core issueshttps://git-r3lab.uni.lu/minerva/core/-/issues2023-11-15T11:44:58+01:00https://git-r3lab.uni.lu/minerva/core/-/issues/1851search and mark submaps anchors on the map2023-11-15T11:44:58+01:00Ewa Smulasearch and mark submaps anchors on the mapWe would like to add new feature - to mark with pins all anchor points for submaps on the map.
Could we have in SUBMAPS tab, in the table the third column, named FIND ANCHOR. In each filed of this column, there would be icon/button ...We would like to add new feature - to mark with pins all anchor points for submaps on the map.
Could we have in SUBMAPS tab, in the table the third column, named FIND ANCHOR. In each filed of this column, there would be icon/button - after click it would return on the canvas the pin(s) marking anchor points. Also it would redirect to left panel SEARCH CONTENT and display search results.
In case there are no anchor points to the submap, the find anchor icon could be inactive; or stay active and return in search left panel info 'no anchor points found'.
![Screen_Shot_2023-03-02_at_15.50.33](/uploads/d2bb8c8a4ca0c9786074abed20c3a05d/Screen_Shot_2023-03-02_at_15.50.33.png)
![Screen_Shot_2023-03-02_at_16.20.30](/uploads/36aa48340ac45dd8a62387efacc34949/Screen_Shot_2023-03-02_at_16.20.30.png)
![Screenshot_2023-03-02_at_14.32.04](/uploads/3a2d42e728d1f9eb199ba5aeb1233f0f/Screenshot_2023-03-02_at_14.32.04.png)v16.3.0~beta.0Piotr GawronPiotr Gawronhttps://git-r3lab.uni.lu/minerva/core/-/issues/53allow admins to configure parameters displayed in the left panel2018-10-23T15:55:01+02:00Piotr Gawronallow admins to configure parameters displayed in the left panelallow to turn on/off visibility of reaction/element typeallow to turn on/off visibility of reaction/element typev12.2.0~beta.0https://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/1993Admin panel - enable sorting users by "Account active"2024-02-22T09:47:42+01:00Marek OstaszewskiAdmin panel - enable sorting users by "Account active"17.0.0-beta.3https://git-r3lab.uni.lu/minerva/core/-/issues/1991Admin panel - check format of manually introduced ORCID2024-03-05T12:53:50+01:00Marek OstaszewskiAdmin panel - check format of manually introduced ORCIDA new field (from v17) allows to store ORCID id, but it's not checked if the formatting of the is correct when it's manually provided.A new field (from v17) allows to store ORCID id, but it's not checked if the formatting of the is correct when it's manually provided.17.0.0-beta.4https://git-r3lab.uni.lu/minerva/core/-/issues/1988minerva service should have a parameter java arguments2024-02-15T14:07:19+01:00Piotr Gawronminerva service should have a parameter java argumentsThis would allow for to increase memory limits used by minerva application (and probably other things).This would allow for to increase memory limits used by minerva application (and probably other things).17.0.0-beta.3https://git-r3lab.uni.lu/minerva/core/-/issues/1949allow to archive project2024-02-13T12:50:46+01:00Piotr Gawronallow to archive projectArchived project:
* should not be browse-able
* should not contain images on the server (remove image files for backgrounds)
* could be revived (images should be regenerated)
* can be interacted with using API
* source file should be do...Archived project:
* should not be browse-able
* should not contain images on the server (remove image files for backgrounds)
* could be revived (images should be regenerated)
* can be interacted with using API
* source file should be downloadable in the frontend (instead of browsing)v17.0.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1944Add BioKC identifiers.org type2023-12-07T16:21:26+01:00Piotr GawronAdd BioKC identifiers.org typehttps://registry.identifiers.org/registry/biokc#!https://registry.identifiers.org/registry/biokc#!v16.3.0~beta.3https://git-r3lab.uni.lu/minerva/core/-/issues/1923New users should be able to log in via ORCID2024-02-13T11:50:06+01:00Marek OstaszewskiNew users should be able to log in via ORCIDMINERVA should enable login using ORCID, to reduce work with account setup, multiple login/password management etc.MINERVA should enable login using ORCID, to reduce work with account setup, multiple login/password management etc.17.0.0~beta.1https://git-r3lab.uni.lu/minerva/core/-/issues/1847table to CellDesigner SBML converter - inclusion of PMID as MIRIAN annotations2023-08-23T08:31:55+02:00Luiz Ladeiratable to CellDesigner SBML converter - inclusion of PMID as MIRIAN annotationsHi all,
I'm using the converter of tables to CellDesigner SBML passing through GPML to create CellDesigner networks from big datasets. We have a column for transcription factors, another for target genes, and a third one for the type o...Hi all,
I'm using the converter of tables to CellDesigner SBML passing through GPML to create CellDesigner networks from big datasets. We have a column for transcription factors, another for target genes, and a third one for the type of interaction. This is easily converted using activity flow SBGN, which works well. However, we do have a fourth column with the PMIDs (sometimes a single one, sometimes more than one separated by ; [e.g. 11753601;9916993]) that we want to keep the information in to be able to track back the literature on the map when visualizing on MINERVA. It would be really useful if it were possible to include these literature identifiers as MIRIAN annotations on the edges automatically!
