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diff --git a/gui/public/jupyter_logo.svg b/gui/public/logo/jupyter.svg
similarity index 100%
rename from gui/public/jupyter_logo.svg
rename to gui/public/logo/jupyter.svg
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diff --git a/gui/public/logo/nionswift.png b/gui/public/logo/nionswift.png
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diff --git a/gui/public/logo/pyarpes.svg b/gui/public/logo/pyarpes.svg
new file mode 100644
index 0000000000000000000000000000000000000000..dd029eb9b89d452f20c9bcc7d095ca6287cb5885
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diff --git a/gui/public/pyiron_logo.png b/gui/public/logo/pyiron.png
similarity index 100%
rename from gui/public/pyiron_logo.png
rename to gui/public/logo/pyiron.png
diff --git a/gui/public/logo/vesta.png b/gui/public/logo/vesta.png
new file mode 100644
index 0000000000000000000000000000000000000000..cbb003a5c7b54681169aeadb10384f063f119991
Binary files /dev/null and b/gui/public/logo/vesta.png differ
diff --git a/gui/tests/artifacts.js b/gui/tests/artifacts.js
index 58f5ed1ee1dbf66a544d8fe4558ed0a5a5dac69f..ff3ceab485504c00dec0301bd7e0f54dde14c4b8 100644
--- a/gui/tests/artifacts.js
+++ b/gui/tests/artifacts.js
@@ -65259,18 +65259,19 @@ window.nomadArtifacts = {
"northTools": {
"jupyter": {
"short_description": "Basic jupyter run with an empty notebook or on given notebook file.",
- "description": "### **Jupyter Notebook**: The Classic Notebook Interface\n\nThe Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience.",
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/jupyter:latest",
+ "description": "### **Jupyter Notebook**: The Classic Notebook Interface\nThe Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience.",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/jupyter:refactor",
"cmd": null,
"image_pull_policy": "Always",
"privileged": false,
+ "default_url": "/lab",
"path_prefix": "lab/tree",
"with_path": true,
"file_extensions": [
"ipynb"
],
"mount_path": "/home/jovyan",
- "icon": "jupyter_logo.svg",
+ "icon": "logo/jupyter.svg",
"maintainer": [
{
"name": "Markus Scheidgen",
@@ -65281,18 +65282,19 @@ window.nomadArtifacts = {
},
"pyiron": {
"short_description": "Jupyterlab with pyiron installed.",
- "description": "## Pyiron: Complex workflows made easy\n\nFrom rapid prototyping to high performance computing in material science. [Homepage](https://pyiron.org/).",
+ "description": "### **Pyiron**: Complex workflows made easy\nFrom rapid prototyping to high performance computing in materials science. [Homepage](https://pyiron.org/).",
"image": "pyiron/pyiron:latest",
"cmd": null,
"image_pull_policy": "Always",
"privileged": false,
+ "default_url": "/lab",
"path_prefix": "lab/tree",
"with_path": true,
"file_extensions": [
"ipynb"
],
"mount_path": "/home/jovyan",
- "icon": "pyiron_logo.png",
+ "icon": "logo/pyiron.png",
"maintainer": [
{
"name": "Markus Scheidgen",
@@ -65302,17 +65304,26 @@ window.nomadArtifacts = {
"external_mounts": []
},
"nionswift": {
- "short_description": "Run NionSwift to analyze data as well as prepare focus series reconstructions",
- "description": "Run Nion Swift to analyze data.",
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/nionswift-webtop",
+ "short_description": "Run Nion Swift to analyze data as well as prepare focus series reconstructions in NOMAD.",
+ "description": "### **Nion Swift**:\nNion Swift is a software package for electron microscopy data analysis and visualization. It is designed to be easy to use and to provide a high degree of interactivity. [Homepage](https://nionswift.readthedocs.io/en/stable/).",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/nionswift:refactor",
"cmd": null,
"image_pull_policy": "Always",
- "privileged": true,
+ "privileged": false,
+ "default_url": "/desktop",
"path_prefix": null,
"with_path": false,
- "file_extensions": [],
- "mount_path": "/config",
- "icon": null,
+ "file_extensions": [
+ "tiff",
+ "tif",
+ "dm3",
+ "dm4",
+ "hdf5",
+ "h5",
+ "nion"
+ ],
+ "mount_path": "/home/jovyan",
+ "icon": "logo/nionswift.png",
"maintainer": [
{
"name": "Sherjeel Shabih",
@@ -65322,14 +65333,15 @@ window.nomadArtifacts = {
"external_mounts": []
},
"nexustools": {
- "short_description": null,
- "description": "Includes multiple NeXus tools for visualization and analysis.",
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/nexus-webtop",
