https://emx2-conception.test.molgenis.org/Conception/tables/#/
doesn't result in error but silently not showing anything
v6.7.1

Describe the bug
When I try to export a separate table in .csv a file without extension is returned.

To Reproduce
Steps to reproduce the behavior:

1. Go to https://emx2-catalogue.test.molgenis.org/LifeCycle4/updownload/
2. Download any table under 'Export specific tables:' as csv
3. a file without extension is downloaded.

Desktop (please complete the following information):

• OS: [e.g. iOS] Windows 10
• Browser [e.g. chrome, safari] chrome
• Version [e.g. 22] 5.31.0

What version of EMX2 are you using (see footer)
6.5.9

Describe the bug

internal server error Error: Cannot invoke "String.equals(Object)" because the return value of "org.molgenis.emx2.web.MolgenisSession.getSessionUser()" is null: {"response":{"errors":[{"message":"Cannot invoke \"String.equals(Object)\" because the return value of \"org.molgenis.emx2.web.MolgenisSession.getSessionUser()\" is null"}],"status":400},"request":{"query":"{_session{email,roles},_settings{key,value},_manifest{ImplementationVersion,SpecificationVersion,DatabaseVersion}}"}}

To Reproduce
Steps to reproduce the behavior:

1. Use the app
2. leave the tab open fore some time
3. go back to using the app
4. See error

Expected behavior
No error , time out msg if appropriate

Screenshots

Desktop (please complete the following information):

• OS: mac
• Browser chrome

Additional context
removing the cookies resolves the issue

What version of EMX2 are you using (see footer)
6.7.4

Describe the bug
When you click on 'Catalogue' you shortly see 'You have to login to view the data' before the Catalogue appears.

To Reproduce
Steps to reproduce the behavior:

1. Go to 'https://emx2.test.molgenis.org' or 'https://data-catalogue.molgeniscloud.org/'
2. Click on 'Catalogue'
3. See error

Expected behavior
I expect to go to the Catalogue immediately.

Describe the bug
When you export an abstract table (e.g. OntologyTerms, Resources, AllVariables), the file is empty.

To Reproduce
Steps to reproduce the behavior:

1. Go to https://emx2-catalogue.test.molgenis.org/LifeCycle4/updownload/
2. Download the whole dataset or specific tables in Excel. The tables OntologyTerms, Resources or AllVariables appear empty, while they are not empty when viewing the data under 'Tables'

Expected behavior
I expect to get an export with the information that I see when I go to the specific tables themselves in the Table view.

• OS: [e.g. iOS] Windows 10
• Browser [e.g. chrome, safari] chrome
• Version [e.g. 22] 5.31.0

See title.

Describe the bug
Cannot upload downloaded model

To Reproduce
Download the schema
some time later ( for example 19 days )
Upload the schema

Expected behavior
Schema is uploadend without errors

or

Message is show that model version is incompatible

What version of EMX2 are you using (see footer)
6.8.0

Describe the bug
While browsing the catalogue i get the message "You have to login to view the data."
I can no longer view any data

To Reproduce
Steps to reproduce the behavior:

1. Go to 'https://emx2.dev.molgenis.org/'
2. Catalogue_test
3. click the molgenis logo top left

Expected behavior
See the catalogue data or an ui element that guides me towards the data

What version of EMX2 are you using (see footer)
6.10.0

Describe the bug
After being on the system for some time I loose the ability to view or edit data. Also customers are bugged by this issue. If you delete cookies the system is functional again.

To Reproduce
Steps to reproduce the behavior:

1. Go to 'https://emx2.test.molgenis.org' or 'https://data-catalogue.molgeniscloud.org/'
2. Click on 'UMCG Data Catalogue' in test or catalogue in data-catalogue
3. Open the Catalogue, click on cohorts, try to add a cohort via forms or edit a cohort (not necessary to save anything), keep forms open (do not know if this is necessary), or just view a cohort
4. Wait a while (5 min may be enough)
5. Return to the web browser and click on Catalogue
6. You will get the message: "You have to login to view the data."
7. You will still be able to view data under 'Tables', but editing is not possible anymore.
8. If you delete cookies or log in you are able to view and edit again.

