref":"../definitions/job.json#/definitions/destination"},
- "tags":{"$ref":"../definitions/job.json#/definitions/tags"},
- "state":{"$ref":"../definitions/job.json#/definitions/state"},
- "attempt":{"$ref":"../definitions/job.json#/definitions/attempt"},
- "created":{"$ref":"../definitions/created-modified.json#/definitions/created"},
- "modified":{"$ref":"../definitions/created-modified.json#/definitions/modified"},
- "config":{"$ref":"../definitions/job.json#/definitions/config"},
- "request":{"$ref":"../definitions/job.json#/definitions/request"},
- "saved_files":{"$ref":"../definitions/job.json#/definitions/saved_files"},
- "produced_metadata":{"$ref":"../definitions/job.json#/definitions/produced_metadata"}
- },
- "additionalProperties":false,
- "required":[
- "_id", "gear_id", "inputs", "config",
- "destination", "tags", "state", "attempt"
- ]
-}
diff --git a/raml/schemas/output/job.json b/raml/schemas/output/job.json
index 46b3ca9fe999c2a5a6768a4a2fc05806e7ae4c9c..1b3149f4ee5896a40bbb61102666c830fd08ae3c 100644
--- a/raml/schemas/output/job.json
+++ b/raml/schemas/output/job.json
@@ -1,26 +1,5 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"type":"object",
- "properties":{
- "id":{"$ref":"../definitions/job.json#/definitions/_id"},
- "origin":{"$ref":"../definitions/job.json#/definitions/origin"},
- "gear_id":{"$ref":"../definitions/job.json#/definitions/gear_id"},
- "previous_job_id":{"$ref":"../definitions/job.json#/definitions/previous_job_id"},
- "inputs":{"$ref":"../definitions/job.json#/definitions/inputs-object"},
- "destination":{"$ref":"../definitions/job.json#/definitions/destination"},
- "tags":{"$ref":"../definitions/job.json#/definitions/tags"},
- "state":{"$ref":"../definitions/job.json#/definitions/state"},
- "attempt":{"$ref":"../definitions/job.json#/definitions/attempt"},
- "created":{"$ref":"../definitions/created-modified.json#/definitions/created"},
- "modified":{"$ref":"../definitions/created-modified.json#/definitions/modified"},
- "config":{"$ref":"../definitions/job.json#/definitions/config"},
- "request":{"$ref":"../definitions/job.json#/definitions/request"},
- "saved_files":{"$ref":"../definitions/job.json#/definitions/saved_files"},
- "produced_metadata":{"$ref":"../definitions/job.json#/definitions/produced_metadata"}
- },
- "additionalProperties":false,
- "required":[
- "id", "gear_id", "inputs", "config",
- "destination", "tags", "state", "attempt"
- ]
+ "allOf":[{"$ref":"../definitions/job.json#/definitions/job-output"}]
}
diff --git a/raml/schemas/output/packfile-start.json b/raml/schemas/output/packfile-start.json
index 41133098cae62c55ff710cf172709cc1d870b268..addf037e72f8b2e18dc129fa142134c892b52753 100644
--- a/raml/schemas/output/packfile-start.json
+++ b/raml/schemas/output/packfile-start.json
@@ -1,7 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "type":"object",
- "properties":{
- "token":{"$ref":"../definitions/objectid.json#"}
- }
+ "$ref": "../definitions/packfile.json#/definitions/packfile-start"
}
diff --git a/raml/schemas/output/report-project.json b/raml/schemas/output/report-project.json
index 96e493cdfd7a7e6270c41e978ed47057cd3536a2..9ead3363d7140f10c94325aa8e8065b3dab250d1 100644
--- a/raml/schemas/output/report-project.json
+++ b/raml/schemas/output/report-project.json
@@ -1,86 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "type":"object",
- "definitions":{
- "gender_count":{
- "type":"object",
- "properties":{
- "Male": {"type":"integer"},
- "Unknown or Not Reported":{"type":"integer"},
- "Female":{"type":"integer"}
- },
- "additionalProperties":false,
- "required":["Male", "Female", "Unknown or Not Reported"]
- },
- "ethnicity_grid":{
- "type":"object",
- "properties":{
- "Not Hispanic or Latino":{
- "allOf":[{"$ref":"#/definitions/gender_count"}]
- },
- "Hispanic or Latino":{
- "allOf":[{"$ref":"#/definitions/gender_count"}]
- },
- "Unknown or Not Reported":{
- "allOf":[{"$ref":"#/definitions/gender_count"}]
- },
- "Total":{"type":"integer"}
- }
- }
- },
- "properties":{
- "projects":{
- "type":"array",
- "items":{
- "type":"object",
- "properties":{
- "demographics_grid":{
- "type":"object",
- "properties":{
- "Black or African American":{
- "allOf":[{"$ref":"#/definitions/ethnicity_grid"}]
- },
- "Unknown or Not Reported":{
- "allOf":[{"$ref":"#/definitions/ethnicity_grid"}]
- },
- "American Indian or Alaska Native":{
- "allOf":[{"$ref":"#/definitions/ethnicity_grid"}]
- },
- "Asian":{
- "allOf":[{"$ref":"#/definitions/ethnicity_grid"}]
- },
- "White":{
- "allOf":[{"$ref":"#/definitions/ethnicity_grid"}]
- },
- "Total":{
- "allOf":[{"$ref":"#/definitions/ethnicity_grid"}]
- },
- "Native Hawaiian or Other Pacific Islander":{
- "allOf":[{"$ref":"#/definitions/ethnicity_grid"}]
- },
- "More Than One Race":{
- "allOf":[{"$ref":"#/definitions/ethnicity_grid"}]
- },
- "male_count": {"type":"integer"},
- "group_label": {"$ref":"../definitions/container.json#/definitions/label"},
- "over_18_count": {"type":"integer"},
- "under_18_count": {"type":"integer"},
- "female_count": {"type":"integer"},
- "subjects_count": {"type":"integer"},
- "other_count": {"type":"integer"},
- "name": {"$ref":"../definitions/container.json#/definitions/label"},
- "session_count": {"type":"integer"},
- "admins": {
- "type":"array",
- "items":{
- "type":"string"
- }
- },
- "demographics_total": {"type":"integer"}
- }
- }
- }
- }
- }
- }
+ "$ref": "../definitions/report.json#/definitions/report-project"
}
diff --git a/raml/schemas/output/report-site.json b/raml/schemas/output/report-site.json
index a764b8e2c092d1f9ddde907cae886e390fd08aa1..da9f8518a668a73ae85177d172a1b085997ca433 100644
--- a/raml/schemas/output/report-site.json
+++ b/raml/schemas/output/report-site.json
@@ -1,27 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "type":"object",
- "properties":{
- "group_count":{"type":"integer"},
- "groups":{
- "type":"array",
- "items":{
- "type":"object",
- "properties":{
- "project_count":{"type":"integer"},
- "label":{
- "oneOf":[
- {"$ref":"../definitions/group.json#/definitions/label"},
- {"type":"null"}
- ]
- },
- "session_count":{"type":"integer"}
- },
- "additionalProperties":false,
- "required":["project_count", "label", "session_count"]
- }
- }
- },
- "additionalProperties":false,
- "required":["group_count", "groups"]
+ "$ref": "../definitions/report.json#/definitions/report-site"
}
diff --git a/raml/schemas/output/session-jobs.json b/raml/schemas/output/session-jobs.json
index e0a35caa3155f78603d4f03fc4f52951fdeab530..2de34142b3cd2a9fb2f2399031deab2558465c66 100644
--- a/raml/schemas/output/session-jobs.json
+++ b/raml/schemas/output/session-jobs.json
@@ -1,41 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "type": "object",
- "properties":{
- "jobs":{
- "type":"array",
- "items":{
- "type":"object",
- "properties":{
- "id":{"$ref":"../definitions/job.json#/definitions/_id"},
- "origin":{"$ref":"../definitions/job.json#/definitions/origin"},
- "gear_id":{"$ref":"../definitions/job.json#/definitions/gear_id"},
- "inputs":{"$ref":"../definitions/job.json#/definitions/inputs-object"},
- "destination":{"$ref":"../definitions/job.json#/definitions/destination"},
- "tags":{"$ref":"../definitions/job.json#/definitions/tags"},
- "state":{"$ref":"../definitions/job.json#/definitions/state"},
- "attempt":{"$ref":"../definitions/job.json#/definitions/attempt"},
- "created":{"$ref":"../definitions/created-modified.json#/definitions/created"},
- "modified":{"$ref":"../definitions/created-modified.json#/definitions/modified"},
- "config":{"$ref":"../definitions/job.json#/definitions/config"},
- "request":{"$ref":"../definitions/job.json#/definitions/request"},
- "saved_files":{"$ref":"../definitions/job.json#/definitions/saved_files"},
- "produced_metadata":{"$ref":"../definitions/job.json#/definitions/produced_metadata"}
- },
- "additionalProperties":false,
- "required":[
- "id", "gear_id", "inputs", "config",
- "destination", "tags", "state", "attempt"
- ]
- }
- },
- "containers":{
- "patternProperties": {
- "^[a-fA-F0-9]{24}$":{
- "type": "object"
- }
- }
- }
- },
- "additionalProperties":false
+ "$ref": "../definitions/session.json#/definitions/session-jobs-output"
}
diff --git a/raml/schemas/output/session-template-recalc.json b/raml/schemas/output/session-template-recalc.json
index b490c631fe33e6d5d8fa024401d3f09cbe9912a9..874ef13fc38b7ff5e38fd0f95a46a2c73d0cace7 100644
--- a/raml/schemas/output/session-template-recalc.json
+++ b/raml/schemas/output/session-template-recalc.json
@@ -1,14 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "type": "object",
- "properties":{
- "sessions_changed":{
- "type":"array",
- "items":{
- "allOf":[{"$ref":"../definitions/objectid.json#"}]
- }
- }
- },
- "additionalProperties":false,
- "required":["sessions_changed"]
+ "$ref": "../definitions/session.json#/definitions/session-template-recalc-output"
}
diff --git a/raml/schemas/output/sites-list.json b/raml/schemas/output/sites-list.json
deleted file mode 100644
index 7e7504b016b3f5db359b9d4bb944accdffe849d9..0000000000000000000000000000000000000000
--- a/raml/schemas/output/sites-list.json
+++ /dev/null
@@ -1,23 +0,0 @@
-{
- "$schema": "http://json-schema.org/draft-04/schema#",
- "type": "array",
- "items": {
- "type": "object",
- "properties": {
- "_id": {
- "type": "string"
- },
- "onload": {
- "type": "boolean"
- },
- "name": {
- "type": "string"
- }
- },
- "required": [
- "_id",
- "onload",
- "name"
- ]
- }
-}
diff --git a/raml/schemas/output/user-delete.json b/raml/schemas/output/user-delete.json
index d9877921d031657143bee32804764331f93cf82a..12e4a66089b694f7d02d9caa54cc14a5d2af1f55 100644
--- a/raml/schemas/output/user-delete.json
+++ b/raml/schemas/output/user-delete.json
@@ -1,12 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "type": "object",
- "properties": {
- "deleted": {
- "type": "integer"
- }
- },
- "required": [
- "deleted"
- ]
+ "$ref": "../definitions/common.json#/definitions/deleted-count"
}
diff --git a/raml/schemas/output/user-new.json b/raml/schemas/output/user-new.json
index 3279fda1c83df826d108138395338bfbf5433aba..e1551ebcd6fdfb01ed035b08a515c437cd78937c 100644
--- a/raml/schemas/output/user-new.json
+++ b/raml/schemas/output/user-new.json
@@ -1,14 +1,6 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "type": "object",
- "properties": {
- "_id": {
- "type": "string"
- }
- },
- "required": [
- "_id"
- ],
+ "$ref": "../definitions/common.json#/definitions/object-created",
"example": {
"$ref": "../../examples/output/user-new.json"
}
diff --git a/raml/schemas/output/user-self.json b/raml/schemas/output/user-self.json
index be5a072af1504eba2f5e2fc7c0975f3dfe7a1794..687a7b62f314db1779f5d0361cfcbf336536116c 100644
--- a/raml/schemas/output/user-self.json
+++ b/raml/schemas/output/user-self.json
@@ -1,26 +1,5 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"type":"object",
- "properties":{
- "_id":{"$ref":"../definitions/user.json#/definitions/_id"},
- "firstname":{"$ref":"../definitions/user.json#/definitions/firstname"},
- "lastname":{"$ref":"../definitions/user.json#/definitions/lastname"},
- "email":{"$ref":"../definitions/user.json#/definitions/email"},
- "avatar":{"$ref":"../definitions/user.json#/definitions/avatar"},
- "avatars":{"$ref":"../definitions/user.json#/definitions/avatars"},
- "root":{"$ref":"../definitions/user.json#/definitions/root"},
- "disabled":{"$ref":"../definitions/user.json#/definitions/disabled"},
- "preferences":{"$ref":"../definitions/user.json#/definitions/preferences"},
- "created":{"$ref":"../definitions/created-modified.json#/definitions/created"},
- "modified":{"$ref":"../definitions/created-modified.json#/definitions/modified"},
