core issueshttps://git-r3lab.uni.lu/minerva/core/-/issues2021-04-20T11:18:43+02:00https://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/1275name/full-name separation in SBML2020-08-04T13:11:04+02:00Piotr Gawronname/full-name separation in SBMLIf glyph name is different than species name then glyph name should become `minerva name` and `species name` should become `minerva full-name`
Suggested by wug[at]ohsu.eduIf glyph name is different than species name then glyph name should become `minerva name` and `species name` should become `minerva full-name`
Suggested by wug[at]ohsu.eduv15.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1255Sort submaps by filename in the upload2020-05-29T10:53:33+02:00Marek OstaszewskiSort submaps by filename in the uploadv15.0.0~beta.4https://git-r3lab.uni.lu/minerva/core/-/issues/1254Handle SBML render:fill in compartments2020-06-22T12:17:49+02:00Marek OstaszewskiHandle SBML render:fill in compartmentsUse SBML render:fill information for the fill colour of the compartments.Use SBML render:fill information for the fill colour of the compartments.v15.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1249Process SWISS-MODEL MIRIAM2020-05-27T13:08:42+02:00Marek OstaszewskiProcess SWISS-MODEL MIRIAMAs in the title.As in the title.v15.0.0~beta.4https://git-r3lab.uni.lu/minerva/core/-/issues/1248Process NCBI Protein MIRIAM2020-05-27T11:18:41+02:00Marek OstaszewskiProcess NCBI Protein MIRIAMAs in the title.As in the title.v15.0.0~beta.4https://git-r3lab.uni.lu/minerva/core/-/issues/1246InfoTab > EXPORT > NETWORK - suggestion2022-02-03T12:48:41+01:00Ewa SmulaInfoTab > EXPORT > NETWORK - suggestionCurrently in the Export > NETWORK tab there are listed all available reactions. If user ticks catalysis box (or any other modifier) the exported data is empty, as MINERVA keeps state transition reactions even if they contain modifiers. I...Currently in the Export > NETWORK tab there are listed all available reactions. If user ticks catalysis box (or any other modifier) the exported data is empty, as MINERVA keeps state transition reactions even if they contain modifiers. I believe this is misleading for the user.
@marek.ostaszewski suggested to simplify the NETWORK reactions boxes to three items:
- process description (state transition, translation......)
- activity flow (positive influence, negative.....)
- all
Next to the boxes the particular reaction should be displayed.
@piotr.gawron any comments, please? :)v16.1.0~beta.0Piotr GawronPiotr Gawronhttps://git-r3lab.uni.lu/minerva/core/-/issues/1234access to db.properties file2021-09-21T13:58:42+02:00Piotr Gawronaccess to db.properties fileThe file `/etc/minerva/db.properties` created by debian package should not be readable by everybody in the OS but only by the owner and owner should be changed to `tomcat` user
reported by @nils.christianThe file `/etc/minerva/db.properties` created by debian package should not be readable by everybody in the OS but only by the owner and owner should be changed to `tomcat` user
reported by @nils.christianv16.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1229compartment/species aliases are considered as search results2021-11-11T15:37:46+01:00Ewa Smulacompartment/species aliases are considered as search resultsIn case I search for "Ca2+" or "Sa2+" [see PD map here](https://pdmap.uni.lu/minerva/?search=ca2+&x=13090&y=6047&zoom=4&),
in the search results there is "Compartment: neuron", not Ca2+ related entity. It looks like the search query ta...In case I search for "Ca2+" or "Sa2+" [see PD map here](https://pdmap.uni.lu/minerva/?search=ca2+&x=13090&y=6047&zoom=4&),
in the search results there is "Compartment: neuron", not Ca2+ related entity. It looks like the search query takes also into searching the compartments aliases ("ca", "sa"). Is it correct behaviour? If it is let's add the warning dialog suggesting to narrow search results by adding prefix ION, molecule or RNA (e.g. ION:Ca2+) or informing that there might appear additional outcomes (like "Compartment: neuron").
![Screen_Shot_2020-05-04_at_17.24.48](/uploads/c6c66b230ad9b322ab6d8763bfc9ea3b/Screen_Shot_2020-05-04_at_17.24.48.png)v16.1.0~beta.0Piotr GawronPiotr Gawronhttps://git-r3lab.uni.lu/minerva/core/-/issues/1208add merge functionality to convert API2020-04-01T12:59:18+02:00Piotr Gawronadd merge functionality to convert APIrequested by @marek.ostaszewski
API endpoint should accept list of files as zipped content, merge them and export to specified format.requested by @marek.ostaszewski
API endpoint should accept list of files as zipped content, merge them and export to specified format.v15.0.0~beta.3https://git-r3lab.uni.lu/minerva/core/-/issues/1205Add 'Forgotten password' to request an account2020-06-19T19:58:40+02:00Ewa SmulaAdd 'Forgotten password' to request an accountPlease change 'request an account' on 'request an account/forgotten password' on authorisation-form page and when log in in user view.
