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View Code? Open in Web Editor NEWA web-based life science omics and imaging data management solution
License: MIT License
A web-based life science omics and imaging data management solution
License: MIT License
Is your feature request related to a problem? Please describe.
Currently the users are not informed in a harmonized way. Notifications are shown sometimes on top and on the bottom left. This concerns the following notifications (Thanks SP for collecting):
Success notifications (Toasts)
Usage: Triggered after successful completion of each task
Warning notifications (Dialogs)
Usage: To warn the user of potential risks that may arise during an interaction.
Information notifications (Dialogs)
Confirmation msg on dialog cancellation
cancel project creation
cancel project editing
cancel experiment creation
cancel experiment editing
cancel exp. variable creation
cancel exp. variable editing
cancel sample batch registration
PAT copy
TSV conversion in dialogs (Register and Edit measurements)
Error Notifications
Usage: To inform users of critical issues and guide them to resolution.
File upload : exceeding size, improper TSV, technical errors (DB, network, etc)
Editing experiment design after samples are registered.
Deleting measurements when no item is selected.
Describe the solution you'd like
Notifications are shown as "toast" notifications with a clear warning/error/success indication instead of stacking on top of each other
Describe alternatives you've considered
There is no alternative!
Additional context
To see an example: This is already done after experimental group registration to guide the user to the sample registration.
Describe the bug
Currently experiment details such as species, specimen and analyte are editable even though samples have been registered.
This means that a user can remove the species even though it has been associated with a sample, which leads to an inconsistent state.
To Reproduce
Steps to reproduce the behavior:
In Design Experiment, after samples are registered, click on "edit experiment" and remove the selected species and add another, click on save and it still saves the new species.
Expected behavior
Species, Specimen and Analyte are not editable after samples have been registered.
Is your feature request related to a problem? Please describe.
When downloading the following files for multiple projects, I get confused as they are called the same.
Download Raw Data
View Measurements
View Measurements
Register Sample Batch
Describe the solution you'd like
Simply prefix the file names with the project so I know for which projects they were downloaded.
Is your feature request related to a problem? Please describe.
The spreadsheet component has proven to be less usable after some user testing since it has limited functionality as compared to excel sheets and is cumbersome to maintain.
Describe the solution you'd like
Measurement registration via .XLSX sheet upload is tested to be a rather easy-to-use and preferred way of metadata handling. It can also be extended for registering sample metadata.
Is your feature request related to a problem? Please describe.
Please make it possible to mute projects or unsubscribe from notificaitons!
Is your feature request related to a problem? Please describe.
As the proteomics labs switched their process and do always do technical replicates now, we want this information in the measurement metadata. The technical replicate column can be optional and freetext but should be one of the first columns so measurements can easily be identified.
Describe the solution you'd like
Add technical replicates to the proteomics measurement metadata.
Describe alternatives you've considered
Add information on technical replicates to the comment column. As this column is one of the last columns, it is not very helpful if I want to identify my measurement as a lab person.
Is your feature request related to a problem? Please describe.
As a person working in the lab, when I want to enter experimental variables, I do not know how enter multiple levels.
Describe the solution you'd like
Describe somewhere that each row is one level or help me out here.
Describe alternatives you've considered
Provide multiple fields where I can enter experimental variables.
Provide an option for me to decide how to split my input.
Additional context
Adding levels with a list like one, two, three
leads only to one level in the variable.
the app claims project QBERT already exists, but when I search for it on the HOME page, it does not appear
So what to do?
Is your feature request related to a problem? Please describe.
If my data manager account is already connected with an ORCID, I want to see it in my user profile overview.
Describe the solution you'd like
A visual indication that on ORCID is connected to the account, as well as the ORCID itself as confirmation.
Describe the bug
A clear and concise description of what the bug is.
To Reproduce
Steps to reproduce the behavior:
Expected behavior
I can upload my original excel. Otherwise I need to have multiple excel file on my computer. This confuses me and is additional work I do not think is necessary.
