From 477b88f115c3bb2526aa07be26236a79a5e1d32a Mon Sep 17 00:00:00 2001 From: Tom Kazimiers Date: Mon, 16 Apr 2018 00:00:42 -0400 Subject: [PATCH] Release 2018.04.15 --- API_CHANGELOG.md | 2 +- CHANGELOG.md | 3 +- sphinx-doc/source/_static/api/index.html | 1439 +++++++++++++++++++--- sphinx-doc/source/conf.py | 4 +- 4 files changed, 1283 insertions(+), 165 deletions(-) diff --git a/API_CHANGELOG.md b/API_CHANGELOG.md index 070551b6c2..365bd98b91 100644 --- a/API_CHANGELOG.md +++ b/API_CHANGELOG.md @@ -2,7 +2,7 @@ This changelog notes changes to API endpoints that are documented and listed through Swagger. Changes to undocumented, internal CATMAID APIs are not included in this changelog. -## Under development +## 2018.04.15 ### Additions diff --git a/CHANGELOG.md b/CHANGELOG.md index c366c3be01..93ff3a8574 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,6 @@ -## Under development +## 2018.04.15 +Contributors: Albert Cardona, Andrew Champion, Chris Barnes, Rob Court, Tom Kazimiers ### Notes diff --git a/sphinx-doc/source/_static/api/index.html b/sphinx-doc/source/_static/api/index.html index ac612326f9..6a3525df9e 100644 --- a/sphinx-doc/source/_static/api/index.html +++ b/sphinx-doc/source/_static/api/index.html @@ -282,6 +282,11 @@

Tag: skeletons

POST /{project_id}/skeletons/import

Import a neuron modeled by a skeleton from an uploaded file.

+ + + + GET /{project_id}/skeletons/in-bounding-box +

Get a list of all skeletons that intersect with the passed in bounding

@@ -297,6 +302,11 @@

Tag: skeletons

POST /{project_id}/skeletons/within-spatial-distance

Find skeletons within a given L-infinity distance of a treenode.

+ + + + GET /{project_id}/skeletons/{skeleton_id}/cable-length +

Get the cable length for a skeleton

@@ -396,6 +406,16 @@

Tag: treenodes

+ + POST /{project_id}/treenodes/compact-detail +

Retrieve node information in a compact form. A list of elements of the

+ + + + GET /{project_id}/treenodes/{treenode_id}/compact-detail +

Retrieve node information in a compact form. A list of the following form

+ + POST /{project_id}/treenodes/{treenode_id}/confidence

Update confidence of edge between a node to either its parent or its

@@ -671,6 +691,21 @@

Tag: landmarks

POST /{project_id}/landmarks/groups/import

Import and link landmarks, landmark groups and locations.

+ + + + PUT /{project_id}/landmarks/groups/links/ +

Link a location group to another landmark group. If the passed in

+ + + + DELETE /{project_id}/landmarks/groups/links/{link_id}/ +

Delete the link between two landmark groups. Won't delete links that

+ + + + POST /{project_id}/landmarks/groups/materialize +

Create all passed in landmarks along with a set of groups in one go.

@@ -681,11 +716,6 @@

Tag: landmarks

POST /{project_id}/landmarks/groups/{landmarkgroup_id}/

Update an existing landmark group.

- - - - DELETE /{project_id}/landmarks/groups/{landmarkgroup_id}/ -

Delete one particular landmark group.

@@ -696,6 +726,11 @@

Tag: landmarks

DELETE /{project_id}/landmarks/groups/{landmarkgroup_id}/locations/{location_id}/

Remove the link between a location and a landmark group.

+ + + + GET /{project_id}/landmarks/groups/{landmarkgroup_id}/transitively-linked +

Get a list of landmark groups that are transitively linked to the

@@ -711,6 +746,11 @@

Tag: landmarks

DELETE /{project_id}/landmarks/{landmark_id}/

Delete one particular landmark.

+ + + + DELETE /{project_id}/landmarks/{landmark_id}/groups/{group_id}/ +

Delete the link between a location and a landmark and a group and a

@@ -2235,6 +2275,21 @@

POST /{proje + + + annotation_reference + +

Whether annoation references are IDs or names, can be 'id' or 'name.