- "api_key":{"$ref":"../definitions/user.json#/definitions/api_key"},
- "wechat":{"$ref":"../definitions/user.json#/definitions/wechat"},
- "firstlogin":{"$ref":"../definitions/user.json#/definitions/firstlogin"},
- "lastlogin":{"$ref":"../definitions/user.json#/definitions/lastlogin"}
- },
- "additionalProperties":false,
- "required":[
- "_id", "firstname", "lastname",
- "root", "email", "created", "modified"
- ]
+ "allOf": [{"$ref":"../definitions/user.json#/definitions/user-output-api-key"}]
}
diff --git a/raml/schemas/output/user-update.json b/raml/schemas/output/user-update.json
index 1634f722b1d9b354844375491d4e1b440f1e6c8f..5f028c946741ca44c054e0cdd62fa0e5bdf3a915 100644
--- a/raml/schemas/output/user-update.json
+++ b/raml/schemas/output/user-update.json
@@ -1,12 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "type": "object",
- "properties": {
- "modified": {
- "type": "integer"
- }
- },
- "required": [
- "modified"
- ]
+ "$ref": "../definitions/common.json#/definitions/modified-count"
}
diff --git a/raml/schemas/output/version.json b/raml/schemas/output/version.json
index c01eea8b23d5ade193245c0cbbc4945c9f056ef4..52791553945abd0de204f9f1c8bdd53b1a26d341 100644
--- a/raml/schemas/output/version.json
+++ b/raml/schemas/output/version.json
@@ -1,16 +1,4 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
- "type": "object",
- "properties": {
- "_id": {
- "type": "string"
- },
- "database": {
- "type": "integer"
- }
- },
- "required": [
- "_id",
- "database"
- ]
+ "$ref": "../definitions/version.json#/definitions/version-output"
}
diff --git a/swagger/index.yaml b/swagger/index.yaml
index 221973900acf90ced910c883b4d185ebd06ea281..34626b765d01b8af61eedfda203b1628a3d1a586 100644
--- a/swagger/index.yaml
+++ b/swagger/index.yaml
@@ -26,6 +26,16 @@ tags:
description: Job operations
- name: collections
description: Collection operations
+ - name: sessions
+ description: Session operations
+ - name: acquisitions
+ description: Acquisition operations
+ - name: projects
+ description: Project operations
+ - name: reports
+ description: Site-wide reports
+ - name: batch
+ description: Batch job operations
paths:
$include:
@@ -45,6 +55,12 @@ paths:
- paths/devices.yaml
- paths/groups.yaml
- paths/collections.yaml
+ - paths/sessions.yaml
+ - paths/acquisitions.yaml
+ - paths/projects.yaml
+ - paths/report.yaml
+ - paths/batch.yaml
+
securityDefinitions:
ApiKey:
diff --git a/swagger/package-lock.json b/swagger/package-lock.json
index d5ed24392e0c091c806085a1cefeda6cd230fac9..6add6536d94a5523d1a92a7da6fae16102c69a9b 100644
--- a/swagger/package-lock.json
+++ b/swagger/package-lock.json
@@ -1250,6 +1250,12 @@
"find-up": "1.1.2"
}
},
+ "pluralize": {
+ "version": "7.0.0",
+ "resolved": "https://registry.npmjs.org/pluralize/-/pluralize-7.0.0.tgz",
+ "integrity": "sha512-ARhBOdzS3e41FbkW/XWrTEtukqqLoK5+Z/4UeDaLuSW+39JPeFgs4gCGqsrJHVZX0fUrx//4OF0K1CUGwlIFow==",
+ "dev": true
+ },
"portscanner": {
"version": "1.2.0",
"resolved": "https://registry.npmjs.org/portscanner/-/portscanner-1.2.0.tgz",
diff --git a/swagger/package.json b/swagger/package.json
index 2f57b4a9d27cb8d609802b9e1ba8e3c70d165945..2eb3771879be6ddc0c542f99024076fba4281625 100644
--- a/swagger/package.json
+++ b/swagger/package.json
@@ -20,6 +20,7 @@
"load-grunt-tasks": "^3.5.2",
"lodash": "^4.17.4",
"mustache": "^2.3.0",
+ "pluralize": "^7.0.0",
"swagger-ui-dist": "^3.6.0"
}
}
diff --git a/swagger/paths/acquisitions.yaml b/swagger/paths/acquisitions.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..325ad7499da4051d90a4a6474b9d121d2f934f7e
--- /dev/null
+++ b/swagger/paths/acquisitions.yaml
@@ -0,0 +1,56 @@
+$template_arguments:
+ resource: acquisition
+ tag: acquisitions
+ parameter: AcquisitionId
+
+/acquisitions:
+ $template: templates/container.yaml
+ arguments:
+ list-output-schema: schemas/output/acquisition-list.json
+ create-input-schema: schemas/input/acquisition.json
+
+/acquisitions/{AcquisitionId}:
+ $template: templates/container-item.yaml
+ arguments:
+ update-input-schema: schemas/input/acquisition-update.json
+ get-output-schema: schemas/output/acquisition.json
+
+# ===== Tags =====
+/acquisitions/{AcquisitionId}/tags:
+ $template: templates/tags.yaml
+/acquisitions/{AcquisitionId}/tags/{TagValue}:
+ $template: templates/tags-tag.yaml
+
+# ===== Packfile =====
+/acquisitions/{AcquisitionId}/packfile-start:
+ $template: templates/packfile-start.yaml
+/acquisitions/{AcquisitionId}/packfile:
+ $template: templates/packfile.yaml
+/acquisitions/{AcquisitionId}/packfile-end:
+ $template: templates/packfile-end.yaml
+
+# ===== Files =====
+/acquisitions/{AcquisitionId}/files:
+ $template: templates/file-list-upload.yaml
+/acquisitions/{AcquisitionId}/files/{FileName}:
+ $template: templates/file-item.yaml
+
+# ===== Notes =====
+/acquisitions/{AcquisitionId}/notes:
+ $template: templates/notes.yaml
+/acquisitions/{AcquisitionId}/notes/{NoteId}:
+ $template: templates/notes-note.yaml
+
+# ===== Analyses =====
+/acquisitions/{AcquisitionId}/analyses:
+ $template: templates/analyses-list.yaml
+/acquisitions/{AcquisitionId}/analyses/{AnalysisId}:
+ $template: templates/analysis-item.yaml
+/acquisitions/{AcquisitionId}/analyses/{AnalysisId}/files:
+ $template: templates/analysis-files.yaml
+/acquisitions/{AcquisitionId}/analyses/{AnalysisId}/files/{Filename}:
+ $template: templates/analysis-files-create-ticket-filename.yaml
+/acquisitions/{AcquisitionId}/analyses/{AnalysisId}/notes:
+ $template: templates/analysis-notes.yaml
+/acquisitions/{AcquisitionId}/analyses/{AnalysisId}/notes/{NoteId}:
+ $template: templates/analysis-notes-item.yaml
diff --git a/swagger/paths/batch.yaml b/swagger/paths/batch.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..564bcd75927babe2f8b45c6e806e8d46f82056e9
--- /dev/null
+++ b/swagger/paths/batch.yaml
@@ -0,0 +1,87 @@
+/batch:
+ get:
+ summary: Get a list of batch jobs the user has created.
+ description: Requires login.
+ operationId: get_all_batch_jobs
+ tags:
+ - batch
+ responses:
+ '200':
+ schema:
+ $ref: schemas/output/batch-list.json
+ post:
+ summary: Create a batch job proposal and insert it as 'pending'.
+ operationId: create_batch_job
+ tags:
+ - batch
+ parameters:
+ - name: body
+ in: body
+ schema:
+ $ref: schemas/input/batch-insert.json
+ responses:
+ '200':
+ schema:
+ $ref: schemas/output/batch-insert.json
+
+/batch/{BatchId}:
+ parameters:
+ - in: path
+ type: string
+ name: BatchId
+ required: true
+ get:
+ summary: Get batch job details.
+ parameters:
+ - in: query
+ type: boolean
+ name: jobs
+ description: If true, return job objects instead of job ids
+ operationId: get_batch_job
+ tags:
+ - batch
+ responses:
+ '200':
+ schema:
+ $ref: schemas/output/batch.json
+ '404':
+ $ref: '#/responses/404:resource-not-found'
+
+/batch/{BatchId}/run:
+ parameters:
+ - in: path
+ type: string
+ name: BatchId
+ required: true
+ post:
+ summary: Launch a job.
+ description: |
+ Creates jobs from proposed inputs, returns jobs enqueued.
+ Moves 'pending' batch job to 'running'.
+ operationId: run_batch_job
+ tags:
+ - batch
+ responses:
+ '200':
+ schema:
+ $ref: schemas/output/job-list.json
+
+/batch/{BatchId}/cancel:
+ parameters:
+ - in: path
+ type: string
+ name: BatchId
+ required: true
+ post:
+ summary: Cancel a Job
+ description: |
+ Cancels jobs that are still pending, returns number of jobs cancelled.
+ Moves a 'running' batch job to 'cancelled'.
+ operationId: cancel_batch_job
+ tags:
+ - batch
+ responses:
+ '200':
+ schema:
+ example:
+ canceled_jobs: 4
diff --git a/swagger/paths/config-js.yaml b/swagger/paths/config-js.yaml
index 09ffa6a754ccf10ff83ac5349f9f98ca5f953021..c26b420e2effe42ea8742fa9b38038a39f7cd637 100644
--- a/swagger/paths/config-js.yaml
+++ b/swagger/paths/config-js.yaml
@@ -7,8 +7,8 @@
responses:
'200':
description: ''
- schema:
- example: |
+ examples:
+ 'application/javascript': |
config = {
"auth": {
"auth_endpoint": "https://accounts.google.com/o/oauth2/auth",
diff --git a/swagger/paths/jobs.yaml b/swagger/paths/jobs.yaml
index b65e2e513286cb476485fd9f2372a0cf5ab02beb..04c328ef3560987d2d6690330c3dff0aad9224d5 100644
--- a/swagger/paths/jobs.yaml
+++ b/swagger/paths/jobs.yaml
@@ -26,8 +26,13 @@
tags:
- jobs
responses:
- default:
+ '200':
description: ''
+ schema:
+ $ref: schemas/output/job.json
+ examples:
+ response:
+ $ref: examples/output/job.json
/jobs/stats:
get:
summary: Get stats about all current jobs
diff --git a/swagger/paths/projects.yaml b/swagger/paths/projects.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..d499e8af6dd633981395dc25676c287564457adb
--- /dev/null
+++ b/swagger/paths/projects.yaml
@@ -0,0 +1,227 @@
+$template_arguments:
+ resource: project
+ tag: projects
+ parameter: ProjectId
+
+/projects:
+ $template: templates/container.yaml
+ arguments:
+ list-output-schema: schemas/output/project-list.json
+ create-input-schema: schemas/input/project.json
+
+/projects/{ProjectId}:
+ $template: templates/container-item.yaml
+ arguments:
+ update-input-schema: schemas/input/project-update.json
+ get-output-schema: schemas/output/project.json
+
+/projects/groups:
+ get:
+ summary: List all groups which have a project in them
+ operationId: get_all_projects_groups
+ tags:
+ - 'projects'
+ responses:
+ '200':
+ description: ''
+ schema:
+ $ref: schemas/output/groups-list.json
+
+'/projects/{ProjectId}/sessions':
+ parameters:
+ - in: path
+ type: string
+ name: ProjectId
+ required: true
+ get:
+ summary: List all sessions for the given project.
+ operationId: get_project_sessions
+ tags:
+ - 'projects'
+ responses:
+ '200':
+ schema:
+ $ref: schemas/output/session-list.json
+
+'/projects/{ProjectId}/acquisitions':
+ get:
+ summary: List all acquisitions for the given project.
+ operationId: get_project_acquisitions
+ tags:
+ - 'projects'
+ responses:
+ '200':
+ schema:
+ $ref: schemas/output/acquisition-list.json
+
+'/projects/{ProjectId}/rules':
+ parameters:
+ - in: path
+ type: string
+ name: ProjectId
+ required: true
+ get:
+ operationId: get_project_rules
+ tags:
+ - 'projects'
+ responses:
+ '200':
+ schema:
+ $ref: schemas/output/rule-list.json
+ post:
+ summary: Create a new rule for a project.
+ operationId: add_project_rule
+ tags:
+ - 'projects'
+ responses:
+ default:
+ description: ''
+ parameters:
+ - in: body
+ name: body
+ schema:
+ $ref: schemas/input/rule-new.json
+
+'/projects/{ProjectId}/rules/{RuleId}':
+ parameters:
+ - in: path
+ type: string
+ name: ProjectId
+ required: true
+ - in: path
+ type: string
+ name: RuleId
+ required: true
+ put:
+ summary: Update a rule on a project.
+ operationId: modify_project_rule
+ tags:
+ - 'projects'
+ responses:
+ default:
+ description: ''
+ parameters:
+ - in: body
+ name: body
+ schema:
+ $ref: schemas/input/rule-update.json
+
+
+'/projects/{ProjectId}/template':
+ parameters:
+ - in: path
+ type: string
+ name: ProjectId
+ required: true
+ post:
+ summary: Set the session template for a project.
+ operationId: set_project_template
+ tags:
+ - 'projects'
+ parameters:
+ - in: body
+ name: body
+ schema:
+ $ref: schemas/input/project-template.json
+ responses:
+ '200':
+ $ref: '#/responses/200:modified-with-count'
+ '404':
+ $ref: '#/responses/404:resource-not-found'
+ delete:
+ summary: Remove the session template for a project.
+ operationId: remove_project_template
+ tags:
+ - 'projects'
+ responses:
+ '200':
+ $ref: '#/responses/200:deleted-with-count'
+ '404':
+ $ref: '#/responses/404:resource-not-found'
+
+'/projects/{ProjectId}/recalc':
+ parameters:
+ - in: path
+ type: string
+ name: ProjectId
+ required: true
+ post:
+ summary: Recalculate if sessions in the project satisfy the template.