Alternatively let me know that I uploaded/and probably edited the wrong file.
Additional context
I use a local excel file to have an overview over my measurements and the steps in my experiment. I want to upload that file instead of always copying information to a new file.
Describe the bug
When adding a lot of experimental variables I have to scroll to the right to see all of them.
To Reproduce
Steps to reproduce the behavior:
Expected behavior
The variables are in multiple rows.
Smartphone (please complete the following information):
Is your feature request related to a problem? Please describe.
Currently, after measurement registration, when I go to the next step Raw Data
, I get directed back to measurement registration. It would be great to get some information on how to proceed here.
Describe the solution you'd like
You could provide information on how to upload data to the data manager instead of taking me back one step.
Describe alternatives you've considered
Show a message with detailled instructions on the raw data page when I never did the step before.
Additional context
Raw data upload does not happen in the data manager so I do not know what happens next.
Is your feature request related to a problem? Please describe.
The current design of the sample main component is outdated.
Describe the solution you'd like
The sample main component looks similiar to the measurement main component and as drafted in the figma prototype.
Describe alternatives you've considered
No alternative for now.
Additional context
Add any other context or screenshots about the feature request here.
Is your feature request related to a problem? Please describe.
Some properties in e.g. the NGS measurement template are not very straight forward to understand, what the required values look like.
Describe the solution you'd like
An additional column with examples in the template. Also, for the ontology CURI it would be very helpful to link the ontology lookup service.
Describe the bug
Project overview cards are overlapping with the footer.
To Reproduce
Steps to reproduce the behavior:
Expected behavior
The project overview items not overflowing to the footer
Desktop (please complete the following information):
Hello QbicSoftware. We bought and used Qbic TD-0350. But right now we can't connect to NFC and control the Light. All results return: Not Supported
Hope you help. Thanks.
Describe the bug
For some users the measurement registration sheet could not be read. This was caused by the encoding chosen for the file. While UTF-16
was required some do not know or cannot save in UTF-16
and try using UTF-8
encoding. This should be checked by us.
To Reproduce
Steps to reproduce the behavior:
UTF-8
Expected behavior
Get an error helping you to save it as UTF-16
or accept UTF-8
as well.
Additional context
Add any other context about the problem here.
Is your feature request related to a problem? Please describe.
The export of XLSX to UTF-16 is just another step the user gets confronted with alerts and warnings about the information loss, etc. Also, it offers a lot of room for errors, since the users are overwhelmed with export file format options.
Describe the solution you'd like
Support the upload of the downloaded template or the downloaded metadata for updates.
Is your feature request related to a problem? Please describe.
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
Describe the solution you'd like
A clear and concise description of what you want to happen.
Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.
Additional context
Add any other context or screenshots about the feature request here.
Is your feature request related to a problem? Please describe.
Usernames can be all funny combinations of characters, people think of. Identifying users as the actual person, you want to collaborate with, can be a challenging task then.
Example: user's username is "researchCat007". You dont know who this person is. Exchanging that information with several collaborators can become very cumbersome for project managers and thus increases frustration easily.
However: Full names fall under the protection by the GDPR, since they are Art 6 data. In order the use them within the platform, we need to adjust the data privacy agreement.
Describe the solution you'd like
Render the actual user full name next to the username, and enable the search for both. Bonus points: Enable search by the ORDiD and render the ORCiD (with URL to the public ORCiD entry!).
Describe alternatives you've considered
No alternative imo.
Additional context
Add any other context or screenshots about the feature request here.
During processes in a dialog window, users can close the dialog by hitting the ESC key and sth. even when clicking outside of the dialog.
An enhancement can be to provide a confirm modal, so users can prevent accidental dialog window closings.
Describe the bug
When providing umlaut in the user full name during registration, the email confirmation mail can not decode it.
To Reproduce
Steps to reproduce the behavior:
Expected behavior
The umlauts are encoded in UTF-8
Is your feature request related to a problem? Please describe.
