qbicsoftware/data-manager-app

A web-based life science omics and imaging data management solution

data-manager-app's Issues

`please provide a name` appears 2 times when selecting a PI

Provide a notification based feedback system

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

• Project creation and editing
• Experiment creation and editing
• Experimental variables creation and editing
• Experimental groups creation and editing
• Offer upload and remove
• QC upload and remove
• PAT token creation, copying and deletion
• Project Access person add and remove (also email notifications for the same)
• Sample batch add, update, remove
• Sample batch dialog add, remove row
• Measurement register, edit, delete
• Measurements - RAW data available

Warning notifications (Dialogs)

Usage: To warn the user of potential risks that may arise during an interaction.

• Confirmation msgs on delete Sample batch
• Confirmation msgs on delete PAT
• Confirmation msgs on delete measurement

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.

Experiment Information is editable even if samples are registered

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.

Add project identifier to downloaded files

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 urls file in Download Raw Data
• download measurement metdata file ngs in View Measurements
• download measurement metadta file proteomics in View Measurements
• download sample metadata in 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.

Move from the spreadsheet component for sample batch registration to .XLSX upload

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.

I do not want to get emails for everything that happens on projects.

Is your feature request related to a problem? Please describe.
Please make it possible to mute projects or unsubscribe from notificaitons!

Please add `technical replicate` to proteomics measurement metadata

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.

Add information on how to enter experimental variables

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

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?

View ORCID in user profile

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.

I cannot edit my measurements

Describe the bug
A clear and concise description of what the bug is.

To Reproduce
Steps to reproduce the behavior:

1. Download template
2. add measurement information
3. register measurement using the filled out template
4. edit information in the excel
5. upload the excel
6. error unknown measurement id

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.

When having a lot of experimental variables in an experiment I have to scroll to the right

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:

1. Add a lot (>15) experimental variables
2. You have to scroll to the right

Expected behavior
The variables are in multiple rows.

Screenshots

Smartphone (please complete the following information):

• Version data manager 1.2.3

Unclear next steps after measurement registration

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.

Sample and Batch Page should be in accordance with figma mockup

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.

Enhance XLSX templates with examples for expected properties

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.

Project list overlaps with footer

Describe the bug
Project overview cards are overlapping with the footer.

To Reproduce
Steps to reproduce the behavior:

1. Log in
2. Reduce the window height
3. See error

Expected behavior
The project overview items not overflowing to the footer

Screenshots

Desktop (please complete the following information):

• OS: macOS
• Browser: Firefox 127.0

Additional context

Please make it more clear that some fields are there to search for specific entities and can't be used as a drop-down.

Hi there, both in Firefox and Chromium I am stuck at 4 Experimental Information.
The drop-down lists for Species, Specimen, Analytes do not appear even when I frantically click on them. But they are mandatory.

Best,
Simon

PS: A screenshot of where I got stuck:

issue when running TD-0350

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.

Measurement Registration file could not be read

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:

1. Save as UTF-8
2. Upload measurement file for registration
3. Get an error.

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.

Support XLSX upload for measurement metadata registration / update

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.

Testissue

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.

Search for other users by their fullname

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.

Confirm cancel or abort actions

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.

German umlaut not encoded in UTF-8 when sending the confirmation email

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:

1. Register as a user with umlaut in the full name, e.g. "Svän Bäm"

Expected behavior
The umlauts are encoded in UTF-8

Screenshots

The user should get notified about RAW data availability via email and in-app notifications

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.

Improve "Prefill Spreadsheat" feature to account for more permuations

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

Preserve the ontology term CURI when downloading metadata

Is your feature request related to a problem? Please describe

We go along the road of being precise by using ontology terms, but then dont provide the CURI when downloading metadata.

Describe the solution you'd like

Provide the CURI next to the term, e.g. metagenomes [NCBITaxon:408169] in the cells when downloading metadata in the app.

Authentication cookies do not prevent CSRF attacks

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.

Improve experimental groups visualisation for complex setups

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

Editing registered metadata to add confounding variables

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.

Please cache project creation progress

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.

Visualization problem in "Cancel Edit Project Information"

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:

1. Go to a Project
2. Click on Edit Project Information
3. Click on Cancel
4. See error

Expected behavior
Both options should be clearly visible.

Screenshots

Desktop

• MacOs Sonoma 14.5
• Firefox 128.0 (64-Bit)
• Build on qpylon/dev

Inform user on reason for password invalidity during password reset

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:

1. Progress the password reset process until a new password can be specified.
2. In this New Password screen input a password string that is invalid (e.g. due to length being too short)
3. The data manager application will show a general exception error message instead of specifying to the user why the provided password is invalid.

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.

Screenshots

Desktop (please complete the following information):

• MacOs Sonoma 14.5
• Firefox 127.0.2 (64-Bit)
• Build on qpylon/dev

When having a lot of experimental groups in an experiment I have to scroll to the right

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:

1. Add a lot (>10) experimental groups
2. You have to scroll to the right

Expected behavior
The variables are in multiple rows.

Screenshots

Smartphone (please complete the following information):

• Version data manager 1.2.3

Modify error list in Register Measurements dialog

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"

`timsTOF fleX MALDI-2` not found in ontology search

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.

Visualization of End users' affiliation and e-mail

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.

Delete Session Cookies on Session Invalidation

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?

I want to link my affiliation to my profile

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.

Improvement of UI for upcoming sprint release

What happened?

• Sorting breaks for sample name
  Go to Register sample batch; Sort sample name multiple times
• Placeholder in project user management
  In the search box for users change the placeholder from please search for username to please search for username or fullname or ORCiD
• Font size change in project user management
  Make the fullname the same size as the username (but not bold)
• Measurement selection information moves view
  When selecting measurements, the buttons in the view jump;Move the selection information below the separator to the grid

What browsers are you seeing the problem on?

No response

Relevant log output

No response

Link ORCiD to existing account

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.

Provide user groups

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.

Define the term `Organism Id`

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.

Favor sample name over sample label

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.

Filter ontology term suggestions by ontology during experiment creation

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.

Possibility to download the project information

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.

I can't create a new project

Please see the screenshot

unfortunately, it does not tell me, what is going wrong