+ description: Returns list of modified session ids.
+ operationId: recalc_project
+ tags:
+ - 'projects'
+ responses:
+ '200':
+ description: |
+ Project's sessions' compliance was recalculated.
+ Returns list of session that were modified.
+ schema:
+ $ref: schemas/output/session-template-recalc.json
+ '404':
+ $ref: '#/responses/404:resource-not-found'
+
+/projects/recalc:
+ post:
+ summary: Recalculate all sessions against their project templates.
+ description: |
+ Iterates all projects that have a session template.
+ Recalculate if projects' sessions satisfy the template.
+ Returns list of modified session ids.
+ operationId: recalc_all_projects
+ tags:
+ - 'projects'
+ responses:
+ '200':
+ description: |
+ Projects' sessions' compliance was recalculated.
+ Returns list of session that were modified.
+ schema:
+ $ref: schemas/output/session-template-recalc.json
+
+
+# ===== Tags =====
+/projects/{ProjectId}/tags:
+ $template: templates/tags.yaml
+/projects/{ProjectId}/tags/{TagValue}:
+ $template: templates/tags-tag.yaml
+
+# ===== Packfile =====
+/projects/{ProjectId}/packfile-start:
+ $template: templates/packfile-start.yaml
+/projects/{ProjectId}/packfile:
+ $template: templates/packfile.yaml
+/projects/{ProjectId}/packfile-end:
+ $template: templates/packfile-end.yaml
+
+# ===== Files =====
+/projects/{ProjectId}/files:
+ $template: templates/file-list-upload.yaml
+/projects/{ProjectId}/files/{FileName}:
+ $template: templates/file-item.yaml
+
+# ===== Permissions =====
+/projects/{ProjectId}/permissions:
+ $template: templates/permissions.yaml
+/projects/{ProjectId}/permissions/{UserId}:
+ $template: templates/permissions-user.yaml
+
+# ===== Notes =====
+/projects/{ProjectId}/notes:
+ $template: templates/notes.yaml
+/projects/{ProjectId}/notes/{NoteId}:
+ $template: templates/notes-note.yaml
+
+# ===== Analyses =====
+/projects/{ProjectId}/analyses:
+ $template: templates/analyses-list.yaml
+/projects/{ProjectId}/analyses/{AnalysisId}:
+ $template: templates/analysis-item.yaml
+/projects/{ProjectId}/analyses/{AnalysisId}/files:
+ $template: templates/analysis-files.yaml
+/projects/{ProjectId}/analyses/{AnalysisId}/files/{Filename}:
+ $template: templates/analysis-files-create-ticket-filename.yaml
+/projects/{ProjectId}/analyses/{AnalysisId}/notes:
+ $template: templates/analysis-notes.yaml
+/projects/{ProjectId}/analyses/{AnalysisId}/notes/{NoteId}:
+ $template: templates/analysis-notes-item.yaml
diff --git a/swagger/paths/report.yaml b/swagger/paths/report.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..000a9ec1f184cd00ade166c89df098420f770091
--- /dev/null
+++ b/swagger/paths/report.yaml
@@ -0,0 +1,34 @@
+/report/site:
+ get:
+ operationId: get_site_report
+ tags:
+ - 'reports'
+ responses:
+ '200':
+ description: ''
+ schema:
+ $ref: schemas/output/report-site.json
+
+/report/project:
+ get:
+ operationId: get_project_report
+ tags:
+ - 'reports'
+ parameters:
+ - in: query
+ type: string
+ name: projects
+ description: Specify multiple times to include projects in the report
+ - in: query
+ type: string
+ name: start_date
+ description: Report start date
+ - in: query
+ type: string
+ name: end_date
+ description: Report end date
+ responses:
+ '200':
+ description: ''
+ schema:
+ $ref: schemas/output/report-project.json
diff --git a/swagger/paths/sessions.yaml b/swagger/paths/sessions.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..d78452b3c560194cc8e437ef4743ae89f0dd0a03
--- /dev/null
+++ b/swagger/paths/sessions.yaml
@@ -0,0 +1,126 @@
+$template_arguments:
+ resource: session
+ tag: sessions
+ parameter: SessionId
+
+/sessions:
+ $template: templates/container.yaml
+ arguments:
+ list-output-schema: schemas/output/session-list.json
+ create-input-schema: schemas/input/session.json
+
+/sessions/{SessionId}:
+ $template: templates/container-item.yaml
+ arguments:
+ update-input-schema: schemas/input/session.json
+ get-output-schema: schemas/output/session.json
+
+'/sessions/{SessionId}/jobs':
+ parameters:
+ - in: path
+ type: string
+ name: SessionId
+ required: true
+ get:
+ summary: Return any jobs that use inputs from this session
+ operationId: get_session_jobs
+ tags:
+ - 'sessions'
+ parameters:
+ - in: query
+ type: string
+ name: states
+ description: filter results by job state
+ - in: query
+ type: string
+ name: tags
+ description: filter results by job tags
+ responses:
+ '200':
+ schema:
+ $ref: schemas/output/session-jobs.json
+
+# ===== Tags =====
+/sessions/{SessionId}/tags:
+ $template: templates/tags.yaml
+/sessions/{SessionId}/tags/{TagValue}:
+ $template: templates/tags-tag.yaml
+
+# ===== Packfile =====
+/sessions/{SessionId}/packfile-start:
+ $template: templates/packfile-start.yaml
+/sessions/{SessionId}/packfile:
+ $template: templates/packfile.yaml
+/sessions/{SessionId}/packfile-end:
+ $template: templates/packfile-end.yaml
+
+# ===== Files =====
+/sessions/{SessionId}/files:
+ $template: templates/file-list-upload.yaml
+/sessions/{SessionId}/files/{FileName}:
+ $template: templates/file-item.yaml
+
+# ===== Notes =====
+/sessions/{SessionId}/notes:
+ $template: templates/notes.yaml
+/sessions/{SessionId}/notes/{NoteId}:
+ $template: templates/notes-note.yaml
+
+'/sessions/{SessionId}/acquisitions':
+ parameters:
+ - in: path
+ type: string
+ name: SessionId
+ required: true
+ get:
+ summary: List acquisitions in a session
+ operationId: get_session_acquisitions
+ tags:
+ - 'sessions'
+ responses:
+ '200':
+ description: ''
+ schema:
+ $ref: schemas/output/acquisition-list.json
+
+# ===== Analyses =====
+/sessions/{SessionId}/analyses:
+ parameters:
+ - required: true
+ type: string
+ in: path
+ name: 'SessionId'
+ post:
+ summary: Create an analysis and upload files.
+ description: |
+ When query param "job" is "true", send JSON to create
+ an analysis and job. Otherwise, multipart/form-data
+ to upload files and create an analysis.
+ operationId: add_session_analysis
+ tags:
+ - 'sessions'
+ parameters:
+ - in: body
+ name: body
+ schema:
+ $ref: schemas/input/analysis-job.json
+ - in: query
+ type: boolean
+ name: job
+ responses:
+ '200':
+ description: ''
+
+
+
+/sessions/{SessionId}/analyses/{AnalysisId}:
+ $template: templates/analysis-item.yaml
+/sessions/{SessionId}/analyses/{AnalysisId}/files:
+ $template: templates/analysis-files.yaml
+/sessions/{SessionId}/analyses/{AnalysisId}/files/{Filename}:
+ $template: templates/analysis-files-create-ticket-filename.yaml
+/sessions/{SessionId}/analyses/{AnalysisId}/notes:
+ $template: templates/analysis-notes.yaml
+/sessions/{SessionId}/analyses/{AnalysisId}/notes/{NoteId}:
+ $template: templates/analysis-notes-item.yaml
+
diff --git a/swagger/paths/users.yaml b/swagger/paths/users.yaml
index dcccc30a454f265ab61f5ffad0d751bea6b7621d..f2af9b8fadea368a0d42844861396b1f18ec9d16 100644
--- a/swagger/paths/users.yaml
+++ b/swagger/paths/users.yaml
@@ -53,10 +53,10 @@
Redirects to the image file of the current user's avatar
/users/{UserId}:
parameters:
- - required: true
+ - in: path
type: string
- in: path
name: UserId
+ required: true
get:
summary: Get information about the specified user
operationId: get_user
diff --git a/swagger/responses/index.yaml b/swagger/responses/index.yaml
index bd2d076f3585d8fa91f2b34dbff82bc4cd02f6ec..03986aaa24bbe3161ddf006b40892decca28bdc9 100644
--- a/swagger/responses/index.yaml
+++ b/swagger/responses/index.yaml
@@ -24,4 +24,8 @@
'400:invalid-body-json':
description: |
- JSON did not validate against schema for this endpoint
+ JSON did not validate against schema for this endpoint.
+
+'404:resource-not-found':
+ description: |
+ The specified resource could not be found.
\ No newline at end of file
diff --git a/swagger/support/swagger-resolver.js b/swagger/support/swagger-resolver.js
index d40b27276d97083f5568b1e4a6d1852a984697a9..ee2575df0ebc65b58b23793d6e2039275aa380f8 100644
--- a/swagger/support/swagger-resolver.js
+++ b/swagger/support/swagger-resolver.js
@@ -5,10 +5,24 @@ var path = require('path');
var fs = require('fs');
var process = require('process');
var yaml = require('js-yaml');
+var pluralize = require('pluralize');
var Mustache = require('mustache');
var walk = require('./walk');
+var TEMPLATE_FUNCS = {
+ 'pluralize': function() {
+ return function(text, render) {
+ return pluralize.plural(render(text));
+ };
+ },
+ 'singularize': function() {
+ return function(text, render) {
+ return pluralize.singular(render(text));
+ };
+ }
+};
+
// Throws if args are missing
function validateTemplateArgs(tmplpath, template, args) {
var i, param;
@@ -73,18 +87,20 @@ SwaggerResolver.prototype.loadFile = function(relpath) {
};
SwaggerResolver.prototype.visit = function(obj) {
+ if( !obj ) {
+ return obj;
+ }
+
// obj will have $template or $include, not both
if( obj.hasOwnProperty('$include') ) {
obj = this.resolveIncludes(obj);
-
- // Recursively resolve content
- obj = this.resolveObject(obj);
} else if( obj.hasOwnProperty('$template') ) {
obj = this.resolveTemplate(obj);
// Recursively resolve content
obj = this.resolveObject(obj);
} else if( obj.hasOwnProperty('$template_arguments') ) {
+ // Save off template arguments for later
this.templateArguments = obj['$template_arguments'];
delete obj['$template_arguments'];
}
@@ -102,8 +118,10 @@ SwaggerResolver.prototype.resolveIncludes = function(obj) {
delete obj['$include'];
for( i = 0; i < includes.length; i++ ) {
- // Load the include file
+ // Load and resolve the include file
inc = this.loadFile(includes[i]);
+ inc = this.resolveObject(inc);
+
// And merge its contents into obj
_.extend(obj, inc);
}
@@ -124,7 +142,7 @@ SwaggerResolver.prototype.resolveTemplate = function(obj) {
}
// Validate arguments?