![Screen_Shot_2020-03-25_at_13.23.56](/uploads/a115d85e34edad4d4a79d0818054ff29/Screen_Shot_2020-0...Please change 'request an account' on 'request an account/forgotten password' on authorisation-form page and when log in in user view.
![Screen_Shot_2020-03-25_at_13.23.56](/uploads/a115d85e34edad4d4a79d0818054ff29/Screen_Shot_2020-03-25_at_13.23.56.png)v15.1.0~beta.0Piotr GawronPiotr Gawronhttps://git-r3lab.uni.lu/minerva/core/-/issues/1194add support for uri qualifiers2020-03-16T15:07:01+01:00Piotr Gawronadd support for uri qualifiersThose qualifiers are not supported yet:
* `bqbiol:hasProperty`
* `bqbiol:isPropertyOf`Those qualifiers are not supported yet:
* `bqbiol:hasProperty`
* `bqbiol:isPropertyOf`v15.0.0~beta.2https://git-r3lab.uni.lu/minerva/core/-/issues/1193add support for SBO annotation2020-03-16T15:07:01+01:00Piotr Gawronadd support for SBO annotationSBO miriam type is not supportedSBO miriam type is not supportedv15.0.0~beta.2https://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/1153Can't access generated overlays2020-06-18T17:24:48+02:00Matti Hochmatti.hoch@uni-rostock.deCan't access generated overlays```javascript
minervaProxy.project.data.getDataOverlays();
```
... does not get overlays that have been added before in the same function. So I guess refreshing is required to do so. Is there a way to overcome this?
I am creating overl...```javascript
minervaProxy.project.data.getDataOverlays();
```
... does not get overlays that have been added before in the same function. So I guess refreshing is required to do so. Is there a way to overcome this?
I am creating overlays through a curl statement:
```
curl -X POST --data "content=name%09color%0ACAPN1%09%2300FF00%0APARK7%09....
```
Or is there a plugin API addOverlay() function?v15.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1141Transcription site should have color2021-11-16T08:47:35+01:00Piotr GawronTranscription site should have color* Coloring shouldn't depend on the getActive status
* clearing colors from map #1132 should work on the color* Coloring shouldn't depend on the getActive status
* clearing colors from map #1132 should work on the colorv16.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1118adding new project format *.sbml does not change Type in Add project window2024-02-08T09:41:09+01:00Ewa Smulaadding new project format *.sbml does not change Type in Add project windowadding new project format *.sbml does not change Type in Add project window.
![Screen_Shot_2020-02-07_at_15.51.40](/uploads/56b392a242630e8b1bb2c9a5fd01b69a/Screen_Shot_2020-02-07_at_15.51.40.png)adding new project format *.sbml does not change Type in Add project window.
![Screen_Shot_2020-02-07_at_15.51.40](/uploads/56b392a242630e8b1bb2c9a5fd01b69a/Screen_Shot_2020-02-07_at_15.51.40.png)v17.0.0~beta.0Piotr GawronPiotr Gawronhttps://git-r3lab.uni.lu/minerva/core/-/issues/1106When removing the project, its status isn't changed 'immediately'2020-02-07T13:39:06+01:00Ewa SmulaWhen removing the project, its status isn't changed 'immediately'After clicking on project "remove button", changing the status to "Project removing(0%)" takes few seconds.After clicking on project "remove button", changing the status to "Project removing(0%)" takes few seconds.v15.0.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1102Prevent hiding glyphs when clicking overlays?2022-02-03T08:01:30+01:00Matti Hochmatti.hoch@uni-rostock.dePrevent hiding glyphs when clicking overlays?Would be great to keep glyphs displayed when activating overlays. Ofc it's possible to click the "Pathways and compartments" overlay afterwards, but is there another way?Would be great to keep glyphs displayed when activating overlays. Ofc it's possible to click the "Pathways and compartments" overlay afterwards, but is there another way?v16.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1089allow plugin to add data overlay2022-02-01T12:53:33+01:00Piotr Gawronallow plugin to add data overlayrequested by matti.hoch[at]uni-rostock.derequested by matti.hoch[at]uni-rostock.dev16.1.0~beta.0