Expected behavior
I expect being able to edit and view the data. Especially since this is a public database, and for now settings are set so that everyone can edit.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: windows 10
• Browser [e.g. chrome, safari] chrome
• Version [e.g. 22]

Additional context
This was reported and discussed before.

Describe the bug
When downloading all tables in xlsx or csv the metadata of empty tables is not exported.

To Reproduce
Steps to reproduce the behavior:

1. Go to https://emx2-catalogue.test.molgenis.org/LifeCycle4/updownload/
2. Click on Export all data as Excel
3. See empty tabs, e.g. 'Prompts', 'Status'.

Expected behavior
I expect to get an exports with all tables (in separate csvs or in Excel tabs) and all column names for these tables if the tables are empty.

Desktop (please complete the following information):

• OS: [e.g. iOS] Windows 10
• Browser [e.g. chrome, safari] chrome
• Version [e.g. 22] 5.31.0

What version of EMX2 are you using (see footer)
6.7.1
Describe the bug
After first being able to see data in the Catalogue app, the data is not visible anymore.

To Reproduce
Steps to reproduce the behavior:

1. Go to https://emx2.test.molgenis.org/UMCG%20Data%20Catalogue/catalogue/#/
2. Wait a while
3. Click on Catalogue
4. Unable to see data - you have to log in..... (also when schema is public...)

Expected behavior
Still being able to see data

• right format
• rotation

What version of EMX2 are you using (see footer)
7.4.1

Describe the bug
When two schemas have identical names but different capitalization, their user permissions are shared.

To Reproduce
Steps to reproduce the behavior:

1. Go to 'https://data-catalogue-staging.molgeniscloud.org/'
2. Click on 'testcohort'
3. Add a user via settings
4. See user back in 'testCohort' settings
5. Try to delete either one of the databases, get error message.

Expected behavior
I expect user permissions to be separated for separate schemas. I expect to be able to delete either one of the databases.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Browser [e.g. chrome, safari]
• Version [e.g. 22]

Smartphone (please complete the following information):

• Device: [e.g. iPhone6]
• OS: [e.g. iOS8.1]
• Browser [e.g. stock browser, safari]
• Version [e.g. 22]

Additional context
Add any other context about the problem here.

Is your feature request related to a problem? Please describe.
In forms, the appearance of datatype ref and ref_array are different. When you need to select an item of a ref, a pop-up screen appears, for a ref_array there is a checkbox. The checkbox is handier and faster.

Describe the solution you'd like
I would like to be able to select an item of a ref datatype with a checkbox, or otherwise a dropdown.

see the difference between 'design' and 'collectionType' here https://emx2.test.molgenis.org/UMCG%20test/catalogue/#/cohorts

What version of EMX2 are you using (see footer)
6.9.1

Describe the bug
When a route includes a query param ( ?foo=bar) the bread crumb a the top of de app becomes a / b / c?foo=bar

To Reproduce
Steps to reproduce the behavior:

1. go to the tables app
2. select a table
3. add a filter
4. See breadcrumb path

Expected behavior
query param a not added to bread crumb

Screenshots

Zoekfunctie werkt soms ineens niet en werkt dan wel weer als je uitlogt.

Go to emx2 demo lifecycle schema
Create a zip from the files:
Keywords.csv
Variables.csv

import the zip:

Expected:

The data is successfully imported

Observed
Error during import , data is not imported

Sommige LifeCycle topics (in nieuwe EMX2 Catalogue model zijn dat keywords) zijn zinnen en soms staat er dan ook een komma in.
keywords met komma's erin worden wel goed ingeladen in de tabel Keywords, maar worden dan niet goed herkend bij het inladen in de tabel Variables

Describe the bug
No table data is shown

To Reproduce
Steps to reproduce the behaviour:

• Go to the tables menu item
• Select a table to view ( https://emx2-catalogue.test.molgenis.org/LifeCycle4/tables/#/Variables)
• Expected data , but nothing is shown

Expected behaviour
Table with data

Additional context
Version: 5.36.2

What version of EMX2 are you using (see footer)
6.7.0

Describe the bug
Variable detail alignment broken

To Reproduce
Steps to reproduce the behavior:
Go to the catalog
Go to the variable list
Unfold one of the variables

Expected behavior
Left alignment

Permissions do not get imported

To Reproduce

• Create cde schema
• Import
  emx2-cde-fdp-rml-compat-v2.xlsx
• Go to cde schema settings

Expected behavior

• anonymous is Viewer

Actual behavior

• No entry for anonymous

Version
5.25.0

What version of EMX2 are you using (see footer)
5.44.0

Describe the bug
The filters options does not show the selected filters.

