core issueshttps://git-r3lab.uni.lu/minerva/core/-/issues2024-03-22T19:58:24+01:00https://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").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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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)