xpub-epmc issueshttps://gitlab.coko.foundation/xpub/xpub-epmc/-/issues2020-02-25T08:42:54Zhttps://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/949Add internal XML QA stats to Admin Metrics page2020-02-25T08:42:54ZMichele Ide-SmithAdd internal XML QA stats to Admin Metrics pageI'd like to add the number of manuscripts which undergo internal (Helpdesk) XML QA each month here: https://plus.europepmc.org/admin-metrics
@XP Has already done a query to add the numbers to a spreadsheet here: https://docs.google.com/...I'd like to add the number of manuscripts which undergo internal (Helpdesk) XML QA each month here: https://plus.europepmc.org/admin-metrics
@XP Has already done a query to add the numbers to a spreadsheet here: https://docs.google.com/spreadsheets/d/1xzsZoxbJbrS6GxNG3nv4ZC-NU_VerzYgUU07uucOxiY/edit?usp=sharing
This is useful management information for the 2021-2026 grant application.2020-03-06https://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/948Add optional fields for acceptance and/or publication dates in submission wor...2020-02-07T11:48:41ZMichele Ide-SmithAdd optional fields for acceptance and/or publication dates in submission workflowIn our REF blog post we mentioned that we would be adding optional fields for acceptance date and first publication date to the submission workflow, to assist institutions with compliance checking. See http://blog.europepmc.org/2018/05/e...In our REF blog post we mentioned that we would be adding optional fields for acceptance date and first publication date to the submission workflow, to assist institutions with compliance checking. See http://blog.europepmc.org/2018/05/europepmc-REF2021.html for information under 'Accepted Manuscripts Submitted to Europe PMC'. Back in May 2018 we said this would be included in the new MSS. But we have recently updated the blog post to say we are 'planning' to include these dates as I gather they are not in the system yet.https://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/947Admin Dashboard - No alert message while searching with a invalid data on the...2020-01-24T16:15:22ZRakesh NambiarAdmin Dashboard - No alert message while searching with a invalid data on the Title fieldNo alert message while searching with invalid data on the Title field.
![image](/uploads/1fa0faefaabf4c63730e96b23bdf3695/image.png)No alert message while searching with invalid data on the Title field.
![image](/uploads/1fa0faefaabf4c63730e96b23bdf3695/image.png)Audrey HamelersAudrey Hamelershttps://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/940XSweet - bold text is not bold2020-01-09T16:15:36ZAudrey HamelersXSweet - bold text is not bold<img src="https://gitlab.coko.foundation/xpub/xpub-epmc/uploads/8680353e876d4cb71cfcf7c496e7ed37/image.png"><img src="https://gitlab.coko.foundation/xpub/xpub-epmc/uploads/8680353e876d4cb71cfcf7c496e7ed37/image.png">Work package 19https://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/934Xsweet does not render tables correctly2020-01-09T16:15:42ZDavid StephensonXsweet does not render tables correctlyXsweet isn't very good at rendering tables from .docx files. Can we get this improved?
This is how the table looks in the .docx:
![image](/uploads/79a999b6a265c278e3afabd3def0c499/image.png)
This is how the table looks in the xsweet pr...Xsweet isn't very good at rendering tables from .docx files. Can we get this improved?
This is how the table looks in the .docx:
![image](/uploads/79a999b6a265c278e3afabd3def0c499/image.png)
This is how the table looks in the xsweet preview
![image](/uploads/cb0bdfead12b2fb42f7b988e6259022b/image.png)Work package 19https://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/933Xsweet does not render equations correctly in preview2020-01-09T16:15:39ZDavid StephensonXsweet does not render equations correctly in previewA few users have pointed out that the xsweet preview does not do a good job. (see below). This needs to be improved.
Submitters manuscript:
![image__4_](/uploads/18ad7d49cb7ea2a0287aba4558cc420f/image__4_.png)
preview:
![image__5_](/u...A few users have pointed out that the xsweet preview does not do a good job. (see below). This needs to be improved.
Submitters manuscript:
![image__4_](/uploads/18ad7d49cb7ea2a0287aba4558cc420f/image__4_.png)
preview:
![image__5_](/uploads/2e3c10eae62e7140ec44f8039da6d2bd/image__5_.png)
(examples taken from EMS85114)Work package 19https://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/926Improve admin metrics2020-01-06T11:01:48ZAudrey HamelersImprove admin metricsAllow more granularity of querying to reduce page load times.
Currently the full last year is loaded. Only the last 5 months should be queried on page load, and then more months should only be loaded on request.
Potentially we could ad...Allow more granularity of querying to reduce page load times.
Currently the full last year is loaded. Only the last 5 months should be queried on page load, and then more months should only be loaded on request.
Potentially we could add more refined date filtering as well, if there's an admin need for that.Work package 19https://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/921NLM abbrevations/name varients of journals indexed by NLM need to be findable...2020-01-23T16:44:10ZDavid StephensonNLM abbrevations/name varients of journals indexed by NLM need to be findable for usersA recurrent problem is that the autocomplete for journals only displays the main title, and none of the varients.
