From 9353e01c78d814312d9c01fd8ebec8052d60b50d Mon Sep 17 00:00:00 2001
From: Markus Scheidgen <markus.scheidgen@gmail.com>
Date: Mon, 20 Jul 2020 12:30:22 +0200
Subject: [PATCH] Fixed various links (for new web page).
---
README.md | 4 +-
docs/api.rst | 4 +-
docs/api_tutorial.md | 42 +++++++++----------
docs/client/cli_use_cases.rst | 2 +-
docs/client/install.rst | 2 +-
docs/conf.py | 2 +-
docs/introduction.md | 8 ++--
docs/metainfo.rst | 8 ++--
docs/upload.rst | 10 +++--
examples/api_use.py | 2 +-
examples/api_use_authenticated.py | 4 +-
gui/public/env.js | 8 ++--
gui/src/components/About.js | 16 ++++---
gui/src/components/App.js | 4 +-
.../metaInfoBrowser/MetaInfoBrowser.js | 3 +-
gui/src/components/uploads/UploadPage.js | 7 +++-
gui/src/config.js | 4 +-
nomad/cli/client/statistics.py | 4 +-
nomad/config.py | 6 +--
nomad/doi.py | 2 +-
nomad/metainfo/example.py | 2 +-
.../material_theme/account/theme.properties | 2 +-
.../material_theme/login/theme.properties | 2 +-
ops/docker-compose/nomad-oasis/README.md | 4 +-
ops/docker-compose/nomad-oasis/env.js | 2 +-
ops/helm/nomad/ci-dev-values.yaml | 2 +-
ops/helm/nomad/values.yaml | 8 ++--
27 files changed, 86 insertions(+), 78 deletions(-)
diff --git a/README.md b/README.md
index a0e3909203..f43b48ef64 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@ This project implements the new *nomad@FAIRDI* infrastructure. Contrary to its N
predecessor, it implements the NOMAD Repository and NOMAD Archive functionality within
a single cohesive application. This project provides all necessary artifacts to develop,
test, deploy, and operate the NOMAD Respository and Archive, e.g. at
-[https://repository.nomad-coe.eu/app/gui](https://repository.nomad-coe.eu/app/gui).
+[https://nomad-lab.eu](https://nomad-lab.eu).
In the future, this project's aim is to integrate more NOMAD CoE components, like the NOMAD
Encyclopedia and NOMAD Analytics Toolkit, to fully integrate NOMAD with one GUI and consistent
@@ -37,7 +37,7 @@ nomad parse --show-backend <your-file-to-parse>
### For NOMAD developer
-Read the [docs](https://repository.nomad-coe.eu/app/docs/index.html). The documentation is also part
+Read the [docs](https://nomad-lab.eu/prod/rae/docs/index.html). The documentation is also part
of the source code. It covers aspects like introduction, architecture, development setup/deployment,
contributing, and API reference.
diff --git a/docs/api.rst b/docs/api.rst
index 97332aaf4c..a74fa951ce 100644
--- a/docs/api.rst
+++ b/docs/api.rst
@@ -4,8 +4,8 @@ API Reference
This is just a brief summary of all API endpoints of the NOMAD API. For a more compelling documention
consult our *swagger* dashboards:
-- (NOMAD API)[swagger dashboard](https://repository.nomad-coe.eu/app/api/)
-- (NOMAD's Optimade API)[swagger dashboard](https://repository.nomad-coe.eu/app/optimade/)
+- (NOMAD API)[swagger dashboard](https://nomad-lab.eu/prod/rae/api/)
+- (NOMAD's Optimade API)[swagger dashboard](https://nomad-lab.eu/prod/rae/optimade/)
Summary
diff --git a/docs/api_tutorial.md b/docs/api_tutorial.md
index 999ec1385a..d4bd1abd20 100644
--- a/docs/api_tutorial.md
+++ b/docs/api_tutorial.md
@@ -12,7 +12,7 @@ trade-offs between expressiveness, learning curve, and convinience:
- use a generic Python HTTP library like [requests](https://requests.readthedocs.io/en/master/)
- use more specific Python libraries like [bravado](https://github.com/Yelp/bravado) that turn HTTP requests into NOMAD
specific function calls based on an [OpenAPI spec](https://swagger.io/specification/) that NOMAD offers and that describes our API
-- directly in the browser via our generated [swagger dashboard](https://repository.nomad-coe.eu/app/api/)
+- directly in the browser via our generated [swagger dashboard](../api/)
- use the NOMAD Python client library, which offers custom and more powerful
implementations for certain tasks (currently only for accessing the NOMAD Archive)
@@ -39,7 +39,7 @@ our gui) for entries that fit search criteria, like compounds having atoms *Si*
it:
```
-curl -X GET "http://repository.nomad-coe.eu/app/api/repo/?atoms=Si&atoms=O"
+curl -X GET "http://nomad-lab.eu/prod/rae/api/repo/?atoms=Si&atoms=O"
```
Here we used curl to send an HTTP GET request to return the resource located by the given URL.