+ "short_description": "Analyse your NeXus files in NOMAD with several NeXus-compatible tools.",
+ "description": "### **NeXus**:\nIncludes multiple NeXus tools for visualization and analysis.",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/nexus:weptop-replacement",
"cmd": null,
"image_pull_policy": "Always",
- "privileged": true,
+ "privileged": false,
+ "default_url": "/lab",
"path_prefix": null,
- "with_path": false,
+ "with_path": true,
"file_extensions": [
"nxs",
"nx",
@@ -65340,8 +65352,8 @@ window.nomadArtifacts = {
"hdf",
"ipynb"
],
- "mount_path": "/config",
- "icon": null,
+ "mount_path": "/home/jovyan",
+ "icon": "logo/nexus.png",
"maintainer": [
{
"name": "Sandor Brockhauser",
@@ -65350,67 +65362,133 @@ window.nomadArtifacts = {
],
"external_mounts": []
},
- "ellips": {
- "short_description": "An example for analyzing ellipsometric data.",
- "description": "This example presents the capabilities of the NOMAD platform to store and standardize ellipsometry data. It shows the generation of a NeXus file according to the [NXellipsometry](https://manual.nexusformat.org/classes/contributed_definitions/NXellipsometry.html#nxellipsometry) application definition and a successive analysis of a SiO2 on Si Psi/Delta measurement.",
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/ellips/jupyter:latest",
+ "fiji": {
+ "short_description": "Use FIJI to analyze and visualize your images in your NOMAD files.",
+ "description": "### **FIJI** (Fiji Is Just ImageJ): Image processing package\nIt can be used for tasks such as image editing, image analysis, and image processing. [Homepage](https://fiji.sc/).",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/fiji:weptop-replacement",
"cmd": null,
"image_pull_policy": "Always",
"privileged": false,
- "path_prefix": "lab/tree",
+ "default_url": "/desktop",
+ "path_prefix": null,
"with_path": false,
"file_extensions": [
- "ipynb",
- "nxs"
+ "tif",
+ "tiff",
+ "jpeg",
+ "png",
+ "gif",
+ "bmp",
+ "avi"
],
"mount_path": "/home/jovyan",
- "icon": "jupyter_logo.svg",
+ "icon": "logo/fiji.png",
"maintainer": [
{
- "name": "Florian Dobener",
- "email": "florian.dobener@physik.hu-berlin.de"
- },
- {
- "name": "Carola Emminger",
- "email": "emminger.carola@physik.hu-berlin.de"
+ "name": "Markus K\u00fchbach",
+ "email": "markus.kuehbach@physik.hu-berlin.de"
}
],
"external_mounts": []
},
- "mpes": {
- "short_description": "An example for analyzing mpes data.",
- "description": "This example presents the capabilities of the NOMAD platform to store and standardize multi photoemission spectroscopy (MPES) experimental data. It contains three major examples:\n\n- Taking a pre-binned file, here stored in a h5 file, and converting it into the standardized MPES NeXus format. There exists a [NeXus application definition for MPES](https://manual.nexusformat.org/classes/contributed_definitions/NXmpes.html#nxmpes) which details the internal structure of such a file.\n- Binning of raw data (see [here](https://www.nature.com/articles/s41597-020-00769-8) for additional resources) into a h5 file and consecutively generating a NeXus file from it.\n- An analysis example using data in the NeXus format and employing the [pyARPES](https://github.com/chstan/arpes) analysis tool to reproduce the main findings of [this paper](https://arxiv.org/pdf/2107.07158.pdf).",
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/mpes/webtop",
+ "vesta": {
+ "short_description": "Run VESTA to analyse and visualize your crystal structures in your NOMAD files.",
+ "description": "### **VESTA**: Visualization for Electronic and STructural Analysis\nVESTA is a software program used for visualizing and analyzing crystal structures, electron density maps, and other three-dimensional data related to materials science and crystallography. [Homepage](http://jp-minerals.org/vesta/en/).",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/abtem:refactor",
"cmd": null,
"image_pull_policy": "Always",
- "privileged": true,
+ "privileged": false,
+ "default_url": "/desktop",
"path_prefix": null,
"with_path": false,
+ "file_extensions": [
+ "vesta",
+ "cif",
+ "res",
+ "vasp",
+ "xyz",
+ "pdb",
+ "mcif",
+ "fsf",
+ "fcf",
+ "shelx",
+ "stl",
+ "cgo",
+ "wrl",
+ "pov",
+ "spf"
+ ],
+ "mount_path": "/home/jovyan",
+ "icon": "logo/vesta.png",
+ "maintainer": [
+ {
+ "name": "Markus K\u00fchbach",
+ "email": "markus.kuehbach@physik.hu-berlin.de"
+ }
+ ],