This makes it harder for users (including helpdesk!) to add journals to submissions.
Eg."Otology & neurotology" brings u...A recurrent problem is that the autocomplete for journals only displays the main title, and none of the varients.
This makes it harder for users (including helpdesk!) to add journals to submissions.
Eg."Otology & neurotology" brings up the correct title, but the NLM title "Otol Neurotol" does not return any results, and neither does Other Title(s): "Otology and neurotology"
Can we have title variants appear in the journal picker?
Thanks!Work package 19Koosum Y RoochunKoosum Y Roochunhttps://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/886Tagger Export - The utility is excluding the duplicate files2020-01-06T10:37:43ZRakesh NambiarTagger Export - The utility is excluding the duplicate filesThe utility is excluding the duplicate files.
Refer the comments in #878 for more detail.
![image](/uploads/2ac0ac4f894c638d9de0276dc83e925e/image.png)The utility is excluding the duplicate files.
Refer the comments in #878 for more detail.
![image](/uploads/2ac0ac4f894c638d9de0276dc83e925e/image.png)Work package 19Audrey HamelersAudrey Hamelershttps://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/883Spaces in XML attributes cause silent errors2019-07-03T15:09:59ZPetra Smith JeglikovaSpaces in XML attributes cause silent errorsTable doesn't display in web preview but it does in pdf preview in EMS83497Table doesn't display in web preview but it does in pdf preview in EMS83497Audrey HamelersAudrey Hamelershttps://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/867File list carousel2020-01-06T10:37:40ZAudrey HamelersFile list carouselAllow us to cycle through attached images/files—It would be great for usability if there were arrow buttons allowing us move between images in the preview pane. (@davids @FranRogers)Allow us to cycle through attached images/files—It would be great for usability if there were arrow buttons allowing us move between images in the preview pane. (@davids @FranRogers)Work package 19Audrey HamelersAudrey Hamelershttps://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/841Searching GRIST API with backslashes in grant IDs fails2019-06-04T15:26:29ZMichael ParkinSearching GRIST API with backslashes in grant IDs failsThe funder 'Academy of Medical Sciences' use backslashes in their grant IDs. The GRIST API doesn't handle these well, and converts them to forward slashes in the response. E.g. CSF004\1001
https://europepmc.org/grantfinder/grantdetails?...The funder 'Academy of Medical Sciences' use backslashes in their grant IDs. The GRIST API doesn't handle these well, and converts them to forward slashes in the response. E.g. CSF004\1001
https://europepmc.org/grantfinder/grantdetails?query=pi:%22Church+D%22+gid:%22CSF004%5C1001%22+ga:%22Academy+of+Medical+Sciences%22
Searching for this grant will not give a hit.
The appropriate URL encoding is '%255c'.
Searching for 'DTF008%255c1002' gives the error `We're experiencing a problem with our grants search. Please try again later.`.
Could someone see if they can add 'Academy of Medical Sciences' grants successfully to a submission, and advise whether this is something that can be handled by the MSS, or whether the GRIST API needs fixing instead to handle backslashes.
Please note that searching by PI and adding the grant works correctly.XINGJUN PIXINGJUN PIhttps://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/827Activity Page - The blank row is displayed on the table for the manuscript `E...2020-01-06T10:53:17ZRakesh NambiarActivity Page - The blank row is displayed on the table for the manuscript `EMS90096`The blank row is displayed on the table for the manuscript `EMS90096`. I just deleted the files like PDF, HTML, NXML and one supporting file and clicked the `Process` button again.
![image](/uploads/c34a442e8b5f1d70803c3d582aee4da0/imag...The blank row is displayed on the table for the manuscript `EMS90096`. I just deleted the files like PDF, HTML, NXML and one supporting file and clicked the `Process` button again.
![image](/uploads/c34a442e8b5f1d70803c3d582aee4da0/image.png)https://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/803Embargo period compliance2019-08-01T07:34:11ZLynne FaulkEmbargo period complianceWe had an issue a while back, where a user was confused about what date to measure his embargo date from, and we were equally confused about what constitutes the publication date. This conversation is recorded in the now-archived mss-ui-...We had an issue a while back, where a user was confused about what date to measure his embargo date from, and we were equally confused about what constitutes the publication date. This conversation is recorded in the now-archived mss-ui-feedback Slack channel. We ended with the following discussion. Was this ever resolved? It's not clear to me.
audrey [15:51]
I have an objection
@michele @lynne what you've changed the message to is not, as far as I am aware, what the system actually DOES (edited)
michele [15:56]
So what happens now?
In the live system?
franrogers [15:57]
ah, I think the user is confused
thanks God
As stated in Section 3.5 (i) of the RCUK policy, “where the RCUK OA block grant is used to pay Article Processing Charges for a paper, the paper must be made Open Access immediately at the time of on‐line publication, using the Creative Commons Attribution (CC BY) licence - https://www.ukri.org/files/legacy/documents/rcukopenaccesspolicy-pdf/.”