- args = obj['arguments']||this.templateArguments||{};
+ args = _.extend({}, TEMPLATE_FUNCS, this.templateArguments, obj['arguments']);
validateTemplateArgs(tmplpath, tmpl, args);
// Render the template, and parse
diff --git a/swagger/support/tasks/schemas-to-defs.js b/swagger/support/tasks/schemas-to-defs.js
index a81d1243d5f4d5f6e7ba314b51550f7d7f925106..efcaa87a1239f3acc96eb42735bfaa5c39e4d3aa 100644
--- a/swagger/support/tasks/schemas-to-defs.js
+++ b/swagger/support/tasks/schemas-to-defs.js
@@ -59,7 +59,7 @@ module.exports = function(grunt) {
if( !root.definitions ) {
root.definitions = {};
}
- _.extend(root.definitions, schemas.getComplexDefinitions());
+ // _.extend(root.definitions, schemas.getComplexDefinitions());
// Write destination file
var data = JSON.stringify(root, null, 2);
diff --git a/swagger/templates/container-item.yaml b/swagger/templates/container-item.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..c7a864df8b4c7037a4042c53e73fa9276033ce49
--- /dev/null
+++ b/swagger/templates/container-item.yaml
@@ -0,0 +1,49 @@
+parameters:
+ - name: resource
+ type: string
+ - name: tag
+ type: string
+ - name: parameter
+ type: string
+ - name: update-input-schema
+ type: string
+ - name: get-output-schema
+ type: string
+template: |
+ parameters:
+ - in: path
+ type: string
+ name: '{{parameter}}'
+ required: true
+ get:
+ summary: Get a single {{resource}}
+ operationId: get_{{resource}}
+ tags:
+ - '{{tag}}'
+ responses:
+ '200':
+ schema:
+ $ref: {{{get-output-schema}}}
+ put:
+ summary: Update a {{resource}}
+ operationId: modify_{{resource}}
+ tags:
+ - '{{tag}}'
+ parameters:
+ - in: body
+ name: body
+ schema:
+ $ref: {{{update-input-schema}}}
+ responses:
+ '200':
+ $ref: '#/responses/200:modified-with-count'
+ '400':
+ $ref: '#/responses/400:invalid-body-json'
+ delete:
+ summary: Delete a {{resource}}
+ operationId: delete_{{resource}}
+ tags:
+ - '{{tag}}'
+ responses:
+ '200':
+ $ref: '#/responses/200:deleted-with-count'
diff --git a/swagger/templates/container.yaml b/swagger/templates/container.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..72d87c9ea0f3ddf7109e90a247788a18cb9872c0
--- /dev/null
+++ b/swagger/templates/container.yaml
@@ -0,0 +1,35 @@
+parameters:
+ - name: resource
+ type: string
+ - name: tag
+ type: string
+ - name: list-output-schema
+ type: string
+ - name: create-input-schema
+ type: string
+template: |
+ get:
+ summary: Get a list of {{#pluralize}}{{resource}}{{/pluralize}}
+ operationId: get_all_{{#pluralize}}{{resource}}{{/pluralize}}
+ tags:
+ - '{{tag}}'
+ responses:
+ '200':
+ schema:
+ $ref: {{{list-output-schema}}}
+ post:
+ summary: Create a new {{resource}}
+ operationId: create_{{resource}}
+ tags:
+ - '{{tag}}'
+ parameters:
+ - in: body
+ name: body
+ schema:
+ $ref: {{{create-input-schema}}}
+ responses:
+ '200':
+ schema:
+ $ref: schemas/output/container-new.json
+ '400':
+ $ref: '#/responses/400:invalid-body-json'
diff --git a/tests/bin/run-tests-ubuntu.sh b/tests/bin/run-tests-ubuntu.sh
index 8c7d94fa559a903b6091b5b606f26acecdb28386..688119f08352527a9eee89b748f57957c17214a6 100755
--- a/tests/bin/run-tests-ubuntu.sh
+++ b/tests/bin/run-tests-ubuntu.sh
@@ -19,7 +19,6 @@ Options:
-l, --lint Run linting
-u, --unit Run unit tests
-i, --integ Run integration tests
- -a, --abao Run abao tests
-h, --help Print this help and exit
-- PYTEST_ARGS Arguments passed to py.test
@@ -40,7 +39,6 @@ function main() {
local RUN_LINT=false
local RUN_UNIT=false
local RUN_INTEG=false
- local RUN_ABAO=false
local PYTEST_ARGS=
while [[ "$#" > 0 ]]; do
@@ -48,7 +46,6 @@ function main() {
-l|--lint) RUN_ALL=false; RUN_LINT=true ;;
-u|--unit) RUN_ALL=false; RUN_UNIT=true ;;
-i|--integ) RUN_ALL=false; RUN_INTEG=true ;;
- -a|--abao) RUN_ALL=false; RUN_ABAO=true ;;
-h|--help) usage; exit 0 ;;
--) PYTEST_ARGS="${@:2}"; break ;;
*) echo "Invalid argument: $1" >&2; usage; exit 1 ;;
@@ -61,8 +58,7 @@ function main() {
RUN_LINT=true
RUN_UNIT=true
RUN_INTEG=true
- RUN_ABAO=true
- elif ${RUN_LINT} && ${RUN_UNIT} && ${RUN_INTEG} && ${RUN_ABAO}; then
+ elif ${RUN_LINT} && ${RUN_UNIT} && ${RUN_INTEG}; then
# All filtering options were used, the same as none
RUN_ALL=true
fi
@@ -100,7 +96,7 @@ function main() {
py.test --cov=api --cov-report= tests/unit_tests/python $PYTEST_ARGS
fi
- if ${RUN_INTEG} || ${RUN_ABAO}; then
+ if ${RUN_INTEG}; then
echo "Spinning up dependencies ..."
uwsgi --http "localhost:8081" --master --http-keepalive \
--so-keepalive --add-header "Connection: Keep-Alive" \
@@ -123,38 +119,10 @@ function main() {
printf '.'
sleep 1
done
- fi
- if ${RUN_INTEG}; then
echo "Running integration tests ..."
py.test tests/integration_tests/python $PYTEST_ARGS
fi
-
- if ${RUN_ABAO}; then
- echo "Running abao tests ..."
- # Create resources that Abao relies on
- python tests/integration_tests/abao/load_fixture.py
-
- # If no VIRTUAL_ENV, make sure /usr/local/bin is in the path
- if [[ -z "${VIRTUAL_ENV:-}" ]]; then
- PATH="/usr/local/bin:$PATH"
- npm install tests/integration_tests
- else
- npm install --global tests/integration_tests
- fi
-
- PATH="$(npm bin):$PATH"
-
- # Allow us to require modules from package.json,
- # since abao_test_hooks.js is not being called from the package directory
- integration_test_node_modules="$(pwd)/node_modules/scitran-core-integration-tests/node_modules"
-
- # Have to change into definitions directory to resolve
- # relative $ref's in the jsonschema's
- pushd raml/schemas/definitions
- NODE_PATH="$integration_test_node_modules" abao ../../api.raml "--server=$SCITRAN_SITE_API_URL" "--hookfiles=../../../tests/integration_tests/abao/abao_test_hooks.js"
- popd
- fi
}
diff --git a/tests/bin/setup-integration-tests-ubuntu.sh b/tests/bin/setup-integration-tests-ubuntu.sh
index 9a700f37d2c01d5d9ca6a8d9d47a805cbe349b5c..7719063ccf9a6ea145f8f888894ec13e66994a34 100755
--- a/tests/bin/setup-integration-tests-ubuntu.sh
+++ b/tests/bin/setup-integration-tests-ubuntu.sh
@@ -5,10 +5,3 @@ cd "$( dirname "${BASH_SOURCE[0]}" )/../.."
sudo pip install -U -r "tests/integration_tests/requirements-integration-test.txt"
-NODE_URL="https://nodejs.org/dist/v6.4.0/node-v6.4.0-linux-x64.tar.gz"
-
-if [[ -z "${VIRTUAL_ENV:-}" ]]; then
- curl $NODE_URL | sudo tar xz -C /usr/local --strip-components 1
-else
- curl $NODE_URL | tar xz -C $VIRTUAL_ENV --strip-components 1
-fi
diff --git a/tests/integration_tests/abao/abao_test_hooks.js b/tests/integration_tests/abao/abao_test_hooks.js
deleted file mode 100644
index 270c43aae48f9001f1b0db69ca091a30da8a16f3..0000000000000000000000000000000000000000
--- a/tests/integration_tests/abao/abao_test_hooks.js
+++ /dev/null
@@ -1,1463 +0,0 @@
-var hooks = require('hooks');
-var chai = require('chai');
-var assert = chai.assert;
-
-// Variables for passing results as input to subsequent tests
-var gear_name = 'test-case-gear';
-var group_id = 'test-group';
-var delete_group_id = 'example_group';
-var test_group_tag = 'test-group-tag';
-var collection_id = 'test-collection-1';
-var delete_collection_id = '';
-var test_collection_1 = null;
-var test_collection_tag = 'test-collection-tag';
-var test_session_1 = null;
-var test_session_2_id = null;
-var test_session_tag = 'test-session-tag';
-var test_session_1_analysis_2_id = null;
-var test_acquisition_1 = null;
-var test_acquisition_tag = 'test-acq-tag';
-var example_acquisition_id = '';
-var test_project_1 = null;
-var test_project_tag = 'test-project-tag';
-var delete_project_id = '';
-var device_id = 'bootstrapper_Bootstrapper'
-var injected_api_key = 'XZpXI40Uk85eozjQkU1zHJ6yZHpix+j0mo1TMeGZ4dPzIqVPVGPmyfeK'
-
-// Tests we're skipping, fix these
-
-// Fails only in travis
-hooks.skip("GET /version -> 200");
-
-// Should 400 to say invalid json
-hooks.skip("GET /download -> 400");
-
-// Should 422 for missing metadata field
-hooks.skip("POST /upload/label -> 402");
-hooks.skip("POST /upload/uid -> 402");
-hooks.skip("POST /upload/uid-match -> 402");
-
-// Should 404
-hooks.skip("GET /jobs/{JobId} -> 404");
-
-// Can only retry a failed job
-hooks.skip("POST /jobs/{JobId}/retry -> 200");
-
-// Cannot get JobId without GET /jobs endpoint
-hooks.skip("GET /jobs/{JobId} -> 200");
-hooks.skip("GET /jobs/{JobId}/config.json -> 200");
-hooks.skip("POST /jobs/{JobId}/retry -> 200");
-hooks.skip("GET /jobs/{JobId} -> 404");
-
-// https://github.com/cybertk/abao/issues/160
-hooks.skip("GET /users/self/avatar -> 307");
-hooks.skip("GET /users/{UserId}/avatar -> 307");
-
-// drones currently use shared secret, allow when using API keys
-hooks.skip("POST /devices -> 200")
-hooks.skip("GET /devices/self -> 200")
-
-// Tests that are skipped because we do them in python
-
-// Skipping because abao doesn't support file fields
-hooks.skip("POST /download -> 200");
-hooks.skip("GET /download -> 200");
-hooks.skip("POST /upload/label -> 200");
-hooks.skip("POST /upload/uid -> 200");
-hooks.skip("POST /upload/uid-match -> 200");
-hooks.skip("POST /upload/uid-match -> 404");
-hooks.skip("POST /engine -> 200");
-hooks.skip("POST /collections/{CollectionId}/packfile-start -> 200");
-hooks.skip("POST /collections/{CollectionId}/packfile -> 200");
-hooks.skip("GET /collections/{CollectionId}/packfile-end -> 200");
-hooks.skip("POST /sessions/{SessionId}/packfile-start -> 200");
-hooks.skip("POST /sessions/{SessionId}/packfile -> 200");
-hooks.skip("GET /sessions/{SessionId}/packfile-end -> 200");
-hooks.skip("POST /acquisitions/{AcquisitionId}/packfile-start -> 200");
-hooks.skip("POST /acquisitions/{AcquisitionId}/packfile -> 200");
-hooks.skip("GET /acquisitions/{AcquisitionId}/packfile-end -> 200");
-hooks.skip("POST /projects/{ProjectId}/packfile-start -> 200");
-hooks.skip("POST /projects/{ProjectId}/packfile -> 200");
-hooks.skip("GET /projects/{ProjectId}/packfile-end -> 200");
-
-
-// Skipping until merge with rest of project raml (So we have a ProjectId)
-hooks.skip("POST /projects/{ProjectId}/template -> 200")
-hooks.skip("DELETE /projects/{ProjectId}/template -> 200")
-hooks.skip("POST /projects/{ProjectId}/recalc -> 200")
-hooks.skip("GET /projects/{ProjectId}/rules -> 200")
-
-// Porting to python as per #600
-hooks.skip("POST /jobs/add -> 200")
-hooks.skip("PUT /jobs/{JobId} -> 200")
-hooks.skip("GET /gears/{GearId} -> 200")
-hooks.skip("GET /sessions/{SessionId}/jobs -> 200")
-
-// Cannot be ran due to gear IDs being used as per #
-hooks.skip("POST /sessions/{SessionId}/analyses -> 200")
-hooks.skip("GET /sessions/{SessionId}/analyses/{AnalysisId} -> 200")
-hooks.skip("DELETE /sessions/{SessionId}/analyses/{AnalysisId} -> 200")
-// Related, ref #696
-hooks.skip("DELETE /gears/{GearId} -> 200")
-
-
-hooks.before("POST /login -> 200", function(test, done) {
- test.request.body = {
- 'code': injected_api_key,
- 'auth_type': 'api-key'
- };
- done();
-});
-
-hooks.beforeEach(function (test, done) {
- test.request.query.root = "true"
- test.request.headers.Authorization = "scitran-user XZpXI40Uk85eozjQkU1zHJ6yZHpix+j0mo1TMeGZ4dPzIqVPVGPmyfeK";
- done();
-});
-
-hooks.before("GET /download -> 404", function(test, done) {
- test.request.query = {
- ticket: '1234'
- };
- done();
-});
-
-hooks.before("POST /users -> 400", function(test, done) {
- test.request.body = {api_key:{key:"test"}};
- done();
-});
-
-hooks.before("GET /users/{UserId} -> 200", function(test, done) {
- test.request.params = {
- UserId: "jane.doe@gmail.com"
- };
- done();
-});
-
-hooks.before("PUT /users/{UserId} -> 200", function(test, done) {
- test.request.params = {
- UserId: "jane.doe@gmail.com"
- };
- done();
-});
-
-hooks.before("PUT /users/{UserId} -> 400", function(test, done) {
- test.request.params = {
- UserId: "jane.doe@gmail.com"
- };
- test.request.body = {"not_a_valid_property":"foo"};
- done();
-});
-
-hooks.before("DELETE /users/{UserId} -> 200", function(test, done) {
- test.request.params = {
- UserId: "jane.doe@gmail.com"
- };
- done();
-});
-
-hooks.before("GET /users/{UserId}/acquisitions -> 200", function(test, done) {
- test.request.params = {
- UserId: "admin@user.com"
- };
- done();
-});
-
-hooks.before("GET /users/{UserId}/collections -> 200", function(test, done) {
- test.request.params = {
- UserId: "admin@user.com"
- };
- done();
-});
-
-hooks.before("GET /users/{UserId}/projects -> 200", function(test, done) {
- test.request.params = {
- UserId: "admin@user.com"
- };
- done();
-});
-
-hooks.before("GET /users/{UserId}/sessions -> 200", function(test, done) {
- test.request.params = {