@@ -47,20 +47,20 @@ In practice you can omit the `-X GET` (which is the default) and you might want
the output:
```
-curl "http://repository.nomad-coe.eu/app/api/repo/?atoms=Si&atoms=O" | python -m json.tool
+curl "http://nomad-lab.eu/prod/rae/api/repo/?atoms=Si&atoms=O" | python -m json.tool
```
You'll see the the metadata of the first 10 entries that match your criteria. There
are various other query parameters. You find a full list in the generated [swagger dashboard
-of our API](https://repository.nomad-coe.eu/app/api/).
+of our API](https://nomad-lab.eu/prod/rae/api/).
Besides search criteria you can determine how many results (`per_page`) and what page of
results should be returned (`page`). If you want to go beyond the first 10.000 results
you can use our *scroll* API (`scroll=true`, `scroll_after`). You can limit what properties
should be returned (`include`, `exclude`). See the the generated [swagger dashboard
-of our API](https://repository.nomad-coe.eu/app/api/) for more parameters.
+of our API](https://nomad-lab.eu/prod/rae/api/) for more parameters.
-If you use the [NOMAD Repository and Archive search interface](https://repository.nomad-coe.eu/app/gui/search)
+If you use the [NOMAD Repository and Archive search interface](https://nomad-lab.eu/prod/rae/gui/search)
and create a query, you can click th a **<>**-button (right and on top of the result list).
This will give you some code examples with URLs for your search query.
@@ -69,21 +69,21 @@ identified an entry (given via a `upload_id`/`calc_id`, see the query output), a
you want to download it:
```
-curl "http://repository.nomad-coe.eu/app/api/raw/calc/JvdvikbhQp673R4ucwQgiA/k-ckeQ73sflE6GDA80L132VCWp1z/*" -o download.zip
+curl "http://nomad-lab.eu/prod/rae/api/raw/calc/JvdvikbhQp673R4ucwQgiA/k-ckeQ73sflE6GDA80L132VCWp1z/*" -o download.zip
```
With `*` you basically requests all the files under an entry or path..
If you need a specific file (that you already know) of that calculation:
```
-curl "http://repository.nomad-coe.eu/app/api/raw/calc/JvdvikbhQp673R4ucwQgiA/k-ckeQ73sflE6GDA80L132VCWp1z/INFO.OUT"
+curl "http://nomad-lab.eu/prod/rae/api/raw/calc/JvdvikbhQp673R4ucwQgiA/k-ckeQ73sflE6GDA80L132VCWp1z/INFO.OUT"
```
You can also download a specific file from the upload (given a `upload_id`), if you know
the path of that file:
```
-curl "http://repository.nomad-coe.eu/app/api/raw/JvdvikbhQp673R4ucwQgiA/exciting_basis_set_error_study/monomers_expanded_k8_rgkmax_080_PBE/72_Hf/INFO.OUT"
+curl "http://nomad-lab.eu/prod/rae/api/raw/JvdvikbhQp673R4ucwQgiA/exciting_basis_set_error_study/monomers_expanded_k8_rgkmax_080_PBE/72_Hf/INFO.OUT"
```
If you have a query
@@ -91,19 +91,19 @@ that is more selective, you can also download all results. Here all compounds th
consist of Si, O, bulk material simulations of cubic systems (currently ~100 entries):
```
-curl "http://repository.nomad-coe.eu/app/api/raw/query?only_atoms=Si&only_atoms=O&system=bulk&crystal_system=cubic" -o download.zip
+curl "http://nomad-lab.eu/prod/rae/api/raw/query?only_atoms=Si&only_atoms=O&system=bulk&crystal_system=cubic" -o download.zip
```
In a similar way you can see the archive of an entry:
```
-curl "http://repository.nomad-coe.eu/app/api/archive/f0KQE2aiSz2KRE47QtoZtw/6xe9fZ9xoxBYZOq5lTt8JMgPa3gX" | python -m json.tool
+curl "http://nomad-lab.eu/prod/rae/api/archive/f0KQE2aiSz2KRE47QtoZtw/6xe9fZ9xoxBYZOq5lTt8JMgPa3gX" | python -m json.tool
```
Or query and display the first page of 10 archives:
```
-curl "http://repository.nomad-coe.eu/app/api/archive/query?only_atoms=Si&only_atoms=O" | python -m json.tool
+curl "http://nomad-lab.eu/prod/rae/api/archive/query?only_atoms=Si&only_atoms=O" | python -m json.tool
```
## Using Python's *request* library
@@ -115,7 +115,7 @@ client library that allows you to send requests:
import requests
import json
-response = requests.get("http://repository.nomad-coe.eu/app/api/archive/query?only_atoms=Si&only_atoms=O")
+response = requests.get("http://nomad-lab.eu/prod/rae/api/archive/query?only_atoms=Si&only_atoms=O")
data = response.json()
print(json.dumps(data), indent=2)
```
@@ -128,7 +128,7 @@ specific functions for you.