+ "external_mounts": []
+ },
+ "abtem": {
+ "short_description": "Electronic structure supported image simulation for transmission electron microscopy.",
+ "description": "### **abTEM, GPAW and VESTA**:\nVESTA, GPAW, and abTEM configured in one container for simulating images and diffraction patterns in transmission electron microscopy.",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/abtem:refactor",
+ "cmd": null,
+ "image_pull_policy": "Always",
+ "privileged": false,
+ "default_url": "/lab",
+ "path_prefix": null,
+ "with_path": true,
+ "file_extensions": [
+ "ipynb"
+ ],
+ "mount_path": "/home/jovyan",
+ "icon": "logo/abtem.png",
+ "maintainer": [
+ {
+ "name": "Markus K\u00fchbach",
+ "email": "markus.kuehbach@physik.hu-berlin.de"
+ }
+ ],
+ "external_mounts": []
+ },
+ "ellips": {
+ "short_description": "An example for analyzing ellipsometric data.",
+ "description": "### **Ellipsometry**:\nThis example presents the capabilities of the NOMAD platform to store and standardize ellipsometry data. It shows the generation of a NeXus file according to the [NXellipsometry](https://manual.nexusformat.org/classes/contributed_definitions/NXellipsometry.html#nxellipsometry) application definition and a successive analysis of a SiO2 on Si Psi/Delta measurement.",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/ellips:refactor",
+ "cmd": null,
+ "image_pull_policy": "Always",
+ "privileged": false,
+ "default_url": "/lab",
+ "path_prefix": "lab/tree",
+ "with_path": true,
"file_extensions": [
"ipynb",
- "nxs",
- "h5",
- "hdf5"
+ "nxs"
],
- "mount_path": "/config",
- "icon": null,
+ "mount_path": "/home/jovyan",
+ "icon": "logo/jupyter.svg",
"maintainer": [
{
"name": "Florian Dobener",
"email": "florian.dobener@physik.hu-berlin.de"
+ },
+ {
+ "name": "Carola Emminger",
+ "email": "emminger.carola@physik.hu-berlin.de"
}
],
"external_mounts": []
},
"xps": {
"short_description": "An example for analyzing XPS data.",
- "description": "Includes tools for analyzing X-ray Photoelectron Spectroscopy (XPS) spectra and converting SPECS SLE files into NeXus.",
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/xps/jupyter:master",
+ "description": "### **XPES**: X-ray Photoelectron Spectroscopy\nIncludes tools for analyzing X-ray Photoelectron Spectroscopy (XPS) spectra and converting SPECS SLE files into NeXus.",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/xps:refactor",
"cmd": null,
"image_pull_policy": "Always",
"privileged": false,
+ "default_url": "/lab",
"path_prefix": "lab/tree",
- "with_path": false,
+ "with_path": true,
"file_extensions": [
"ipynb",
"nxs",
@@ -65418,7 +65496,7 @@ window.nomadArtifacts = {
"hdf5"
],
"mount_path": "/home/jovyan",
- "icon": "jupyter_logo.svg",
+ "icon": "logo/jupyter.svg",
"maintainer": [
{
"name": "Florian Dobener",
@@ -65437,13 +65515,14 @@ window.nomadArtifacts = {
},
"sts": {
"short_description": "An example for analyzing SPM (STM / STS) experiment.",
- "description": "This example is for two types of experiments: Scanning Tunneling Microscopy (STM) and Scanning Tunneling Spectroscopy (STS) from Scanning Probe Microscopy. It can transform the data from files generated by a the nanonis software into the NeXus application definition NXsts. The example contains data files from the two specific nanonis software versions generic 5e and generic 4.5.",
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/sts-jupyter",
+ "description": "### **STS**: Scanning Tunneling Spectroscopy\nThis example is for two types of experiments: Scanning Tunneling Microscopy (STM) and Scanning Tunneling Spectroscopy (STS) from Scanning Probe Microscopy. It can transform the data from files generated by a the nanonis software into the NeXus application definition NXsts. The example contains data files from the two specific nanonis software versions generic 5e and generic 4.5.",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/sts:refactor",
"cmd": null,
"image_pull_policy": "Always",
"privileged": false,
+ "default_url": "/lab",
"path_prefix": "lab/tree",
- "with_path": false,
+ "with_path": true,
"file_extensions": [
"ipynb",
"nxs",
@@ -65451,7 +65530,7 @@ window.nomadArtifacts = {
"hdf5"
],
"mount_path": "/home/jovyan",
- "icon": "jupyter_logo.svg",
+ "icon": "logo/jupyter.svg",
"maintainer": [
{
"name": "Rubel Mozumder",
@@ -65460,98 +65539,21 @@ window.nomadArtifacts = {
],
"external_mounts": []
},
- "webtop": {
- "short_description": null,
