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Commit 8fd1965d authored by Colton Leekley-Winslow's avatar Colton Leekley-Winslow
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Add RAML for ContainerHandler based routes

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raml/examples/output/container-delete.json 0 → 100644
+ 1
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{"deleted":1}
raml/examples/output/container-new.json 0 → 100644
+ 3
− 0
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{
"_id":"57bb486a9e512c41c8b7fdd5"
}
raml/examples/output/container-update.json 0 → 100644
+ 1
− 0
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{"modified":1}
raml/examples/output/job-list.json
+ 8
− 2
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...@@ -20,7 +20,10 @@ ...@@ -20,7 +20,10 @@
"modified": "2016-08-11T12:46:12.593000+00:00", "modified": "2016-08-11T12:46:12.593000+00:00",
"created": "2016-08-11T12:46:12.593000+00:00", "created": "2016-08-11T12:46:12.593000+00:00",
"state": "pending", "state": "pending",
"_id": "57ac7394c700190017123fb8" "_id": "57ac7394c700190017123fb8",
"config":{
"speed":3
}
}, },
{ {
"inputs": [ "inputs": [
...@@ -44,6 +47,9 @@ ...@@ -44,6 +47,9 @@
"modified": "2016-08-11T13:02:09.055000+00:00", "modified": "2016-08-11T13:02:09.055000+00:00",
"created": "2016-08-11T13:02:09.055000+00:00", "created": "2016-08-11T13:02:09.055000+00:00",
"state": "pending", "state": "pending",
"_id": "57ac77515e325c0018cd17cf" "_id": "57ac77515e325c0018cd17cf",
"config":{
"speed":3
} }
}
] ]
raml/examples/output/job-next.json 0 → 100755
+ 44
− 0
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{
"inputs": [{
"input": "dicom",
"type": "acquisition",
"id": "57e45279a74e91000ed6898f",
"name": "4784_1_1_localizer_dicom.zip"
}],
"attempt": 1,
"name": "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
}
raml/examples/output/job.json
+ 4
− 1
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...@@ -19,5 +19,8 @@ ...@@ -19,5 +19,8 @@
"modified": "2016-08-11T13:02:09.055000+00:00", "modified": "2016-08-11T13:02:09.055000+00:00",
"created": "2016-08-11T13:02:09.055000+00:00", "created": "2016-08-11T13:02:09.055000+00:00",
"state": "pending", "state": "pending",
"id": "57ac77515e325c0018cd17cf" "id": "57ac77515e325c0018cd17cf",
"config":{
"speed":3
}
} }
raml/examples/output/project-list.json 0 → 100644
+ 60
− 0
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[{
"group": "scitran",
"created": "2016-09-22T21:51:53.151000+00:00",
"modified": "2016-09-22T21:51:53.151000+00:00",
"label": "Neuroscience",
"_id": "57e452791cff88b85f9f9c97",
"public": false,
"permissions": [{
"access": "admin",
"_id": "coltonlw@flywheel.io",
"site": "local"
}]
}, {
"group": "scitran",
"created": "2016-09-22T21:52:27.576000+00:00",
"modified": "2016-09-22T21:52:27.576000+00:00",
"label": "Psychology",
"_id": "57e4529b1cff88b85f9f9c98",
"public": false,
"permissions": [{
"access": "admin",
"_id": "coltonlw@flywheel.io",
"site": "local"
}]
}, {
"group": "scitran",
"created": "2016-09-22T21:52:52.539000+00:00",
"modified": "2016-09-22T21:52:52.539000+00:00",
"label": "Testdata",
"_id": "57e452b41cff88b85f9f9c99",
"public": false,
"permissions": [{
"access": "admin",
"_id": "coltonlw@flywheel.io",
"site": "local"
}]
}, {
"group": "test-group",
"created": "2016-09-22T21:54:47.925000+00:00",
"modified": "2016-09-22T21:54:47.925000+00:00",
"label": "test-project",
"_id": "57e45327466d8e000e33a859",
"public": false,
"permissions": [{
"access": "admin",
"_id": "coltonlw@flywheel.io",
"site": "local"
}]
}, {
"group": "scitran",
"created": "2016-09-29T18:53:06.199000+00:00",
"modified": "2016-09-29T18:53:06.199000+00:00",
"label": "test2",
"_id": "57ed6312466d8e01c91ee427",
"permissions": [{
"access": "admin",
"_id": "coltonlw@flywheel.io",
"site": "local"
}]
}]
raml/examples/output/project.json 0 → 100644
+ 13
− 0
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{
"group": "scitran",
"created": "2016-09-22T21:51:53.151000+00:00",
"modified": "2016-09-22T21:51:53.151000+00:00",
"label": "Neuroscience",
"_id": "57e452791cff88b85f9f9c97",
"public": false,
"permissions": [{
"access": "admin",
"_id": "coltonlw@flywheel.io",
"site": "local"
}]
}
raml/examples/output/session-jobs.json 0 → 100644
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{
"57ebe5adf0a2c90027d2bd44": [
{
"inputs": {
"dicom": {
"type": "acquisition",
"id": "57ebe5adf0a2c90027d2bd44",
"name": "1_1_dicom.zip"
}
},
"attempt": 1,
"name": "dcm_convert",
"tags": [
"dcm_convert",
"spectroscopy"
],