```python
from bravado.client import SwaggerClient
-nomad_url = 'http://repository.nomad-coe.eu/app/api'
+nomad_url = 'http://nomad-lab.eu/prod/rae/api'
# create the bravado client
client = SwaggerClient.from_url('%s/swagger.json' % nomad_url)
@@ -194,7 +194,7 @@ data you also need an account (email, password). The toy account used here, shou
available on most nomad installations:
```python
-nomad_url = 'https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/latest/api'
+nomad_url = 'https://nomad-lab.eu/prod/rae/api'
user = 'leonard.hofstadter@nomad-fairdi.tests.de'
password = 'password'
```
@@ -220,7 +220,7 @@ class KeycloakAuthenticator(Authenticator):
self.password = password
self.token = None
self.__oidc = KeycloakOpenID(
- server_url='https://repository.nomad-coe.eu/fairdi/keycloak/auth/',
+ server_url='https://nomad-lab.eu/fairdi/keycloak/auth/',
realm_name='fairdi_nomad_prod',
client_id='nomad_public')
@@ -296,7 +296,7 @@ if upload.tasks_status != 'SUCCESS':
```
Of course, you can also visit the nomad GUI
-([https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/latest/gui/uploads](https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/latest/gui/uploads))
+([https://nomad-lab.eu/prod/rae/gui/uploads](https://nomad-lab.eu/prod/rae/gui/uploads))
to inspect your uploads. (You might click reload, if you had the page already open.)
@@ -379,7 +379,7 @@ or downloading data are only **GET** operations controlled by URL parameters. Fo
Downloading data:
```
-curl http://repository.nomad-coe.eu/app/api/raw/query?upload_id=<your_upload_id> -o download.zip
+curl http://nomad-lab.eu/prod/rae/api/raw/query?upload_id=<your_upload_id> -o download.zip
```
It is a litle bit trickier, if you need to authenticate yourself, e.g. to download
@@ -387,18 +387,18 @@ not yet published or embargoed data. All endpoints support and most require the
an access token. To acquire an access token from our usermanagement system with curl:
```
curl --data 'grant_type=password&client_id=nomad_public&username=<your_username>&password=<your password>' \
- https://repository.nomad-coe.eu/fairdi/keycloak/auth/realms/fairdi_nomad_prod/protocol/openid-connect/token
+ https://nomad-lab.eu/fairdi/keycloak/auth/realms/fairdi_nomad_prod/protocol/openid-connect/token
```
You can use the access-token with:
```
curl -H 'Authorization: Bearer <you_access_token>' \
- http://repository.nomad-coe.eu/app/api/raw/query?upload_id=<your_upload_id> -o download.zip
+ http://nomad-lab.eu/prod/rae/api/raw/query?upload_id=<your_upload_id> -o download.zip
```
### Conclusions
This was just a small glimpse into the nomad API. You should checkout our
-[swagger-ui](https://repository.nomad-coe.eu/app/api/)
+[swagger-ui](nomad-lab.eu/prod/rae/api/)
for more details on all the API endpoints and their parameters. You can explore the
API via the swagger-ui and even try it in your browser.
diff --git a/docs/client/cli_use_cases.rst b/docs/client/cli_use_cases.rst
index cc55cfbaf1..871d74c888 100644
--- a/docs/client/cli_use_cases.rst
+++ b/docs/client/cli_use_cases.rst
@@ -27,7 +27,7 @@ Here is a breakdown of the different arguments:
* :code:`-n <url>`: Url to the API endpoint in the source deployment. This API will
be queried to fetch the data to be mirrored. E.g.
- http://repository.nomad-coe.eu/api
+ http://nomad-lab.eu/prod/rae/api
* :code:`-u <username>`: Your username that is used for authentication in the API call.
* :code:`-w <password>`: Your password that is used for authentication in the API call.
* :code:`mirror <query>`: Your query as a JSON dictionary. See the documentation for
diff --git a/docs/client/install.rst b/docs/client/install.rst
index d4eb101e08..14957a2304 100644
--- a/docs/client/install.rst
+++ b/docs/client/install.rst
@@ -14,7 +14,7 @@ Download and install latest release from nomad
.. code-block:: sh
- curl https://repository.nomad-coe.eu/app/dist/nomad-lab.tar.gz -o nomad-lab.tar.gz
+ curl https://nomad-lab.eu/prod/rae/dist/nomad-lab.tar.gz -o nomad-lab.tar.gz
pip install ./nomad-lab.tar.gz
There are different layers of dependencies that you have to install, in order to use
diff --git a/docs/conf.py b/docs/conf.py
index 7ce7e127d6..67f30366c3 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -200,4 +200,4 @@ def setup(app):
# }, True)
# app.add_transform(AutoStructify)
-extlinks = {'api': ('https://repository.nomad-coe.eu/app/api/%s', 'NOMAD API ')}
\ No newline at end of file
+extlinks = {'api': ('https://nomad-lab.eu/prod/rae/api/%s', 'NOMAD API ')}
\ No newline at end of file
diff --git a/docs/introduction.md b/docs/introduction.md
index 9babf75946..0783f4220d 100644
--- a/docs/introduction.md
+++ b/docs/introduction.md
@@ -14,9 +14,10 @@ This is the documentation of **nomad@FAIRDI**, the Open-Source continuation of t
original NOMAD-coe software that reconciles the original code base,
integrate it's services, allows 3rd parties to run individual and federated instance of
the nomad infrastructure, provides nomad to other material science domains, and applies
-the FAIRDI principles as proliferated by the [FAIRDI Data Infrastructure e.V.](http://fairdi.eu).