- UserId: "admin@user.com"
- };
- done();
-});
-
-hooks.before("PUT /groups/{GroupId} -> 400", function(test, done) {
- test.request.params = {
- GroupId: group_id
- };
- test.request.body = {"not_a_real_property":"foo"};
- done();
-});
-
-hooks.before("POST /groups -> 400", function(test, done) {
- test.request.body = {"not_a_real_property":"foo"};
- done();
-});
-
-
-hooks.before("GET /groups/{GroupId} -> 200", function(test, done) {
- test.request.params = {
- GroupId: group_id
- };
- done();
-});
-
-hooks.before("DELETE /groups/{GroupId} -> 200", function(test, done) {
- test.request.params = {
- GroupId: delete_group_id
- };
- done();
-});
-
-hooks.before("POST /groups/{GroupId}/permissions -> 200", function(test, done) {
- test.request.params = {
- GroupId: group_id
- };
- test.request.body = {
- _id: "test@user.com",
- access: "ro"
- }
- done();
-});
-
-hooks.before("POST /groups/{GroupId}/permissions -> 400", function(test, done) {
- test.request.params = {
- GroupId: group_id
- };
- test.request.body.foo = "bar";
- done();
-});
-
-hooks.before("GET /groups/{GroupId}/permissions/{UserId} -> 200", function(test, done) {
- test.request.params = {
- GroupId: group_id,
- UserId: "test@user.com"
- };
- done();
-});
-
-hooks.before("PUT /groups/{GroupId}/permissions/{UserId} -> 200", function(test, done) {
- test.request.params = {
- GroupId: group_id,
- UserId: "test@user.com"
- };
- test.request.body = {
- _id: "test@user.com",
- access: "admin"
- };
- done();
-});
-
-hooks.before("PUT /groups/{GroupId}/permissions/{UserId} -> 400", function(test, done) {
- test.request.params = {
- GroupId: group_id,
- UserId:"test@user.com"
- };
- test.request.body = {
- _id: "test@user.com",
- access: "rw",
- not_a_real_property: "foo"
- };
- done();
-});
-
-hooks.before("DELETE /groups/{GroupId}/permissions/{UserId} -> 200", function(test, done) {
- test.request.params = {
- GroupId: group_id,
- UserId: "test@user.com"
- };
- done();
-});
-
-hooks.before("POST /groups/{GroupId}/tags -> 200", function(test, done) {
- test.request.params = {
- GroupId: group_id
- };
- test.request.body = {
- "value":test_group_tag
- };
- done();
-});
-
-hooks.before("POST /groups/{GroupId}/tags -> 400", function(test, done) {
- test.request.params = {
- GroupId: group_id
- };
- test.request.body = {
- "value":test_group_tag,
- "bad property": "foo"
- };
- done();
-});
-
-hooks.before("GET /groups/{GroupId}/tags/{TagValue} -> 200", function(test, done) {
- test.request.params = {
- GroupId: group_id,
- TagValue: test_group_tag
- };
- done();
-});
-
-hooks.before("PUT /groups/{GroupId}/tags/{TagValue} -> 200", function(test, done) {
- test.request.params = {
- GroupId: group_id,
- TagValue: test_group_tag
- };
- test_group_tag = "a-new-tag";
- test.request.body = {
- "value":test_group_tag
- };
- done();
-});
-
-hooks.before("PUT /groups/{GroupId}/tags/{TagValue} -> 400", function(test, done) {
- test.request.params = {
- GroupId: group_id,
- TagValue: test_group_tag
- };
- test.request.body = {
- "value":test_group_tag,
- "bad proeprty":"blah"
- };
- done();
-});
-
-hooks.before("DELETE /groups/{GroupId}/tags/{TagValue} -> 200", function(test, done) {
- test.request.params = {
- GroupId: group_id,
- TagValue: test_group_tag
- };
- done();
-});
-
-hooks.before("GET /groups/{GroupId}/projects -> 200", function(test, done) {
- test.request.params = {
- GroupId: group_id
- };
- done();
-});
-
-
-// set initial test_collection_1
-hooks.after("GET /collections -> 200", function(test, done) {
- test_collection_1 = test.response.body[0];
- collection_id = test.response.body[0]._id;
- delete_collection_id = test.response.body[1]._id;
- done();
-});
-
-hooks.before("GET /collections/{CollectionId} -> 200", function(test, done) {
- test.request.params.CollectionId = collection_id;
- done();
-});
-
-// set detailed test_collection_1 (including analyses, that are omitted during listing)
-hooks.after("GET /collections/{CollectionId} -> 200", function(test, done) {
- test_collection_1 = test.response.body;
- done();
-});
-
-hooks.before("GET /collections/{CollectionId}/sessions -> 200", function(test, done) {
- test.request.params.CollectionId = collection_id;
- done();
-});
-
-hooks.before("GET /collections/{CollectionId}/acquisitions -> 200", function(test, done) {
- test.request.params.CollectionId = collection_id;
- done();
-});
-
-hooks.before("POST /collections -> 400", function(test, done) {
- test.request.params.CollectionId = collection_id;
- test.request.body.foo = "not an allowed property";
- done();
-});
-
-hooks.before("PUT /collections/{CollectionId} -> 400", function(test, done) {
- test.request.params.CollectionId = collection_id;
- test.request.body.foo = "not an allowed property";
- done();
-});
-
-hooks.before("DELETE /collections/{CollectionId} -> 200", function(test, done) {
- test.request.params.CollectionId = delete_collection_id;
- done();
-});
-
-hooks.before("POST /collections/{CollectionId}/tags -> 200", function(test, done) {
- test.request.params.CollectionId = collection_id;
- test.request.body = {
- "value":test_collection_tag
- };
- done();
-});
-
-hooks.before("POST /collections/{CollectionId}/tags -> 400", function(test, done) {
- test.request.params.CollectionId = collection_id;
- test.request.body = {
- "value":""
- };
- done();
-});
-
-hooks.before("GET /collections/{CollectionId}/tags/{TagValue} -> 200", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- TagValue : test_collection_tag
- };
- done();
-});
-
-hooks.before("PUT /collections/{CollectionId}/tags/{TagValue} -> 200", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- TagValue : test_collection_tag
- };
- test_collection_tag = "new-tag-value";
- test.request.body = {
- "value":test_collection_tag
- };
- done();
-});
-
-hooks.before("PUT /collections/{CollectionId}/tags/{TagValue} -> 400", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- TagValue : test_collection_tag
- };
- test.request.body = {
- "value":""
- };
- done();
-});
-
-hooks.before("DELETE /collections/{CollectionId}/tags/{TagValue} -> 200", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- TagValue : test_collection_tag
- };
- done();
-});
-
-hooks.before("GET /collections/{CollectionId}/files/{FileName} -> 200", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- FileName : "notes.txt"
- };
- test.request.query = {
- "ticket":""
- };
- done();
-});
-
-hooks.before("POST /collections/{CollectionId}/permissions -> 200", function(test, done) {
- test.request.params = {
- CollectionId : collection_id
- };
- test.request.body = {
- "_id":"test@user.com",
- "access":"ro"
- };
- done();
-});
-
-hooks.before("POST /collections/{CollectionId}/permissions -> 400", function(test, done) {
- test.request.params = {
- CollectionId : collection_id
- };
- test.request.body = {
- "not a valid":"permissions entry"
- };
- done();
-});
-
-hooks.before("GET /collections/{CollectionId}/permissions/{UserId} -> 200", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- UserId: "test@user.com"
- };
- done();
-});
-
-hooks.before("PUT /collections/{CollectionId}/permissions/{UserId} -> 200", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- UserId: "test@user.com"
- };
- test.request.body = {
- "access":"rw",
- "_id":"test@user.com"
- };
- done();
-});
-
-hooks.before("PUT /collections/{CollectionId}/permissions/{UserId} -> 400", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- UserId: "test@user.com"
- };
- test.request.body = {
- "not a valid":"permissions entry"
- };
- done();
-});
-
-hooks.before("DELETE /collections/{CollectionId}/permissions/{UserId} -> 200", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- UserId: "test@user.com"
- };
- done();
-});
-
-hooks.before("POST /collections/{CollectionId}/notes -> 200", function(test, done) {
- test.request.params = {
- CollectionId : collection_id
- };
- done();
-});
-
-hooks.before("POST /collections/{CollectionId}/notes -> 400", function(test, done) {
- test.request.params = {
- CollectionId : collection_id
- };
- test.request.body = {
- "not real":"property"
- };
- done();
-});
-
-hooks.before("GET /collections/{CollectionId}/notes/{NoteId} -> 200", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- NoteId: test_collection_1.notes[0]._id
- };
- done();
-});
-
-hooks.before("PUT /collections/{CollectionId}/notes/{NoteId} -> 200", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- NoteId: test_collection_1.notes[0]._id
- };
- test.request.body = {
- "text":"new note"
- };
- done();
-});
-
-hooks.before("PUT /collections/{CollectionId}/notes/{NoteId} -> 400", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- NoteId: test_collection_1.notes[0]._id
- };
- test.request.body = {
- "note a":"real property"
- };
- done();
-});
-
-hooks.before("DELETE /collections/{CollectionId}/notes/{NoteId} -> 200", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- NoteId: test_collection_1.notes[0]._id
- };
- done();
-});
-
-hooks.before("GET /collections/{CollectionId}/analyses/{AnalysisId} -> 200", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- AnalysisId: test_collection_1.analyses[0]._id
- };
- done();
-});
-
-hooks.before("DELETE /collections/{CollectionId}/analyses/{AnalysisId} -> 200", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- AnalysisId: test_collection_1.analyses[1]._id
- };
- done();
-});
-
-hooks.before("GET /collections/{CollectionId}/analyses/{AnalysisId}/files -> 200", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- AnalysisId: test_collection_1.analyses[0]._id
- };
- test.request.query.ticket = "";
- done();
-});
-
-hooks.before("GET /collections/{CollectionId}/analyses/{AnalysisId}/files/{Filename} -> 200", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- AnalysisId: test_collection_1.analyses[0]._id,
- Filename: "test-1.dcm"
- };
- test.request.query.ticket = "";
- done();
-});
-
-hooks.before("POST /collections/{CollectionId}/analyses/{AnalysisId}/notes -> 200", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- AnalysisId: test_collection_1.analyses[0]._id
- };
- done();
-});
-
-hooks.before("POST /collections/{CollectionId}/analyses/{AnalysisId}/notes -> 400", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- AnalysisId: test_collection_1.analyses[0]._id
- };
- test.request.body = {
- "not a":"real property"
- };
- done();
-});
-
-hooks.before("DELETE /collections/{CollectionId}/analyses/{AnalysisId}/notes/{NoteId} -> 200", function(test, done) {
- test.request.params = {
- CollectionId : collection_id,
- AnalysisId: test_collection_1.analyses[0]._id,
- NoteId: test_collection_1.analyses[0].notes[0]._id
- };
- done();
-});
-
-
-// set initial test_session_1
-hooks.after("GET /sessions -> 200", function(test, done) {
- test_session_1 = test.response.body[0];
- assert.equal(test_session_1.label, "test-session-1");
- done();
-});
-
-hooks.before("GET /sessions/{SessionId} -> 200", function(test, done) {
- test.request.params.SessionId = test_session_1._id;
- done();
-});
-
-// set detailed test_session_1 (including analyses, that are omitted during listing)
-hooks.after("GET /sessions/{SessionId} -> 200", function(test, done) {
- test_session_1 = test.response.body;
- done();
-});
-
-hooks.after("GET /sessions/{SessionId} -> 200", function(test, done) {
- test_session_1 = test.response.body;
- assert.equal(test_session_1.label, "test-session-1");
- done();
-});
-
-hooks.before("POST /sessions -> 200", function(test, done) {
- test.request.body.project = test_session_1.project;
- done();
-});
-
-hooks.after("POST /sessions -> 200", function(test, done) {
- test_session_2_id = test.response.body._id
- done();
-});
-
-hooks.before("POST /sessions -> 400", function(test, done) {
- test.request.body.foo = "not an allowed property";
- test.request.body.project = test_session_1.project;
- done();
-});
-
-hooks.before("PUT /sessions/{SessionId} -> 200", function(test, done) {
- test.request.params.SessionId = test_session_1._id;
- test.request.body = {
- project: test_session_1.project,
- label: "new-label-test-session-1"
- };
- done();
-});
-
-hooks.before("PUT /sessions/{SessionId} -> 400", function(test, done) {
- test.request.params.SessionId = test_session_1._id;
- test.request.body = {
- project: test_session_1.project,
- "not_a_real_property": "new-label-test-session-1"
- };
- done();
-});
-
-hooks.before("DELETE /sessions/{SessionId} -> 200", function(test, done) {