+ + formData + + string + + + + + + @@ -3117,9 +3172,9 @@

GET /{projec - node_type + project_id -

Either 'connector', 'treenode' or 'location'

+

Project containing node of interest

formData @@ -3133,9 +3188,9 @@

GET /{projec - project_id + node_type -

Project containing node of interest

+

Either 'connector', 'treenode' or 'location'

formData @@ -3451,6 +3506,51 @@

GET /{projec + + + with_names + +

Whether to return location with their landmark names

+ + formData + + string + + + + + + + + + with_links + +

Whether to return links to other groups

+ + formData + + string + + + + + + + + + with_relations + +

Whether to return a map of used relation IDs to their names

+ + formData + + string + + + + + + @@ -3728,21 +3828,30 @@

POST /{proje - -
+ +
-
Delete one particular landmark group.
-

DELETE /{project_id}/landmarks/groups/{landmarkgroup_id}/

+
Link a location group to another landmark group. If the passed in
+

PUT /{project_id}/landmarks/groups/links/

Tags: landmarks
-

Delete one particular landmark group.

+

Link a location group to another landmark group. If the passed in + groups already are in relation to each other using the passed in + relation, no new link is created. Instead, the existing link will be + returned. A flag in the result indicates whether the returned object is + new.

- + +
+ +

application/x-www-form-urlencoded +

+
@@ -3759,7 +3868,7 @@

DELETE /{pro

- - - + + + + + + + + + + + + + + + - - - + + - - + @@ -4017,9 +4133,9 @@

POST /{proje

- - + + + + + + + @@ -4073,21 +4205,27 @@

POST /{proje - -
+ +
-
Remove the link between a location and a landmark group.
-

DELETE /{project_id}/landmarks/groups/{landmarkgroup_id}/locations/{location_id}/

+
Get details on one particular landmarkgroup group, including its
+

GET /{project_id}/landmarks/groups/{landmarkgroup_id}/

Tags: landmarks
-

Remove the link between a location and a landmark group.

+

Get details on one particular landmarkgroup group, including its + members.

- + +
+ +

application/x-www-form-urlencoded +

+

project_id

The project the landmark group is part of.

+

Project of landmark group

 path @@ -3773,11 +3882,43 @@

DELETE /{pro

- landmarkgroup_id + group_1_id

The ID of the landmark group to delete.

+

The first landmark group, has role of subject.

pathformData + integer + + + + +
+ relation_id +

The relation between group 1 and 2, has role of predicate.

+ 		formData + integer + + + + +
+ group_2_id +

The first landmark group, has role of object.

+ 		formData integer @@ -3794,11 +3935,11 @@

DELETE /{pro
-
- 204 No Content +
+ 200 OK
-
+
@@ -3814,26 +3955,23 @@

DELETE /{pro

-
+ + +
-
Get details on one particular landmarkgroup group, including its
-

GET /{project_id}/landmarks/groups/{landmarkgroup_id}/

+
Delete the link between two landmark groups. Won't delete links that
+

DELETE /{project_id}/landmarks/groups/links/{link_id}/

Tags: landmarks
-

Get details on one particular landmarkgroup group, including its - members.

+

Delete the link between two landmark groups. Won't delete links that + don't connect to landmark groups.

- -
- -

application/x-www-form-urlencoded -

-
+
@@ -3850,7 +3988,7 @@

GET /{projec

- - - - - - - - - - - - - - - -
project_id

The project the landmark group is part of.

+

Project of landmark group

 path @@ -3864,9 +4002,9 @@

GET /{projec

- landmarkgroup_id + link_id

The ID of the landmark group.

+

The link to delete

 path @@ -3878,36 +4016,6 @@

GET /{projec

- with_members -

Whether to return group members

- 		formData - boolean - - - -
- with_locations -

Whether to return linked locations

- 		formData - string - - - -
@@ -3915,11 +4023,11 @@

GET /{projec
-
- 200 OK +
+ 204 No Content
-
+
@@ -3935,18 +4043,25 @@

GET /{projec

-
+ + +
-
Update an existing landmark group.
-

POST /{project_id}/landmarks/groups/{landmarkgroup_id}/

+
Create all passed in landmarks along with a set of groups in one go.
+

POST /{project_id}/landmarks/groups/materialize

Tags: landmarks
-

Update an existing landmark group.

-

Currently, only the name and group members can be updated. Edit - permissions are only needed when removing group members.

+

Create all passed in landmarks along with a set of groups in one go.

+

The format for the passed in landmarks is expected to be [name, x1, y1, + z1, x2, y2, z2], representing a shared landmark at locations (x1, y1, + z1) for group A and (x2, y2, z2) for group B.

+

The format for the optionally passed in links is: [group_name_1, + relation_name, group_name_2] elements, representing a relation between + two groups. Whether group A and B map to 1 and 2 or vice versa depends + on the semantics of the relation.