+the FAIRDI principles as proliferated by the [FAIRDI Data Infrastructure e.V.](https://fairdi.eu).
A central and publically available instance of the nomad software is run at the
-[MPCDF](https://www.mpcdf.mpg.de/) in Garching, Germany.
+[MPCDF](https://www.mpcdf.mpg.de/) in Garching, Germany. Software development and the
+operation of NOMAD is done by the [NOMAD Laboratory](https://nomad-lab.eu)
The nomad software runs SAAS on a server and is used via web-based GUI and ReSTful
API. Originally developed and hosted as individual services, **nomad@FAIRDI**
@@ -24,8 +25,7 @@ provides all services behind one GUI and API into a single coherent, integrated,
modular software project.
This documentation is only about the nomad *software*; it is about architecture,
-how to contribute, code reference, engineering and operation of nomad. It is not a
-nomad user manual.
+how to contribute, code reference, engineering and operation of nomad.
## Architecture
diff --git a/docs/metainfo.rst b/docs/metainfo.rst
index fdd4d5afd3..4cc884d372 100644
--- a/docs/metainfo.rst
+++ b/docs/metainfo.rst
@@ -10,7 +10,7 @@ The NOMAD Metainfo stores descriptive and structured information about materials
data contained in the NOMAD Archive. The Metainfo can be understood as the schema of
the Archive. The NOMAD Archive data is
structured to be independent of the electronic-structure theory code or molecular-simulation,
-(or beyond). The NOMAD Metainfo can be browsed as part of the `NOMAD Repository and Archive web application <https://repository.nomad-coe.eu/app/gui/metainfo>`_.
+(or beyond). The NOMAD Metainfo can be browsed as part of the `NOMAD Repository and Archive web application <https://nomad-lab.eu/prod/rae/gui/metainfo>`_.
Typically (meta-)data definitions are generated only for a predesigned and specific scientific field,
application or code. In contrast, the NOMAD Metainfo considers all pertinent information
@@ -29,10 +29,8 @@ the archive data is solely served by NOMAD's API.
The NOMAD Metainfo started within the `NOMAD Laboratory <https://nomad-lab.eu>`_. It was discussed at the
`CECAM workshop Towards a Common Format for Computational Materials Science Data <https://th.fhi-berlin.mpg.de/meetings/FCMSD2016/>`_
-and is open to external contributions and extensions. More information can be found in:
-
-- `Towards a Common Format for Computational Materials Science Data (Psi-K 2016 Highlight) <http://th.fhi-berlin.mpg.de/site/uploads/Publications/Psik_Highlight_131-2016.pdf>`_ provides a description on how to establish code-independent formats in detail and presents the challenges and practical strategies for achieving a common format for the representation of computational material-science data.
-- `The Novel Materials Discovery Laboratory - Data formats and compression, D1.1 <https://www.nomad-coe.eu/uploads/outreach/Public%20Deliverables/NOMAD%20D1.1%20public%20KO20June2016.pdf>`_ outlines possible data formats, concepts, and compression techniques used to build a homogeneous (code-independent) data archive, called the NOMA
+and is open to external contributions and extensions. More information can be found in
+`Towards a Common Format for Computational Materials Science Data (Psi-K 2016 Highlight) <http://th.fhi-berlin.mpg.de/site/uploads/Publications/Psik_Highlight_131-2016.pdf>`_.
Metainfo Python Interface
diff --git a/docs/upload.rst b/docs/upload.rst
index 6c98dd3582..abc9cb18f0 100644
--- a/docs/upload.rst
+++ b/docs/upload.rst
@@ -2,13 +2,14 @@
Uploading Data to the NOMAD Repository
======================================
-To contribute your data to the repository, please, login to our `upload page <../uploads>`_ (you need to register first, if you do not have a NOMAD account yet).
+To contribute your data to the repository, please, login to our `upload page <../gui/uploads>`_
+(you need to register first, if you do not have a NOMAD account yet).
*A note for returning NOMAD users!* We revised the upload process with browser based upload
alongside new shell commands. The new Upload page allows you to monitor upload processing
and verify processing results before publishing your data to the Repository.
-The `upload page <../uploads>`_ acts as a staging area for your data. It allows you to
+The `upload page <../gui/uploads>`_ acts as a staging area for your data. It allows you to
upload data, to supervise the processing of your data, and to examine all metadata that
NOMAD extracts from your uploads. The data on the upload page will be private and can be
deleted again. If you are satisfied with our processing, you can publish the data.
@@ -29,8 +30,9 @@ extract the most important information of POTCAR files and store it in the files
POTCAR files are only available to the uploader and assigned co-authors.
This is done automatically; you don't need to do anything.
-Once published, data cannot be erased. Linking a corrected version to a corresponding older one ("erratum") will be possible soon.
-Files from an improved calculation, even for the same material, will be handled as a new entry.