To Reproduce
Steps to reproduce the behavior:

1. Go to 'https://emx2-conception.test.molgenis.org/ARS/tables/#/SourceVariables' (need to be logged in)
2. Click on 'filters'
3. Choose a few.
4. Filters are not applied.

Expected behavior
The table is refreshed an shows only the chosen columns.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS] win 10
• Browser [e.g. chrome, safari] chrome
• Version [e.g. 22]

Smartphone (please complete the following information):

• Device: [e.g. iPhone6]
• OS: [e.g. iOS8.1]
• Browser [e.g. stock browser, safari]
• Version [e.g. 22]

Additional context
Add any other context about the problem here.

Describe the bug
Missing tables after import, even though they are there

To Reproduce
Unsure. Happened a couple of times. A rough idea of what we did:

• Delete existing filled cde database.
• Create new cde database
• Grant Viewer permission to anonymous user
• Upload
  emx2-cde-fdp-rml-compat-v2.xlsx into the cde schema
• Go to the tables list
• sometimes nothing is present
• The tables suddenly appear if you repeat a combination of
  • refresh the tables list
  • go to the schema page
  • log out and log back in again

Expected behavior
The tables are there right away

Screenshots
If applicable, add screenshots to help explain your problem.

Version
5.25.0

What version of EMX2 are you using (see footer)
7.4.1

Describe the bug
Images from the molgenis guide (help) are missing for some databases (testcohort)

To Reproduce

• Go to: https://data-catalogue-staging.molgeniscloud.org/testcohort/docs/#/cat_general-information
• Figure 1 is not shown

Expected behavior

• Go to: https://data-catalogue-staging.molgeniscloud.org/apps/docs/#/cat_general-information
• Figure 1 is shown

What version of EMX2 are you using (see footer)
7.4.1

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

To Reproduce
Steps to reproduce the behavior:

1. Go to e.g. 'https://data-catalogue.molgeniscloud.org/catalogue/catalogue/#/cohorts/ELFE'
2. See error message; Error: Validation error of type FieldUndefined: Field 'linkageOptions' in type 'Cohorts' is undefined @ 'Cohorts/linkageOptions'

Expected behavior
Catalogue app and model should fit together

What version of EMX2 are you using (see footer)
documentation

Describe the bug
When following the development manual for setup after using yarn in the apps folder
I should also cd into styleguide and do yarn build there, else you get the following error

This dependency was not found:

* @mswertz/emx2-styleguide in ../node_modules/cache-loader/dist/cjs.js??ref--0-0!../node_modules/vue-loader/lib??vue-loader-options!./src/App.vue?vue&type=script&lang=js&, ../node_modules/cache-loader/dist/cjs.js??ref--0-0!../node_modules/vue-loader/lib??vue-loader-options!./src/components/ListTables.vue?vue&type=script&lang=js&

To install it, you can run: npm install --save @mswertz/emx2-styleguide

Expected behavior
Should be in de docs

Describe the feature request
I want to remove all the data from a table/entity so i can re-upload a new version of the data ( or just remove the data from the system).

To Reproduce
Sign in with right to 'delete' data in table x
navigate to a data table x
click a button to remove all rows of data in table x

and / or

Have endpoint / mutation to remove all rows from a table x, if client passes correct token

Expected behavior
System asks for confirmation ( api can assume auto confirm )
All the data rows are removed from the table / system
If data in the table is being referenced by another table, the system should warn about this and not remove the data (, or clear out the links, or remove the referenced rows (cascade delete) .)

Additional context
UI / Docs should make it clear what happens to data used in other tables.