@@ -3972,7 +4087,7 @@

POST /{proje

project_id

The project the landmark group is part of.

+

The project to operate in.

 path @@ -3986,10 +4101,11 @@

POST /{proje

- landmarkgroup_id + group_a_name path

The name of landmark group A.

+ 		formData string @@ -4001,13 +4117,13 @@

POST /{proje

- landmark_id + group_b_name

The ID of the landmark group.

+

The name of landmark group B.

pathformData - integer + string
- name + landmarks

The new name of the landmark group.

+

A list of landmark definitions for group B.

 formData @@ -4028,17 +4144,33 @@

POST /{proje

+
- members + links

The new members of the landmark group.

+

A list of link definitions between group A and B.

 formData - string[] + string + + + +
+ reuse_existing_landmarks +

If existing landmarks can be reused, no error will be thrown if a landmark with the same name exists alrady.

+ 		formData + string
@@ -4102,9 +4240,9 @@

DELETE /{pro

- - + + + + + + + + + + + + + + + + + + + + + + + + + + +
- location_id + project_id

Existing location ID

+

The project the landmark group is part of.

 path @@ -4118,9 +4256,294 @@

DELETE /{pro

- project_id + landmarkgroup_id

Project of landmark group

+

The ID of the landmark group.

+ 		path + integer + + + + +
+ with_members +

Whether to return group members

+ 		formData + boolean + + + +
+ with_locations +

Whether to return linked locations

+ 		formData + string + + + +
+ with_names +

Whether to return linked landmark names

+ 		formData + string + + + +
+
+ +
+ +
+
+ 200 OK + +
+
+
+
+ +
+
+
+ +
+
+ +
+
+
+
+
+
+
+
Update an existing landmark group.
+

POST /{project_id}/landmarks/groups/{landmarkgroup_id}/

+ Tags: + landmarks +
+
+
+

Update an existing landmark group.

+

Currently, only the name and group members can be updated. Edit + permissions are only needed when removing group members.

+ +
+ + +
+ +

application/x-www-form-urlencoded +

+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ project_id +

The project the landmark group is part of.

+ 		path + integer + + + + +
+ landmarkgroup_id + path + string + + + + +
+ landmark_id +

The ID of the landmark group.

+ 		path + integer + + + + +
+ name +

The new name of the landmark group.

+ 		formData + string + + + +
+ members +

The new members of the landmark group.

+ 		formData + string[] + + + +
+ append_members +

Whether the existing members should be extended by the + passed in members. No members will be removed.

+ 		formData + boolean + + + +
+
+ +
+ +
+
+ 201 Created + +
+
+
+
+ +
+
+
+ +
+
+ +
+
+
+
+
+ + +
+
+
Remove the link between a location and a landmark group.
+

DELETE /{project_id}/landmarks/groups/{landmarkgroup_id}/locations/{location_id}/

+ Tags: + landmarks +
+
+
+

Remove the link between a location and a landmark group.

+ +
+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ project_id +

Project of landmark group

+ 		path + integer + + + + +
+ location_id +

Existing location ID

 path @@ -4201,6 +4624,22 @@

PUT /{projec

+ project_id +

Project of landmark group

+ 		path + integer + + + + +
location_id @@ -4217,11 +4656,88 @@

PUT /{projec

+ landmarkgroup_id +

The landmark group to link

+ 		path + integer + + + + +
+
+ +
+ +
+
+ 200 OK + +
+
+
+
+ +
+
+
+ +
+
+ +
+
+
+
+
+ + +
+
+
Get a list of landmark groups that are transitively linked to the
+

GET /{project_id}/landmarks/groups/{landmarkgroup_id}/transitively-linked

+ Tags: + landmarks +
+
+
+

Get a list of landmark groups that are transitively linked to the + input group with the passed in relation.

+ +
+ + +
+ +

application/x-www-form-urlencoded +

+
+
+ + + + + + + + + + + - - + + + + + + + + + + + + + +
project_id

Project of landmark group

+

Project of landmark groups

 path @@ -4237,7 +4753,7 @@

PUT /{projec

landmarkgroup_id

The landmark group to link

+

The starting landmark group

 path @@ -4249,6 +4765,37 @@

PUT /{projec

+ relation_id +

The relation a valid group link has to have

+ 		formData + integer + + + + +
+ max_depth +

(optional) Maximum number of hops from the source group. 0 to disable.

+ 		formData + integer + + + +
@@ -4306,9 +4853,9 @@

DELETE /{pro - landmark_id + project_id -

The ID of the landmark.