+Once published, data cannot be erased. Linking a corrected version to a corresponding older
+one ("erratum") will be possible soon. Files from an improved calculation, even for the
+same material, will be handled as a new entry.
You can publish data as being open access or restricted for up to three years (with embargo).
For the latter you may choose with whom you want to share your data. We strongly support the
diff --git a/examples/api_use.py b/examples/api_use.py
index ef0bb27740..9b345d0f52 100644
--- a/examples/api_use.py
+++ b/examples/api_use.py
@@ -4,7 +4,7 @@ This is a brief example on how to use the public nomad@FAIRDI API.
from bravado.client import SwaggerClient
-nomad_url = 'http://repository.nomad-coe.eu/app/api'
+nomad_url = 'http://nomad-lab.eu/prod/rae/api'
# create the bravado client
client = SwaggerClient.from_url('%s/swagger.json' % nomad_url)
diff --git a/examples/api_use_authenticated.py b/examples/api_use_authenticated.py
index 297cf12012..5bb9d2394e 100644
--- a/examples/api_use_authenticated.py
+++ b/examples/api_use_authenticated.py
@@ -8,7 +8,7 @@ from urllib.parse import urlparse
from keycloak import KeycloakOpenID
from time import time
-nomad_url = 'http://repository.nomad-coe.eu/app/api'
+nomad_url = 'http://nomad-lab.eu/prod/rae/api'
user = 'yourusername'
password = 'yourpassword'
@@ -21,7 +21,7 @@ class KeycloakAuthenticator(Authenticator):
self.password = password
self.token = None
self.__oidc = KeycloakOpenID(
- server_url='https://repository.nomad-coe.eu/fairdi/keycloak/auth/',
+ server_url='https://nomad-lab.eu/fairdi/keycloak/auth/',
realm_name='fairdi_nomad_prod',
client_id='nomad_public')
diff --git a/gui/public/env.js b/gui/public/env.js
index 27d5456db3..1bc990b0f7 100644
--- a/gui/public/env.js
+++ b/gui/public/env.js
@@ -1,16 +1,16 @@
window.nomadEnv = {
- 'keycloakBase': 'https://repository.nomad-coe.eu/fairdi/keycloak/auth/',
+ 'keycloakBase': 'https://nomad-lab.eu/fairdi/keycloak/auth/',
'keycloakRealm': 'fairdi_nomad_test',
'keycloakClientId': 'nomad_gui_dev',
'appBase': 'http://localhost:8000/fairdi/nomad/latest',
'debug': false,
- 'matomoEnabled': true,
- 'matomoUrl': 'https://repository.nomad-coe.eu/fairdi/stat',
+ 'matomoEnabled': false,
+ 'matomoUrl': 'https://nomad-lab.eu/prod/stat',
'matomoSiteId': '2',
'version': {
"label": "0.8.3",
"isBeta": false,
"usesBetaData": false,
- "officialUrl": "https://repository.nomad-coe.eu/app/gui"
+ "officialUrl": "https://nomad-lab.eu/prod/rae/gui"
}
}
diff --git a/gui/src/components/About.js b/gui/src/components/About.js
index ff4fecf3f8..e5cd720a90 100644
--- a/gui/src/components/About.js
+++ b/gui/src/components/About.js
@@ -100,7 +100,7 @@ export default function About() {
window.location.href = 'https://encyclopedia.nomad-coe.eu/gui/#/search'
})
makeClickable('analytics', () => {
- window.location.href = 'https://www.nomad-coe.eu/index.php?page=bigdata-analyticstoolkit'
+ window.location.href = 'https://nomad-lab.eu/index.php?page=AItutorials'
})
makeClickable('search', () => {
history.push('/search')
@@ -144,10 +144,14 @@ export default function About() {
This is the *graphical user interface* (GUI) for the NOMAD Repository and
Archive. It allows you to **search, access, and download all NOMAD data** in its
raw (Repository) and processed (Archive) form. You can **upload and manage your own
- raw materials science data**. Learn more about what data can be uploaded
- and how to prepare your data on the [NOMAD Repository homepage](https://repository.nomad-coe.eu/).
- You can access all published data without an account. If you want to provide
- your own data, please login or register for an account.
+ raw materials science data**. You can access all published data without an account.
+ If you want to provide your own data, please login or register for an account.
+
+ You can learn more about on the NOMAD Repository and Archive
+ [homepage](https://nomad-lab.eu/index.php?page=repo-arch), our
+ [documentation](${appBase}/docs/index.html).
+ There is also an [FAQ](https://nomad-lab.eu/index.php?page=repository-archive-faqs)
+ and the more detailed [uploader documentation](${appBase}/docs/upload.html).
`}</Markdown>
</Grid>
<InfoCard xs={6} title="Interactive Search" top>
@@ -217,7 +221,7 @@ export default function About() {
There is a [tutorial on how to use the API with plain Python](${appBase}/docs/api_tutorial.html).
Another [tutorial covers how to install and use NOMAD's Python client library](${appBase}/docs/archive_tutorial.html).