- "description": "Baseline webtop image for test",
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/webtop",
- "cmd": null,
- "image_pull_policy": "Always",
- "privileged": true,
- "path_prefix": null,
- "with_path": false,
- "file_extensions": [],
- "mount_path": "/config",
- "icon": null,
- "maintainer": [
- {
- "name": "Sherjeel Shabih",
- "email": "sherjeel.shabih@hu-berlin.de"
- }
- ],
- "external_mounts": []
- },
"apmtools": {
"short_description": "An example for analyzing atom probe data.",
- "description": "Miscellaneous tools from the atom probe community:\nCurrently APTyzer, paraprobe-toolbox, and APAV",
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/apmtools-webtop",
- "cmd": null,
- "image_pull_policy": "Always",
- "privileged": true,
- "path_prefix": null,
- "with_path": false,
- "file_extensions": [],
- "mount_path": "/config",
- "icon": "jupyter_logo.svg",
- "maintainer": [
- {
- "name": "Markus K\u00fchbach",
- "email": "markus.kuehbach@physik.hu-berlin.de"
- }
- ],
- "external_mounts": []
- },
- "fiji": {
- "short_description": "ImageJ and Fiji for image processing",
- "description": "ImageJ and Fiji with amongst others several electron-microscopy specific plug-ins",
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/fiji-webtop",
+ "description": "### **APM tools**: Atom Probe Microscopy tools\nMiscellaneous tools from the atom probe community:\nCurrently APTyzer, paraprobe-toolbox, and APAV",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/apmtools:refactor",
"cmd": null,
"image_pull_policy": "Always",
- "privileged": true,
- "path_prefix": null,
- "with_path": false,
- "file_extensions": [],
- "mount_path": "/config",
- "icon": "jupyter_logo.svg",
- "maintainer": [
- {
- "name": "Markus K\u00fchbach",
- "email": "markus.kuehbach@physik.hu-berlin.de"
- }
- ],
- "external_mounts": []
- },
- "frwr": {
- "short_description": "Inline electron holography by C. Koch",
- "description": "FRWR3 in-line holography/focus series reconstruction code",
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/frwr-webtop",
- "cmd": null,
- "image_pull_policy": "Always",
- "privileged": true,
+ "privileged": false,
+ "default_url": "/lab",
"path_prefix": null,
- "with_path": false,
- "file_extensions": [],
- "mount_path": "/config",
- "icon": "jupyter_logo.svg",
- "maintainer": [
- {
- "name": "Markus K\u00fchbach",
- "email": "markus.kuehbach@physik.hu-berlin.de"
- }
+ "with_path": true,
+ "file_extensions": [
+ "ipynb"
],
- "external_mounts": []
- },
- "abtem": {
- "short_description": "Electronic structure supported image simulation for transmission electron microscopy.",
- "description": "VESTA, GPAW, and abTEM configured in one container for simulating images and diffraction patterns in transmission electron microscopy",
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/abtem-webtop",
- "cmd": null,
- "image_pull_policy": "Always",
- "privileged": true,
- "path_prefix": null,
- "with_path": false,
- "file_extensions": [],
- "mount_path": "/config",
- "icon": "jupyter_logo.svg",
+ "mount_path": "/home/jovyan",
+ "icon": "logo/jupyter.svg",
"maintainer": [
{
"name": "Markus K\u00fchbach",
diff --git a/nomad/app/v1/routers/north.py b/nomad/app/v1/routers/north.py
index 63ece466b3297bff41dc51a3c7480b24b4040d4a..8dc994e712da4d5e8814b5dbdd4a41f7e4ebcb38 100644
--- a/nomad/app/v1/routers/north.py
+++ b/nomad/app/v1/routers/north.py
@@ -242,7 +242,12 @@ async def start_tool(
user_id=user.user_id, expires_in=config.north.nomad_access_token_expiry_time
)
body = {
- 'tool': {'image': tool.image, 'cmd': tool.cmd, 'privileged': tool.privileged},
+ 'tool': {
+ 'image': tool.image,
+ 'cmd': tool.cmd,
+ 'privileged': tool.privileged,
+ 'default_url': tool.default_url,
+ },
'environment': {
'SUBFOLDER': f'{config.services.api_base_path.rstrip("/")}/north/user/{user.username}/',
'JUPYTERHUB_CLIENT_API_URL': f'{config.north_url()}/hub/api',
diff --git a/nomad/config/defaults.yaml b/nomad/config/defaults.yaml
index a76412e2ca5d42bf528ad86fe0b201432f97a922..8e43a1d57507ff3a24ef8bf2959e958a9fd0bb2e 100644
--- a/nomad/config/defaults.yaml
+++ b/nomad/config/defaults.yaml
@@ -227,16 +227,16 @@ north:
jupyter:
description: '### **Jupyter Notebook**: The Classic Notebook Interface
-
The Jupyter Notebook is the original web application for creating and sharing
computational documents. It offers a simple, streamlined, document-centric
experience.'
