core issueshttps://git-r3lab.uni.lu/minerva/core/-/issues2024-01-11T07:23:04+01:00https://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/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/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/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/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/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/5reaction to compartment2021-02-01T09:57:39+01:00Piotr Gawronreaction to compartmentmodel should allow to have reactions going to compartmentsmodel should allow to have reactions going to compartmentshttps://git-r3lab.uni.lu/minerva/core/-/issues/4Validation of miriam2018-08-27T10:35:25+02:00Piotr GawronValidation of miriamWhen url from miriam uri is created there should be validation added if the link goes to existing website.
This is tricky because depending on the database the resulting webpage can be
* 404 error
* 500 error
* no error with some info ...When url from miriam uri is created there should be validation added if the link goes to existing website.
This is tricky because depending on the database the resulting webpage can be
* 404 error
* 500 error
* no error with some info that it doesn't exist
* etc.https://git-r3lab.uni.lu/minerva/core/-/issues/3TargetType enum2018-08-27T10:35:25+02:00Piotr GawronTargetType enumTargetType should be replaced or include Class<? extends Species>. In such a way every target (of mirna, drug, chemical etc.) will be targeting specific class of elements.TargetType should be replaced or include Class<? extends Species>. In such a way every target (of mirna, drug, chemical etc.) will be targeting specific class of elements.https://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.v18.0https://git-r3lab.uni.lu/minerva/core/-/issues/18export to excel file2018-08-27T10:35:25+02:00Piotr Gawronexport to excel filehttps://git-r3lab.uni.lu/minerva/core/-/issues/17upload data from excel file2018-08-27T10:35:25+02:00Piotr Gawronupload data from excel fileThere should be a possibility of uploading overlays from Excel file.There should be a possibility of uploading overlays from Excel file.https://git-r3lab.uni.lu/minerva/core/-/issues/7Gene homology2018-08-27T10:35:25+02:00Piotr GawronGene homologyCreate a page where user can easily change identifier of one organism to the other. For instance from mouse MGD identifier into human HGNC.Create a page where user can easily change identifier of one organism to the other. For instance from mouse MGD identifier into human HGNC.https://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/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/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/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/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/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/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/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/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/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/1192automatic layout for non-layouted sbml2020-03-12T12:27:22+01:00Piotr Gawronautomatic layout for non-layouted sbmlwe can consider using graphviz (https://www.graphviz.org/) to improve automatic layout (keeping in mind separations of compartments, complexes, etc)we can consider using graphviz (https://www.graphviz.org/) to improve automatic layout (keeping in mind separations of compartments, complexes, etc)https://git-r3lab.uni.lu/minerva/core/-/issues/1250Permalinks for maps? URL shortening service for MINERVA maps? - Not a high pr...2024-01-09T15:20:27+01:00Alexander MazeinPermalinks for maps? URL shortening service for MINERVA maps? - Not a high priority but easy to implement?We have long URLs for MINERVA maps, and they do not look too good in papers or emails, especially if one wants to go with zoom level https://asthma.uni.lu/minerva/index.xhtml?id=AA_V42_SBGN&x=2050&y=1050&zoom=4 or even shorter version is...We have long URLs for MINERVA maps, and they do not look too good in papers or emails, especially if one wants to go with zoom level https://asthma.uni.lu/minerva/index.xhtml?id=AA_V42_SBGN&x=2050&y=1050&zoom=4 or even shorter version is not too short https://asthma.uni.lu/minerva/index.xhtml?id=AA_V42_SBGN
On our Disease Maps website, all pages have short URL via permalinks. For example, it is
https://disease-maps.org/parkinsons
and not
https://disease-maps.org/pages/projects/parkinsons.
Maybe we can do something like that?
So for that AA map we could have, for example:
https://asthma.uni.lu/aav42tx
or at least
https://asthma.uni.lu/minerva/aav42tx
instead of
https://asthma.uni.lu/minerva/index.xhtml?id=AA_V42_SBGN&x=2050&y=1050&zoom=4
The permalink can be generated or customised.
It has covered me for some time, I thought of using one of URL shorteners but maybe could be done for all MINERVA users?