- The [NOMAD Analytics Toolkit](https://analytics-toolkit.nomad-coe.eu) allows to use
+ The [NOMAD Analytics Toolkit](https://nomad-lab.eu/index.php?page=AIToolkit) allows to use
this without installation and directly on NOMAD servers.
`}</Markdown></InfoCard>
<Grid item xs={12}>
diff --git a/gui/src/components/App.js b/gui/src/components/App.js
index d257cc64d4..96feb8cadf 100644
--- a/gui/src/components/App.js
+++ b/gui/src/components/App.js
@@ -278,7 +278,7 @@ function MainMenu() {
/>
<MainMenuItem
title="FAQ"
- path="/faq"
+ href="https://nomad-lab.eu/index.php?page=repository-archive-faqs"
tooltip="Frequently Asked Questions (FAQ)"
icon={<FAQIcon/>}
/>
@@ -456,7 +456,7 @@ class NavigationUnstyled extends React.Component {
disableGutters
>
<div className={classes.title}>
- <a href="https://nomad-coe.eu">
+ <a href="https://nomad-lab.eu">
<img alt="The NOMAD logo" className={classes.logo} src={`${guiBase}/nomad.png`}></img>
</a>
<Typography variant="h6" color="inherit" noWrap>
diff --git a/gui/src/components/metaInfoBrowser/MetaInfoBrowser.js b/gui/src/components/metaInfoBrowser/MetaInfoBrowser.js
index dd52834622..0539736268 100644
--- a/gui/src/components/metaInfoBrowser/MetaInfoBrowser.js
+++ b/gui/src/components/metaInfoBrowser/MetaInfoBrowser.js
@@ -8,6 +8,7 @@ import MetainfoSearch from './MetainfoSearch'
import { FormControl, Select, Input, MenuItem, ListItemText, InputLabel, makeStyles } from '@material-ui/core'
import { schema } from '../MetaInfoRepository'
import { errorContext } from '../errors'
+import { appBase } from '../../config'
export const help = `
The NOMAD *metainfo* defines all quantities used to represent archive data in
@@ -37,7 +38,7 @@ reference (blue) relations.
If you bookmark this page, you can save the definition represented by the highlighted
*main* card.
-To learn more about the meta-info, visit the [meta-info homepage](https://metainfo.nomad-coe.eu/nomadmetainfo_public/archive.html).
+To learn more about the meta-info, visit the [meta-info documentation](${appBase}/docs/metainfo.html).
`
const MenuProps = {
PaperProps: {
diff --git a/gui/src/components/uploads/UploadPage.js b/gui/src/components/uploads/UploadPage.js
index 68e4050daa..150e3d5f9f 100644
--- a/gui/src/components/uploads/UploadPage.js
+++ b/gui/src/components/uploads/UploadPage.js
@@ -14,13 +14,14 @@ import { withApi } from '../api'
import { withCookies, Cookies } from 'react-cookie'
import Pagination from 'material-ui-flat-pagination'
import { CopyToClipboard } from 'react-copy-to-clipboard'
-import { guiBase } from '../../config'
+import { guiBase, appBase } from '../../config'
import qs from 'qs'
import { CodeList } from '../About'
+import { Link } from '@material-ui/core'
export const help = `
NOMAD allows you to upload data. After upload, NOMAD will process your data: it will
-identify the main output files of [supported codes](https://www.nomad-coe.eu/the-project/nomad-repository/nomad-repository-howtoupload)
+identify the main output files of supported codes.
and then it will parse these files. The result will be a list of entries (one per each identified mainfile).
Each entry is associated with metadata. This is data that NOMAD acquired from your files and that
describe your calculations (e.g. chemical formula, used code, system type and symmetry, etc.).
@@ -275,6 +276,8 @@ class UploadPage extends React.Component {
NOMAD will search through all files and identify the relevant files automatically.
Each uploaded file can be <b>up to 32GB</b> in size, you can have <b>up to 10 unpublished
uploads</b> simultaneously. Your uploaded data is not published right away.
+ Find more details about uploading data in our <Link href={`${appBase}/docs/upload.html`}>documentation</Link> or visit
+ our <Link href="https://nomad-lab.eu/index.php?page=repository-archive-faqs">FAQs</Link>.
</Typography>
<Typography>
The following codes are supported: <CodeList/>.
diff --git a/gui/src/config.js b/gui/src/config.js
index a5bbcf59ad..f6978b1f18 100644
--- a/gui/src/config.js
+++ b/gui/src/config.js
@@ -3,7 +3,7 @@ import { createMuiTheme } from '@material-ui/core'
window.nomadEnv = window.nomadEnv || {}
export const version = window.nomadEnv.version
export const appBase = window.nomadEnv.appBase.replace(/\/$/, '')
-// export const apiBase = 'http://repository.nomad-coe.eu/v0.8/api'
+// export const apiBase = 'http://nomad-lab.eu/prod/rae/api'
export const apiBase = `${appBase}/api`
export const optimadeBase = `${appBase}/optimade`
export const guiBase = process.env.PUBLIC_URL
@@ -19,7 +19,7 @@ export const maxLogsToShow = 50
export const consent = `
By using this web-site and by uploading and downloading data, you agree to the
-[terms of use](https://www.nomad-coe.eu/the-project/nomad-repository/nomad-repository-terms).
