Changes for page API Catalogue

Last modified by lupascu on 2022/05/23 22:36
From version 7.1
edited by adavison
on 2021/12/17 13:28
Change comment: There is no comment for this version
To version 15.1
edited by rowanthorpe
on 2021/12/17 14:31
Change comment: Add Headless Jupyter Notebook Testing service entry

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1 -XWiki.adavison
1 +XWiki.rowanthorpe
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1 -This page catalogues the [[web API>>https://en.wikipedia.org/wiki/Web_API||rel="noopener noreferrer" target="_blank"]]s available for users and developers of [[EBRAINS tools and services>>https://ebrains.eu||rel="noopener noreferrer" target="_blank"]].
1 +
2 2  
3 -Please note this is a work in progress. Further information is available in [[this spreadsheet>>https://drive.ebrains.eu/lib/c11f95c0-59fd-428f-b02e-2238566c8499/file/EA-WG/list_of_APIs.xlsx]].
3 +This page catalogues the [[web API>>https://en.wikipedia.org/wiki/Web_API]]s available for users and developers of [[EBRAINS tools and services>>https://ebrains.eu]].
4 4  
5 +(% class="box warningmessage" %)
6 +(((
7 +Please note this is a work in progress.
8 +)))
9 +
5 5  ----
6 6  
12 +{{toc/}}
13 +
14 +----
15 +
7 7  == Core services / Collaboratory ==
8 8  
9 9  === Authentication / Authorization (IAM) ===
10 10  
11 -[[[[image:1635154142156-729.png]]>>https://www.keycloak.org/documentation.html||rel="noopener noreferrer" target="_blank"]]
20 +[[[[image:documentation-icon.png]]>>https://www.keycloak.org/documentation.html||rel="noopener noreferrer" target="_blank"]]
12 12  
13 -IAM is the EBRAINS **I**dentity and **A**ccess **M**anagement service which is delivered by the Collaboratory and manages user identification and permission management for all EBRAINS users and services.
22 +IAM is the EBRAINS **I**dentity and **A**ccess **M**anagement service which is delivered by the Collaboratory and manages user identification and permission management for all EBRAINS users and services.
14 14  
15 15  === Collaboratory wiki ===
16 16  
17 -[[[[image:1635154142156-729.png]]>>https://www.xwiki.org/xwiki/bin/view/Documentation/UserGuide/Features/XWikiRESTfulAPI||rel="noopener noreferrer" target="_blank"]]
26 +[[[[image:documentation-icon.png]]>>https://www.xwiki.org/xwiki/bin/view/Documentation/UserGuide/Features/XWikiRESTfulAPI||rel="noopener noreferrer" target="_blank"]]
18 18  
19 -The [[Wiki service>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Getting%20Started/#HWikipages]] of the Collaboratory hosts the main interface to access all the other Collaboratory services. As such, it embodies the full concept of collab workspaces and most users consider it to be the collab service. The Wiki in itself offers a handy way of documenting a user's work with a simple wiki user interface.
28 +The [[Wiki service>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Getting%20Started/#HWikipages]] of the Collaboratory hosts the main interface to access all the other Collaboratory services. As such, it embodies the full concept of collab workspaces and most users consider it to be the collab service. The Wiki in itself offers a handy way of documenting a user's work with a simple wiki user interface.
20 20  
21 21  === Drive ===
22 22  
23 -[[[[image:1635154142156-729.png]]>>https://download.seafile.com/published/web-api/home.md||rel="noopener noreferrer" target="_blank"]]
32 +[[[[image:documentation-icon.png]]>>https://download.seafile.com/published/web-api/home.md||rel="noopener noreferrer" target="_blank"]]
24 24  
25 25  The Collaboratory offers two storage solutions for collabs: the Drive and the Bucket. The Drive is especially well suited for files and documents that need to be worked on in a more agile manner, possibly also collaboratively. For larger files, datasets, and videos the [[Bucket>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation%20Bucket/]] offers a better solution.
