core issueshttps://git-r3lab.uni.lu/minerva/core/-/issues2020-03-04T14:11:36+01:00https://git-r3lab.uni.lu/minerva/core/-/issues/1160Access default project (+ basmap) easily through API2020-03-04T14:11:36+01:00Matti Hochmatti.hoch@uni-rostock.deAccess default project (+ basmap) easily through APIIs there a way to access the basemap of the currently selected default project through the API without entering the respective ID?
E.g. for the image export:
```
https://minerva-dev.lcsb.uni.lu/minerva/api/projects/default/models/basem...Is there a way to access the basemap of the currently selected default project through the API without entering the respective ID?
E.g. for the image export:
```
https://minerva-dev.lcsb.uni.lu/minerva/api/projects/default/models/basemap:downloadImage?handlerClass=lcsb.mapviewer.converter.graphics.PngImageGenerator
```
https://git-r3lab.uni.lu/minerva/core/-/issues/1039Visualizing Layer Arrows in MINERVA2019-11-28T11:24:55+01:00Matti Hochmatti.hoch@uni-rostock.deVisualizing Layer Arrows in MINERVALayer arrows drawn in Celldesigner are currently not visible hen uploading the map to Minerva.
Example:
CellDesigner
![image](/uploads/6b43c870ead4947627462f4dcbe3f2b9/image.png)
MINERVA
![image](/uploads/2e7d980330d3f3a88a7d784b529ac3...Layer arrows drawn in Celldesigner are currently not visible hen uploading the map to Minerva.
Example:
CellDesigner
![image](/uploads/6b43c870ead4947627462f4dcbe3f2b9/image.png)
MINERVA
![image](/uploads/2e7d980330d3f3a88a7d784b529ac3d6/image.png)https://git-r3lab.uni.lu/minerva/core/-/issues/952Changes in the layout of the window "Select annotators"2024-01-09T15:25:17+01:00Ewa SmulaChanges in the layout of the window "Select annotators"Please change window *Annotate model automatically:* as below:
- adjust right side windows *available annotators* and *selected annotators*,
- move "Please click on selected annotator to display details at the bottom" next to the *Selec...Please change window *Annotate model automatically:* as below:
- adjust right side windows *available annotators* and *selected annotators*,
- move "Please click on selected annotator to display details at the bottom" next to the *Selected annotator* window, at height of the first annotator,
- shorten the let panel and place Copy from and dropdown list below the list,
- sort the list and categorised as per below. Please put spacing or linr between the categories.
hi @marek.ostaszewski Do you agree with theses changes?
![Screen_Shot_2019-09-13_at_15.59.41](/uploads/2516577fbf9ff495f7e08ad70e042ae0/Screen_Shot_2019-09-13_at_15.59.41.png)![Screen_Shot_2019-09-13_at_15.18.47](/uploads/ebcbcf4211fb3a205c8db64da151cb59/Screen_Shot_2019-09-13_at_15.18.47.png)https://git-r3lab.uni.lu/minerva/core/-/issues/888Z-Index for compartments/pathways not working2021-04-20T11:34:47+02:00Ewa SmulaZ-Index for compartments/pathways not workingIn case the compartment/pathway is entirely covered by bigger compartment/pathway, the Z-Index does not work. The small compartment is not put to the front of the big compartment, although the small one has higher Z-Index. In case the el...In case the compartment/pathway is entirely covered by bigger compartment/pathway, the Z-Index does not work. The small compartment is not put to the front of the big compartment, although the small one has higher Z-Index. In case the elements are overlapping, Z-Index works ok.
[test.xml](/uploads/4369e005c986cdcf9d3c279e4faf25b7/test.xml)https://git-r3lab.uni.lu/minerva/core/-/issues/852Unit tests should (generally) not persist changes to DB2019-06-28T09:34:30+02:00Sascha HerzingerUnit tests should (generally) not persist changes to DBA unit test that calls a transactional service will persist database changes.
This can lead to a couple of issues, especially w.r.t. other tests.
Annotating unit tests with @Transactional in combination with @Rollback will trigger rollb...A unit test that calls a transactional service will persist database changes.
This can lead to a couple of issues, especially w.r.t. other tests.
Annotating unit tests with @Transactional in combination with @Rollback will trigger rollback after a test is performed.https://git-r3lab.uni.lu/minerva/core/-/issues/846Create CRUD EventListener EventHandler framework2022-03-03T14:14:15+01:00Sascha HerzingerCreate CRUD EventListener EventHandler frameworkSascha HerzingerSascha Herzingerhttps://git-r3lab.uni.lu/minerva/core/-/issues/795Stylesheets accessible for all MINERVA users - Improved aesthetics2019-06-13T10:09:37+02:00Alexander MAZEINStylesheets accessible for all MINERVA users - Improved aestheticsJust an idea.