+[terms of use](https://nomad-lab.eu/index.php?page=terms).
Uploaded data is licensed under the Creative Commons Attribution license
([CC BY 4.0](https://creativecommons.org/licenses/by/4.0/)). You can publish
diff --git a/nomad/cli/client/statistics.py b/nomad/cli/client/statistics.py
index 02812074ef..3b94ece86b 100644
--- a/nomad/cli/client/statistics.py
+++ b/nomad/cli/client/statistics.py
@@ -537,7 +537,7 @@ def statistics_table(html, geometries, public_path):
</ul>
<p>
For more and interactive statistics, use the <i>metadata</i> view of
- the <a href="https://repository.nomad-coe.eu/app/gui/search">NOMAD Repository and Archvi search</a>.
+ the <a href="https://nomad-lab.eu/prod/rae/gui/search">NOMAD Repository and Archvi search</a>.
</p>
<p>
90% of VASP calculations are provided by
@@ -554,7 +554,7 @@ def statistics_table(html, geometries, public_path):
<p>
The archive data is represented in a code-independent, structured
form. The archive structure and all quantities are described via the
- <a href="https://www.nomad-coe.eu/the-project/nomad-archive/archive-meta-info">NOMAD Metainfo</a>.
+ <a href="https://nomad-lab.eu/prod/rae/gui/metainfo">NOMAD Metainfo</a>.
The NOMAD Metainfo defines a conceptual model to store the values connected
to atomistic or <i>ab initio</i> calculations. A clear and usable metadata definition
is a prerequisites to preparing the data for analysis that everybody
diff --git a/nomad/config.py b/nomad/config.py
index 2311680625..69a41bdcbf 100644
--- a/nomad/config.py
+++ b/nomad/config.py
@@ -120,7 +120,7 @@ elastic = NomadConfig(
)
keycloak = NomadConfig(
- server_url='https://repository.nomad-coe.eu/fairdi/keycloak/auth/',
+ server_url='https://nomad-lab.eu/fairdi/keycloak/auth/',
realm_name='fairdi_nomad_test',
username='admin',
password='password',
@@ -250,7 +250,7 @@ normalize = NomadConfig(
client = NomadConfig(
user='leonard.hofstadter@nomad-fairdi.tests.de',
password='password',
- url='http://repository.nomad-coe.eu/app/api'
+ url='http://nomad-lab.eu/prod/rae/api'
)
datacite = NomadConfig(
@@ -269,7 +269,7 @@ meta = NomadConfig(
service='unknown nomad service',
name='novel materials discovery (NOMAD)',
description='A FAIR data sharing platform for materials science data',
- homepage='https://repository.nomad-coe.eu/v0.8',
+ homepage='https://https://nomad-lab.eu',
source_url='https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR',
maintainer_email='markus.scheidgen@physik.hu-berlin.de'
)
diff --git a/nomad/doi.py b/nomad/doi.py
index 8582a2fd12..c4a4ef25e3 100644
--- a/nomad/doi.py
+++ b/nomad/doi.py
@@ -30,7 +30,7 @@ from nomad import config, utils
def edit_url(doi: str, url: str = None):
''' Changes the URL of an already findable DOI. '''
if url is None:
- url = 'https://repository.nomad-coe.eu/app/gui/datasets/doi/%s' % doi
+ url = 'https://nomad-lab.eu/prod/rae/gui/datasets/doi/%s' % doi
metadata_url = '%s/doi/%s' % (config.datacite.mds_host, doi)
response = requests.put(
diff --git a/nomad/metainfo/example.py b/nomad/metainfo/example.py
index e7ad6f57cc..ca57f59519 100644
--- a/nomad/metainfo/example.py
+++ b/nomad/metainfo/example.py
@@ -22,7 +22,7 @@ from nomad.metainfo import (
MSection, MCategory, Section, Quantity, Package, SubSection, MEnum,
Datetime, constraint)
-m_package = Package(links=['http://metainfo.nomad-coe.eu'])
+m_package = Package(links=['https://nomad-lab.eu/prod/rae/docs/metainfo.html'])
class SystemHash(MCategory):
diff --git a/ops/containers/keycloak/material_theme/account/theme.properties b/ops/containers/keycloak/material_theme/account/theme.properties
index 8293dd1e46..6ec78a16c8 100644
--- a/ops/containers/keycloak/material_theme/account/theme.properties
+++ b/ops/containers/keycloak/material_theme/account/theme.properties
@@ -1,5 +1,5 @@
parent=base
styles=css/material-components-web.min.css css/bootstrap-material-design-alerts.css css/material-keycloak-theme.css
scripts=js/polyfill/nodelist-foreach.js js/material-components-web.min.js js/material-keycloak-theme.js
-kcLogoLink=https://nomad-coe.eu/
+kcLogoLink=https://nomad-lab.eu/
diff --git a/ops/containers/keycloak/material_theme/login/theme.properties b/ops/containers/keycloak/material_theme/login/theme.properties
index 8293dd1e46..6ec78a16c8 100644
--- a/ops/containers/keycloak/material_theme/login/theme.properties
+++ b/ops/containers/keycloak/material_theme/login/theme.properties
@@ -1,5 +1,5 @@
parent=base
styles=css/material-components-web.min.css css/bootstrap-material-design-alerts.css css/material-keycloak-theme.css
scripts=js/polyfill/nodelist-foreach.js js/material-components-web.min.js js/material-keycloak-theme.js
-kcLogoLink=https://nomad-coe.eu/
+kcLogoLink=https://nomad-lab.eu/
diff --git a/ops/docker-compose/nomad-oasis/README.md b/ops/docker-compose/nomad-oasis/README.md
index cd98b90434..2a375787c8 100644
--- a/ops/docker-compose/nomad-oasis/README.md
+++ b/ops/docker-compose/nomad-oasis/README.md
@@ -203,7 +203,7 @@ The GUI also has a config file, called `env.js` with a similar function than `no
```js
window.nomadEnv = {
'appBase': '/nomad-oasis/',
- 'keycloakBase': 'https://repository.nomad-coe.eu/fairdi/keycloak/auth/',
+ 'keycloakBase': 'https://nomad-lab.eu/fairdi/keycloak/auth/',
'keycloakRealm': 'fairdi_nomad_prod',
'keycloakClientId': 'nomad_public',
'debug': false,
@@ -352,7 +352,7 @@ Will will probably provide functionality in the API of the central NOMAD to uplo