Not a high priority but easy to implement? Maybe via creating redirections, or using permalinks, or somehow else.https://git-r3lab.uni.lu/minerva/core/-/issues/1276allow for automatic break of name text into few lines2021-04-20T11:18:43+02:00Piotr Gawronallow for automatic break of name text into few linesrequested by Guanming Wu wug[at]ohsu.edurequested by Guanming Wu wug[at]ohsu.eduhttps://git-r3lab.uni.lu/minerva/core/-/issues/1422API "configuration" call: restructure the response2022-05-06T07:36:54+02:00Marek OstaszewskiAPI "configuration" call: restructure the responseCurrently in the API "configuration" call the response JSON is flat; the parameters should follow the grouping in the Admin panel in the GUI.Currently in the API "configuration" call the response JSON is flat; the parameters should follow the grouping in the Admin panel in the GUI.https://git-r3lab.uni.lu/minerva/core/-/issues/1443Error Importing Minerva SBGNML into Newt SBGN Editor2021-01-22T21:10:53+01:00Augustin LunaError Importing Minerva SBGNML into Newt SBGN EditorI have tried exporting the apoptosis map SBGNML via the Minerva website interface
https://covid19map.elixir-luxembourg.org/minerva/?submap=591&x=690&y=566&zoom=4&searchCoordinates=626,502,591,4&
I receive this message:
Incorrect file ...I have tried exporting the apoptosis map SBGNML via the Minerva website interface
https://covid19map.elixir-luxembourg.org/minerva/?submap=591&x=690&y=566&zoom=4&searchCoordinates=626,502,591,4&
I receive this message:
Incorrect file format!https://git-r3lab.uni.lu/minerva/core/-/issues/1480User Groups2021-06-09T11:22:02+02:00Matti Hochmatti.hoch@uni-rostock.deUser GroupsPossibility to put users into customized groups to facilitate assignment of access to projects, etc.Possibility to put users into customized groups to facilitate assignment of access to projects, etc.https://git-r3lab.uni.lu/minerva/core/-/issues/1594rewrite API2024-02-29T14:52:38+01:00Piotr Gawronrewrite APICurrent API implementation is becoming hard to extend and maintain. Here are base points that should be considered when rewriting API:
* all input/output should be entity based json (except when passing file content)
* serialization shou...Current API implementation is becoming hard to extend and maintain. Here are base points that should be considered when rewriting API:
* all input/output should be entity based json (except when passing file content)
* serialization should be done automatically using Jackson
* patch/post/delete requests should handle properly simultaneous modifications of the objects (https://www.mscharhag.com/api-design/rest-concurrent-updates)
* when accessing collections use Pageable interface
* use JPA validation for input parametershttps://git-r3lab.uni.lu/minerva/core/-/issues/1616Add support for kinetics MathML functions2021-12-16T11:12:17+01:00Piotr GawronAdd support for kinetics MathML functionsFull list can be found here:
http://co.mbine.org/specifications/sbml.level-3.version-2.core.release-2.pdf
Implement at least those:
* arithmetic operators: plus, minus, times, divide, power, root, abs, exp, ln, log, floor, ceiling, fact...Full list can be found here:
http://co.mbine.org/specifications/sbml.level-3.version-2.core.release-2.pdf
Implement at least those:
* arithmetic operators: plus, minus, times, divide, power, root, abs, exp, ln, log, floor, ceiling, factorial, quotient, max, min, rem
* trigonometric operators: sin, cos, tan, sec, csc, cot, sinh, cosh, tanh, sech, csch, coth, arcsin, arccos, arctan, arcsec, arccsc, arccot, arcsinh, arccosh, arctanh, arcsech, arccsch, arccothhttps://git-r3lab.uni.lu/minerva/core/-/issues/1655remove project validation and change it to plugin2023-11-09T12:25:52+01:00Piotr Gawronremove project validation and change it to pluginhttps://git-r3lab.uni.lu/minerva/core/-/issues/1656cache drugs/mirnas/chemicals in the background2023-11-09T12:25:55+01:00Piotr Gawroncache drugs/mirnas/chemicals in the backgroundCaching of data for every project should be done in the background.
Moreover, changing organism/disease should trigger re-caching.Caching of data for every project should be done in the background.