26 26  
27 27  === Bucket (Data Proxy) ===
28 28  
29 -[[[[image:1635154142156-729.png]]>>https://data-proxy-ppd.ebrains.eu/api/docs||rel="noopener noreferrer" target="_blank"]]
38 +[[[[image:documentation-icon.png]]>>https://data-proxy-ppd.ebrains.eu/api/docs||rel="noopener noreferrer" target="_blank"]]
30 30  
31 31  The Collaboratory offers two storage solutions for collabs: the Drive and the Bucket. The Drive is especially well suited for files and documents that need to be worked on in a more agile manner, possibly also collaboratively. For larger files, datasets, and videos the [[Bucket>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation%20Bucket/]] offers a better solution.
32 32  
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36 36  
37 37  === Knowledge Graph core ===
38 38  
39 -[[[[image:1635154142156-729.png]]>>https://core.kg.ebrains.eu/swagger-ui/index.html?configUrl=/v3/api-docs/swagger-config||rel="noopener noreferrer" target="_blank"]]
48 +[[[[image:documentation-icon.png]]>>https://core.kg.ebrains.eu/swagger-ui/index.html?configUrl=/v3/api-docs/swagger-config||rel="noopener noreferrer" target="_blank"]]
40 40  
41 41  The EBRAINS Knowledge Graph is a multi-modal metadata store which brings together information from different fields on brain research. At the core of the EBRAINS Knowledge Graph, a graph database tracks the linkage between experimental data and neuroscientific data science supporting more extensive data reuse and complex computational research than would be possible otherwise.
42 42  
43 43  === Knowledge Space ===
44 44  
45 -[[[[image:1635154142156-729.png]]>>https://api.knowledge-space.org/docs||rel="noopener noreferrer" target="_blank"]]
54 +[[[[image:documentation-icon.png]]>>https://api.knowledge-space.org/docs||rel="noopener noreferrer" target="_blank"]]
46 46  
47 47  KnowledgeSpace aims to be a globally-used, community-based, data-driven encyclopedia for neuroscience that links brain research concepts to data, models, and the literature that support them. Further it aims to serve as a framework where large-scale neuroscience projects can expose their data to the neuroscience community-at-large. KS is a framework that combines general descriptions of neuroscience concepts found in wikipedia with more detailed content from InterLex. It then integrates the content from those two sources with the latest neuroscience citations found in PubMed and data found in some of the world’s leading neuroscience repositories. KS is a joint development between the Human Brain Project (HBP), the International Neuroinformatics Coordinating Facility (INCF), and the Neuroscience Information Framework (NIF).
48 48  
49 49  === Neural Activity Resource ===
50 50  
51 -[[[[image:1635154142156-729.png]]>>https://neural-activity-resource.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
60 +[[[[image:documentation-icon.png]]>>https://neural-activity-resource.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
52 52  
53 53  The Neural Activity Resource provides a simplified interface to data and metadata from the KG about neural activity recordings.
54 54  
55 55  === Provenance API ===
56 56  
57 -[[[[image:1635154142156-729.png]]>>https://prov.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
66 +[[[[image:documentation-icon.png]]>>https://prov.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
58 58  
59 59  The Provenance API provides a simplified interface to computational provenance information in the KG.
60 60  
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64 64  
65 65  === Image service ===
66 66  
67 -[[[[image:1635154142156-729.png]]>>https://img-svc.apps.hbp.eu/api-docs||rel="noopener noreferrer" target="_blank"]]
76 +[[[[image:documentation-icon.png]]>>https://img-svc.apps.hbp.eu/api-docs||rel="noopener noreferrer" target="_blank"]]
68 68  
69 -The Image Service was designed to allow users to process imaging data in order to be used with interactive HBP tools. These tools often need special formats and data descriptors to work, and the Image Service's goal is to provide streamlined workflows with which datasets can be made available to these tools with the simplest possible input, on-demand, using resources allocated in the FENIX Research Infrastructure.
78 +The Image Service was designed to allow users to process imaging data in order to be used with interactive HBP tools. These tools often need special formats and data descriptors to work, and the Image Service's goal is to provide streamlined workflows with which datasets can be made available to these tools with the simplest possible input, on-demand, using resources allocated in the FENIX Research Infrastructure.