external_mounts: []
file_extensions:
- ipynb
- icon: jupyter_logo.svg
- image: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/jupyter:latest
+ icon: logo/jupyter.svg
+ image: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/jupyter:refactor
image_pull_policy: Always
+ default_url: /lab
maintainer:
- email: markus.scheidgen@physik.hu-berlin.de
name: Markus Scheidgen
@@ -247,17 +247,17 @@ north:
file.
with_path: true
pyiron:
- description: '## Pyiron: Complex workflows made easy
-
+ description: '### **Pyiron**: Complex workflows made easy
- From rapid prototyping to high performance computing in material science.
+ From rapid prototyping to high performance computing in materials science.
[Homepage](https://pyiron.org/).'
external_mounts: []
file_extensions:
- ipynb
- icon: pyiron_logo.png
+ icon: logo/pyiron.png
image: pyiron/pyiron:latest
image_pull_policy: Always
+ default_url: /lab
maintainer:
- email: markus.scheidgen@physik.hu-berlin.de
name: Markus Scheidgen
@@ -267,21 +267,36 @@ north:
short_description: Jupyterlab with pyiron installed.
with_path: true
nionswift:
- description: Run Nion Swift to analyze data.
+ description: '### **Nion Swift**:
+
+ Nion Swift is a software package for electron microscopy data
+ analysis and visualization. It is designed to be easy to use and to provide
+ a high degree of interactivity. [Homepage](https://nionswift.readthedocs.io/en/stable/).'
+ icon: logo/nionswift.png
external_mounts: []
- file_extensions: []
- image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/nionswift-webtop
+ file_extensions:
+ - tiff
+ - tif
+ - dm3
+ - dm4
+ - hdf5
+ - h5
+ - nion
+ image: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/nionswift:refactor
image_pull_policy: Always
+ default_url: /desktop
maintainer:
- email: sherjeel.shabih@hu-berlin.de
name: Sherjeel Shabih
- mount_path: /config
- privileged: true
- short_description: Run NionSwift to analyze data as well as prepare focus
- series reconstructions
+ mount_path: /home/jovyan
+ privileged: false
+ short_description: Run Nion Swift to analyze data as well as prepare focus
+ series reconstructions in NOMAD.
with_path: false
nexustools:
- description: Includes multiple NeXus tools for visualization and analysis.
+ description: '### **NeXus**:
+
+ Includes multiple NeXus tools for visualization and analysis.'
external_mounts: []
file_extensions:
- nxs
@@ -292,27 +307,113 @@ north:
- h5
- hdf
- ipynb
- image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/nexus-webtop
+ icon: logo/nexus.png
+ image: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/nexus:weptop-replacement
image_pull_policy: Always
+ default_url: /lab
maintainer:
- email: sandor.brockhauser@physik.hu-berlin.de
name: Sandor Brockhauser
- mount_path: /config
- privileged: true
+ mount_path: /home/jovyan
+ privileged: false
+ short_description: Analyse your NeXus files in NOMAD with several NeXus-compatible tools.
+ with_path: true
+ fiji:
+ description: '### **FIJI** (Fiji Is Just ImageJ): Image processing package
+
+ It can be used for tasks such as image editing, image analysis,
+ and image processing. [Homepage](https://fiji.sc/).'