** EMX2 version
v38.0

Describe the bug
Upload of LifeCycle4 example has slow variables upload (100 instead of 2000 items/sec)

To Reproduce
Steps to reproduce the behavior:

1. Go to emx2-catalogue.test.molgenis.org
2. Download Excel from LifeCycle4
3. Create new schema
4. Upload

Expected behavior
2000+ items/sec for the 'Variables'

How to reproduce:

Go to server: https://emx2-catalogue.test.molgenis.org/
Upload:

data csv file, with a semicolon separator

Expected behaviour:
Succesfull import of data
( or error message indicating semicolon separator is not supported )

Observed behaviour:
No data is imported

notes:
v5.17.0 krijg import 'succes', maar geen data in systeem

Is your feature request related to a problem? Please describe.
I'm always frustrated when I cannot find the right tab back in my web browser, because emx2 opens that many tabs.

Describe the solution you'd like
Less opening of new tabs

Describe alternatives you've considered
The alternative is already present: we can navigate the system via the breadcrumbs and the banner.

Additional context
Add any other context or screenshots about the feature request here.

Describe the bug
When trying to view the docs i get an error

To Reproduce
Steps to reproduce the behavior:

1. Go to https://emx2-catalogue.test.molgenis.org/
2. Click on 'Docs;
3. See error

Expected behavior
Expected to see the docs ( did not expect new tab)

Additional context
Version: 5.17.0 .

Describe the bug
Does not auto (hot)reload frontend in dev mode

To Reproduce
Run 'yarn serve' in one of the frontend apps.
Change some app code ( example change text in html element)

Expected behavior
Dev preview is updated to reflect changes (hot)reload

Actual behavior
Page needs to be fully reloaded by hand ( full page relaod)

Describe the bug
Build test should consistently pass or fail

To Reproduce
Create PR ( no backend changes)
org.molgenis.emx2.graphql.TestGraphqlDatabaseFields > testCreateAndDeleteSchema FAILED java.lang.AssertionError: expected:<8> but was:<9> at org.junit.Assert.fail(Assert.java:89) at org.junit.Assert.failNotEquals(Assert.java:835) at org.junit.Assert.assertEquals(Assert.java:647) at org.junit.Assert.assertEquals(Assert.java:633) at org.molgenis.emx2.graphql.TestGraphqlDatabaseFields.testCreateAndDeleteSchema(TestGraphqlDatabaseFields.java:41) 14 tests completed, 1 failed
Expected behavior
Backend test should always pass or fail ( no backend code it touched in PR)

Describe the bug
Export of the Catalogue model in Excel or csv contains duplicates. All duplicates are in tables that are extended tables of an 'abstract' table.

See highlighted in Excel:
extendedTables_duplicates_in_export.xlsx

Desktop (please complete the following information):

• OS: [e.g. iOS] Windows 10
• Browser [e.g. chrome, safari] chrome
• Version [e.g. 22] 5.31.0

What version of EMX2 are you using (see footer)
Inferred version: 6.7.5-SNAPSHOT

Describe the bug
org.molgenis.emx2.sql.TestGrantRolesToUsers > testRole FAILED
java.lang.AssertionError: expected:<0> but was:<1>
at org.junit.Assert.fail(Assert.java:89)
at org.junit.Assert.failNotEquals(Assert.java:835)
at org.junit.Assert.assertEquals(Assert.java:647)
at org.junit.Assert.assertEquals(Assert.java:633)
at org.molgenis.emx2.sql.TestGrantRolesToUsers.testRole(TestGrantRolesToUsers.java:145)

To Reproduce
Steps to reproduce the behavior:
gradle build

Expected behavior
All test succeed

Desktop (please complete the following information):

• OS: mac os
  Model Name: MacBook Pro
  Model Identifier: MacBookPro15,2
  Processor Name: Quad-Core Intel Core i5
  Processor Speed: 2,4 GHz
  Number of Processors: 1
  Total Number of Cores: 4
  L2 Cache (per Core): 256 KB
  L3 Cache: 6 MB
  Hyper-Threading Technology: Enabled
  Memory: 16 GB

What version of EMX2 are you using (see footer)
Software version: 6.5.6. Database version: 6.4.2.

Describe the bug
On emx2.dev.molgenis.org you cannot return to the schema overview when clicking Molgenis or in any other way.