Currently the user can be informed about the availability of RAW data only through the RAW data status column (to be implemented) in the measurements view. But this is not enough as it is important for the user to know when the RAW data attached to their measurements is available for download and the column could be overlooked.
Describe the solution you'd like
The user can be explicitly informed via a toast notification in the app and an email notification in addition to the RAW data status column in the measurements tab.
@KochTobi mentioned that technically this is not straightforward and needs further investigation into how this notification can be triggered. The status information can be retrieved from the openbis but since the data manager is not aware of when the RAW data upload happens on the sftp server, it is not pushed to the data manager.
Is your feature request related to a problem? Please describe.
Not all permutations are currently considered when registering a sample batch in case of multiple analytes present.
Describe the solution you'd like
Might be nice to have permutations also with analytes, that seem to be not considered right now (my imaginary example had DNA & RNA, and I wanted DNA and RNA analyzed for each sample
We go along the road of being precise by using ontology terms, but then dont provide the CURI when downloading metadata.
Provide the CURI next to the term, e.g. metagenomes [NCBITaxon:408169]
in the cells when downloading metadata in the app.
Is your feature request related to a problem? Please describe.
For every successful authentication, the app currently stores the SESSION-ID in a cookie on the client. The cookie's SameSite
parameter is set to None
though, which allows attackers to intercept e.g. credentials via foreign domain forms.
Read https://owasp.org/www-community/SameSite for more information.
Describe the solution you'd like
Set SameSite
property to at least lax
.
Describe alternatives you've considered
none.
Additional context
The lax setting should still allow the usage of links to our data management ressources while not enforcing users to re-login if they are already authenticated. This maintains the UX while increasing the mitigation against CSRF attacks afaik.
Is your feature request related to a problem? Please describe.
When having many groups the visualisation was not easy to see, I had one row (over 2 screens) with many imaginary combinations (3 columns, 2x3x3 factors, e.g. 2 treatments, 3 timepoints, 3 genotypes/environments). But maybe 2x3x3 is too much anyway for that view.
Describe the solution you'd like
Maybe would be nice to have in several rows (to scroll down instead of to the right
Is your feature request related to a problem? Please describe.
I would like to be able to add confounding variables to already registered samples.
Describe the solution you'd like
After registration of a batch, it would be nice to be able to add confounding variables (ex. age, sex, BMI, cell culture medium, etc.) when editing the metadata of the batch.
Describe alternatives you've considered
At the moment the information can only be added as a comment, but it would be better to have it as a separate column. The new columns could be added through the browser editing function or, if not possible, by downloading the metadata as txt and uploading it with the additional columns.
When I am in the middle of creating a project and I accidentally press ESC, I have to restart the whole process again. None of my information already entered is saved.
Hi all!
Describe the bug
There is a little visualization problem in the “discard changes” window from the Edit Project Information (see image). Not all options are fully visible.
To Reproduce
Steps to reproduce the behavior:
Expected behavior
Both options should be clearly visible.
Desktop
Describe the bug
If an invalid password is provided as a to be set password during password reset the user is shown a general exception instead of being informed on why the provided password is invalid.
To Reproduce
Steps to reproduce the behavior:
Expected behavior
The user is informed about the reason why the provided password is too short instead of being shown a general application error. Ideally below the password setting textfield similiar to how it's done during user registration.
Desktop (please complete the following information):
Describe the bug
When adding a lot of experimental groups I have to scroll to the right to see all of them.
To Reproduce
Steps to reproduce the behavior:
Expected behavior
The variables are in multiple rows.
Smartphone (please complete the following information):
Is your feature request related to a problem? Please describe.
The errors in the measurement registration dialog are not specific and don't help the user to recognise the issue.
Describe the solution you'd like
The errors should follow a common format:
Column header of the column containing the error : The error message. Solution suggesting an example of correct input.
For e.g.,QBiC Sample ID : Unknown sample with sample ID "Test". QBiC Sample ID should be in the format Q98KK007A1.