+ external_mounts: []
+ file_extensions:
+ - tif
+ - tiff
+ - jpeg
+ - png
+ - gif
+ - bmp
+ - avi
+ icon: logo/fiji.png
+ image: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/fiji:weptop-replacement
+ image_pull_policy: Always
+ default_url: /desktop
+ maintainer:
+ - email: markus.kuehbach@physik.hu-berlin.de
+ name: "Markus K\xFChbach"
+ mount_path: /home/jovyan
+ privileged: false
+ short_description: Use FIJI to analyze and visualize your images in your NOMAD files.
with_path: false
+ vesta:
+ description: '### **VESTA**: Visualization for Electronic and STructural Analysis
+
+ VESTA is a software program used for visualizing and analyzing crystal structures,
+ electron density maps, and other three-dimensional data related to materials
+ science and crystallography. [Homepage](http://jp-minerals.org/vesta/en/).'
+ external_mounts: []
+ file_extensions:
+ - vesta
+ - cif
+ - res
+ - vasp
+ - xyz
+ - pdb
+ - mcif
+ - fsf
+ - fcf
+ - shelx
+ - stl
+ - cgo
+ - wrl
+ - pov
+ - spf
+ icon: logo/vesta.png
+ image: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/abtem:refactor
+ image_pull_policy: Always
+ default_url: /desktop
+ maintainer:
+ - email: markus.kuehbach@physik.hu-berlin.de
+ name: "Markus K\xFChbach"
+ mount_path: /home/jovyan
+ privileged: false
+ short_description: Run VESTA to analyse and visualize your crystal structures in
+ your NOMAD files.
+ with_path: false
+ abtem:
+ description: '### **abTEM, GPAW and VESTA**:
+
+ VESTA, GPAW, and abTEM configured in one container for simulating
+ images and diffraction patterns in transmission electron microscopy.'
+ external_mounts: []
+ file_extensions:
+ - ipynb
+ icon: logo/abtem.png
+ image: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/abtem:refactor
+ image_pull_policy: Always
+ default_url: /lab
+ maintainer:
+ - email: markus.kuehbach@physik.hu-berlin.de
+ name: "Markus K\xFChbach"
+ mount_path: /home/jovyan
+ privileged: false
+ short_description: Electronic structure supported image simulation for transmission
+ electron microscopy.
+ with_path: true
ellips:
- description: This example presents the capabilities of the NOMAD platform
+ description: '### **Ellipsometry**:
+
+ This example presents the capabilities of the NOMAD platform
to store and standardize ellipsometry data. It shows the generation of a
NeXus file according to the [NXellipsometry](https://manual.nexusformat.org/classes/contributed_definitions/NXellipsometry.html#nxellipsometry)
application definition and a successive analysis of a SiO2 on Si Psi/Delta
- measurement.
+ measurement.'
external_mounts: []
file_extensions:
- ipynb
- nxs
- icon: jupyter_logo.svg
- image: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/ellips/jupyter:latest
+ icon: logo/jupyter.svg
+ image: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/ellips:refactor
image_pull_policy: Always
+ default_url: /lab
maintainer:
- email: florian.dobener@physik.hu-berlin.de
name: Florian Dobener
@@ -322,50 +423,21 @@ north:
path_prefix: lab/tree
privileged: false
short_description: An example for analyzing ellipsometric data.
- with_path: false
- mpes:
- description: 'This example presents the capabilities of the NOMAD platform
- to store and standardize multi photoemission spectroscopy (MPES) experimental
- data. It contains three major examples:
-
-
- - Taking a pre-binned file, here stored in a h5 file, and converting it
- into the standardized MPES NeXus format. There exists a [NeXus application
- definition for MPES](https://manual.nexusformat.org/classes/contributed_definitions/NXmpes.html#nxmpes)
- which details the internal structure of such a file.
-
- - Binning of raw data (see [here](https://www.nature.com/articles/s41597-020-00769-8)
- for additional resources) into a h5 file and consecutively generating a
- NeXus file from it.
-
- - An analysis example using data in the NeXus format and employing the [pyARPES](https://github.com/chstan/arpes)
- analysis tool to reproduce the main findings of [this paper](https://arxiv.org/pdf/2107.07158.pdf).'
- external_mounts: []
- file_extensions:
- - ipynb
- - nxs
- - h5
- - hdf5
- image: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/mpes/webtop
- image_pull_policy: Always
- maintainer:
- - email: florian.dobener@physik.hu-berlin.de
- name: Florian Dobener
- mount_path: /config
- privileged: true
- short_description: An example for analyzing mpes data.
- with_path: false
+ with_path: true
xps:
- description: Includes tools for analyzing X-ray Photoelectron Spectroscopy
- (XPS) spectra and converting SPECS SLE files into NeXus.