To Reproduce
Steps to reproduce the behavior:

1. Go to 'https://emx2.dev.molgenis.org/apps/central/#/'
2. Click on any schema, you can now view the tables in this schema
3. Click on Molgenis, you can still view the tables in the schema and are not returned to 'https://emx2.dev.molgenis.org/apps/central/#/'

Expected behavior
Return to overview of all available schemas

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Browser [e.g. chrome, safari]
• Version [e.g. 22]

Smartphone (please complete the following information):

• Device: [e.g. iPhone6]
• OS: [e.g. iOS8.1]
• Browser [e.g. stock browser, safari]
• Version [e.g. 22]

Additional context
Add any other context about the problem here.

What version of EMX2 are you using (see footer)
6.1.1

Describe the bug
click on checkbox label does not select checkbox

To Reproduce
Steps to reproduce the behavior:

1. Go to https://emx2.dev.molgenis.org/lifecycle/catalogue/#/list/Institutions
2. Click on 'any checkbox label

Expected behavior
Check box should be (de)selected

Additional context
Previously fixes in: 0b54ab7
Reintroduced in: 89043b2

What version of EMX2 are you using (see footer)
6.5.4

Describe the bug
When a new data-set / data model is uploaded ( or 'large' data change) the application becomes broken ( session errors) while the data is being indexed ( 5 , 10 , 15 min maybe more )

To Reproduce
Steps to reproduce the behavior:

1. Go to server -> import
2. Import non trivial data set ( 30 + tables , 3000 records)
3. after import is done , click around in the app
4. pages are loaded with error messages or not al all and java error is shown

Expected behavior
App works , or user is notified that the app is down and asked to check back in n minutes

What version of EMX2 are you using (see footer)
6.10.0.

Describe the bug
Menu items set to 'editor' cannot be seen by users with editor or manager role

To Reproduce
Steps to reproduce the behavior:

1. Go to 'https://data-catalogue-staging.molgeniscloud.org/'
2. Log in as admin
3. Make a test user account with editor right for a schema of choice
4. Log in as this test user
5. You cannot see the up/download menu item
6. repeat with test user set to manager

Expected behavior
I expect to see menu items that should be visible for an editor role

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Browser [e.g. chrome, safari]
• Version [e.g. 22]

Smartphone (please complete the following information):

• Device: [e.g. iPhone6]
• OS: [e.g. iOS8.1]
• Browser [e.g. stock browser, safari]
• Version [e.g. 22]

Additional context
Add any other context about the problem here.

Describe the bug
Tests running in CI sometime fail (without code change)

for example:

Task :backend:molgenis-emx2-webapi:compileTestJava

Note: /home/jenkins/agent/workspace/molgenis_molgenis-emx2_PR-233/backend/molgenis-emx2-webapi/src/test/java/org.molgenis.emx2.web/TestWebApi.java uses unchecked or unsafe operations.

Note: Recompile with -Xlint:unchecked for details.

Task :backend:molgenis-emx2-sql:test FAILED

org.molgenis.emx2.sql.TestCompositeForeignKeys > testCompositeRefArray FAILED

Add user failed: duplicate key value violates unique constraint "pg_authid_rolname_index".Key (rolname)=(MG_USER_admin) already exists.: SQL [CREATE ROLE "MG_USER_admin" WITH NOLOGIN]; ERROR: duplicate key value violates unique constraint "pg_authid_rolname_index"

  Detail: Key (rolname)=(MG_USER_admin) already exists.

    at org.molgenis.emx2.sql.SqlDatabaseExecutor.executeCreateUser(SqlDatabaseExecutor.java:34)

    at org.molgenis.emx2.sql.SqlDatabase.lambda$addUser$4(SqlDatabase.java:212)

    at org.molgenis.emx2.sql.SqlDatabase.lambda$tx$8(SqlDatabase.java:324)

    at org.jooq.impl.DefaultDSLContext$3.run(DefaultDSLContext.java:615)

    at org.jooq.impl.DefaultDSLContext$3.run(DefaultDSLContext.java:612)

    at org.jooq.impl.DefaultDSLContext.lambda$transactionResult0$0(DefaultDSLContext.java:543)

    at org.jooq.impl.Tools$35$1.block(Tools.java:5242)

    at java.base/java.util.concurrent.ForkJoinPool.managedBlock(ForkJoinPool.java:3137)

    at org.jooq.impl.Tools$35.get(Tools.java:5239)