"destination": {
"type": "acquisition",
"id": "57ebe5adf0a2c90027d2bd44"
},
"request": {
"inputs": [
{
"type": "scitran",
"uri": "/jobs/57ebe5adf0a2c90027d2bd48/config.json",
"location": "/flywheel/v0"
},
{
"type": "scitran",
"uri": "/acquisitions/57ebe5adf0a2c90027d2bd44/files/1_1_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=57ebe5adf0a2c90027d2bd44&job=57ebe5adf0a2c90027d2bd48",
"location": "/flywheel/v0/output"
}
]
},
"modified": "2016-09-28T15:45:52.607000+00:00",
"created": "2016-09-28T15:45:49.975000+00:00",
"state": "running",
"config": {},
"id": "57ebe5adf0a2c90027d2bd48"
}
]
}
raml/examples/output/session-list.json 0 → 100644
+ 52
− 0
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[{
"group": "scitran",
"created": "2016-09-19T17:13:48.164000+00:00",
"subject": {
"code": "ex4784",
"_id": "57e01cccb1dc04000fb83f02"
},
"modified": "2016-09-19T17:13:48.164000+00:00",
"label": "control_1",
"project": "57e01cccf6b5d5edbcb4e1cf",
"_id": "57e01cccb1dc04000fb83f03",
"public": false,
"permissions": [{
"access": "admin",
"_id": "coltonlw@flywheel.io",
"site": "local"
}]
}, {
"group": "scitran",
"created": "2016-09-19T17:13:54.873000+00:00",
"subject": {
"code": "ex6879",
"_id": "57e01cd2b1dc04000eb83f05"
},
"modified": "2016-09-19T17:13:54.873000+00:00",
"label": "control_2",
"project": "57e01cccf6b5d5edbcb4e1cf",
"_id": "57e01cd2b1dc04000eb83f06",
"public": false,
"permissions": [{
"access": "admin",
"_id": "coltonlw@flywheel.io",
"site": "local"
}]
}, {
"group": "scitran",
"created": "2016-09-19T17:14:02.228000+00:00",
"subject": {
"code": "ex8403",
"_id": "57e01cdab1dc04000eb83f10"
},
"modified": "2016-09-19T17:14:02.228000+00:00",
"label": "patient_1",
"project": "57e01cccf6b5d5edbcb4e1cf",
"_id": "57e01cdab1dc04000eb83f11",
"public": false,
"permissions": [{
"access": "admin",
"_id": "coltonlw@flywheel.io",
"site": "local"
}]
}]
raml/examples/output/session.json 0 → 100644
+ 18
− 0
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{
"group": "scitran",
"created": "2016-09-19T17:13:48.164000+00:00",
"subject": {
"code": "ex4784",
"_id": "57e01cccb1dc04000fb83f02"
},
"modified": "2016-09-19T17:13:48.164000+00:00",
"label": "control_1",
"project": "57e01cccf6b5d5edbcb4e1cf",
"_id": "57e01cccb1dc04000fb83f03",
"public": false,
"permissions": [{
"access": "admin",
"_id": "coltonlw@flywheel.io",
"site": "local"
}]
}
raml/resourceTypes/container-item.raml 0 → 100644
+ 25
− 0
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get:
description: Get a single <<resourcePathName|!singularize>>
responses:
200:
body:
application/json:
put:
description: Update a <<resourcePathName|!singularize>>
is: ["validates-json-body"]
body:
application/json:
responses:
200:
body:
application/json:
schema: !include ../schemas/output/container-update.json
example: !include ../examples/output/container-update.json
delete:
description: Delete a <<resourcePathName|!singularize>>
responses:
200:
body:
application/json:
schema: !include ../schemas/output/container-delete.json
example: !include ../examples/output/container-delete.json
raml/resourceTypes/container.raml 0 → 100644
+ 19
− 0
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description: <<resourcePathName|!pluralize>> in the Scitran Core API
get:
description: Get a list of <<resourcePathName>>
responses:
200:
body:
application/json:
post:
description: |
Add a new <<resourcePathName|!singularize>>
is: ["validates-json-body"]
body:
application/json:
responses:
200:
body:
application/json:
schema: !include ../schemas/output/container-new.json
example: !include ../examples/output/container-new.json
raml/resources/acquisitions.raml 0 → 100644
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− 0
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type: container
get:
responses:
200:
body:
application/json:
example: !include ../examples/output/acquisition-list.json
schema: !include ../schemas/output/acquisition-list.json
post:
description: Create a acquisition
body:
application/json:
example: !include ../examples/input/acquisition.json
schema: !include ../schemas/input/acquisition.json
/{AcquisitionId}:
type: container-item
get:
responses:
200:
body:
application/json:
example: !include ../examples/output/acquisition.json
schema: !include ../schemas/output/acquisition.json
put:
body:
application/json:
example: !include ../examples/input/acquisition-update.json
schema: !include ../schemas/input/acquisition-update.json
raml/resources/collections.raml
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− 1