+

The project the landmark is part of.

path @@ -4322,9 +4869,9 @@

DELETE /{pro - project_id + landmark_id -

The project the landmark is part of.

+

The ID of the landmark.

path @@ -4399,9 +4946,9 @@

GET /{projec - landmark_id + project_id -

The ID of the landmark.

+

The project the landmark is part of.

path @@ -4415,9 +4962,9 @@

GET /{projec - project_id + landmark_id -

The project the landmark is part of.

+

The ID of the landmark.

path @@ -4505,9 +5052,9 @@

POST /{proje - landmark_id + project_id -

The ID of the landmark.

+

The project the landmark is part of.

path @@ -4521,9 +5068,9 @@

POST /{proje - project_id + landmark_id -

The project the landmark is part of.

+

The ID of the landmark.

path @@ -4561,7 +5108,128 @@

POST /{proje 201 Created -
+
+
+
+ +
+
+
+ +
+
+ +
+ + +

+
+ + +
+
+
Delete the link between a location and a landmark and a group and a
+

DELETE /{project_id}/landmarks/{landmark_id}/groups/{group_id}/

+ Tags: + landmarks +
+
+
+

Delete the link between a location and a landmark and a group and a + location, if and only if both exist. If the last link to a location is + deleted, the location is removed as well.

+ +
+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ project_id +

Project of landmark group

+ 		path + integer + + + + +
+ landmark_id +

The landmark to unlink from

+ 		path + integer + + + + +
+ group_id +

The group to unlink from

+ 		path + integer + + + + +
+ keep_points +

Wheter only links should be deleted and points should be kept.

+ 		path + boolean + + + + +
+
+ +
+ +
+
+ 204 No Content + +
+
@@ -4613,9 +5281,9 @@

PUT /{projec - landmark_id + project_id -

The landmark to link

+

Project of landmark group

path @@ -4629,9 +5297,9 @@

PUT /{projec - project_id + landmark_id -

Project of landmark group

+

The landmark to link

path @@ -4761,9 +5429,9 @@

DELETE /{pro - landmark_id + project_id -

The landmark to unlink

+

Project of landmark group

path @@ -4777,9 +5445,9 @@

DELETE /{pro - location_id + landmark_id -

The location to unlink

+

The landmark to unlink

path @@ -4793,9 +5461,9 @@

DELETE /{pro - project_id + location_id -

Project of landmark group

+

The location to unlink

path @@ -5202,8 +5870,8 @@

POST /{proje limited to constrain query execution time. Optionally, lists of treenodes and connector IDs can be provided to make sure they are included in the result set, regardless of intersection.

-

Returned is an array with four entries:

-

[[treenodes], [connectors], {labels}, node_limit_reached, {relation_map}]

+

Returned is an array with five entries, plus optionally a sixth one

+

[[treenodes], [connectors], {labels}, node_limit_reached, {relation_map}, {exstraNodes}]

The list of treenodes has elements of this form:

[id, parent_id, location_x, location_y, location_z, confidence, radius, skeleton_id, edition_time, user_id]

The list connectors has elements of this form:

@@ -5410,6 +6078,22 @@

POST /{proje + + + with_relation_map + +

Whether an ID to name mapping for the used relations should be included + and which extent it should have.

+ + formData + + string + + + + + +

@@ -6822,13 +7506,12 @@

POST /{proje - interval_id + project_id -

Interval the connector is part of

- - formData + + path - integer + string @@ -6838,12 +7521,13 @@

POST /{proje - project_id + interval_id - - path +

Interval the connector is part of

+ + formData - string + integer @@ -6924,7 +7608,7 @@

GET /{projec - interval_id + project_id path @@ -6939,7 +7623,7 @@

GET /{projec - project_id + interval_id path @@ -7014,13 +7698,12 @@

POST /{proje - interval_id + project_id -

Interval to update state of

- - formData + + path - integer + string @@ -7030,12 +7713,13 @@

POST /{proje - project_id + interval_id - - path +

Interval to update state of

+ + formData - string + integer @@ -7486,7 +8170,7 @@

POST /{proje

If the sampler was created with allowing the creation of new boundary nodes, these nodes are removed by default if they have not been modified since their insertion. This can optionally be disabled using the

-

parameter.

+

<delete_created_nodes> parameter.

