micropublication issueshttps://gitlab.coko.foundation/groups/micropublication/-/issues2020-06-04T20:36:23Zhttps://gitlab.coko.foundation/micropublication/micropublication/-/issues/181Bioentity linking2020-06-04T20:36:23ZYannis BarlasBioentity linking“Linking” refers to highlighting genes or similar entities in the main description and methods text.
The goal is to have a navigable list of entities on the final article. Linking will be achieved by
communicating with an external API (w...“Linking” refers to highlighting genes or similar entities in the main description and methods text.
The goal is to have a navigable list of entities on the final article. Linking will be achieved by
communicating with an external API (which will be handled by Nicholas Stiffler). The Coko
application will send over the text and the API will respond with the links it found in the text.
Linking should be done early on by the submitting author (before the initial submission), quite
possibly with a “link” button next to the text. After the API response is received, the author will
be presented with a table of the links found and will be able to correct mistakes in the text and
running the linking function again.
The editors should also have access to the linking feature, so that they can check the
manuscript links and communicate to the author changes that they deem necessary.nickstifflernickstifflerhttps://gitlab.coko.foundation/micropublication/micropublication/-/issues/180Dashboard filtering2020-09-26T00:59:54ZYannis BarlasDashboard filteringWe discussed a filtering feature for the dashboard, where the editors could select a status from
the dropdown menu, thereby filtering the manuscripts to only those that are in the selected
status.
Articles that are “done” (published, re...We discussed a filtering feature for the dashboard, where the editors could select a status from
the dropdown menu, thereby filtering the manuscripts to only those that are in the selected
status.
Articles that are “done” (published, rejected etc) will be automatically archived (but not deleted),
so that they are by default not in the dashboard view.
The proposed states were as follows (wording subject to change):
* Needs datatype/curator QC - done ->initial submission ready
* Needs SO approval
* Needs reviewer invites
* Reviewer has been invited - done
* Needs reviewer chasing (needs a date step)
* Reviewer reviewing - done -> pending
* Author needs to revise
* Reviewers want to see revision
* Editor needs to make decision
* Needs to be publishedUpcomingnickstifflernickstifflerhttps://gitlab.coko.foundation/micropublication/micropublication/-/issues/166Chat window open by default2019-03-20T17:13:18ZDaniela RacitiChat window open by defaultCan the chat window stay open by default?
When the editor sends the message to the SO and vice versa, having the chat expanded will allow to immediately see what needs to be addressed.
I would like to hear what @karenyook also thinks ab...Can the chat window stay open by default?
When the editor sends the message to the SO and vice versa, having the chat expanded will allow to immediately see what needs to be addressed.
I would like to hear what @karenyook also thinks about thishttps://gitlab.coko.foundation/micropublication/micropublication/-/issues/138email template announcements2021-05-05T20:43:08ZDaniela Racitiemail template announcements@yannis let @karen and @daniela know when you want the e-mail templates from us@yannis let @karen and @daniela know when you want the e-mail templates from ushttps://gitlab.coko.foundation/micropublication/micropublication/-/issues/137Dashboard view should show next action needed2021-05-05T20:42:04ZDaniela RacitiDashboard view should show next action neededDashboard view needs to show next action needed for an article in addition to the previous action doneDashboard view needs to show next action needed for an article in addition to the previous action donehttps://gitlab.coko.foundation/micropublication/micropublication/-/issues/120not all author names are recognized by the autocomplete2019-02-07T13:17:19ZDaniela Racitinot all author names are recognized by the autocompleteBy typing in the author’s last name- Ihara- the autocomplete does not return any results. By typing in Shinji (first name) the autocomplete works. Make sure that the autocomplete works regardless if an author starts typing in the first o...By typing in the author’s last name- Ihara- the autocomplete does not return any results. By typing in Shinji (first name) the autocomplete works. Make sure that the autocomplete works regardless if an author starts typing in the first or last name. This seems to happen only with Shinji Ihara.
@draciti wrote to JuancarlosDaniela RacitiDaniela Racitihttps://gitlab.coko.foundation/micropublication/micropublication/-/issues/115Console error while using autocomplete2021-05-05T20:42:09ZYannis BarlasConsole error while using autocompleteWhen selecting an autocomplete result, there's sometimes the following error in the browser console:
```
Warning: `handleChange` has triggered and you forgot to pass an `id` or `name` attribute to your input
```
There is an id or name...When selecting an autocomplete result, there's sometimes the following error in the browser console:
```
Warning: `handleChange` has triggered and you forgot to pass an `id` or `name` attribute to your input
```
There is an id or name on all fields, and everything seems to work as expected, but still worth looking into.https://gitlab.coko.foundation/micropublication/micropublication/-/issues/114Autocomplete validation2021-05-05T20:42:13ZYannis BarlasAutocomplete validationIf an option in the autocomplete fields is not selected from the results (via click / enter), then I don't get the wormbase ID, which means that validation will fail, even if a valid value gets typed in.
Solution: If what the typed valu...If an option in the autocomplete fields is not selected from the results (via click / enter), then I don't get the wormbase ID, which means that validation will fail, even if a valid value gets typed in.