To be compliant, the MRC also requires all publications to be deposited in Europe PubMed Central (PMC) (https://europepmc.org/) at the earliest opportunity, and certainly within 6 months of publication. Being available on the publisher’s website is not sufficient to be compliant. For further information, please see section 9.2 of the RCUK Policy on OA - Frequently Asked Questions
europepmc.org
Europe PMC
Europe PMC is an archive of life sciences journal literature.
so
If it is gold OA it has to be OA at time of online publication (edited)
if it’s in EPMC they just use publication
audrey [15:59]
@michele the release delay is calculated from the print publication date—except for Nature publications, where they send us a list of exact embargo dates and we use those (It's not clear exactly how those are calculated by them) (edited)
franrogers [15:59]
for Nature it is ePub date of final version
I believe
audrey [15:59]
Right but it doesn't necessarily line up with the epub date in our system
franrogers [16:00]
true
michele [16:07]
Ok, so going back to @franrogers comment earlier, “we are probably inherently non-compliant on the online publication thing, unless we are chatting VoR online rather than ePub ahead of print”
I’m not sure how to resolve this confusion for users where they (or their authors) are funded by an organisation who has a policy such as UKRI.
Hopefully it is not a biggie.
franrogers [16:08]
well we have to wait for the PubMed publication date
and I am not sure when that is in existencehttps://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/802Non-author admin often review manuscripts2019-08-01T07:34:19ZLynne FaulkNon-author admin often review manuscriptsAdmin type users who are responsible for submitting manuscripts for a number of authors, sometimes find themselves responsible for approving those manuscripts. They are concerned the language in our submission system makes it clear that ...Admin type users who are responsible for submitting manuscripts for a number of authors, sometimes find themselves responsible for approving those manuscripts. They are concerned the language in our submission system makes it clear that they shouldn't be doing this, but they don't see a way around it, and don't think their authors would ever get around to approving the manuscripts. What should we do about this?https://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/800File upload - how is bibliography labeled?2019-08-01T07:34:38ZLynne FaulkFile upload - how is bibliography labeled?During the file upload process, the user was unsure what file type to assign the Bibliography document. When this section is remade, perhaps we need to clarify this with the copy.During the file upload process, the user was unsure what file type to assign the Bibliography document. When this section is remade, perhaps we need to clarify this with the copy.https://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/797Progress saved indicator and Cancel buttons not found quickly2019-08-01T07:34:33ZLynne FaulkProgress saved indicator and Cancel buttons not found quicklyNeither the Progress saved indicator nor the Cancel button was found very quickly when users were asked to find them. The positioning does not seem to be intuitive, users seemed to look for the progress saved indicator near the call to ...Neither the Progress saved indicator nor the Cancel button was found very quickly when users were asked to find them. The positioning does not seem to be intuitive, users seemed to look for the progress saved indicator near the call to action buttons at the bottom, and the cancel the function at the top. We didn't do this initially because Hindawi had used the layout we currently use. I think reversing them is probably worth trying.https://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/796Citation label causes slight confusion2019-08-01T07:33:10ZLynne FaulkCitation label causes slight confusionI have brought this issue up before, but a user brought it up unprompted, and my observations of users is that although it's not a big deal, it causes slight confusion at the beginning of the process. It would be good to have a short dis...I have brought this issue up before, but a user brought it up unprompted, and my observations of users is that although it's not a big deal, it causes slight confusion at the beginning of the process. It would be good to have a short discussion about it to discuss our options.
The first stage of the submission process is labeled "Citation." While our users will know this term, it's not plain language, and not always clear why it's called that or needs to be found at this point, while "Title" makes more sense to people. I know Audrey you said that the label "Title" is incorrect in this context so we may not be able to use that. But I think its worth discussing because one user said he was taken aback by the word "Citation" and said it was not as classic as say something like "Title". Also, when NCBI did their show and tell, "Title" was the label they used for this initial stage.https://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/794User session management problems2020-01-06T10:37:11ZAudrey HamelersUser session management problemsWhen a user's session has ended, the page still allows user actions, but then loads forever, or comes back with mysterious error messages. Here's one example (I will put in more as I come across them again):
![Screenshot_2019-05-17_at_0...When a user's session has ended, the page still allows user actions, but then loads forever, or comes back with mysterious error messages. Here's one example (I will put in more as I come across them again):
![Screenshot_2019-05-17_at_09.51.00](/uploads/a0b4738f2d20ef38df983ee6de1cae1c/Screenshot_2019-05-17_at_09.51.00.png)
There is no clear indication to the user that they are no longer logged in and that that is the cause of their problem—it appears that something is wrong with the system. It would be much better if the page would refresh back to the login screen once a user session has ended.Work package 19Yuci GouYuci Gouhttps://gitlab.coko.foundation/xpub/xpub-epmc/-/issues/776Site does not load in IE112020-01-06T10:49:31ZAudrey HamelersSite does not load in IE11Work package 19Yuci GouYuci Gou