70 70  
71 71  === siibra ===
72 72  
73 -[[[[image:1635154142156-729.png]]>>https://siibra-api.readthedocs.io||rel="noopener noreferrer" target="_blank"]]
82 +[[[[image:documentation-icon.png]]>>https://siibra-api.readthedocs.io||rel="noopener noreferrer" target="_blank"]]
74 74  
75 75  The siibra toolsuite provides both interactive and programmatic user interfaces for working with “multilevel” brain atlases, that is, brain atlases composed of multiple reference spaces, parcellation maps, and data modalities. siibra-API is a RESTful API service exposing the core functionalities for integration with other applications.
76 76  
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80 80  
81 81  === Neo-Viewer ===
82 82  
83 -[[[[image:1635154142156-729.png]]>>https://neo-viewer.brainsimulation.eu/||rel="noopener noreferrer" target="_blank"]]
92 +[[[[image:documentation-icon.png]]>>https://neo-viewer.brainsimulation.eu/||rel="noopener noreferrer" target="_blank"]]
84 84  
85 85  Neo Viewer provides web-based visualisation of electrophysiology data, with support for** **most of the widely-used file formats in neurophysiology, including community standards such as NIX and NWB. It consists of a REST API for transforming electrophysiology data files into JSON format and a Javascript component that can be embedded in any web page.
86 86  
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90 90  
91 91  === Model Validation service ===
92 92  
93 -[[[[image:1635154142156-729.png]]>>https://validation-v2.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
102 +[[[[image:documentation-icon.png]]>>https://validation-v2.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
94 94  
95 -The Model Validation Service provides web-based tools for working with computational models, and the validation of such models against experimental data. It consists of a REST web service and two clients: the Model Catalog collaboratory app and a Python client. Underlying metadata are stored in the Knowledge Graph. The service allows users (i) to create, edit, search and view metadata about models and validation tests, (ii) to register, search, view and compare the results of validation tests.
104 +The Model Validation Service provides web-based tools for working with computational models, and the validation of such models against experimental data.  It consists of a REST web service and two clients: the Model Catalog collaboratory app and a Python client. Underlying metadata are stored in the Knowledge Graph. The service allows users (i) to create, edit, search and view metadata about models and validation tests, (ii) to register, search, view and compare the results of validation tests.
96 96  
97 97  === The Virtual Brain ===
98 98  
99 -[[[[image:1635154142156-729.png]]>>https://thevirtualbrain-rest.apps.hbp.eu/doc||rel="noopener noreferrer" target="_blank"]]
108 +[[[[image:documentation-icon.png]]>>https://thevirtualbrain-rest.apps.hbp.eu/doc||rel="noopener noreferrer" target="_blank"]]
100 100  
101 101  REST API for TVB.
102 102  
103 103  === MoDEL-CNS ===
104 104  
105 -[[[[image:1635154142156-729.png]]>>https://mmb.irbbarcelona.org/MoDEL-CNS/api/rest/docs/||rel="noopener noreferrer" target="_blank"]]
114 +[[[[image:documentation-icon.png]]>>https://mmb.irbbarcelona.org/MoDEL-CNS/api/rest/docs/||rel="noopener noreferrer" target="_blank"]]
106 106  
107 107  Molecular Dynamics Extended Library: Central Nervous System (MoDEL-CNS) is a platform designed to provide web-access to **atomistic-MD trajectories** for relevant **signal transduction proteins**.
108 108  
109 109  === Cellular Level Simulation ===
110 110  
111 -[[[[image:1635154142156-729.png]]>>https://humanbrainproject.github.io/hbp-bsp-service-account/introduction/introduction.html||rel="noopener noreferrer" target="_blank"]]
120 +[[[[image:documentation-icon.png]]>>https://humanbrainproject.github.io/hbp-bsp-service-account/introduction/introduction.html||rel="noopener noreferrer" target="_blank"]]
112 112  
113 113  Web applications that allow running simulations in different scales (single cell, multiple cells, regions).