- test.request.params.SessionId = test_session_2_id;
- done();
-});
-
-
-hooks.before("GET /sessions/{SessionId}/jobs -> 200", function(test, done) {
- test.request.params.SessionId = test_session_1._id;
- done();
-});
-
-hooks.before("POST /sessions/{SessionId}/tags -> 200", function(test, done) {
- test.request.params.SessionId = test_session_1._id;
- test.request.body = {
- value: test_session_tag
- };
- done();
-});
-
-hooks.before("POST /sessions/{SessionId}/tags -> 400", function(test, done) {
- test.request.params.SessionId = test_session_1._id;
- test.request.body = {
- value: ""
- };
- done();
-});
-
-hooks.before("GET /sessions/{SessionId}/tags/{TagValue} -> 200", function(test, done) {
- test.request.params = {
- SessionId : test_session_1._id,
- TagValue: test_session_tag
- };
- done();
-});
-
-hooks.before("PUT /sessions/{SessionId}/tags/{TagValue} -> 200", function(test, done) {
- test.request.params = {
- SessionId : test_session_1._id,
- TagValue: test_session_tag
- };
- test_session_tag = 'new-tag-value';
- test.request.body = {
- value: test_session_tag
- };
- done();
-});
-
-hooks.before("PUT /sessions/{SessionId}/tags/{TagValue} -> 400", function(test, done) {
- test.request.params = {
- SessionId : test_session_1._id,
- TagValue: test_session_tag
- };
- test.request.body = {
- value: ""
- };
- done();
-});
-
-hooks.before("DELETE /sessions/{SessionId}/tags/{TagValue} -> 200", function(test, done) {
- test.request.params = {
- SessionId : test_session_1._id,
- TagValue: test_session_tag
- };
- done();
-});
-
-hooks.before("GET /sessions/{SessionId}/files/{FileName} -> 200", function(test, done) {
- test.request.params = {
- SessionId : test_session_1._id,
- FileName : "notes.txt"
- };
- test.request.query = {
- "ticket":""
- };
- done();
-});
-
-hooks.before("POST /sessions/{SessionId}/notes -> 200", function(test, done) {
- test.request.params = {
- SessionId : test_session_1._id
- };
- test.request.body = {
- "text":"test note"
- };
- done();
-});
-
-hooks.before("POST /sessions/{SessionId}/notes -> 400", function(test, done) {
- test.request.params = {
- SessionId : test_session_1._id
- };
- test.request.body = {
- "note a real":"property"
- };
- done();
-});
-
-hooks.before("GET /sessions/{SessionId}/notes/{NoteId} -> 200", function(test, done) {
- test.request.params = {
- SessionId : test_session_1._id,
- NoteId: test_session_1.notes[0]._id
- };
- done();
-});
-
-hooks.before("PUT /sessions/{SessionId}/notes/{NoteId} -> 200", function(test, done) {
- test.request.params = {
- SessionId : test_session_1._id,
- NoteId: test_session_1.notes[0]._id
- };
- test.request.body = {
- "text":"new note"
- };
- done();
-});
-
-hooks.before("PUT /sessions/{SessionId}/notes/{NoteId} -> 400", function(test, done) {
- test.request.params = {
- SessionId : test_session_1._id,
- NoteId: test_session_1.notes[0]._id
- };
- test.request.body = {
- "not a real":"property"
- };
- done();
-});
-
-hooks.before("DELETE /sessions/{SessionId}/notes/{NoteId} -> 200", function(test, done) {
- test.request.params = {
- SessionId : test_session_1._id,
- NoteId: test_session_1.notes[0]._id
- };
- done();
-});
-
-hooks.before("GET /sessions/{SessionId}/acquisitions -> 200", function(test, done) {
- test.request.params.SessionId = test_session_1._id;
- done();
-});
-
-hooks.before("POST /sessions/{SessionId}/analyses -> 200", function(test, done) {
- test.request.params.SessionId = test_session_1._id;
- test.request.query = {"job":"true"};
- test.request.body = {
- "analysis": {
- "label": "Test Analysis 1"
- },
- "job" : {
- "gear": "test-case-gear",
- "inputs": {},
- "tags": ["example"]
- }
- }
- done();
-});
-
-hooks.after("POST /sessions/{SessionId}/analyses -> 200", function(test, done) {
- test_session_1_analysis_2_id = test.response.body._id;
- done();
-});
-
-hooks.before("GET /sessions/{SessionId}/analyses/{AnalysisId} -> 200", function(test, done) {
- test.request.params.SessionId = test_session_1._id;
- test.request.params.AnalysisId = test_session_1_analysis_2_id;
- done();
-});
-
-hooks.before("DELETE /sessions/{SessionId}/analyses/{AnalysisId} -> 200", function(test, done) {
- test.request.params.SessionId = test_session_1._id;
- test.request.params.AnalysisId = test_session_1_analysis_2_id;
- done();
-});
-
-hooks.before("GET /sessions/{SessionId}/analyses/{AnalysisId}/files -> 200", function(test, done) {
- test.request.params.SessionId = test_session_1._id;
- test.request.params.AnalysisId = test_session_1.analyses[0]._id;
- test.request.query.ticket = "";
- done();
-});
-
-hooks.before("GET /sessions/{SessionId}/analyses/{AnalysisId}/files/{Filename} -> 200", function(test, done) {
- test.request.params.SessionId = test_session_1._id;
- test.request.params.AnalysisId = test_session_1.analyses[0]._id;
- test.request.params.Filename = "test-1.dcm";
- test.request.query.ticket = "";
- done();
-});
-
-hooks.before("POST /sessions/{SessionId}/analyses/{AnalysisId}/notes -> 200", function(test, done) {
- test.request.params.SessionId = test_session_1._id;
- test.request.params.AnalysisId = test_session_1.analyses[0]._id;
- done();
-});
-
-hooks.before("POST /sessions/{SessionId}/analyses/{AnalysisId}/notes -> 400", function(test, done) {
- test.request.params.SessionId = test_session_1._id;
- test.request.params.AnalysisId = test_session_1.analyses[0]._id;
- test.request.body = {
- "not a":"real property"
- };
- done();
-});
-
-hooks.before("DELETE /sessions/{SessionId}/analyses/{AnalysisId}/notes/{NoteId} -> 200", function(test, done) {
- test.request.params.SessionId = test_session_1._id;
- test.request.params.AnalysisId = test_session_1.analyses[0]._id;
- test.request.params.NoteId = test_session_1.analyses[0].notes[0]._id;
- done();
-});
-
-
-
-// set initial test_acquisition_1
-hooks.after("GET /acquisitions -> 200", function(test, done) {
- test_acquisition_1 = test.response.body[0];
- assert.equal(test_acquisition_1.label, "test-acquisition-1");
- done();
-});
-
-hooks.before("GET /acquisitions/{AcquisitionId} -> 200", function(test, done) {
- test.request.params.AcquisitionId = test_acquisition_1._id;
- done();
-});
-
-// set detailed test_acquisition_1 (including analyses, that are omitted during listing)
-hooks.after("GET /acquisitions/{AcquisitionId} -> 200", function(test, done) {
- test_acquisition_1 = test.response.body;
- done();
-});
-
-hooks.before("POST /acquisitions -> 200", function(test, done) {
- test.request.body.session = test_session_1._id;
- done();
-});
-
-hooks.after("POST /acquisitions -> 200", function(test, done) {
- example_acquisition_id = test.response.body._id;
- done();
-});
-
-hooks.before("POST /acquisitions -> 400", function(test, done) {
- test.request.body.session = test_session_1._id;
- test.request.body.foo = "bar";
- done();
-});
-
-hooks.before("PUT /acquisitions/{AcquisitionId} -> 200", function(test, done) {
- test.request.params.AcquisitionId = test_acquisition_1._id;
- test.request.body = {"label":"test-acquisition-1-new-label"};
- done();
-});
-
-
-hooks.before("PUT /acquisitions/{AcquisitionId} -> 400", function(test, done) {
- test.request.params.AcquisitionId = test_acquisition_1._id;
- test.request.body = {"not-real":"an invalid property"};
- done();
-});
-
-hooks.before("DELETE /acquisitions/{AcquisitionId} -> 200", function(test, done) {
- test.request.params.AcquisitionId = example_acquisition_id;
- done();
-});
-
-hooks.before("POST /acquisitions/{AcquisitionId}/tags -> 200", function(test, done) {
- test.request.params.AcquisitionId = test_acquisition_1._id;
- test.request.body = {
- "value": test_acquisition_tag
- };
- done();
-});
-
-hooks.before("POST /acquisitions/{AcquisitionId}/tags -> 400", function(test, done) {
- test.request.params.AcquisitionId = test_acquisition_1._id;
- test.request.body = {
- "value": test_acquisition_tag,
- "bad property": "not a real property"
- };
- done();
-});
-
-hooks.before("GET /acquisitions/{AcquisitionId}/tags/{TagValue} -> 200", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id,
- TagValue : test_acquisition_tag
- };
- done();
-});
-
-hooks.before("PUT /acquisitions/{AcquisitionId}/tags/{TagValue} -> 200", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id,
- TagValue : test_acquisition_tag
- };
- test_acquisition_tag = "new-tag-value";
- test.request.body = {
- "value": test_acquisition_tag
- };
- done();
-});
-
-hooks.before("PUT /acquisitions/{AcquisitionId}/tags/{TagValue} -> 400", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id,
- TagValue : test_acquisition_tag
- };
- test.request.body = {
- "value": test_acquisition_tag,
- "bad property": "not a real property"
- };
- done();
-});
-
-hooks.before("DELETE /acquisitions/{AcquisitionId}/tags/{TagValue} -> 200", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id,
- TagValue : test_acquisition_tag
- };
- done();
-});
-
-hooks.before("GET /acquisitions/{AcquisitionId}/files/{FileName} -> 200", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id,
- FileName : "test-1.dcm"
- };
- test.request.query = {
- "ticket":""
- };
- done();
-});
-
-hooks.before("POST /acquisitions/{AcquisitionId}/notes -> 200", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id
- };
- done();
-});
-
-hooks.before("POST /acquisitions/{AcquisitionId}/notes -> 400", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id
- };
- test.request.body.not_real = "invalid property";
- done();
-});
-
-hooks.before("GET /acquisitions/{AcquisitionId}/notes/{NoteId} -> 200", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id,
- NoteId: test_acquisition_1.notes[0]._id
- };
- done();
-});
-
-hooks.before("PUT /acquisitions/{AcquisitionId}/notes/{NoteId} -> 200", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id,
- NoteId: test_acquisition_1.notes[0]._id
- };
- test.request.body = {
- "text":"updated note text"
- };
- done();
-});
-
-hooks.before("PUT /acquisitions/{AcquisitionId}/notes/{NoteId} -> 400", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id,
- NoteId: test_acquisition_1.notes[0]._id
- };
- test.request.body = {
- "invalid property":"specified"
- };
- done();
-});
-
-hooks.before("DELETE /acquisitions/{AcquisitionId}/notes/{NoteId} -> 200", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id,
- NoteId: test_acquisition_1.notes[0]._id
- };
- done();
-});
-
-hooks.before("GET /acquisitions/{AcquisitionId}/analyses/{AnalysisId} -> 200", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id,
- AnalysisId: test_acquisition_1.analyses[0]._id
- };
- done();
-});
-
-hooks.before("DELETE /acquisitions/{AcquisitionId}/analyses/{AnalysisId} -> 200", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id,
- AnalysisId: test_acquisition_1.analyses[1]._id
- };
- done();
-});
-
-hooks.before("GET /acquisitions/{AcquisitionId}/analyses/{AnalysisId}/files -> 200", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id,
- AnalysisId: test_acquisition_1.analyses[0]._id
- };
- test.request.query.ticket = "";
- done();
-});
-
-hooks.before("GET /acquisitions/{AcquisitionId}/analyses/{AnalysisId}/files/{Filename} -> 200", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id,
- AnalysisId: test_acquisition_1.analyses[0]._id,
- Filename: "test-1.dcm"
- };
- test.request.query.ticket = "";
- done();
-});
-
-hooks.before("POST /acquisitions/{AcquisitionId}/analyses/{AnalysisId}/notes -> 200", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id,
- AnalysisId: test_acquisition_1.analyses[0]._id
- };
- done();
-});
-
-hooks.before("POST /acquisitions/{AcquisitionId}/analyses/{AnalysisId}/notes -> 400", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id,
- AnalysisId: test_acquisition_1.analyses[0]._id
- };
- test.request.body = {
- "not a":"real property"
- };
- done();
-});
-
-hooks.before("GET /acquisitions/{AcquisitionId}/analyses/{AnalysisId}/notes/{NoteId} -> 200", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id,
- AnalysisId: test_acquisition_1.analyses[0]._id,
- NoteId: test_acquisition_1.analyses[0].notes[0]._id
- };
- done();
-});
-
-hooks.before("DELETE /acquisitions/{AcquisitionId}/analyses/{AnalysisId}/notes/{NoteId} -> 200", function(test, done) {
- test.request.params = {
- AcquisitionId : test_acquisition_1._id,
- AnalysisId: test_acquisition_1.analyses[0]._id,
- NoteId: test_acquisition_1.analyses[0].notes[0]._id
- };
- done();
-});
-
-
-// set initial test_project_1
-hooks.after("GET /projects -> 200", function(test, done) {