+ description: '### **XPES**: X-ray Photoelectron Spectroscopy
+
+ Includes tools for analyzing X-ray Photoelectron Spectroscopy
+ (XPS) spectra and converting SPECS SLE files into NeXus.'
external_mounts: []
file_extensions:
- ipynb
- nxs
- h5
- hdf5
- icon: jupyter_logo.svg
- image: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/xps/jupyter:master
+ icon: logo/jupyter.svg
+ image: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/xps:refactor
+ default_url: /lab
image_pull_policy: Always
maintainer:
- email: florian.dobener@physik.hu-berlin.de
@@ -378,9 +450,11 @@ north:
path_prefix: lab/tree
privileged: false
short_description: An example for analyzing XPS data.
- with_path: false
+ with_path: true
sts:
- description: 'This example is for two types of experiments: Scanning Tunneling
+ description: '### **STS**: Scanning Tunneling Spectroscopy
+
+ This example is for two types of experiments: Scanning Tunneling
Microscopy (STM) and Scanning Tunneling Spectroscopy (STS) from Scanning
Probe Microscopy. It can transform the data from files generated by a the
nanonis software into the NeXus application definition NXsts. The example
@@ -392,9 +466,10 @@ north:
- nxs
- h5
- hdf5
- icon: jupyter_logo.svg
- image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/sts-jupyter
+ icon: logo/jupyter.svg
+ image: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/sts:refactor
image_pull_policy: Always
+ default_url: /lab
maintainer:
- email: rubel.mozumder@physik.hu-berlin.de
name: Rubel Mozumder
@@ -402,80 +477,27 @@ north:
path_prefix: lab/tree
privileged: false
short_description: An example for analyzing SPM (STM / STS) experiment.
- with_path: false
- webtop:
- description: Baseline webtop image for test
- external_mounts: []
- file_extensions: []
- image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/webtop
- image_pull_policy: Always
- maintainer:
- - email: sherjeel.shabih@hu-berlin.de
- name: Sherjeel Shabih
- mount_path: /config
- privileged: true
- with_path: false
+ with_path: true
apmtools:
- description: 'Miscellaneous tools from the atom probe community:
+ description: '### **APM tools**: Atom Probe Microscopy tools
+
+ Miscellaneous tools from the atom probe community:
Currently APTyzer, paraprobe-toolbox, and APAV'
external_mounts: []
- file_extensions: []
- icon: jupyter_logo.svg
- image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/apmtools-webtop
+ file_extensions:
+ - ipynb
+ icon: logo/jupyter.svg
+ image: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/apmtools:refactor
image_pull_policy: Always
+ default_url: /lab
maintainer:
- email: markus.kuehbach@physik.hu-berlin.de
name: "Markus K\xFChbach"
- mount_path: /config
- privileged: true
+ mount_path: /home/jovyan
+ privileged: false
short_description: An example for analyzing atom probe data.
- with_path: false
- fiji:
- description: ImageJ and Fiji with amongst others several electron-microscopy
- specific plug-ins
- external_mounts: []
- file_extensions: []
- icon: jupyter_logo.svg
- image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/fiji-webtop
- image_pull_policy: Always
- maintainer:
- - email: markus.kuehbach@physik.hu-berlin.de
- name: "Markus K\xFChbach"
- mount_path: /config
- privileged: true
- short_description: ImageJ and Fiji for image processing
- with_path: false
- frwr:
- description: FRWR3 in-line holography/focus series reconstruction code
- external_mounts: []
- file_extensions: []
- icon: jupyter_logo.svg
- image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/frwr-webtop
- image_pull_policy: Always
- maintainer:
- - email: markus.kuehbach@physik.hu-berlin.de
- name: "Markus K\xFChbach"
- mount_path: /config
- privileged: true
- short_description: Inline electron holography by C. Koch
- with_path: false
- abtem:
- description: VESTA, GPAW, and abTEM configured in one container for simulating
- images and diffraction patterns in transmission electron microscopy
- external_mounts: []
- file_extensions: []
- icon: jupyter_logo.svg
- image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/abtem-webtop
- image_pull_policy: Always
- maintainer:
- - email: markus.kuehbach@physik.hu-berlin.de
- name: "Markus K\xFChbach"
- mount_path: /config
- privileged: true
- short_description: Electronic structure supported image simulation for transmission
- electron microscopy.
- with_path: false
+ with_path: true
windows: true
ui:
entry:
diff --git a/nomad/config/models/north.py b/nomad/config/models/north.py
index f65370af0e85e7b14b7f06b9698e55a27c245ad9..594cfc7a59fe2176c37fbf33955648b756973879 100644
--- a/nomad/config/models/north.py
+++ b/nomad/config/models/north.py
@@ -65,11 +65,18 @@ class NORTHTool(BaseModel):
privileged: bool = Field(
False, description='Whether the tool needs to run in privileged mode.'