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...@@ -4,4 +4,72 @@ get: ...@@ -4,4 +4,72 @@ get:
200: 200:
body: body:
application/json: application/json:
example: example: !include ../examples/output/collection-list.json
schema: !include ../schemas/output/collection-list.json
post:
is: ["validates-json-body"]
description: Create a collection
body:
application/json:
example: !include ../examples/input/collection.json
schema: !include ../schemas/input/collection.json
responses:
200:
body:
application/json:
example: !include ../examples/output/collection-new.json
schema: !include ../schemas/output/collection-new.json
/{CollectionId}:
uriParameters:
CollectionId:
type: string
get:
description: Retrieve a single collection
responses:
200:
body:
application/json:
example: !include ../examples/output/collection.json
schema: !include ../schemas/output/collection.json
put:
is: ["validates-json-body"]
description: Update a collection and its contents
body:
application/json:
example: !include ../examples/input/collection-update.json
schema: !include ../schemas/input/collection-update.json
responses:
200:
description: Collection updated
delete:
description: Delete a collection
responses:
200:
description: Collection was deleted
/sessions:
get:
description: List sessions in a collection
responses:
200:
body:
application/json:
example: !include ../examples/output/session-list.json
schema: !include ../schemas/output/session-list.json
/acquisitions:
get:
description: List acquisitions in a collection
responses:
200:
body:
application/json:
example: !include ../examples/output/acquisition-list.json
schema: !include ../schemas/output/acquisition-list.json
/curators:
get:
description: List all curators of collections
responses:
200:
body:
application/json:
example: !include ../examples/output/collection-curators-list.json
schema: !include ../schemas/output/collection-curators-list.json
raml/resources/groups.raml
+ 1
− 1
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...@@ -31,7 +31,7 @@ post: ...@@ -31,7 +31,7 @@ post:
body: body:
application/json: application/json:
example: !include ../examples/output/group.json example: !include ../examples/output/group.json
schema: !include ../schemas/definitions/group-output.json schema: !include ../schemas/output/group.json
put: put:
is: [validates-json-body] is: [validates-json-body]
description: Update group description: Update group
......
raml/resources/jobs.raml
+ 2
− 2
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...@@ -30,8 +30,8 @@ get: ...@@ -30,8 +30,8 @@ get:
200: 200:
body: body:
application/json: application/json:
example: !include ../examples/output/job.json example: !include ../examples/output/job-next.json
schema: !include ../schemas/output/job.json schema: !include ../schemas/output/job-next.json
/stats: /stats:
description: Job stats description: Job stats
get: get:
......
raml/resources/projects.raml
+ 60
− 34
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/{ProjectId}/template: type: container
uriParameters: get:
ProjectId: responses:
type: string 200:
required: true body:
post: application/json:
description: Set the session template for a project example: !include ../examples/output/project-list.json
body: schema: !include ../schemas/output/project-list.json
application/json: post:
example: !include ../examples/input/project-template.json description: Create a project
schema: !include ../schemas/input/project-template.json body:
application/json:
example: !include ../examples/input/project.json
schema: !include ../schemas/input/project.json
/{ProjectId}:
type: container-item
get:
responses: responses:
200: 200:
description: Template was saved
body: body:
application/json: application/json:
example: | example: !include ../examples/output/project.json
{"modified": 1} schema: !include ../schemas/output/project.json
404: put:
description: Project was not found body:
application/json:
example: !include ../examples/input/project-update.json
schema: !include ../schemas/input/project-update.json
/{ProjectId}/template:
uriParameters:
ProjectId:
type: string
required: true
post:
description: Set the session template for a project
body:
application/json:
example: !include ../examples/input/project-template.json
schema: !include ../schemas/input/project-template.json
responses:
200:
description: Template was saved
body:
application/json:
example: |
{"modified": 1}
404:
description: Project was not found
/recalc:
uriParameters:
ProjectId:
type: string
required: true
post:
description: |
Recalculate if sessions in the project satisfy the template.
