core issueshttps://git-r3lab.uni.lu/minerva/core/-/issues2021-04-20T09:02:15+02:00https://git-r3lab.uni.lu/minerva/core/-/issues/1358SBGN view: unit of information is shown twice for a multimer2021-04-20T09:02:15+02:00Alexander MAZEINSBGN view: unit of information is shown twice for a multimerFor some reason, the unit of information "N:2" is shown twice for a homodimer https://osteoarthritis.uni.lu/ The map was created in CellDesigner.For some reason, the unit of information "N:2" is shown twice for a homodimer https://osteoarthritis.uni.lu/ The map was created in CellDesigner.v16.0.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1457generate process rectangles for SBML render layout2021-03-19T09:48:55+01:00Piotr Gawrongenerate process rectangles for SBML render layoutv16.0.0~alpha.1https://git-r3lab.uni.lu/minerva/core/-/issues/1456SBML layout/render should contain information about modification states2021-03-19T08:48:25+01:00Piotr GawronSBML layout/render should contain information about modification statesv16.0.0~alpha.1https://git-r3lab.uni.lu/minerva/core/-/issues/1055COPASI does not preserve elements shape2021-02-12T10:20:03+01:00Ewa SmulaCOPASI does not preserve elements shapeCOPASI draws all elements as rectangles, what causes that reactions arrows are hidden.
![Screen_Shot_2019-12-16_at_10.56.47](/uploads/8dff9b7d6d3f2b58205e931f1351bd75/Screen_Shot_2019-12-16_at_10.56.47.png)![Screen_Shot_2019-12-16_at_1...COPASI draws all elements as rectangles, what causes that reactions arrows are hidden.
![Screen_Shot_2019-12-16_at_10.56.47](/uploads/8dff9b7d6d3f2b58205e931f1351bd75/Screen_Shot_2019-12-16_at_10.56.47.png)![Screen_Shot_2019-12-16_at_10.55.03](/uploads/8d31a978004c434c0ba754a40672a31b/Screen_Shot_2019-12-16_at_10.55.03.png)v16.0.0~alpha.1https://git-r3lab.uni.lu/minerva/core/-/issues/1056COPASI moving element without its name2021-02-12T10:10:05+01:00Ewa SmulaCOPASI moving element without its nameMoving the species grabs only rectangle without text inside it.
![Screen_Shot_2019-12-16_at_11.13.59](/uploads/a154aac8ce8c7368d416cae585c6ea1d/Screen_Shot_2019-12-16_at_11.13.59.png)Moving the species grabs only rectangle without text inside it.
![Screen_Shot_2019-12-16_at_11.13.59](/uploads/a154aac8ce8c7368d416cae585c6ea1d/Screen_Shot_2019-12-16_at_11.13.59.png)v16.0.0~alpha.1https://git-r3lab.uni.lu/minerva/core/-/issues/1376Perfect search via URL2021-02-09T13:58:27+01:00Marek OstaszewskiPerfect search via URLThe status of the tick box "Perfect search" should be reflected in the MINERVA URL.
It should be possible to invoke perfect search via the URL as well.The status of the tick box "Perfect search" should be reflected in the MINERVA URL.
It should be possible to invoke perfect search via the URL as well.v16.0.0~alpha.1https://git-r3lab.uni.lu/minerva/core/-/issues/1420handle additional miriam2021-02-09T09:17:09+01:00Piotr Gawronhandle additional miriam* http://identifiers.org/complexportal/CPX-5686
* Invalid miriam uri: urn:miriam:bind:31392488
reported by @marcio.acencio* http://identifiers.org/complexportal/CPX-5686
* Invalid miriam uri: urn:miriam:bind:31392488
reported by @marcio.acenciov16.0.0~alpha.1https://git-r3lab.uni.lu/minerva/core/-/issues/1450Handle MIRIAM PMC2021-02-09T09:13:55+01:00Marek OstaszewskiHandle MIRIAM PMCCurrently MINERVA throws
Invalid miriam uri: urn:miriam:pmc:___Currently MINERVA throws
Invalid miriam uri: urn:miriam:pmc:___v16.0.0~alpha.1https://git-r3lab.uni.lu/minerva/core/-/issues/137provide export to SBtab2021-02-01T09:55:11+01:00Piotr Gawronprovide export to SBtablink to the standard: https://sbtab.net/link to the standard: https://sbtab.net/https://git-r3lab.uni.lu/minerva/core/-/issues/1379hypothetical complex information should be accessible via API2020-10-22T13:17:22+02:00Marek Ostaszewskihypothetical complex information should be accessible via APIas aboveas abovev15.1.0https://git-r3lab.uni.lu/minerva/core/-/issues/1330add instance name to 'request an account' email's title2020-08-14T12:23:04+02:00Ewa Smulaadd instance name to 'request an account' email's titleconfiguration > Email content used for requesting an account
please add the instance's name in the title, so we know on which instance create new accountconfiguration > Email content used for requesting an account
please add the instance's name in the title, so we know on which instance create new accountv15.1.0~beta.1Piotr GawronPiotr Gawronhttps://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/1322gpml OVAL not imported2020-07-14T11:14:52+02:00Ewa Smulagpml OVAL not importedgraphical element OVAL is not displayed in MINERVA.
[kolko.gpml](/uploads/f6df0aaacef8f2ba0efa8db37a37b16a/kolko.gpml)graphical element OVAL is not displayed in MINERVA.
[kolko.gpml](/uploads/f6df0aaacef8f2ba0efa8db37a37b16a/kolko.gpml)Piotr GawronPiotr Gawronhttps://git-r3lab.uni.lu/minerva/core/-/issues/1314Make text area glyphs with z-index < 0 non-clickable2020-06-26T15:07:13+02:00Marek OstaszewskiMake text area glyphs with z-index < 0 non-clickableText areas which have a glyph and a z-index lower than 0 should not be interactive, e.g. a user should not be able to click them.Text areas which have a glyph and a z-index lower than 0 should not be interactive, e.g. a user should not be able to click them.v15.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1312confirm login by press Enter key - nice to have2020-06-26T13:48:51+02:00Ewa Smulaconfirm login by press Enter key - nice to haveIn case user logs in User View (INFO/OVERLAYS tab or via locker icon) the AUTHORIZATION FORM dialog is displayed. Only way to send user's login details is by clicking the LOGIN button, please allow to send data by press "Enter" key.In case user logs in User View (INFO/OVERLAYS tab or via locker icon) the AUTHORIZATION FORM dialog is displayed. Only way to send user's login details is by clicking the LOGIN button, please allow to send data by press "Enter" key.v15.1.0~beta.0Piotr GawronPiotr Gawronhttps://git-r3lab.uni.lu/minerva/core/-/issues/1308"Show overview" behaves incorrectly when unused images in "images" folder2020-06-26T12:17:16+02:00Marek Ostaszewski"Show overview" behaves incorrectly when unused images in "images" folderWhen there are unused image files (not mentioned in the "coords.txt" file) in the "images" folder, "Show overview" picks up the unused image instead of the first one in the "coords.txt". See attached example.
[Archive.zip](/uploads/c5af...When there are unused image files (not mentioned in the "coords.txt" file) in the "images" folder, "Show overview" picks up the unused image instead of the first one in the "coords.txt". See attached example.
[Archive.zip](/uploads/c5afb745ca682ed938370e88925592a6/Archive.zip)v15.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1300change export as gpml of unknown reaction to line-arrow-solid2020-06-26T09:07:14+02:00Ewa Smulachange export as gpml of unknown reaction to line-arrow-solidCurrently 'Unknown reaction' is exported as gpml to 'mim-gap reaction'.
Please export 'Unknown reaction' as gpml to line-arrow-solid (the same way as state transition).Currently 'Unknown reaction' is exported as gpml to 'mim-gap reaction'.
Please export 'Unknown reaction' as gpml to line-arrow-solid (the same way as state transition).v15.1.0~beta.0Piotr GawronPiotr Gawronhttps://git-r3lab.uni.lu/minerva/core/-/issues/1302export as SBGN - change mapping of some state transition reaction2020-06-25T17:56:04+02:00Ewa Smulaexport as SBGN - change mapping of some state transition reactionIn case of exporting below reactions as SBGN, map these the same way as state transition reaction
(production-proccess-consumption). Currently these three reactions are omitted during export.
- transport
- translation
- transcriptionIn case of exporting below reactions as SBGN, map these the same way as state transition reaction
(production-proccess-consumption). Currently these three reactions are omitted during export.
- transport
- translation
- transcriptionv15.1.0~beta.0Piotr GawronPiotr Gawronhttps://git-r3lab.uni.lu/minerva/core/-/issues/1292allow to store process coordinates2020-06-24T18:17:16+02:00Piotr Gawronallow to store process coordinatesthis should be alternative to current process drawn in the center of the reaction line,
import it from SBML:
> Regarding the reaction node thing (item 3 below): In our format, we use a position for a reaction indicating where the reactio...this should be alternative to current process drawn in the center of the reaction line,
import it from SBML:
> Regarding the reaction node thing (item 3 below): In our format, we use a position for a reaction indicating where the reaction node should be drawn. The SBML layout extension doesn't provide such a thing as you observed. However, the ReactionGraph layout still can take a BoundingBox element together with a list of LineSegments, though the spec said that the BoundingBox should be ignored if LineSegments are provided. Do you think we can try to hack this by providing the Reaction node as a BoundingBox for the Minerva? It is easy for me to convert the position into a BoundingBox.
by wug[at]ohsu.eduv15.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/1298allow to remove plugin data2020-06-24T18:17:16+02:00Piotr Gawronallow to remove plugin datarequested by @MattiHochrequested by @MattiHochv15.1.0~beta.0