    at org.jooq.impl.DefaultDSLContext.transactionResult0(DefaultDSLContext.java:595)

    at org.jooq.impl.DefaultDSLContext.transactionResult(DefaultDSLContext.java:512)

    at org.jooq.impl.DefaultDSLContext.transaction(DefaultDSLContext.java:612)

    at org.molgenis.emx2.sql.SqlDatabase.tx(SqlDatabase.java:316)

    at org.molgenis.emx2.sql.SqlDatabase.addUser(SqlDatabase.java:212)

    at org.molgenis.emx2.sql.SqlDatabase.init(SqlDatabase.java:112)

    at org.molgenis.emx2.sql.SqlDatabase.<init>(SqlDatabase.java:83)

    at org.molgenis.emx2.sql.TestDatabaseFactory.getTestDatabase(TestDatabaseFactory.java:30)

    at org.molgenis.emx2.sql.TestCompositeForeignKeys.setUp(TestCompositeForeignKeys.java:25)



    Caused by:

    org.jooq.exception.DataAccessException: SQL [CREATE ROLE "MG_USER_admin" WITH NOLOGIN]; ERROR: duplicate key value violates unique constraint "pg_authid_rolname_index"

What version of EMX2 are you using (see footer)
6.7.4 (very old)

Describe the bug
After error described here #357 occurred and reloading the previous page in my web browser, the Catalogue option in the menu disappeared.

To Reproduce
Steps to reproduce the behavior:

1. Go to 'https://data-catalogue.molgeniscloud.org/'

2. Click on 'Catalogue', click on cohorts, view a cohort

3. wait a while (5 min may be enough)

4. return to web browser

5. Click on Catalogue, error described under #357 occurs

6. if you click on Molgenis logo, a 404 error is given
   

7. Return to previous page

8. Catalogue is not accessible anymore via the ribbon
   

Expected behavior
I expect navigation through the database to work properly and not give errors after reloading pages.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Browser [e.g. chrome, safari]
• Version [e.g. 22]

Smartphone (please complete the following information):

• Device: [e.g. iPhone6]
• OS: [e.g. iOS8.1]
• Browser [e.g. stock browser, safari]
• Version [e.g. 22]

Additional context
Add any other context about the problem here.

What version of EMX2 are you using (see footer)
6.7.1

Describe the bug
If you make a new schema and enter a description, the description does not show once the schema is made.

To Reproduce
Steps to reproduce the behavior:

1. Go to an emx2 server
2. Click on + to make a new schema/database
3. Fill out name and description
4. No description is visible

Expected behavior
I expect the description to be visible

Is your feature request related to a problem? Please describe.
When you upload your data and navigate to another window. Then navigate back to the upload the progress is gone. This encourages users to reupload the data which breaks the whole system.

Describe the solution you'd like
When you navigate back to the upload window you see the active upload and disable the upload function when a current upload is in progress

Additional context
Postgres is running out of memory when you upload a large data set twice.

What version of EMX2 are you using (see footer)
7.0.1

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

To Reproduce
Steps to reproduce the behavior:

1. Go to 'https://emx2.test.molgenis.org'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Browser [e.g. chrome, safari]
• Version [e.g. 22]

Smartphone (please complete the following information):

• Device: [e.g. iPhone6]
• OS: [e.g. iOS8.1]
• Browser [e.g. stock browser, safari]
• Version [e.g. 22]

Additional context
Add any other context about the problem here.

What version of EMX2 are you using (see footer)
5.41.0

Describe the bug
I uploaded molgenis.csv succesfully. Then I looked at schema but was empty. I had to logout/login to fix.

Expected behavior
I expected schema to be updated with the schema I just uploaded

What version of EMX2 are you using (see footer)
7.4.1

Describe the bug
I uploaded this schema:
cohort_model.zip

and some data
CohortDictionary_testCohort.xlsx

when I download the data, the column 'refSchema' is not correct anymore. It does not refer to CatalogueOntologies, but repeats the refTable column.
testcohort1627285922583.xlsx

Also, I am not able to edit columns that refer to CatalogueOntologies tables via forms.