Returns list of modified session ids.
responses:
200:
description: |
Project's sessions' compliance was recalculated.
Returns list of session that were modified.
404:
description: Project was not found
delete: delete:
description: Remove the session template for a project description: Remove the session template for a project
...@@ -42,21 +86,3 @@ ...@@ -42,21 +86,3 @@
description: | description: |
Projects' sessions' compliance was recalculated. Projects' sessions' compliance was recalculated.
Returns list of session that were modified. Returns list of session that were modified.
/{ProjectId}/recalc:
uriParameters:
ProjectId:
type: string
required: true
post:
description: |
Recalculate if sessions in the project satisfy the template.
Returns list of modified session ids.
responses:
200:
description: |
Project's sessions' compliance was recalculated.
Returns list of session that were modified.
404:
description: Project was not found
raml/resources/sessions.raml 0 → 100644
+ 44
− 0
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type: container
get:
responses:
200:
body:
application/json:
example: !include ../examples/output/session-list.json
schema: !include ../schemas/output/session-list.json
post:
description: Create a session
body:
application/json:
example: !include ../examples/input/session.json
schema: !include ../schemas/input/session.json
/{SessionId}:
type: container-item
get:
responses:
200:
body:
application/json:
example: !include ../examples/output/session.json
schema: !include ../schemas/output/session.json
put:
body:
application/json:
example: !include ../examples/input/session.json
schema: !include ../schemas/input/session.json
/jobs:
get:
description: Return any jobs that use inputs from this session
queryParameters:
states:
type: string
description: filter results by job state
tags:
type: string
description: filter results by job tags
responses:
200:
body:
application/json:
example: !include ../examples/output/session-jobs.json
schema: !include ../schemas/output/session-jobs.json
raml/schemas/definitions/acquisition.json 0 → 100644
+ 53
− 0
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{
"$schema": "http://json-schema.org/draft-04/schema#",
"definitions":{
"instrument": {"type": "string"},
"measurement": {"type": "string"},
"timestamp": {"type": ["string", "null"], "format": "date-time"},
"timezone": {"type": "string"},
"acquisition-input":{
"type": "object",
"properties": {
"public": {"$ref": "../definitions/container.json#/definitions/public"},
"label": {"$ref": "../definitions/container.json#/definitions/label"},
"metadata": {"$ref": "../definitions/container.json#/definitions/metadata"},
"archived": {"$ref":"../definitions/container.json#/definitions/archived"},
"session": {"$ref":"../definitions/objectid.json#"},
"uid": {"$ref":"../definitions/user.json#/definitions/_id"},
"instrument": {"$ref": "#/definitions/instrument"},
"measurement": {"$ref": "#/definitions/measurement"},
"timestamp": {"$ref":"#/definitions/timestamp"},
"timezone": {"$ref":"#/definitions/timezone"}
},
"additionalProperties":false
},
"acquisition-output":{
"type":"object",
"properties": {
"_id":{"$ref":"../definitions/objectid.json#"},
"public": {"$ref": "../definitions/container.json#/definitions/public"},
"label": {"$ref": "../definitions/container.json#/definitions/label"},
"metadata": {"$ref": "../definitions/container.json#/definitions/metadata"},
"session": {"$ref":"../definitions/objectid.json#"},
"collections":{
"type":"array",
"items":{"$ref":"../definitions/objectid.json#"}
},
"files":{
"type":"array",
"items":{"$ref":"../definitions/file.json#/definitions/file-output"}
},
"instrument": {"$ref": "#/definitions/instrument"},
"measurement": {"$ref": "#/definitions/measurement"},
"timestamp": {"$ref":"#/definitions/timestamp"},
"created":{"$ref":"../definitions/created-modified.json#/definitions/created"},
"modified":{"$ref":"../definitions/created-modified.json#/definitions/modified"},
"permissions":{
"type":"array",
"items":{"$ref":"../definitions/permission.json#"}
}
},
"additionalProperties":false
}
}
}
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