Solution: If what the typed value matches one of the results 100%, auto-select that and get the id.https://gitlab.coko.foundation/micropublication/micropublication/-/issues/113Typing performance2021-05-05T20:42:16ZYannis BarlasTyping performanceThere is considerable lag when typing in the form in development mode.
It is much better in production mode, but there is still room for improvement.There is considerable lag when typing in the form in development mode.
It is much better in production mode, but there is still room for improvement.https://gitlab.coko.foundation/micropublication/micropublication/-/issues/110Make comments area expandable2021-05-05T20:42:23ZYannis BarlasMake comments area expandablehttps://gitlab.coko.foundation/micropublication/micropublication/-/issues/109Detection method: "other" option2021-05-05T20:42:30ZYannis BarlasDetection method: "other" optionWe need an extra "other" option in the radio buttons.We need an extra "other" option in the radio buttons.https://gitlab.coko.foundation/micropublication/micropublication/-/issues/108Species2021-05-05T20:42:27ZYannis BarlasSpeciesFor now this should read Organism and should be a drop down of “Nematode, Fruitfly, Frog, Fission Yeast, Budding Yeast, Fish, Rat, Mouse, Human” in the future, this should trigger a species specific gene set.For now this should read Organism and should be a drop down of “Nematode, Fruitfly, Frog, Fission Yeast, Budding Yeast, Fish, Rat, Mouse, Human” in the future, this should trigger a species specific gene set.https://gitlab.coko.foundation/micropublication/micropublication/-/issues/103Suggested reviewer enhancements2021-05-05T20:46:15ZYannis BarlasSuggested reviewer enhancementsA couple of things here:
* Allow more than one suggested reviewers
* Ask for an optional email
* Possibly also allow for free text instead of forcing wormbase validated autocomplete data
Also update placeholder to "Please suggest at lea...A couple of things here:
* Allow more than one suggested reviewers
* Ask for an optional email
* Possibly also allow for free text instead of forcing wormbase validated autocomplete data
Also update placeholder to "Please suggest at least one reviewer"https://gitlab.coko.foundation/micropublication/micropublication/-/issues/101Allow video upload2021-05-05T20:40:42ZYannis BarlasAllow video uploadWe need to look into how storage and network limitations can create a problem for us with this.We need to look into how storage and network limitations can create a problem for us with this.https://gitlab.coko.foundation/micropublication/micropublication/-/issues/98Make dashboard searchable2018-12-12T16:40:43ZYannis BarlasMake dashboard searchableAs a first iteration, simply by name (and probably for the whole dashboard, not per section).
We can look into search enhancements down the line.As a first iteration, simply by name (and probably for the whole dashboard, not per section).
We can look into search enhancements down the line.julientaqjulien@coko.foundationjulientaqjulien@coko.foundationhttps://gitlab.coko.foundation/micropublication/micropublication/-/issues/97Make dashboard sections sortable2018-12-12T16:39:38ZYannis BarlasMake dashboard sections sortableWe can start with a couple of simple options (name and status) and enhance later.We can start with a couple of simple options (name and status) and enhance later.julientaqjulien@coko.foundationjulientaqjulien@coko.foundationhttps://gitlab.coko.foundation/micropublication/micropublication/-/issues/96Draw attention to actionable articles2018-12-12T16:38:31ZYannis BarlasDraw attention to actionable articlesWe need a smart way to show in the dashboard that an action is currently required of the user for an article.
Things to think about:
* We should probably float articles where an action is required to the top.
* Not all actions are the...We need a smart way to show in the dashboard that an action is currently required of the user for an article.
Things to think about:
* We should probably float articles where an action is required to the top.
* Not all actions are the same (we could do better than "you need to do something" and possibly provide some context as to what that might be)julientaqjulien@coko.foundationjulientaqjulien@coko.foundationhttps://gitlab.coko.foundation/micropublication/micropublication/-/issues/91Submission form redesign2020-09-29T18:43:39ZYannis BarlasSubmission form redesignWe need to put some design work into the submission form to make it more manageable.
The two ideas that have been floated so far are:
* The form should work with steps (author input, then article metadata etc.)
* Using the same separati...We need to put some design work into the submission form to make it more manageable.
The two ideas that have been floated so far are:
* The form should work with steps (author input, then article metadata etc.)
* Using the same separation, but in the same page with a navigable table of contents-like menu on the lefthttps://gitlab.coko.foundation/micropublication/micropublication/-/issues/88User manager2020-08-07T06:31:03ZYannis BarlasUser managerAdmins should have access to a user manager, where they can view and (if there are no legal issues) create / delete users.Admins should have access to a user manager, where they can view and (if there are no legal issues) create / delete users.Upcomingnickstifflernickstifflerhttps://gitlab.coko.foundation/micropublication/micropublication/-/issues/87Multiple admins2021-05-05T20:34:19ZYannis BarlasMultiple adminsLook into the use case of having >1 admin user.
This would definitely require some UI to manage permissions (most likely in the current admin team manager interface).Look into the use case of having >1 admin user.
This would definitely require some UI to manage permissions (most likely in the current admin team manager interface).