To Reproduce
Steps to reproduce the behavior:

1. Go to 'https://data-catalogue-staging.molgeniscloud.org/', log in as admin
2. Create a new test schema
3. Upload model
   cohort_model.zip
   and data
   CohortDictionary_testCohort.xlsx
4. Download data and see column 'refSchema' for error.
5. Try to add variable via forms, it is not possible to add a keyword, error message: 'Table OntologyTerms not found'

Describe the bug
RDF export of id is wrong

To Reproduce
Steps to reproduce the behavior:

1. Upload fair genomes example file
2. Export to TTL
3. See http://purl.obolibrary.org/obo/NCIT_C154415 "http://purl.obolibrary.org/obo/HP_0000011";

Expected behavior
3. See http://purl.obolibrary.org/obo/NCIT_C154415 http://purl.obolibrary.org/obo/HP_0000011

What version of EMX2 are you using (see footer)
Software version: 6.2.0. Database version: 6.1.1.

Describe the bug
When loading large zip it seems to hang at and (while committing)

To Reproduce
Download and upload lifecycle example.

Expected behavior
Last step should not seem to hang but instead a message 'commiting all data' should be shown.
Unfortunately no way to know how long that takes but we could make time that goes up so user can see the server is still there

Screenshots

What version of EMX2 are you using (see footer)
7.4.1, also happens in 7.0.0 (test)

Describe the bug
The table AllVariables (or AllSourceVariables or AllTargetVariables) cannot be viewed most of the time. Sometimes it does load.

To Reproduce
Steps to reproduce the behavior:

1. Go to 'https://emx2.test.molgenis.org'
2. Click on 'Catalogue', table AllVariables
3. See variables appear or not, try again and see variables appear or not, etc.

Expected behavior
I expect to be able to view all variables all of the time.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Browser [e.g. chrome, safari]
• Version [e.g. 22]

Smartphone (please complete the following information):

• Device: [e.g. iPhone6]
• OS: [e.g. iOS8.1]
• Browser [e.g. stock browser, safari]
• Version [e.g. 22]

Additional context
Add any other context about the problem here.

What version of EMX2 are you using (see footer)
5.38.0
Describe the bug
When entering via forms of you click outside the form the form closes and the data is lost.

To Reproduce
Steps to reproduce the behavior:

1. Go to 'https://emx2-catalogue.test.molgenis.org/LifeCycle4/tables'
2. Click on a table
3. Start adding an entry with the plus sign
4. Click outside the form
5. The form disappears, data is not saved.

Expected behavior
The form stays on the screen.

Desktop (please complete the following information):

• OS: [e.g. iOS] windows 10
• Browser [e.g. chrome, safari] chrome
• Version [e.g. 22] 90.0.4430.212

In a single table csv export, I get string ids of the shape 1.0, 2.0, 3.0

To Reproduce

• Create cde scheme
• Import
  emx2-cde-fdp-rml-compat-v2.xlsx
• In cde settings, grant Viewer permission to anonymous user
• Export to csv: wget http://localhost:8080/cde/api/csv/cde_Patient -O cde_Patient.csv
• Look at the uniqid column of the csv:

uniqid,pid,genderLabel,genderURI,sexQualityURI,birthdate,birthdateQualityURI,first_contact_date,symptom_onset_age,hgvs_variant,date,ordo_uri,status_label,death_date,status_uri,HP1,HP2,HP3,HP4,HP5,HP6,HP7,HP8,HP9,HP10,HP1L,HP2L,HP3L,HP4L,HP5L,HP6L,HP7L,HP8L,HP9L,HP10L
1.0,Patient001,Male,http://purl.obolibrary.org/obo/NCIT_C20197,http://purl.obolibrary.org/obo/NCIT_C28421,1958-01-10,http://purl.obolibrary.org/obo/NCIT_C68615,2008-03-11,2005-03-02,DOCK8:c.494C>T,1994-02-27,http://www.orpha.net/ORDO/Orphanet_166260,Alive,2035-10-23,http://purl.obolibrary.org/obo/NCIT_C37987,http://purl.obolibrary.org/obo/HP_0000001,http://purl.obolibrary.org/obo/HP_0000011,http://purl.obolibrary.org/obo/HP_0000021,http://purl.obolibrary.org/obo/HP_0000031,http://purl.obolibrary.org/obo/HP_0000041,http://purl.obolibrary.org/obo/HP_0000051,http://purl.obolibrary.org/obo/HP_0000061,http://purl.obolibrary.org/obo/HP_0000071,http://purl.obolibrary.org/obo/HP_0000081,http://purl.obolibrary.org/obo/HP_0000091,HP:0000001,HP:0000011,HP:0000021,HP:0000031,HP:0000041,HP:0000051,HP:0000061,HP:0000071,HP:0000081,HP:0000091
2.0,Patient002,Female,http://purl.obolibrary.org/obo/NCIT_C16576,http://purl.obolibrary.org/obo/NCIT_C28421,1992-02-13,http://purl.obolibrary.org/obo/NCIT_C68615,1974-05-19,1997-12-24,APOL1:c.980C>T,1994-07-13,http://www.orpha.net/ORDO/Orphanet_166261,Alive,2020-04-27,http://purl.obolibrary.org/obo/NCIT_C37987,http://purl.obolibrary.org/obo/HP_0000002,http://purl.obolibrary.org/obo/HP_0000012,http://purl.obolibrary.org/obo/HP_0000022,http://purl.obolibrary.org/obo/HP_0000032,http://purl.obolibrary.org/obo/HP_0000042,http://purl.obolibrary.org/obo/HP_0000052,http://purl.obolibrary.org/obo/HP_0000062,http://purl.obolibrary.org/obo/HP_0000072,http://purl.obolibrary.org/obo/HP_0000082,http://purl.obolibrary.org/obo/HP_0000092,HP:0000002,HP:0000012,HP:0000022,HP:0000032,HP:0000042,HP:0000052,HP:0000062,HP:0000072,HP:0000082,HP:0000092
3.0,Patient003,Male,http://purl.obolibrary.org/obo/NCIT_C20197,http://purl.obolibrary.org/obo/NCIT_C28421,1933-10-02,http://purl.obolibrary.org/obo/NCIT_C68615,2000-11-18,1997-04-13,PRPF6T>C:c.1344T>C,1996-08-18,http://www.orpha.net/ORDO/Orphanet_166262,Dead,2029-09-28,http://purl.obolibrary.org/obo/NCIT_C28554,http://purl.obolibrary.org/obo/HP_0000003,http://purl.obolibrary.org/obo/HP_0000013,http://purl.obolibrary.org/obo/HP_0000023,http://purl.obolibrary.org/obo/HP_0000033,http://purl.obolibrary.org/obo/HP_0000043,http://purl.obolibrary.org/obo/HP_0000053,http://purl.obolibrary.org/obo/HP_0000063,http://purl.obolibrary.org/obo/HP_0000073,http://purl.obolibrary.org/obo/HP_0000083,http://purl.obolibrary.org/obo/HP_0000093,HP:0000003,HP:0000013,HP:0000023,HP:0000033,HP:0000043,HP:0000053,HP:0000063,HP:0000073,HP:0000083,HP:0000093
4.0,Patient004,Female,http://purl.obolibrary.org/obo/NCIT_C16576,http://purl.obolibrary.org/obo/NCIT_C28421,1941-01-17,http://purl.obolibrary.org/obo/NCIT_C68615,1979-03-08,1999-09-25,GRIN1:c.1471G>C,2007-08-26,http://www.orpha.net/ORDO/Orphanet_166263,Dead,2012-05-12,http://purl.obolibrary.org/obo/NCIT_C28554,http://purl.obolibrary.org/obo/HP_0000004,http://purl.obolibrary.org/obo/HP_0000014,http://purl.obolibrary.org/obo/HP_0000024,http://purl.obolibrary.org/obo/HP_0000034,http://purl.obolibrary.org/obo/HP_0000044,http://purl.obolibrary.org/obo/HP_0000054,http://purl.obolibrary.org/obo/HP_0000064,http://purl.obolibrary.org/obo/HP_0000074,http://purl.obolibrary.org/obo/HP_0000084,http://purl.obolibrary.org/obo/HP_0000094,HP:0000004,HP:0000014,HP:0000024,HP:0000034,HP:0000044,HP:0000054,HP:0000064,HP:0000074,HP:0000084,HP:0000094

Expected behavior
Values are just like they got entered, so 1,2,3,4,5 instead of 1.0, 2.0, 3.0, 4.0, 5.0

Version
5.25.0