Thanks!v16.3.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1839Could we add 'loading' icon in EXPORT tab ?2023-11-15T11:45:40+01:00Ewa SmulaCould we add 'loading' icon in EXPORT tab ?For maps with a lot of pathways/compartments there is few seconds delay to display _Included/Excluded compartment/pathways_ lists and _Download_ button. Maybe we could add there loading icon? So user knows the page is not ready yet?For maps with a lot of pathways/compartments there is few seconds delay to display _Included/Excluded compartment/pathways_ lists and _Download_ button. Maybe we could add there loading icon? So user knows the page is not ready yet?v16.3.0~beta.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/1792error report sent to minerva-net should contain server side stacktrace2023-09-15T13:02:07+02:00Piotr Gawronerror report sent to minerva-net should contain server side stacktracev16.3.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1726every project should have license defined2023-09-21T13:58:49+02:00Piotr Gawronevery project should have license defined@marek.ostaszewski Please provide list of licenses together with the content@marek.ostaszewski Please provide list of licenses together with the contentv16.3.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1725import/export authors from SBGN-ML2023-12-01T12:54:57+01:00Piotr Gawronimport/export authors from SBGN-ML16.3.0~beta.1https://git-r3lab.uni.lu/minerva/core/-/issues/1721behaviour of projects whose creators are removed2024-02-29T11:11:24+01:00Ewa Smulabehaviour of projects whose creators are removedhi @marek.ostaszewski, if I remove user from minerva, how should projects that user created behave? Currently the projects are still available for other users, but the backgrounds and overlays are removed, as the owner of backgrounds/ove...hi @marek.ostaszewski, if I remove user from minerva, how should projects that user created behave? Currently the projects are still available for other users, but the backgrounds and overlays are removed, as the owner of backgrounds/overlays does not exist. Opening such. map occurs with warning/error display: `Project doesn't have a background defined. Please re-upload map in admin panel.`. Are we happy with this solution?
![Screenshot_2022-06-22_at_11.24.45](/uploads/b5fd7927a990772247b9606c4f752f57/Screenshot_2022-06-22_at_11.24.45.png)
![Screenshot_2022-06-22_at_11.25.11](/uploads/cd83dfdd6c57243db8daefa78786cc36/Screenshot_2022-06-22_at_11.25.11.png)v17.1.0Piotr GawronPiotr Gawronhttps://git-r3lab.uni.lu/minerva/core/-/issues/1700"Privacy policy" notification functionality2022-06-01T14:19:22+02:00Marek Ostaszewski"Privacy policy" notification functionalitySome remarks:
- the text "Cookie policy (url)" should be "Privacy policy (url)"
- this functionality should be available under “Server configuration”, not “Legend and logo”
The default text of the privacy policy (default for MINERVA ins...Some remarks:
- the text "Cookie policy (url)" should be "Privacy policy (url)"
- this functionality should be available under “Server configuration”, not “Legend and logo”
The default text of the privacy policy (default for MINERVA installation) should be:
```
# MINERVA - Cookie and privacy policy
Last updated: May 23, 2022
**The MINERVA Platform** is provided by the Luxembourg Centre for Systems Biomedicine (LCSB), an interdisciplinary centre at the University of Luxembourg to visualize, explore and analyze molecular interaction maps.