114 114  
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118 118  
119 119  === NRP Frontend-Backend comms ===
120 120  
121 -[[[[image:1635154142156-729.png]]>>https://neurorobotics.net/Documentation/nrp/developer_manual/ExDbackend/index.html||rel="noopener noreferrer" target="_blank"]]
130 +[[[[image:documentation-icon.png]]>>https://neurorobotics.net/Documentation/nrp/developer_manual/ExDbackend/index.html||rel="noopener noreferrer" target="_blank"]]
122 122  
123 123  === NRP-core ===
124 124  
125 -[[[[image:1635154142156-729.png]]>>https://hbpneurorobotics.bitbucket.io/index.html||rel="noopener noreferrer" target="_blank"]]
134 +[[[[image:documentation-icon.png]]>>https://hbpneurorobotics.bitbucket.io/index.html||rel="noopener noreferrer" target="_blank"]]
126 126  
127 127  The neurorobotics platform core (referred throughout this document as NRP-core) is the mechanism through which NRP users can implement simulations whereby multiple pieces of simulation software can coexist, synchronize their execution and exchange data in tightly ordered fashion. In previous versions of the NRP, NRP-core was referred to as the "Closed Loop Engine" (CLE), the task of which was to orchestrate the dialogue between the Gazebo robotic simulator and brain models implemented in NEST, Nengo, etc. For those of our users familiar with the CLE, NRP-core is a generalization of the latter, with new generic mechanisms provided to users who want to integrate new simulation engines into their NRP simulations. NRP-core is still built on the so-called Transfer Function framework, although the latter was adapted and renamed [[Transceiver Functions>>url:https://hbpneurorobotics.bitbucket.io/transceiver_function.html]] framework. This renaming is not only cosmetic: users familiar with the NRP up to v3.2 should indeed remain aware of some limited but meaningful evolutions between these two frameworks.
128 128  
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138 138  
139 139  === Job Queue service ===
140 140  
141 -[[[[image:1635154142156-729.png]]>>https://nmpi.hbpneuromorphic.eu/api/v2/||rel="noopener noreferrer" target="_blank"]]
150 +[[[[image:documentation-icon.png]]>>https://nmpi.hbpneuromorphic.eu/api/v2/||rel="noopener noreferrer" target="_blank"]]
142 142  REST API for submitting jobs to the BrainScaleS and SpiNNaker platforms, and for retrieving job results.
143 143  
144 144  === Quotas service ===
145 145  
146 -[[[[image:1635154142156-729.png]]>>]]
155 +[[[[image:documentation-icon.png]]>>]]
147 147  REST API for requesting and managing compute quotas for the BrainScaleS and SpiNNaker platforms.
148 148  
149 149  ----
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152 152  
153 153  === UNICORE ===
154 154  
155 -[[[[image:1635154142156-729.png]]>>https://sourceforge.net/p/unicore/wiki/REST_API/||rel="noopener noreferrer" target="_blank"]]
164 +[[[[image:documentation-icon.png]]>>https://sourceforge.net/p/unicore/wiki/REST_API/||rel="noopener noreferrer" target="_blank"]]
156 156  
157 157  UNICORE (UNiform Interface to COmputing REsources) provides tools and services for making high-performance computing and data resources accessible in a seamless and secure way for a wide variety of applications.
158 158  
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160 160  
161 161  === Supercomputing Proxy ===
162 162  
163 -[[[[image:1635154142156-729.png]]>>https://unicore-job-proxy.apps.hbp.eu/docs||rel="noopener noreferrer" target="_blank"]]
172 +[[[[image:documentation-icon.png]]>>https://unicore-job-proxy.apps.hbp.eu/docs||rel="noopener noreferrer" target="_blank"]]
164 164  
165 165  Supercomputing proxy provides services which run on supercomputers a means of running a job on behalf of an EBRAINS user without requesting that the user have an HPAC account. The job is launched using a service account in the name of the service provider. The service is limited to running jobs which use pre-determined executables. The end-user cannot use the supercomputing resources for purposes not intended by the service provider.
166 166  
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170 170  
171 171  === OpenStack ===
172 172  
173 -[[[[image:1635154142156-729.png]]>>https://wiki.ebrains.eu/bin/view/Collabs/openstack/||rel="noopener noreferrer" target="_blank"]]
182 +[[[[image:documentation-icon.png]]>>https://wiki.ebrains.eu/bin/view/Collabs/openstack/||rel="noopener noreferrer" target="_blank"]]
174 174  
175 175  Red Hat OpenStack Platform provides the foundation to build a private or public Infrastructure-as-a-Service (IaaS) cloud on top of Red Hat Enterprise Linux. It offers a highly scalable, fault-tolerant platform for the development of cloud-enabled workloads.