)
+ default_url: str = Field(
+ None,
+ description=(
+ 'An optional path prefix that is added to the container URL to '
+ 'reach the tool, e.g. "/lab" for jupyterlab.'
+ ),
+ )
path_prefix: str = Field(
None,
description=(
'An optional path prefix that is added to the container URL to '
- 'reach the tool, e.g. "lab/tree" for jupyterlab.'
+ 'reach the files, e.g. "lab/tree" for jupyterlab.'
),
)
with_path: bool = Field(
diff --git a/nomad/jupyterhub_config.py b/nomad/jupyterhub_config.py
index fcd937ead1f6a4bb556c0dff3da1b98a8562eeab..a4ddc7e34920b005cb1ea6fc4eff50eb924b56d1 100644
--- a/nomad/jupyterhub_config.py
+++ b/nomad/jupyterhub_config.py
@@ -73,6 +73,10 @@ def pre_spawn(spawner):
spawner.image = tool.get('image')
spawner.cmd = tool.get('cmd')
+ # Workaround to have specific default_url for specific containers without using profiles
+ if tool.get('default_url'):
+ spawner.default_url = tool.get('default_url')
+
c.Spawner.pre_spawn_hook = pre_spawn
diff --git a/ops/kubernetes/nomad/updatevalues.py b/ops/kubernetes/nomad/updatevalues.py
index 3a4ba1e04cbb611021e9cc435059a3ec5b0cd637..a902d7fe1c975c40c5c1b1f92ac848c6282ddaaa 100644
--- a/ops/kubernetes/nomad/updatevalues.py
+++ b/ops/kubernetes/nomad/updatevalues.py
@@ -46,12 +46,14 @@ if generate_profiles:
)
)
- if tool.path_prefix:
- profile['kubespawner_override']['default_url'] = tool.path_prefix
+ if tool.default_url:
+ profile['kubespawner_override']['default_url'] = tool.default_url
if tool.cmd:
profile['kubespawner_override']['cmd'] = tool.cmd
if tool.privileged:
profile['kubespawner_override']['privileged'] = tool.privileged
+ profile['kubespawner_override']['allow_privilege_escalation'] = True
+ profile['kubespawner_override']['uid'] = 0
else:
pre_puller = data.setdefault('jupyterhub', {}).setdefault('prePuller', {})
diff --git a/ops/kubernetes/nomad/values.yaml b/ops/kubernetes/nomad/values.yaml
index 0d517f73106fe79bdbaabaff3789fb9b506af91b..98498b784cc8800e26ff77171750414c2d031c2c 100644
--- a/ops/kubernetes/nomad/values.yaml
+++ b/ops/kubernetes/nomad/values.yaml
@@ -524,6 +524,10 @@ jupyterhub:
spawner.image = tool.get('image')
spawner.cmd = tool.get('cmd')
+ # Workaround to have specific default_url for specific containers without using profiles
+ if tool.get('default_url'):
+ spawner.default_url = tool.get('default_url')
+
# Workaround for webtop based images (no connection to jupyterhub itself)
if tool.get('privileged'):
spawner.privileged = True
@@ -549,43 +553,37 @@ jupyterhub:
extraImages:
jupyter:
name: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/jupyter
- tag: latest
+ tag: refactor
pyiron:
name: pyiron/pyiron
tag: latest
nionswift:
- name: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/nionswift-webtop
- tag: latest
+ name: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/nionswift
+ tag: refactor
nexustools:
- name: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/nexus-webtop
- tag: latest
+ name: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/nexus
+ tag: weptop-replacement
+ fiji:
+ name: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/fiji
+ tag: weptop-replacement
+ vesta:
+ name: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/abtem
+ tag: refactor
+ abtem:
+ name: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/abtem
+ tag: refactor
ellips:
- name: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/ellips/jupyter
- tag: latest
- mpes:
- name: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/mpes/webtop
- tag: latest
+ name: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/ellips
+ tag: refactor
xps:
- name: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/xps/jupyter
- tag: master
+ name: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/xps
+ tag: refactor
sts:
- name: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/sts-jupyter
- tag: latest
- webtop:
- name: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/webtop
- tag: latest
+ name: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/sts
+ tag: refactor
apmtools:
- name: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/apmtools-webtop
- tag: latest
- fiji:
- name: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/fiji-webtop
- tag: latest
- frwr:
- name: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/frwr-webtop
- tag: latest
- abtem:
- name: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/abtem-webtop
- tag: latest
+ name: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/apmtools
+ tag: refactor
scheduling:
userScheduler:
enabled: false