In order to work properly, the MINERVA Platform uses cookies. Cookies are bits of information that are created and maintained by your web browser when you visit a website. MINERVA cookies are so-called first-party cookies and will not track your activity once you leave that website.
Additionally, the MINERVA Platform can optionally gather analytics about user activity using Google Analytics platform. You will have to agree for this to happen.
The webserver hosting the MINERVA Platform may collect information about your activity. This depends on the specific configuration of this instance of the MINERVA Platform. Please contact system administrators for information.
Below are the details about our cookie and privacy policy.
# Cookies
## MINERVA cookies
When you visit the MINERVA Platform for the first time you will be notified of our cookie policy. You will have the option to proceed only with technically necessary cookies (i.e. optimisation, security and authentication) or (additionally) allow site analytics cookies (see Section 3.3). This cookie, named "cc_cookie", expires in 6 months. When you work with the MINERVA Platform, we create a session cookie named "MINERVA_AUTH_TOKEN". This cookie expires at the end of the browsing session.
**Legal basis**
Use of cookies is in our legitimate interest (GDPR Article 6(1)(f)) as it is necessary for us to deliver our sites to you in a stable and secure manner.
## Google Analytics of the MINERVA Platform
**Disclaimer:**
**This is optional. If you weren't asked for opt-in, it means that Google Analytics is not configured for this instance of the MINERVA Platform.**
The MINERVA Platform can optionally track your activity using Google Analytics (GA) to analyse its effectiveness and efficiency.
This platform enables the protection of end-user personal data thanks to features such as IP address de-identification and a mechanism for users to opt-out so that their browsing is not processed for analytics purposes.
[Read here about the cookies used by Google Analytics](https://developers.google.com/analytics/devguides/collection/analyticsjs/cookie-usage).
The cookies used by Google Analytics will be transmitted to and stored by Google on servers in the United States which leads to the transfer of personal data to the United States. Google Analytics is configured to store first-party cookies that expire after 2 years.
If you choose to opt-out, we will keep your preference in a cookie named “cc_cookie”, which expires in 6 months.
```v16.2.0https://git-r3lab.uni.lu/minerva/core/-/issues/1697cookie banner2022-05-04T13:43:29+02:00Piotr Gawroncookie bannerit should be customizableit should be customizablev16.2.0https://git-r3lab.uni.lu/minerva/core/-/issues/1685Provide incorrect zip file warning2024-02-27T11:00:35+01:00Marek OstaszewskiProvide incorrect zip file warningIntuitively, some users zip the entire folder with their map build, not its' contents.
Currently there's no warning that such a zip file will not work.
Suggestions:
1. Handle one-level nesting of zipped content (when the unzipped resul...Intuitively, some users zip the entire folder with their map build, not its' contents.
Currently there's no warning that such a zip file will not work.
Suggestions:
1. Handle one-level nesting of zipped content (when the unzipped results are a single directory, use contents of the directory)
2. On file upload, warn the user that the zipped content contains no .xml file that can be used as a root map, suggesting incorrectly zipped buildv17.1.0https://git-r3lab.uni.lu/minerva/core/-/issues/1678change checkbox to radio button for default backgrounds2024-02-27T11:00:53+01:00Ewa Smulachange checkbox to radio button for default backgroundsAs currently user can tick few __default__ views, change checkbox on radio button (and the default view set Pathways&compartments).
![Screenshot_2022-03-21_at_16.36.56](/uploads/914702fe66d7c6b1bf3d90a25f532412/Screenshot_2022-03-21_...As currently user can tick few __default__ views, change checkbox on radio button (and the default view set Pathways&compartments).
![Screenshot_2022-03-21_at_16.36.56](/uploads/914702fe66d7c6b1bf3d90a25f532412/Screenshot_2022-03-21_at_16.36.56.png)v17.1.0