Maybe could be encoded within the SBML renderer project.
The stylesheets idea: I got it from how we have it in Newt sometime ago. You can switch between styles:
http://web.newteditor.org/?URL=http://metabolismregulation....Just an idea.
Maybe could be encoded within the SBML renderer project.
The stylesheets idea: I got it from how we have it in Newt sometime ago. You can switch between styles:
http://web.newteditor.org/?URL=http://metabolismregulation.org/downloads/F006-ACLY.sbgn
(please see the screenshot attached)
![screenshot](/uploads/6fcb3f7187dfc02276ee5c4b6742211c/screenshot.png)
Also, another example: Krayon project uses CSS to store styles
https://github.com/wiese42/krayon4sbgn/tree/master/resources/styles/read-only
Then the styles appear in the editor.
Krayon is a new SBGN editor, I tested, it works nicely, developed by a co-founder of yWorks and now is being managed/improved by Andreas Drager.
The default styles should be really good and probably chosen from existing examples or designed by an artist like it was done, I understand, for the new super-nice blueish MINERVA style.https://git-r3lab.uni.lu/minerva/core/-/issues/699Search panel options (admin panel) - small amendments2023-12-21T14:04:41+01:00Ewa SmulaSearch panel options (admin panel) - small amendments1. Divide the table on two parts, with headers:
* Reactions
* Elements
Please review *Name* fields, "element" and "reaction" can be removed.
2. Please change "Show element title" in *Search panel options* tab onto "Show a pin"1. Divide the table on two parts, with headers:
* Reactions
* Elements
Please review *Name* fields, "element" and "reaction" can be removed.
2. Please change "Show element title" in *Search panel options* tab onto "Show a pin"https://git-r3lab.uni.lu/minerva/core/-/issues/599Add possibility to create link from element to overview image2024-01-09T19:27:56+01:00Piotr GawronAdd possibility to create link from element to overview imagerequested by faiz.khan3@uni-rostock.derequested by faiz.khan3@uni-rostock.dev18.0https://git-r3lab.uni.lu/minerva/core/-/issues/486SBGN - activity flow2021-01-27T11:34:21+01:00Piotr GawronSBGN - activity flowDescription of the format can be found here: http://co.mbine.org/specifications/sbgn.af.level-1.version-1.2.pdf
We already use libsbgn library for parsing SBGN: https://mvnrepository.com/artifact/org.sbgn/libsbgn/0.2
Below you can find...Description of the format can be found here: http://co.mbine.org/specifications/sbgn.af.level-1.version-1.2.pdf
We already use libsbgn library for parsing SBGN: https://mvnrepository.com/artifact/org.sbgn/libsbgn/0.2
Below you can find SBGN AF mapping by Alexander:
> Here is the mapping between CellDesigner's Reduced Notation links and SBGN Activity Flow links. I use exact terms from the CellDesigner's Reduced Notation palette and the terms of the Activity Flow reference card (attached).
>
> Positive Influence -> positive influence
>
> Reduced Physical Stimulation -> positive influence
>
> Unknown Positive Influence -> positive influence
>
> Unknown Reduced Physical Stimulation -> positive influence
>
> Negative Influence -> negative influence
>
> Unknown Negative Influence -> negative influence
>
> Reduced Modulation -> unknown influence
>
> Unknown Reduced Modulation -> unknown influence
>
> Reduced Trigger -> necessary stimulation
>
> Unknown Reduced Trigger -> necessary stimulation
>
> In principle, the unknown (dashed lines) could be kept, it is okay not be strictly AF in this case.
>
> Please note that, as we discussed, we should not change the way you handle the internal model in MINERVA, >we should only modify the visual part when a user checks "Visualise in SBGN Activity Flow" box.
>
> This is the compromise we agreed on: modifying visually, not the model itself. Activity Flow is >conceptually a different language. For example, it would be tricky to try to present multiple state >variable in AF (and it is not needed, not the purpose of this language).
>
> When it comes from CellDesigner: normal pipeline but modified visualisation for AF if a user requests it >(works only for reduced notation, no processes allowed).
>
> When it comes from SBGN-ML, the mapping to CellDesigner Reduced Notation (or internal MINERVA model) is >possible, fewer problems there since in a clean AF we would not introduce state variables etc.
>
> Mapping from SBGN-ML AF to CellDesigner for links:
>
> positive influence -> Positive Influence
>
> negative influence -> Negative Influence
>
> unknown influence -> Reduced Modulation
>
> necessary stimulation -> Reduced Trigger
>
> Mapping from SBGN-ML to CellDesigner for entities: keep labels as they are, use auxiliary units to inform >on the type of shape to be used, for example, macromolecule, RNA, gene etc.Sascha HerzingerSascha Herzingerhttps://git-r3lab.uni.lu/minerva/core/-/issues/388automated load testing2018-04-16T12:27:16+02:00Nils Christianautomated load testingLoad testing should be automated. It should be easy to mimic realistic load of tens to hundreds of users performing different actions (browse map, upload overlay, add comment, ...).Load testing should be automated. It should be easy to mimic realistic load of tens to hundreds of users performing different actions (browse map, upload overlay, add comment, ...).https://git-r3lab.uni.lu/minerva/core/-/issues/278Search and zoom function2024-01-09T19:30:13+01:00Kerstin NeiningerSearch and zoom functionAfter hitting the search button, it is zoomed out completely (which is unfavourable in some applications). I would recommend that the default is not zooming out after a search. But to enable both (zoom out completely or not), an extra bu...After hitting the search button, it is zoomed out completely (which is unfavourable in some applications). I would recommend that the default is not zooming out after a search. But to enable both (zoom out completely or not), an extra button/checkbox that can be checked to enable a zoom out would be nice.v18.0https://git-r3lab.uni.lu/minerva/core/-/issues/229enhancements to plugin API2017-11-08T11:32:09+01:00Piotr Gawronenhancements to plugin API* [ ] there should be a way to provide list of plugin urls in the configuration panel
* object passed to plugin should contain some meta information:
* [ ] BioEntity - should also implement getChildren, getCompartment, getComplex wh...* [ ] there should be a way to provide list of plugin urls in the configuration panel
* object passed to plugin should contain some meta information:
* [ ] BioEntity - should also implement getChildren, getCompartment, getComplex when applicable
* [ ] Reaction
* [ ] Annotation
* [ ] MiRnaDb
* [ ] DrugDb
* [ ] SearchDb
* [ ] ChemicalDb
* [ ] Marker
* [ ] Surface
* [ ] DataOverlay
* [ ] getAllBioEntities(filter) - this method should contain optional filter parameter that can contain type of bioentity
* [ ] addContextSubmenu({submenu}) -allow user to create context menuhttps://git-r3lab.uni.lu/minerva/core/-/issues/225User should be able to change his data2024-01-11T07:14:35+01:00Piotr GawronUser should be able to change his datav18.0https://git-r3lab.uni.lu/minerva/core/-/issues/166Left panel - User data layout2024-01-09T19:34:36+01:00Marek OstaszewskiLeft panel - User data layoutIn the Info panel, User data is clumped together. This layout should be improved, if possible.In the Info panel, User data is clumped together. This layout should be improved, if possible.v18.0https://git-r3lab.uni.lu/minerva/core/-/issues/136Map overlay - flux thickness to big on overview2024-01-11T07:23:04+01:00Alberto NoronhaMap overlay - flux thickness to big on overview![Screenshot_from_2017-07-05_20-52-48](/uploads/43cd33b480124abcd39cc0c366d79f31/Screenshot_from_2017-07-05_20-52-48.png)
The reaction edge thickness for overlay are too thick at the full zoom out.![Screenshot_from_2017-07-05_20-52-48](/uploads/43cd33b480124abcd39cc0c366d79f31/Screenshot_from_2017-07-05_20-52-48.png)
The reaction edge thickness for overlay are too thick at the full zoom out.v18.0https://git-r3lab.uni.lu/minerva/core/-/issues/34multiple links from single area in biolayout2019-02-20T15:08:27+01:00Piotr Gawronmultiple links from single area in biolayoutWhen we process biolayout images the clickable regions should allow to link to more than one region on the map.When we process biolayout images the clickable regions should allow to link to more than one region on the map.https://git-r3lab.uni.lu/minerva/core/-/issues/33entrez annotator - add uniprot when annotating2019-02-21T14:26:21+01:00Piotr Gawronentrez annotator - add uniprot when annotatingThis is not as easy as it sounds.
Entrez data model is so complicated/messy that finding uniprot there is a bit challaning...This is not as easy as it sounds.
Entrez data model is so complicated/messy that finding uniprot there is a bit challaning...https://git-r3lab.uni.lu/minerva/core/-/issues/28unify interfaces of search parser2019-03-11T17:22:26+01:00Piotr Gawronunify interfaces of search parserunify interfaces for external db search engines:
* drugbank
* chembl
* chemical
* mirnaunify interfaces for external db search engines:
* drugbank
* chembl
* chemical
* mirnahttps://git-r3lab.uni.lu/minerva/core/-/issues/20Advanced search2024-01-09T19:42:53+01:00Piotr GawronAdvanced searchThere should be a way to perform advanced search.
Search should allow to limit results by type/name/annotation.There should be a way to perform advanced search.
Search should allow to limit results by type/name/annotation.v18.0