The error list must be a scrollable list after it exceeds a maximum of 4 entries.
Increase the dialog size to increase the spacing and readability of the information.
Additional context
#DM1178
Example: Users edit without measurementId -> for every measurement there is an error no measurement id found. It would be better to see a list of errors "measurement column missing" or "measurement not found"
Is your feature request related to a problem? Please describe.
It was noted that the instrument timsTOF fleX MALDI-2
was not found in our ontology search.
https://ontobee.org/ontology/MS?iri=http://purl.obolibrary.org/obo/MS_1003397
Describe the solution you'd like
The instrument to be included in our ontology search.
Describe alternatives you've considered
Using the more general type described in the ontology.
I have some cases, where the End-Users E-mail has changed either because they got married (women sometimes take the family name of the husband) or because they changed affiliation. This change affects the project management because it breaks communication and also makes difficult the invoice submission.
It would be very useful if the end user is allow to update his/her E-mail and affiliation in their profile and that the Project managers can visualize the updated information.
The HA proxy functions on the session cookie. As vaadin updates the cookie content but not recreates the cookie itself, the draining does not work currently. Only expired cookies lead to a switch away from a drained node.
Is there a way to delete the cookie and re-create it instead of changing its contents?
Is your feature request related to a problem? Please describe.
As a scientist I have an interest in having my affiliation linked to my profile. This could be super helpful in auto-filling my measurement registration sheets (as it is always the same for the place I work at).
It would be great to add the affiliation to my profile.
Describe the solution you'd like
Having a list of affiliations with organisation I am affiliated with in my profile. Use this list when suggesting possible entries for the measurement sheet I upload to register a measurement.
Describe alternatives you've considered
Allow me to store favorite ROR ids somewhere.
Additional context
Add any other context or screenshots about the feature request here.
Register sample batch
; Sort sample name multiple timesplease search for username
to please search for username or fullname or ORCiD
No response
No response
Is your feature request related to a problem? Please describe.
I already have an account that I created with my email and password. I also have an ORCiD. How do I link that ORCiD in my account so that other can see it and find me on ORCiD as well?
Describe the solution you'd like
I need a way to add the orcid to my profile.
Describe alternatives you've considered
None. I do not have any suggestion on how to implement it. I only want to have the opportunity to link the account and login with my ORCiD.
Is your feature request related to a problem? Please describe.
When managing recurring projects with access to the same group of people, it would be simplify the access management, when I can add a user group instead.
Describe the solution you'd like
No idea yet.
Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.
Additional context
Add any other context or screenshots about the feature request here.
Is your feature request related to a problem? Please describe.
For some users it is unclear what is meant by organism id
in the sample batch registration step.
Describe the solution you'd like
Remove the organism id or rename it.
Describe alternatives you've considered
Add a definition and intended use of the organism id to the documentation and teach users about it.
Additional Context
For some users it was clear what was meant by organism id and they used it to differentiate between orignin individuals of their samples.
TL;DR:
Researchers seem to favor the expression "sample name" over "sample label" for what they call their custom sample label printed/written on the tubes.
This feature was originally requested by Daniel S.
Is your feature request related to a problem? Please describe.
Not all ontology terms are relevant for the researchers current use case, when creating an experiment. At the same time, the system cannot make any assumptions yet (e.g. based on keywords in the title or project description)
Describe the solution you'd like
Might be good to be able to select one particular ontology, e.g. if I work with environmental samples I would know I'd like to use ENVO.
Hello!
Is your feature request related to a problem? Please describe.
In some of the downstream analysis reports we need to provide project information, like project title, PI and contact at QBiC. At the moment there is no possibility to download this data from the Data Manager in a table format.
Describe the solution you'd like
I would like to have a feature like the User Database - Download Project Information that we currently have in the qPortal.
Describe alternatives you've considered
Manually copy and paste the information on tables, however this is very cumbersome.
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