- test_project_1 = test.response.body[0];
- assert.equal(test_project_1.label, "test-project-1");
- done();
-});
-
-hooks.after("POST /projects -> 200", function(test, done) {
- delete_project_id = test.response.body._id;
- done();
-});
-
-hooks.before("POST /projects -> 400", function(test, done) {
- test.request.body.not_real = "an invalid property";
- done();
-});
-
-hooks.before("GET /projects/{ProjectId} -> 200", function(test, done) {
- test.request.params.ProjectId = test_project_1._id;
- done();
-});
-
-// set detailed test_project_1 (including analyses, that are omitted during listing)
-hooks.after("GET /projects/{ProjectId} -> 200", function(test, done) {
- test_project_1 = test.response.body;
- done();
-});
-
-hooks.before("PUT /projects/{ProjectId} -> 400", function(test, done) {
- test.request.params.ProjectId = test_project_1._id;
- test.request.body = {"not_real":"fake property"};
- done();
-});
-
-hooks.before("DELETE /projects/{ProjectId} -> 200", function(test, done) {
- test.request.params.ProjectId = delete_project_id;
- done();
-});
-
-hooks.before("POST /projects/{ProjectId}/tags -> 200", function(test, done) {
- test.request.params.ProjectId = test_project_1._id;
- test.request.body = {
- "value":test_project_tag
- };
- done();
-});
-
-hooks.before("POST /projects/{ProjectId}/tags -> 400", function(test, done) {
- test.request.params.ProjectId = test_project_1._id;
- test.request.body = {
- "value":""
- };
- done();
-});
-
-hooks.before("GET /projects/{ProjectId}/tags/{TagValue} -> 200", function(test, done) {
- test.request.params = {
- ProjectId : test_project_1._id,
- TagValue : test_project_tag
- };
- done();
-});
-
-hooks.before("PUT /projects/{ProjectId}/tags/{TagValue} -> 200", function(test, done) {
- test.request.params = {
- ProjectId : test_project_1._id,
- TagValue : test_project_tag
- };
- test_project_tag = "new-tag-value";
- test.request.body = {
- "value":test_project_tag
- };
- done();
-});
-
-hooks.before("PUT /projects/{ProjectId}/tags/{TagValue} -> 400", function(test, done) {
- test.request.params = {
- ProjectId : test_project_1._id,
- TagValue : test_project_tag
- };
- test.request.body = {
- "value":""
- };
- done();
-});
-
-hooks.before("DELETE /projects/{ProjectId}/tags/{TagValue} -> 200", function(test, done) {
- test.request.params = {
- ProjectId : test_project_1._id,
- TagValue : test_project_tag
- };
- done();
-});
-
-hooks.before("GET /projects/{ProjectId}/files/{FileName} -> 200", function(test, done) {
- test.request.params = {
- ProjectId : test_project_1._id,
- FileName : "notes.txt"
- };
- test.request.query = {
- "ticket":""
- };
- done();
-});
-
-hooks.before("POST /projects/{ProjectId}/permissions -> 200", function(test, done) {
- test.request.params = {
- ProjectId : test_project_1._id
- };
- test.request.body = {
- "_id":"test@user.com",
- "access":"ro"
- };
- done();
-});
-
-hooks.before("POST /projects/{ProjectId}/permissions -> 400", function(test, done) {
- test.request.params = {
- ProjectId : test_project_1._id
- };
- test.request.body = {
- "not a valid":"permissions entry"
- };
- done();
-});
-
-hooks.before("GET /projects/{ProjectId}/permissions/{UserId} -> 200", function(test, done) {
- test.request.params = {
- ProjectId : test_project_1._id,
- UserId: "test@user.com"
- };
- done();
-});
-
-hooks.before("PUT /projects/{ProjectId}/permissions/{UserId} -> 200", function(test, done) {
- test.request.params = {
- ProjectId : test_project_1._id,
- UserId: "test@user.com"
- };
- test.request.body = {
- "access":"rw",
- "_id":"test@user.com"
- };
- done();
-});
-
-hooks.before("PUT /projects/{ProjectId}/permissions/{UserId} -> 400", function(test, done) {
- test.request.params = {
- ProjectId : test_project_1._id,
- UserId: "test@user.com"
- };
- test.request.body = {
- "not a valid":"permissions entry"
- };
- done();
-});
-
-hooks.before("DELETE /projects/{ProjectId}/permissions/{UserId} -> 200", function(test, done) {
- test.request.params = {
- ProjectId : test_project_1._id,
- UserId: "test@user.com"
- };
- done();
-});
-
-hooks.before("POST /projects/{ProjectId}/notes -> 200", function(test, done) {
- test.request.params = {
- ProjectId : test_project_1._id
- };
- test.request.body = {
- "text":"test note"
- };
- done();
-});
-
-hooks.before("POST /projects/{ProjectId}/notes -> 400", function(test, done) {
- test.request.params = {
- ProjectId : test_project_1._id
- };
- test.request.body = {
- "not a real":"property"
- };
- done();
-});
-
-hooks.before("GET /projects/{ProjectId}/notes/{NoteId} -> 200", function(test, done) {
- test.request.params = {
- ProjectId : test_project_1._id,
- NoteId: test_project_1.notes[0]._id
- };
- done();
-});
-
-hooks.before("PUT /projects/{ProjectId}/notes/{NoteId} -> 200", function(test, done) {
- test.request.params = {
- ProjectId : test_project_1._id,
- NoteId: test_project_1.notes[0]._id
- };
- test.request.body = {
- "text":"updated note"
- };
- done();
-});
-
-hooks.before("PUT /projects/{ProjectId}/notes/{NoteId} -> 400", function(test, done) {
- test.request.params = {
- ProjectId : test_project_1._id,
- NoteId: test_project_1.notes[0]._id
- };
- test.request.body = {
- "not a real":"property"
- };
- done();
-});
-
-hooks.before("DELETE /projects/{ProjectId}/notes/{NoteId} -> 200", function(test, done) {
- test.request.params = {
- ProjectId : test_project_1._id,
- NoteId: test_project_1.notes[0]._id
- };
- done();
-});
-
-hooks.before("GET /projects/{ProjectId}/sessions -> 200", function(test, done) {
- test.request.params.ProjectId = test_project_1._id;
- done();
-});
-
-hooks.before("GET /projects/{ProjectId}/acquisitions -> 200", function(test, done) {
- test.request.params.ProjectId = test_project_1._id;
- done();
-});
-
-hooks.before("GET /report/project -> 200", function(test, done) {
- test.request.query = {
- "projects":test_project_1._id
- };
- done();
-});
-
-hooks.before("GET /projects/{ProjectId}/analyses/{AnalysisId} -> 200", function(test, done) {
- test.request.params = {
- ProjectId: test_project_1._id,
- AnalysisId: test_project_1.analyses[0]._id
- };
- done();
-});
-
-hooks.before("DELETE /projects/{ProjectId}/analyses/{AnalysisId} -> 200", function(test, done) {
- test.request.params = {
- ProjectId: test_project_1._id,
- AnalysisId: test_project_1.analyses[1]._id
- };
- done();
-});
-
-hooks.before("GET /projects/{ProjectId}/analyses/{AnalysisId}/files -> 200", function(test, done) {
- test.request.params = {
- ProjectId: test_project_1._id,
- AnalysisId: test_project_1.analyses[0]._id
- };
- test.request.query.ticket = "";
- done();
-});
-
-hooks.before("GET /projects/{ProjectId}/analyses/{AnalysisId}/files/{Filename} -> 200", function(test, done) {
- test.request.params = {
- ProjectId: test_project_1._id,
- AnalysisId: test_project_1.analyses[0]._id,
- Filename: "test-1.dcm"
- };
- test.request.query.ticket = "";
- done();
-});
-
-hooks.before("POST /projects/{ProjectId}/analyses/{AnalysisId}/notes -> 200", function(test, done) {
- test.request.params = {
- ProjectId: test_project_1._id,
- AnalysisId: test_project_1.analyses[0]._id
- };
- done();
-});
-
-
-hooks.before("POST /projects/{ProjectId}/analyses/{AnalysisId}/notes -> 400", function(test, done) {
- test.request.params = {
- ProjectId: test_project_1._id,
- AnalysisId: test_project_1.analyses[0]._id
- };
- test.request.body = {
- "not a":"real property"
- }
- done();
-});
-
-hooks.before("DELETE /projects/{ProjectId}/analyses/{AnalysisId}/notes/{NoteId} -> 200", function(test, done) {
- test.request.params = {
- ProjectId: test_project_1._id,
- AnalysisId: test_project_1.analyses[0]._id,
- NoteId: test_project_1.analyses[0].notes[0]._id
- };
- done();
-});
-
-hooks.before("GET /devices/{DeviceId} -> 200", function(test, done) {
- test.request.params.DeviceId = device_id;
- done();
-});
-
-hooks.before("GET /devices/{DeviceId} -> 404", function(test, done) {
- test.request.params.DeviceId = 'bad_device_id';
- done();
-});
diff --git a/tests/integration_tests/abao/load_fixture.py b/tests/integration_tests/abao/load_fixture.py
deleted file mode 100644
index 32c036bdc8cc9ffb735a7658657ef358c5338786..0000000000000000000000000000000000000000
--- a/tests/integration_tests/abao/load_fixture.py
+++ /dev/null
@@ -1,433 +0,0 @@
-import datetime
-import json
-import os
-
-import pymongo
-import requests
-
-
-# load required envvars w/ the same name
-SCITRAN_CORE_DRONE_SECRET = os.environ['SCITRAN_CORE_DRONE_SECRET']
-SCITRAN_PERSISTENT_DB_URI = os.environ['SCITRAN_PERSISTENT_DB_URI']
-SCITRAN_SITE_API_URL = os.environ['SCITRAN_SITE_API_URL']
-
-
-class BaseUrlSession(requests.Session):
- """Requests session subclass using core api's base url"""
- def request(self, method, url, **kwargs):
- return super(BaseUrlSession, self).request(method, SCITRAN_SITE_API_URL + url, **kwargs)
-
-
-def main():
- abao_user = 'abao@user.com'
- abao_api_key = 'XZpXI40Uk85eozjQkU1zHJ6yZHpix+j0mo1TMeGZ4dPzIqVPVGPmyfeK'
-
- as_drone = BaseUrlSession()
- as_drone.headers.update({
- 'X-SciTran-Method': 'bootstrapper',
- 'X-SciTran-Name': 'Bootstrapper',
- 'X-SciTran-Auth': SCITRAN_CORE_DRONE_SECRET,
- })
-
- as_drone.post('/users', json={
- '_id': abao_user,
- 'firstname': 'Abao',
- 'lastname': 'User',
- 'root': True,
- })
- api_db = pymongo.MongoClient(SCITRAN_PERSISTENT_DB_URI).get_default_database()
- api_db.apikeys.insert_one({
- '_id': abao_api_key,
- 'created': datetime.datetime.utcnow(),
- 'last_seen': None,
- 'type': 'user',
- 'uid': abao_user
- })
-
- as_root = BaseUrlSession()
- as_root.headers.update({'Authorization': 'scitran-user {}'.format(abao_api_key)})
- as_root.params.update({'root': 'true'})
-
- # create scitran group
- r = as_root.post('/groups', json={'_id': 'scitran'})
- assert r.ok
-
- # create test-group
- r = as_root.post('/groups', json={'_id': 'test-group'})
- assert r.ok
-
- # upload file to test-project-1/test-session-1/test-acquisition-1
- # depends on 'create test-group'
- r = as_root.post('/upload/label', files={
- 'file': ('test-1.dcm', open('tests/integration_tests/abao/test_files/test-1.dcm', 'rb')),
- 'metadata': ('', json.dumps({
- 'group': { '_id': 'test-group' },
- 'project': {
- 'label': 'test-project-1'
- },
- 'session': {
- 'label': 'test-session-1',
- 'subject': {
- 'age': 25,
- 'sex': 'male',
- 'firstname': 'xyz'
- }
- },
- 'acquisition': {
- 'label': 'test-acquisition-1',
- 'files': [{ 'name': 'test-1.dcm' }]
- }
- }))
- })
- assert r.ok
-
- # list projects
- # depends on 'upload file to test-project-1/test-session-1/test-acquisition-1'
- r = as_root.get('/projects')
- assert r.ok
- assert r.json()[0]['label'] == 'test-project-1'
- test_project = r.json()[0]
-
- # list sessions
- # depends on 'upload file to test-project-1/test-session-1/test-acquisition-1'
- r = as_root.get('/sessions')
- assert r.ok
- assert r.json()[0]['label'] == 'test-session-1'
- test_session = r.json()[0]
-
- # list acquisitions for test-session-1
- # depends on 'upload file to test-project-1/test-session-1/test-acquisition-1'
- r = as_root.get('/sessions/' + test_session['_id'] + '/acquisitions')
- assert r.ok
- assert r.json()[0]['label'] == 'test-acquisition-1'
- test_acquisition = r.json()[0]
-
- # add test-case-gear
- r = as_root.post('/gears/test-case-gear', json={
- 'category': 'converter',
- 'gear': {
- 'inputs': {
- 'dicom': {
- 'base': 'file',
- 'type': { 'enum': [ 'wat' ] }
- }
- },
- 'maintainer': 'Example',
- 'description': 'Example',
- 'license': 'BSD-2-Clause',
- 'author': 'Example',
- 'url': 'https://example.example',
- 'label': 'wat',
- 'flywheel': '0',
- 'source': 'https://example.example',
- 'version': '0.0.1',
- 'config': {},
- 'name': 'test-case-gear'
- },
- 'exchange': {
- 'git-commit': 'aex',
- 'rootfs-hash': 'sha384:oy',
- 'rootfs-url': 'https://example.example'
- }
- })
- assert r.ok
- test_gear = r.json()
-
- # create test-collection-1
- r = as_root.post('/collections', json={
- 'label': 'test-collection-1'
- })
- assert r.ok
- test_collection = r.json()
-
- # add test-session-1 to test-collection-1
- # depends on 'upload file to test-project-1/test-session-1/test-acquisition-1'
- # depends on 'create test-collection-1'
- r = as_root.put('/collections/' + test_collection['_id'], json={
- 'contents':{
- 'operation': 'add',
- 'nodes': [{
- 'level': 'session',
- '_id': test_session['_id']
- }]
- }
- })
- assert r.ok
-
- # upload file to test-collection-1
- # depends on 'create test-collection-1'