### How to maintain an Oasis installation?
#### How to install a NOMAD Oasis?
-Follow our guide: https://repository.nomad-coe.eu/app/docs/ops.html#operating-a-nomad-oasis
+Follow our guide: https://nomad-lab.eu/prod/rae/docs/ops.html#operating-a-nomad-oasis
#### How do version numbers work?
There are still a lot of thing in NOMAD that are subject to change. Currently, changes in the minor version number (0.x.0) designate major changes that require data migration. Changes in the patch version number (0.7.x) just contain minor changes and fixes and do not require data migration. Once we reach 1.0.0, NOMAD will use the regular semantic versioning conventions.
diff --git a/ops/docker-compose/nomad-oasis/env.js b/ops/docker-compose/nomad-oasis/env.js
index c3b12dfa66..d4fd251fd8 100644
--- a/ops/docker-compose/nomad-oasis/env.js
+++ b/ops/docker-compose/nomad-oasis/env.js
@@ -1,6 +1,6 @@
window.nomadEnv = {
'appBase': '/nomad-oasis/',
- 'keycloakBase': 'https://repository.nomad-coe.eu/fairdi/keycloak/auth/',
+ 'keycloakBase': 'https://nomad-lab.eu/fairdi/keycloak/auth/',
'keycloakRealm': 'fairdi_nomad_prod',
'keycloakClientId': 'nomad_public',
'debug': false,
diff --git a/ops/helm/nomad/ci-dev-values.yaml b/ops/helm/nomad/ci-dev-values.yaml
index 69654013ef..24e28cacf6 100644
--- a/ops/helm/nomad/ci-dev-values.yaml
+++ b/ops/helm/nomad/ci-dev-values.yaml
@@ -27,7 +27,7 @@ logstash:
dbname: nomad_dev_v0_8
keycloak:
- serverUrl: "https://repository.nomad-coe.eu/fairdi/keycloak/auth/"
+ serverUrl: "https://nomad-lab.eu/fairdi/keycloak/auth/"
passwordSecret: 'nomad-keycloak-password'
realmName: 'fairdi_nomad_prod'
clientId: 'nomad_public'
diff --git a/ops/helm/nomad/values.yaml b/ops/helm/nomad/values.yaml
index 3471c413b3..56bea48ce5 100644
--- a/ops/helm/nomad/values.yaml
+++ b/ops/helm/nomad/values.yaml
@@ -3,7 +3,7 @@ version:
label: "0.8.3"
isBeta: false
usesBetaData: false
- officialUrl: "https://repository.nomad-coe.eu/app/gui"
+ officialUrl: "https://nomad-lab.eu/prod/rae/gui"
## Everything concerning the container images to be used
image:
@@ -73,7 +73,7 @@ gui:
## This variable is used in the GUI to show or hide additional information
debug: false
## URL for matomo(piwik) user tracking
- matomoUrl: 'https://repository.nomad-coe.eu/fairdi/stat'
+ matomoUrl: 'https://nomad-lab.eu/prod/stat'
## site id for matomo(piwik) user tracking
matomoSiteId: 1
## send matomo(piwik) user tracking data
@@ -140,8 +140,8 @@ client:
username: admin
keycloak:
- serverExternalUrl: "https://repository.nomad-coe.eu/fairdi/keycloak/auth/"
- serverUrl: "https://repository.nomad-coe.eu/fairdi/keycloak/auth/"
+ serverExternalUrl: "https://nomad-lab.eu/fairdi/keycloak/auth/"
+ serverUrl: "https://nomad-lab.eu/keycloak/auth/"
realmName: "fairdi_nomad_test"
username: "admin"
clientId: "nomad_public"
--
GitLab