Merge branch 'main' into nmb

.gitignore

@@ -9,8 +9,10 @@ __pycache__/
 # Distribution / packaging
 .Python
 build/
+
 develop-eggs/
 dist/
+resources/
 downloads/
 eggs/
 .eggs/
@@ -19,14 +21,16 @@ lib64/
 parts/
 sdist/
 var/
+pkgs/
 wheels/
 pip-wheel-metadata/
 share/python-wheels/
 *.egg-info/
 .installed.cfg
 *.egg
 MANIFEST
-
+app/data/genetics/*
+app/static/pkgs/*
 # PyInstaller
 #  Usually these files are written by a python script from a template
 #  before PyInstaller builds the exe, so as to inject date/other infos into it.

README.md

@@ -1,58 +1,66 @@
-# SSAM-lite-server
-
-[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](./LICENSE)
-[![DOI:10.1101/2021.09.2x.xxxxxxxx](http://img.shields.io/badge/DOI-10.1101/2021.09.2x.xxxxxxxx-B31B1B.svg)](https://doi.org/10.1101/2021.09.2x.xxxxxxxx)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5517607.svg)](https://doi.org/10.5281/zenodo.5517607)
-
-... is a lightweight implementation of the [SSAM framework](https://www.nature.com/articles/s41467-021-23807-4).
-It provides the functionality of SSAMs most popular and widely used features in a graphical user interface
-with a few functions added for convenience and ease of use. After installation on a server it can be used by 
-researchers as browser-based web app.
-
-
-Author: Sebastian Tiesmeyer ([email protected])<sup>1</sup>
-
-<sup>1</sup> Digital Health Center, Berlin Institute of Health (BIH) at Charité – Universitätsmedizin, Berlin, Germany
-
-## Choose your flavour
-
-You might also want to check out the [SSAM-lite](https://github.com/HiDiHlabs/ssam-lite) implementation.
-
-For a guide to help you choose read https://ssam-lite.readthedocs.io/en/latest/local_vs_server.html
-
-## Installation
-
-https://ssam-lite.readthedocs.io/en/latest/installation.html#ssam-lite-server
-
-
-## Documentation
-
-https://ssam-lite.readthedocs.io
-
-
-## Versioning
-
-This project follows the [SemVer](https://semver.org) guidelines for versioning.
-
-For a list of versions see the [releases](https://github.com/HiDiHlabs/ssam-lite-server/releases).
-
-
-## Citations
-
-TODO update Citation when ready
-
-Sebastian Tiesmeyer, Shashwat Sahay, Niklas Mueller-Boetticher, Roland Eils, Sebastian Mackowiak, Naveed Ishaque.
-2021.
-"[SSAM-lite: a light-weight web-based framework for analysis of spatially resolved transcriptomics data](https://biorxiv.org)"
-*bioRxiv*. doi: 10.1101/2021....
-
-
-## Sample data
-
-Multiple datasets to try out SSAM-lite have been prepared and are available for download on 
-Zenodo (https://zenodo.org/record/5517607).
-
-
-## License
-
-This project is licensed under the MIT License - for details please refer to the [LICENSE](./LICENSE) file.
+# SSAM-lite-server
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](./LICENSE)
+[![DOI:10.1101/2021.09.2x.xxxxxxxx](http://img.shields.io/badge/DOI-10.1101/2021.09.2x.xxxxxxxx-B31B1B.svg)](https://doi.org/10.1101/2021.09.2x.xxxxxxxx)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5517607.svg)](https://doi.org/10.5281/zenodo.5517607)
+
+... is a lightweight implementation of the [SSAM framework](https://www.nature.com/articles/s41467-021-23807-4).
+It provides the functionality of SSAMs most popular and widely used features in a graphical user interface
+with a few functions added for convenience and ease of use. After installation on a server it can be used by 
+researchers as browser-based web app.
+
+
+Author: Sebastian Tiesmeyer ([email protected])<sup>1</sup>
+
+<sup>1</sup> Digital Health Center, Berlin Institute of Health (BIH) at Charité – Universitätsmedizin, Berlin, Germany
+
+## Choose your flavour
+
+You might also want to check out the [SSAM-lite](https://github.com/HiDiHlabs/ssam-lite) implementation.
+
+For a guide to help you choose read https://ssam-lite.readthedocs.io/en/latest/local_vs_server.html
+
+## Installation
+
+https://ssam-lite.readthedocs.io/en/latest/installation.html#ssam-lite-server
+
+
+## Documentation
+
+https://ssam-lite.readthedocs.io
+
+
+## Versioning
+
+This project follows the [SemVer](https://semver.org) guidelines for versioning.
+
+For a list of versions see the [releases](https://github.com/HiDiHlabs/ssam-lite-server/releases).
+
+
+## Citations
+
+TODO update Citation when ready
+
+Sebastian Tiesmeyer, Shashwat Sahay, Niklas Mueller-Boetticher, Roland Eils, Sebastian Mackowiak, Naveed Ishaque.
+2021.
+"[SSAM-lite: a light-weight web-based framework for analysis of spatially resolved transcriptomics data](https://biorxiv.org)"
+*bioRxiv*. doi: 10.1101/2021....
+
+
+## Sample data
+
+Multiple datasets to try out SSAM-lite have been prepared and are available for download on 
+Zenodo (https://zenodo.org/record/5517607).
+
+
+## License
+
+This project is licensed under the MIT License - for details please refer to the [LICENSE](./LICENSE) file.
+=======
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

flask/app/static/css/style.css → app/static/css/style.css

@@ -320,4 +320,19 @@ body {
   height: 100px;
   width: 100px;
   /* display: none; */
+}
+
+.vf-norm-load{
+  border: 16px solid #f3f3f3; /* Light grey */
+  border-top: 16px solid #3498db; /* Blue */
+  border-radius: 50%;
+  width: 120px;
+  height: 120px;
+  animation: spin 2s linear infinite;
+  display: none;
+}
+
+@keyframes spin {
+  0% { transform: rotate(0deg); }
+  100% { transform: rotate(360deg); }
 }