Moreover, changing organism/disease should trigger re-caching.https://git-r3lab.uni.lu/minerva/core/-/issues/1657annotating should be a separate job that can be run at any time2022-02-28T14:06:08+01:00Piotr Gawronannotating should be a separate job that can be run at any timehttps://git-r3lab.uni.lu/minerva/core/-/issues/1670export boolean to sbgn - incorrect line2022-03-18T15:16:54+01:00Ewa Smulaexport boolean to sbgn - incorrect lineexport as SBGN of boolean reaction from [cellDfile - boolean-and.xml](/uploads/c070b041becfe173df047c6148ac2f7a/boolean-and.xml) is exported incorrectly (image below) [here model-13.sbgn](/uploads/6dbd1bf72984cee04b07c1707106e9ac/model-1...export as SBGN of boolean reaction from [cellDfile - boolean-and.xml](/uploads/c070b041becfe173df047c6148ac2f7a/boolean-and.xml) is exported incorrectly (image below) [here model-13.sbgn](/uploads/6dbd1bf72984cee04b07c1707106e9ac/model-13.sbgn)
![Screenshot_2022-03-18_at_11.47.00](/uploads/117af295c240768feafcf0fdfc015d52/Screenshot_2022-03-18_at_11.47.00.png)
![Screenshot_2022-03-18_at_11.47.12](/uploads/ff47ba5a4aa3f5d678ee57aece5e001d/Screenshot_2022-03-18_at_11.47.12.png)https://git-r3lab.uni.lu/minerva/core/-/issues/1727The field "notification email" should be visible only to admins and project a...2023-11-09T12:25:58+01:00Marek OstaszewskiThe field "notification email" should be visible only to admins and project authorshttps://git-r3lab.uni.lu/minerva/core/-/issues/1740validation of required annotator not working2022-08-25T09:07:36+02:00Ewa Smulavalidation of required annotator not workingParameters selected in "required" are not saved if I change the species. f. ex. if I select required annotator for RNA and close the dialog, they are saved. But if after setting RNA I set up f ex. chemical, required annotators for RNA ar...Parameters selected in "required" are not saved if I change the species. f. ex. if I select required annotator for RNA and close the dialog, they are saved. But if after setting RNA I set up f ex. chemical, required annotators for RNA are forgotten.
![Screen_Shot_2022-08-02_at_18.30.14](/uploads/d022b0689e056091ba99f3e8ab4685db/Screen_Shot_2022-08-02_at_18.30.14.png)Piotr GawronPiotr Gawronhttps://git-r3lab.uni.lu/minerva/core/-/issues/1768downloadModel API call with reactionIds with errors2023-11-09T13:01:07+01:00Marek OstaszewskidownloadModel API call with reactionIds with errorsCurrently the API call to download a diagram part by reactionIds:
`$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/665:downloadModel?handlerClass=lcsb.mapviewer.converter.model.celldesigner.CellDesig...Currently the API call to download a diagram part by reactionIds:
`$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/models/665:downloadModel?handlerClass=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser&reactionIds=1032' -i -X GET`
does not behave properly. In the following example diagram:
[minervar_example](https://minerva-dev.lcsb.uni.lu/minerva/index.xhtml?id=minervar_example)
when calling for:
`curl 'https://minerva-dev.lcsb.uni.lu/minerva/api/projects/minervar_example/models/2578:downloadModel?handlerClass=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser&reactionIds=496329' -i -X GET`
I get the diagram as in the picture, one element (DRD2) should not be there.