- r = as_root.post('/collections/' + test_collection['_id'] + '/files', files={
- 'file': ('notes.txt', open('tests/integration_tests/abao/test_files/notes.txt', 'rb'))
- })
- assert r.ok
-
- # create test-collection-2
- r = as_root.post('/collections', json={
- 'label': 'test-collection-2'
- })
- assert r.ok
-
- # upload file to test-project-1
- # depends on 'upload file to test-project-1/test-session-1/test-acquisition-1'
- r = as_root.post('/projects/' + test_project['_id'] + '/files', files={
- 'file': ('notes.txt', open('tests/integration_tests/abao/test_files/notes.txt', 'rb'))
- })
- assert r.ok
-
- # upload file to test-session-1
- # depends on 'upload file to test-project-1/test-session-1/test-acquisition-1'
- r = as_root.post('/sessions/' + test_session['_id'] + '/files', files={
- 'file': ('notes.txt', open('tests/integration_tests/abao/test_files/notes.txt', 'rb'))
- })
- assert r.ok
-
- # add a note to test-project-1
- # depends on 'upload file to test-project-1/test-session-1/test-acquisition-1'
- r = as_root.post('/projects/' + test_project['_id'] + '/notes', json={
- 'text': 'test note'
- })
- assert r.ok
-
- # add a note to test-session-1
- # depends on 'upload file to test-project-1/test-session-1/test-acquisition-1'
- r = as_root.post('/sessions/' + test_session['_id'] + '/notes', json={
- 'text': 'test note'
- })
- assert r.ok
-
- # add a note to test-acquisition-1
- # depends on 'upload file to test-project-1/test-session-1/test-acquisition-1'
- r = as_root.post('/acquisitions/' + test_acquisition['_id'] + '/notes', json={
- 'text': 'test note'
- })
- assert r.ok
-
- # add a note to test-collection-1
- # depends on 'create test-collection-1'
- r = as_root.post('/collections/' + test_collection['_id'] + '/notes', json={
- 'text': 'test note'
- })
- assert r.ok
-
- # create session 1 test-analysis-1 (job)
- # depends on 'upload file to test-project-1/test-session-1/test-acquisition-1'
- # depends on 'add test-case-gear'
- r = as_root.post('/sessions/' + test_session['_id'] + '/analyses?job=true', json={
- 'analysis': { 'label': 'Test Analysis 1' },
- 'job': {
- 'gear_id': test_gear['_id'],
- 'inputs': {
- 'dicom': {
- 'type': 'acquisition',
- 'id': test_acquisition['_id'],
- 'name': 'test-1.dcm'
- }
- },
- 'tags': ['example']
- }
- })
- assert r.ok
- test_session_analysis = r.json()
-
- # create session 1 test-analysis (file upload)
- # depends on 'upload file to test-project-1/test-session-1/test-acquisition-1'
- r = as_root.post('/sessions/' + test_session['_id'] + '/analyses', files={
- 'file': ('test-1.dcm', open('tests/integration_tests/abao/test_files/test-1.dcm', 'rb')),
- 'metadata': ('', json.dumps({
- 'label': 'test analysis',
- 'inputs': [ { 'name': 'test-1.dcm' } ]
- }))
- })
- assert r.ok
- test_session_analysis_upload = r.json()
-
- # delete session 1 test analysis (file upload)
- # depends on 'create session 1 test-analysis (file upload)'
- r = as_root.delete('/sessions/' + test_session['_id'] + '/analyses/' + test_session_analysis_upload['_id'])
- assert r.ok
-
- # create acquisition 1 test-analysis (file upload)
- # depends on 'upload file to test-project-1/test-session-1/test-acquisition-1'
- r = as_root.post('/acquisitions/' + test_acquisition['_id'] + '/analyses', files={
- 'file': ('test-1.dcm', open('tests/integration_tests/abao/test_files/test-1.dcm', 'rb')),
- 'metadata': ('', json.dumps({
- 'label': 'test analysis',
- 'inputs': [ { 'name': 'test-1.dcm' } ]
- }))
- })
- assert r.ok
- test_acquisition_analysis_upload = r.json()
-
- # create acquisition 1 test-analysis 2 (file upload)
- # depends on 'upload file to test-project-1/test-session-1/test-acquisition-1'
- r = as_root.post('/acquisitions/' + test_acquisition['_id'] + '/analyses', files={
- 'file': ('test-1.dcm', open('tests/integration_tests/abao/test_files/test-1.dcm', 'rb')),
- 'metadata': ('', json.dumps({
- 'label': 'test analysis',
- 'inputs': [ { 'name': 'test-1.dcm' } ]
- }))
- })
- assert r.ok
-
- # create collection 1 test-analysis (file upload)
- # depends on 'create test-collection-1'
- r = as_root.post('/collections/' + test_collection['_id'] + '/analyses', files={
- 'file': ('test-1.dcm', open('tests/integration_tests/abao/test_files/test-1.dcm', 'rb')),
- 'metadata': ('', json.dumps({
- 'label': 'test analysis',
- 'inputs': [ { 'name': 'test-1.dcm' } ]
- }))
- })
- assert r.ok
- test_collection_analysis_upload = r.json()
-
- # create collection 1 test-analysis 2 (file upload)
- # depends on 'create test-collection-1'
- r = as_root.post('/collections/' + test_collection['_id'] + '/analyses', files={
- 'file': ('test-1.dcm', open('tests/integration_tests/abao/test_files/test-1.dcm', 'rb')),
- 'metadata': ('', json.dumps({
- 'label': 'test analysis 2',
- 'inputs': [ { 'name': 'test-1.dcm' } ]
- }))
- })
- assert r.ok
-
- # create project 1 test-analysis (file upload)
- # depends on 'upload file to test-project-1/test-session-1/test-acquisition-1'
- r = as_root.post('/projects/' + test_project['_id'] + '/analyses', files={
- 'file': ('test-1.dcm', open('tests/integration_tests/abao/test_files/test-1.dcm', 'rb')),
- 'metadata': ('', json.dumps({
- 'label': 'test analysis',
- 'inputs': [ { 'name': 'test-1.dcm' } ]
- }))
- })
- assert r.ok
- test_project_analysis_upload = r.json()
-
- # create project 1 test-analysis 2 (file upload)
- # depends on 'upload file to test-project-1/test-session-1/test-acquisition-1'
- r = as_root.post('/projects/' + test_project['_id'] + '/analyses', files={
- 'file': ('test-1.dcm', open('tests/integration_tests/abao/test_files/test-1.dcm', 'rb')),
- 'metadata': ('', json.dumps({
- 'label': 'test analysis',
- 'inputs': [ { 'name': 'test-1.dcm' } ]
- }))
- })
- assert r.ok
-
- # add a note to test-acquisition-1 test-analysis-1
- # depends on 'create acquisition 1 test-analysis (file upload)'
- r = as_root.post('/acquisitions/' + test_acquisition['_id'] + '/analyses/' + test_acquisition_analysis_upload['_id'] + '/notes', json={
- 'text': 'test note'
- })
- assert r.ok
-
- # add a note to test-collection-1 test-analysis-1
- # depends on 'create test-collection-1'
- r = as_root.post('/collections/' + test_collection['_id'] + '/analyses/' + test_collection_analysis_upload['_id'] + '/notes', json={
- 'text': 'test note'
- })
- assert r.ok
-
- # add a note to test-session-1 test-analysis-1
- # depends on 'create session 1 test-analysis (file upload)'
- r = as_root.post('/sessions/' + test_session['_id'] + '/analyses/' + test_session_analysis['_id'] + '/notes', json={
- 'text': 'test note'
- })
- assert r.ok
-
- # add a note to test-project-1 test-analysis-1
- # depends on 'create project 1 test-analysis (file upload)'
- r = as_root.post('/projects/' + test_project['_id'] + '/analyses/' + test_project_analysis_upload['_id'] + '/notes', json={
- 'text': 'test note'
- })
- assert r.ok
-
- # create project
- r = as_root.post('/projects', json={
- 'group': 'test-group',
- 'label': 'Project with template',
- 'public': False
- })
- assert r.ok
- st_project = r.json()
-
- # create compliant session
- # depends on 'create project'
- r = as_root.post('/sessions', json={
- 'subject': { 'code': 'ex8945' },
- 'label': 'Compliant Session',
- 'project': st_project['_id'],
- 'public': False
- })
- assert r.ok
- st_compliant_session = r.json()
-
- # create non-compliant session
- # depends on 'create project'
- r = as_root.post('/sessions', json={
- 'subject': { 'code': 'ex9849' },
- 'label': 'Non-compliant Session',
- 'project': st_project['_id'],
- 'public': False
- })
- assert r.ok
- st_noncompliant_session = r.json()
-
- # create acquisition-1 for compliant session
- # depends on 'create compliant session'
- r = as_root.post('/acquisitions', json={
- 'label': 'c-acquisition-1-t1',
- 'session': st_compliant_session['_id'],
- 'public': False
- })
- assert r.ok
-
- # create acquisition-2 for compliant session
- # depends on 'create compliant session'
- r = as_root.post('/acquisitions', json={
- 'label': 'c-acquisition-2-t1',
- 'session': st_compliant_session['_id'],
- 'public': False
- })
- assert r.ok
-
- # create acquisition-1 for noncompliant session
- # depends on 'create non-compliant session'
- r = as_root.post('/acquisitions', json={
- 'label': 'nc-acquisition-1-t1',
- 'session': st_noncompliant_session['_id'],
- 'public': False
- })
- assert r.ok
-
- # add project template
- r = as_root.post('/projects/' + st_project['_id'] + '/template', json={
- 'session': { 'subject': { 'code' : '^ex' } },
- 'acquisitions': [{
- 'label': 't1',
- 'minimum': 2
- }]
- })
- assert r.ok
- assert r.json()['modified'] == 1
-
- # create acquisition-2 for noncompliant session
- # depends on 'create non-compliant session'
- r = as_root.post('/acquisitions', json={
- 'label': 'nc-acquisition-2-t1',
- 'session': st_noncompliant_session['_id'],
- 'public': False
- })
- assert r.ok
-
- # update session 2 to be non-compliant
- # depends on 'create non-compliant session'
- r = as_root.put('/sessions/' + st_noncompliant_session['_id'], json={
- 'subject': { 'code': 'bad-subject-code' }
- })
- assert r.ok
-
-
-if __name__ == '__main__':
- main()
diff --git a/tests/integration_tests/abao/test_files/engine-analyses-1.txt b/tests/integration_tests/abao/test_files/engine-analyses-1.txt
deleted file mode 100644
index 6686dd9ae599f5946313397b37162b2053445cc8..0000000000000000000000000000000000000000
--- a/tests/integration_tests/abao/test_files/engine-analyses-1.txt
+++ /dev/null
@@ -1 +0,0 @@
-Replace this with something more realistic
diff --git a/tests/integration_tests/abao/test_files/notes.txt b/tests/integration_tests/abao/test_files/notes.txt
deleted file mode 100644
index 907b308167f0880fb2a5c0e1614bb0c7620f9dc3..0000000000000000000000000000000000000000
--- a/tests/integration_tests/abao/test_files/notes.txt
+++ /dev/null
@@ -1 +0,0 @@
-blah
diff --git a/tests/integration_tests/abao/test_files/test-1.dcm b/tests/integration_tests/abao/test_files/test-1.dcm
deleted file mode 100644
index f088aa8f90a25afd9b2b19c1cc9ceaa325d26915..0000000000000000000000000000000000000000
Binary files a/tests/integration_tests/abao/test_files/test-1.dcm and /dev/null differ
diff --git a/tests/integration_tests/python/test_handlers.py b/tests/integration_tests/python/test_handlers.py
index 65b5133cd9682cf23043a086f5a1e14a6e8d4638..668b867ef1bed289f63ed31ab4d28c37501bf665 100644
--- a/tests/integration_tests/python/test_handlers.py
+++ b/tests/integration_tests/python/test_handlers.py
@@ -14,7 +14,7 @@ def test_schemahandler(as_public):
r = as_public.get('/schemas/definitions/user.json')
assert r.ok
schema = r.json()
- assert all(attr in schema['definitions'] for attr in ('_id', 'firstname', 'lastname'))
+ assert all(attr in schema['definitions'] for attr in ('email', 'firstname', 'lastname'))
def test_devicehandler(as_user, as_root, as_drone, api_db):
diff --git a/tests/unit_tests/python/test_validators.py b/tests/unit_tests/python/test_validators.py
index 8e14c1db16e7af86a4fc1d16f6d330fffcea0340..0dcfb157e7f8f2163423a4525132f189a950ee58 100644
--- a/tests/unit_tests/python/test_validators.py
+++ b/tests/unit_tests/python/test_validators.py
@@ -121,13 +121,30 @@ def pytest_generate_tests(metafunc):
# Helper to load the example data from a file
def load_example_data(schema_type, schema_name):
+ example_path = None
example_data = None
- relpath = os.path.join(schema_type, '{0}.json'.format(schema_name))
-
- if relpath in EXAMPLES_MAP:
- example_path = os.path.join(EXAMPLES_PATH, EXAMPLES_MAP[relpath])
- else:
- example_path = os.path.join(EXAMPLES_PATH, relpath)
+ # First check if there is example data in the schema file
+ relpath = os.path.join(SCHEMAS_PATH, schema_type, '{0}.json'.format(schema_name))
+ if os.path.exists(relpath):
+ with open(relpath) as f:
+ schema_data = json.load(f)
+ if schema_data and 'example' in schema_data:
+ example_data = schema_data['example']
+ if '$ref' in example_data:
+ # Resolve ref
+ example_path = os.path.join(relpath, example_data['$ref'])
+ example_data = None
+ else:
+ return schema_data['example']
+
+ # Then check in the examples folder
+ if example_path is None or not os.path.exists(example_path):
+ relpath = os.path.join(schema_type, '{0}.json'.format(schema_name))
+
+ if relpath in EXAMPLES_MAP:
+ example_path = os.path.join(EXAMPLES_PATH, EXAMPLES_MAP[relpath])
+ else:
+ example_path = os.path.join(EXAMPLES_PATH, relpath)
if os.path.exists(example_path):
with open(example_path) as f: