core issueshttps://git-r3lab.uni.lu/minerva/core/-/issues2019-07-22T19:18:10+02:00https://git-r3lab.uni.lu/minerva/core/-/issues/629Remove custom anonymous user authentication2019-07-22T19:18:10+02:00Sascha HerzingerRemove custom anonymous user authenticationlet's switch to this instead
https://docs.spring.io/spring-security/site/docs/4.0.x/reference/html/anonymous.html#anonymouslet's switch to this instead
https://docs.spring.io/spring-security/site/docs/4.0.x/reference/html/anonymous.html#anonymousv14.0.0~alpha.0Sascha HerzingerSascha Herzingerhttps://git-r3lab.uni.lu/minerva/core/-/issues/626Add option to disable `REQUEST AN ACCOUNT`2019-01-31T13:22:35+01:00Nils ChristianAdd option to disable `REQUEST AN ACCOUNT`Add a configuration to option to disable the link `REQUEST AN ACCOUNT` on the login page.
By default, the link should be disabled when the email settings are not configured.Add a configuration to option to disable the link `REQUEST AN ACCOUNT` on the login page.
By default, the link should be disabled when the email settings are not configured.v12.2.0~beta.1https://git-r3lab.uni.lu/minerva/core/-/issues/625Use JWT (or alternatives) over standard token auth2019-07-22T19:10:05+02:00Sascha HerzingerUse JWT (or alternatives) over standard token authv14.0.0~alpha.0Sascha HerzingerSascha Herzingerhttps://git-r3lab.uni.lu/minerva/core/-/issues/618if MeSH ID incorrect - add dialog window2019-03-11T16:07:48+01:00Ewa Smulaif MeSH ID incorrect - add dialog windowPlease provide an error dialog window if user inputs and save an incorrect MeshID during adding a new project.Please provide an error dialog window if user inputs and save an incorrect MeshID during adding a new project.v13.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/615list of reaction2019-04-05T10:59:12+02:00Piotr Gawronlist of reaction> in case of multiple maps, enable to download and report reactions for each map separately as reaction numbers are not unique across multiple maps.
by @erfan.younesi
@nils.christian> in case of multiple maps, enable to download and report reactions for each map separately as reaction numbers are not unique across multiple maps.
by @erfan.younesi
@nils.christianv13.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/614list of publications2019-02-05T15:32:50+01:00Piotr Gawronlist of publications> in case of multiple maps, enable to download publications for individual maps also
by @erfan.younesi
@nils.christian> in case of multiple maps, enable to download publications for individual maps also
by @erfan.younesi
@nils.christianv12.2.0~beta.1https://git-r3lab.uni.lu/minerva/core/-/issues/610automatic Refresh - it would be nice to have2019-04-05T10:20:05+02:00Ewa Smulaautomatic Refresh - it would be nice to haveDuring saving a new project or removing an existing one, please provide automatic refresh of the minerva admin panel page, e.g.every 10sec?
Could we add percentage value of uploading/removing progress next to comments like "parsing", "a...During saving a new project or removing an existing one, please provide automatic refresh of the minerva admin panel page, e.g.every 10sec?
Could we add percentage value of uploading/removing progress next to comments like "parsing", "annotating" in *Status* column? Or an "uploading bar"?
Or maybe display a dialog window, after clicking "save" and "remove" buttons, with information: "please refresh page manually by clicking REFRESH button" ?v13.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/607allow showing and hiding data overlays in plugin API2019-01-10T16:36:58+01:00Piotr Gawronallow showing and hiding data overlays in plugin APIv12.2.0~beta.0https://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/598Check if there is possibility to provide transparency (alpha) for elements2019-10-22T08:20:26+02:00Piotr GawronCheck if there is possibility to provide transparency (alpha) for elementsrequested by faiz.khan3@uni-rostock.derequested by faiz.khan3@uni-rostock.dehttps://git-r3lab.uni.lu/minerva/core/-/issues/597Handle coloring of reaction parts2019-03-18T15:34:13+01:00Marek OstaszewskiHandle coloring of reaction partsCellDesigner allows coloring of reaction parts (see below), these should be handled.
![Screen_Shot_2018-12-12_at_09.05.11](/uploads/a07cb783ca8bf066b8b0301e5fb34478/Screen_Shot_2018-12-12_at_09.05.11.png)CellDesigner allows coloring of reaction parts (see below), these should be handled.
![Screen_Shot_2018-12-12_at_09.05.11](/uploads/a07cb783ca8bf066b8b0301e5fb34478/Screen_Shot_2018-12-12_at_09.05.11.png)v13.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/596Harmonize column names in the overlay datasets2019-03-11T13:19:48+01:00Marek OstaszewskiHarmonize column names in the overlay datasetsThere are discrepancies in the column naming in the overlay datasets. Some are linked by "_" or "-" symbols (gene_name, pubchem-substance), some with a capital letter (lineWidth), some with whitespace (entrez gene).
- All should be harmo...There are discrepancies in the column naming in the overlay datasets. Some are linked by "_" or "-" symbols (gene_name, pubchem-substance), some with a capital letter (lineWidth), some with whitespace (entrez gene).
- All should be harmonized following a similar system
- Whitespace should not be a concatenating symbolv13.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/595allow to open multiple data overlays using url GET param2018-12-27T14:06:51+01:00Piotr Gawronallow to open multiple data overlays using url GET paramoriginally asked by Andrei.Zinovyev@curie.fr:
>However, my question is - can we automate it further? What I want to do is to 1) open browser with minerva project, 2) remotely activate the overlay such that it would be displayed without a...originally asked by Andrei.Zinovyev@curie.fr:
>However, my question is - can we automate it further? What I want to do is to 1) open browser with minerva project, 2) remotely activate the overlay such that it would be displayed without any intervention from the user.
>In other words, I would like to write a small external javascript program which would send an overlay to a dedicated minerva server, open browser and show the visualization, all without requiring intervention from the user. Is it possible with current minerva API functionality?v12.2.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/591add handling of annotations for model2019-03-19T14:41:53+01:00Piotr Gawronadd handling of annotations for modelthis should possible for SBML and CellDesigner SBMLthis should possible for SBML and CellDesigner SBMLv13.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/590process vcard data that can appear in model annotations2019-04-03T11:28:01+02:00Piotr Gawronprocess vcard data that can appear in model annotationsIn the model annotation RDF there can be vcard information that should be stored together with the map file.
It should be supported by SBML and CellDesigner SBML.
Example:
```
<annotation>
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/...In the model annotation RDF there can be vcard information that should be stored together with the map file.
It should be supported by SBML and CellDesigner SBML.
Example:
```
<annotation>
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#"
xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_0000002">
<dc:creator>
<rdf:Bag>
<rdf:li rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Roberts</vCard:Family>
<vCard:Given>Matthew Grant</vCard:Given>
</vCard:N>
<vCard:EMAIL>mroberts@embl.ac.uk</vCard:EMAIL>
<vCard:ORG rdf:parseType="Resource">
<vCard:Orgname>EMBL-EBI</vCard:Orgname>
</vCard:ORG>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Lloyd</vCard:Family>
<vCard:Given>Catherine</vCard:Given>
</vCard:N>
<vCard:EMAIL>c.lloyd@auckland.ac.nz</vCard:EMAIL>
<vCard:ORG rdf:parseType="Resource">
<vCard:Orgname>University of Auckland</vCard:Orgname>
</vCard:ORG>
</rdf:li>
</rdf:Bag>
</dc:creator>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2010-06-25T13:23:00Z</dcterms:W3CDTF>
</dcterms:created>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-08T16:30:35Z</dcterms:W3CDTF>
</dcterms:modified>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-08T16:30:35Z</dcterms:W3CDTF>
</dcterms:modified>
<bqmodel:is>
<rdf:Bag>
<rdf:li
rdf:resource="http://identifiers.org/biomodels.db/MODEL1006230061" />
</rdf:Bag>
</bqmodel:is>
<bqmodel:isDescribedBy>
<rdf:Bag>
<rdf:li
rdf:resource="http://identifiers.org/pubmed/13678598" />
</rdf:Bag>
</bqmodel:isDescribedBy>
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/go/GO:0002250" />
</rdf:Bag>
</bqbiol:isVersionOf>
<bqbiol:hasTaxon>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/taxonomy/9606" />
</rdf:Bag>
</bqbiol:hasTaxon>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li
rdf:resource="http://identifiers.org/pubmed/13678598" />
</rdf:Bag>
</bqbiol:isDescribedBy>
<bqmodel:is>
<rdf:Bag>
<rdf:li
rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000684" />
</rdf:Bag>
</bqmodel:is>
</rdf:Description>
</rdf:RDF>
</annotation>
```v13.1.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/585Add project window - CSZ setup enhancement2018-11-23T11:36:14+01:00Ewa SmulaAdd project window - CSZ setup enhancementCurrently, if user checks only the box *Custom semantic zooming contains multiple overlays* the CSZ is not generated at all. That box must be checked together with *Custom semantic zooming* box to generate CSZ.
Please make the *Custom s...Currently, if user checks only the box *Custom semantic zooming contains multiple overlays* the CSZ is not generated at all. That box must be checked together with *Custom semantic zooming* box to generate CSZ.
Please make the *Custom semantic zooming contains multiple overlays* inactive until box *Custom semantic zoom* is ticked.v12.1.2Piotr GawronPiotr Gawronhttps://git-r3lab.uni.lu/minerva/core/-/issues/584Add '?' description in Add project window2018-11-23T11:36:09+01:00Ewa SmulaAdd '?' description in Add project windowPlease add two **?** icons and put below descriptions, in the Add Project window
1. Custom semantic zooming
Check this checkbox to display semantic zooming of the map, defined in the upload file
2. Custom semantic zooming contains m...Please add two **?** icons and put below descriptions, in the Add Project window
1. Custom semantic zooming
Check this checkbox to display semantic zooming of the map, defined in the upload file
2. Custom semantic zooming contains multiple overlays
Check this checkbox to display each semantic zoom level in the General Overlays
![add](/uploads/3089a1d8571441fe459de92ec5c32c63/add.png)v12.1.2Piotr GawronPiotr Gawronhttps://git-r3lab.uni.lu/minerva/core/-/issues/580Add ClinicalTrials.gov to handled MIRIAMs2018-11-16T16:07:17+01:00Marek OstaszewskiAdd ClinicalTrials.gov to handled MIRIAMsReference of the identifier:
https://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000137Reference of the identifier:
https://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000137v12.2.0~beta.0https://git-r3lab.uni.lu/minerva/core/-/issues/576Genomes - put "waiting icon"2018-11-15T16:17:26+01:00Ewa SmulaGenomes - put "waiting icon"Please put "waiting icon" for changing the version of hg in adding new genome. Awaiting for corresponding url takes a while.
![adding_new_genome](/uploads/29b27e13be86f63034767a7ea4f6baab/adding_new_genome.png)Please put "waiting icon" for changing the version of hg in adding new genome. Awaiting for corresponding url takes a while.
![adding_new_genome](/uploads/29b27e13be86f63034767a7ea4f6baab/adding_new_genome.png)v12.2.0~beta.0Piotr GawronPiotr Gawronhttps://git-r3lab.uni.lu/minerva/core/-/issues/573Allow to set default width of a plugin2018-11-16T15:43:54+01:00David HokszaAllow to set default width of a pluginCurrently, the plugin can set minWidth in minervaDefine. It would be useful if it could also specify its default width. That would be basically a recommended width, but if the user wanted, she still could make it narrower.Currently, the plugin can set minWidth in minervaDefine. It would be useful if it could also specify its default width. That would be basically a recommended width, but if the user wanted, she still could make it narrower.v12.2.0~beta.0