![Screenshot_2022-09-21_at_11.42.06](/uploads/04d74fe3a15ccaa378f2a67ce55a0c82/Screenshot_2022-09-21_at_11.42.06.png)https://git-r3lab.uni.lu/minerva/core/-/issues/1780genome browser isn't working for hg382024-01-09T14:42:03+01:00Ewa Smulagenome browser isn't working for hg38- original ref hg38:[refGene.txt.gz](/uploads/3d473eeca2271a4f6add16cc8ec191dc/refGene.txt.gz)
- corresponding bb file (isn't displaying genes): [refGene38.bb](/uploads/735a7e51e375248e790c5d45cbfa546b/refGene38.bb)
- ref hg38 trimmed...- original ref hg38:[refGene.txt.gz](/uploads/3d473eeca2271a4f6add16cc8ec191dc/refGene.txt.gz)
- corresponding bb file (isn't displaying genes): [refGene38.bb](/uploads/735a7e51e375248e790c5d45cbfa546b/refGene38.bb)
- ref hg38 trimmed to 'basic chromosomes chr1, chr2...': [chromosoms-basic.txt.zip](/uploads/d79819d54cde1dbe9a11d40b1e410ccd/chromosoms-basic.txt.zip)
- bb file that displays hg38 genes in browser (after removing redundant chromosomes): [chromosoms-basic.txt.bb](/uploads/d076008e0acafb03b114839c2c52c151/chromosoms-basic.txt.bb)v18.0Piotr GawronPiotr Gawronhttps://git-r3lab.uni.lu/minerva/core/-/issues/1836Overlay files containing raw numerical data2024-01-09T14:39:12+01:00Luiz LadeiraOverlay files containing raw numerical dataIt would be nice to be able to upload overlay files with one more additional column containing the raw numerical data (without scaling from 0 to 1, or -1 to 1).It would be nice to be able to upload overlay files with one more additional column containing the raw numerical data (without scaling from 0 to 1, or -1 to 1).v18.0https://git-r3lab.uni.lu/minerva/core/-/issues/1867INFO - EXPORT- ELEMENTS - Improved defaults and order?2023-12-21T14:04:55+01:00Alexander MAZEININFO - EXPORT- ELEMENTS - Improved defaults and order?Now I know more about how to export a list of entities with annotation but earlier it was a bit confusing. So, some suggestions:
1. There could be defaults in terms of boxes checked. I would suggest 'Name' in COLUMNS checked together wit...Now I know more about how to export a list of entities with annotation but earlier it was a bit confusing. So, some suggestions:
1. There could be defaults in terms of boxes checked. I would suggest 'Name' in COLUMNS checked together with 'Simple molecule', 'Protein' and 'Gene' in TYPES. When used for the first time, nothing is checked by default and when you click download, you have nothing.
2. The order of checkboxes could be updated, for example 'Name' should go first (top-left corner) as the most needed
3. For some reason I was not noticing options for exporting annotation via the Annotation section. It might to do something with the visual but I simply was ignoring that. Kind of not on the "same level" or not intuitive, I am not sure exactly why. Instead I was focusing on checkboxes, which ones I should actually use. I tried several before discovering that the information I needed was in 'References' in COLUMNS. And now I know that there is a much better way to export it via Annotation section.
4. Defaults could be for Annotation too. I think 'ChEBI', 'HGNC Symbol' and 'UniProt'.https://git-r3lab.uni.lu/minerva/core/-/issues/2002Feature request: handle user overlays across projects on the same platform2024-02-20T13:46:46+01:00Marek OstaszewskiFeature request: handle user overlays across projects on the same platformCurrently, when new versions of a project are uploaded to the same MINERVA PLatform, overlays have to be manually transferred.
This is error-prone and time consuming, with data potentially propagating against users' intention. MINERVA sh...Currently, when new versions of a project are uploaded to the same MINERVA PLatform, overlays have to be manually transferred.
This is error-prone and time consuming, with data potentially propagating against users' intention. MINERVA should support easier handling of the user overlays within the same platform.
Suggested solutions:
Solution 1:
- user overlays are common across projects, visible for their owner on each project (on the same platform) the owner has access to.
- public/global overlays: a given overlay would be decided as public/global per project.
- challenge: removal of a single root overlay would result in removing it from other projects
- suggestion 1: allow this behaviour under a warning prompt
- suggestion 2: block a removal of an overlay until it's made private on all related projects
Solution 2:
- implement a functionality for user data transfer (in bulk) across projects
- challenge: this would be a manual solution, with data potentially propagating against users' intentionhttps://git-r3lab.uni.lu/minerva/core/-/issues/2013SBGN-ML export may produce invalid notes2024-03-22T19:58:24+01:00Adrien RougnySBGN-ML export may produce invalid notesWhen exporting in SBGN-ML, nodes that are skipped because not SBGN-compatible are reported in a \<notes\> element at the end of the \<sbgn\> element; this \<notes\> element is not properly formatted as it is not valid xhtml (the \<body\>...When exporting in SBGN-ML, nodes that are skipped because not SBGN-compatible are reported in a \<notes\> element at the end of the \<sbgn\> element; this \<notes\> element is not properly formatted as it is not valid xhtml (the \<body\> element lacks xmlns="http://www.w3.org/1999/xhtml").