@@ -8660,11 +9344,198 @@

POST /{proje formData - string + string + + + + + + + + + + +
+ +
+
+ 201 Created + +
+
+
+
+ +
+
+
+ +
+
+ +
+
+
+

+
+ + +
+
+
Get a list of all skeletons that intersect with the passed in bounding
+

GET /{project_id}/skeletons/in-bounding-box

+ Tags: + skeletons +
+
+
+

Get a list of all skeletons that intersect with the passed in bounding + box.

+ +
+ + +
+ +

application/x-www-form-urlencoded +

+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -8674,11 +9545,11 @@

POST /{proje
-
- 201 Created +
+ 200 OK
-
+
@@ -9035,6 +9906,93 @@

POST /{proje

+ +
+
+
Get the cable length for a skeleton
+

GET /{project_id}/skeletons/{skeleton_id}/cable-length

+ Tags: + skeletons +
+
+
+

Get the cable length for a skeleton

+ +
+ + +
+

+ project_id + path + string + + + + +
+ limit +

Limit the number of returned nodes.

+ 		formData + integer + + + +
+ left +

Minimum world space X coordinate

+ 		formData + float + + + + +
+ top +

Minimum world space Y coordinate

+ 		formData + float + + + + +
+ z1 +

Minimum world space Z coordinate

+ 		formData + float + + + + +
+ right +

Maximum world space X coordinate

+ 		formData + float + + + + +
+ bottom +

Maximum world space Y coordinate

+ 		formData + float + + + + +
+ z2 +

Maximum world space Z coordinate

+ 		formData + float +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ project_id +

Project of landmark

+ 		path + integer + + + + +
+ skeleton_id +

IDs of the skeleton to get the cable length for

+ 		path + integer + + + + +
+
+ +
+ +
+
+ 200 OK + +
+
+
+
+ +
+
+
+ +
+
+ +
+
+
+
+
+
@@ -10280,6 +11238,165 @@

GET /{projec

+ +
+
+
Retrieve node information in a compact form. A list of elements of the
+

POST /{project_id}/treenodes/compact-detail

+ Tags: + treenodes +
+
+
+

Retrieve node information in a compact form. A list of elements of the + following form is returned: [ID, parent ID, x, y, z, confidence, user_id, + radius, skeleton_id, user_id].

+ +
+ + +
+ + + + + + + + + + + + + + + + + + + +
+ project_id + path + string + + + + +
+
+ +
+ +
+
+ 201 Created + +
+
+
+
+ +
+
+
+ +
+
+ +
+
+
+
+
+ + +
+
+
Retrieve node information in a compact form. A list of the following form
+

GET /{project_id}/treenodes/{treenode_id}/compact-detail

+ Tags: + treenodes +
+
+
+

Retrieve node information in a compact form. A list of the following form + is returned: [ID, parent ID, x, y, z, confidence, user_id, radius, + skeleton_id, user_id].

+ +
+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ project_id + path + string + + + + +
+ treenode_id + path + string + + + + +
+
+ +
+ +
+
+ 200 OK + +
+
+
+
+ +
+
+
+ +
+
+ +
+
+
+
+
+
@@ -10320,7 +11437,7 @@

POST /{proje - treenode_id + project_id path @@ -10335,7 +11452,7 @@

POST /{proje - project_id + treenode_id path @@ -10398,7 +11515,7 @@

POST /{proje partner_confidences -

Set different confidences to connectors in

+

Set different confidences to connectors in <partner_ids>

formData @@ -10466,7 +11583,7 @@

GET /{projec - treenode_id + project_id path @@ -10481,7 +11598,7 @@

GET /{projec - project_id + treenode_id path @@ -10551,7 +11668,7 @@

GET /{projec - treenode_id + project_id path @@ -10566,7 +11683,7 @@

GET /{projec - project_id + treenode_id path @@ -10642,7 +11759,7 @@

POST /{proje - treenode_id + project_id path @@ -10657,7 +11774,7 @@

POST /{proje - project_id + treenode_id path @@ -10761,7 +11878,7 @@

DELETE /{pro - treenode_id + project_id path @@ -10776,7 +11893,7 @@

DELETE /{pro - project_id + treenode_id path diff --git a/sphinx-doc/source/conf.py b/sphinx-doc/source/conf.py index f0d4e218f6..89712b95b5 100644 --- a/sphinx-doc/source/conf.py +++ b/sphinx-doc/source/conf.py @@ -56,9 +56,9 @@ # built documents. # # The short X.Y version. -version = '2018.02.16-dev' +version = '2018.04.15' # The full version, including alpha/beta/rc tags. -release = '2018.02.16-dev' +release = '2018.04.15' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. #language = None