176 176  
177 177  === OpenShift ===
178 178  
179 -[[[[image:1635154142156-729.png]]>>https://wiki.ebrains.eu/bin/view/Collabs/kubernetes/openshift/||rel="noopener noreferrer" target="_blank"]]
188 +[[[[image:documentation-icon.png]]>>https://wiki.ebrains.eu/bin/view/Collabs/kubernetes/openshift/||rel="noopener noreferrer" target="_blank"]]
180 180  
181 181  OpenShift is a family of containerization software products developed by Red Hat.
182 182  
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186 186  
187 187  === Gitlab ===
188 188  
189 -[[[[image:1635154142156-729.png]]>>https://docs.gitlab.com/ee/api/||rel="noopener noreferrer" target="_blank"]]
198 +[[[[image:documentation-icon.png]]>>https://docs.gitlab.com/ee/api/||rel="noopener noreferrer" target="_blank"]]
190 190  
191 191  EBRAINS hosts a self-managed instance of GitLab for source code management and CI/CD.
192 192  
193 193  === Docker registry (Harbor) ===
194 194  
195 -[[[[image:1635154142156-729.png]]>>https://docker-registry.ebrains.eu/devcenter-api-2.0||rel="noopener noreferrer" target="_blank"]]
204 +[[[[image:documentation-icon.png]]>>https://docker-registry.ebrains.eu/devcenter-api-2.0||rel="noopener noreferrer" target="_blank"]]
196 196  
197 -(% class="wikigeneratedid" %)
198 198  The EBRAINS Docker registry uses Harbor, an an open source trusted cloud native registry project that stores, signs, and scans content.
199 199  
208 +=== Headless Jupyter Notebook Testing service ===
209 +
210 +[[[[image:documentation-icon.png]]>>]]
211 +
212 +The [[EBRAINS Headless Jupyter Notebook Testing service>>https://test-notebooks.apps.hbp.eu/get_notebooks||rel="noopener noreferrer" target="_blank"]] periodically executes automatic browser tests by running notebook cells one-by one to assess/evaluate their successful execution.
213 +
200 200  === Logging/monitoring APIs ===
201 201  
202 -[[[[image:1635154142156-729.png]]>>]]
216 +[[[[image:documentation-icon.png]]>>]]
203 203  
204 204  TO DO
205 205  
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209 209  
210 210  === PLUS ===
211 211  
212 -[[[[image:1635154142156-729.png]]>>https://lab.ch.ebrains.eu/user-redirect/lab/tree/drive/Shared%20with%20all/PLUS-LAB/PLUS%20KPI-PrI%20API.ipynb||rel="noopener noreferrer" target="_blank"]]
226 +[[[[image:documentation-icon.png]]>>https://lab.ch.ebrains.eu/user-redirect/lab/tree/drive/Shared%20with%20all/PLUS-LAB/PLUS%20KPI-PrI%20API.ipynb||rel="noopener noreferrer" target="_blank"]]
213 213  
214 214  PLUS is a project management tool for the Human Brain Project.
215 215  
216 216  ----
217 217  
218 -(% class="box infomessage" %)
219 -(((
220 -The book icon used on this page is from a [[set of icons by Boca Tutor>>https://www.iconfinder.com/iconsets/tutor-icon-set||rel="noopener noreferrer" target="_blank"]] and is licensed under the [[Creative Commons>>https://en.wikipedia.org/wiki/en:Creative_Commons||rel="noopener noreferrer" target="_blank"]] [[Attribution-Share Alike 3.0 Unported>>https://creativecommons.org/licenses/by-sa/3.0/deed.en||rel="noopener noreferrer" target="_blank"]] license.
221 -)))
232 +The book icon used on this page is from a [[set of icons by Boca Tutor>>https://www.iconfinder.com/iconsets/tutor-icon-set]] and is licensed under the [[Creative Commons>>https://en.wikipedia.org/wiki/en:Creative_Commons]] [[Attribution-Share Alike 3.0 Unported>>https://creativecommons.org/licenses/by-sa/3.0/deed.en]] license.
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API Catalogue