nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2024-03-25T11:57:35Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1750Added support for topologies with multiple roots and no atomic structure.2024-03-25T11:57:35ZLauri HimanenAdded support for topologies with multiple roots and no atomic structure.Closes #1953Closes #1953https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1733Resolve "add reference to elabftw parser"2024-03-15T00:49:13ZAmir GolparvarResolve "add reference to elabftw parser"Closes #1937Closes #1937Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1678Resolve "Scatter plots with multiple values per entry"2024-02-27T15:46:39ZLauri HimanenResolve "Scatter plots with multiple values per entry"Closes #1732Closes #1732Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1676Resolve "Packages aliases in metainfo"2024-03-01T11:03:53ZMarkus ScheidgenResolve "Packages aliases in metainfo"This MR uses the `alias` property on `Package` definitions, e.g.
```python
m_package = Package(aliases=['some.other.python.package.name'])
class MySection(MSection):
...
m_package.__init__metainfo__()
```
I checked that you can now:
...This MR uses the `alias` property on `Package` definitions, e.g.
```python
m_package = Package(aliases=['some.other.python.package.name'])
class MySection(MSection):
...
m_package.__init__metainfo__()
```
I checked that you can now:
- [x] process an `.archive.json` file with an `"m_def": "some.other.python.package.name.MySection"` in it.
- [x] you can reprocess an entry that was previously processed and has an `"m_def": "some.other.python.package.name.MySection"` in the archive.
- [x] the gui shows the data for an entry with `"m_def": "some.other.python.package.name.MySection"` in it.
This should cover most cases when refactoring package names:
- using the ArchiveQuery on old data (or instantiating it otherwise)
- showing old data in the gui
There are use cases were this does not work:
- querying with for a python based section definition name as a search criteria
!!! This is only for refactoring python package names. This is not about changing sub-section names. This will require another MR.
!!! This also only works for packages that are known and loaded in the backend. Therefore, this only works for python packages in nomad-lab or plugins. It does not work for any uploaded ".yaml" schemas.
Closes #1886Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1649Add coauthor, reviewer groups2024-01-29T13:47:24ZSascha KlawohnAdd coauthor, reviewer groups- Add user groups, API `/groups`
- Add coauthor, reviewer groups
- Add writer, viewer groups
- Add groups to ES owner query
- Add tests for groups, uploads, search
Closes #1760- Add user groups, API `/groups`
- Add coauthor, reviewer groups
- Add writer, viewer groups
- Add groups to ES owner query
- Add tests for groups, uploads, search
Closes #1760Sascha KlawohnSascha Klawohnhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1646Resolve "Config option to disable optimade API."2024-02-26T11:46:23ZMarkus ScheidgenResolve "Config option to disable optimade API."Closes #1866Closes #1866https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1628Resolve "Converter for json to and from pd dataframe"2024-02-29T10:43:49ZAmir GolparvarResolve "Converter for json to and from pd dataframe"- [x] flatten json into a pandas dataframe
- [x] reconstruct dataframe to json
- [x] options: depth of the json to flatten
- [x] options: order resultant dataframe alphabetically or by a list of strings
Closes #1849- [x] flatten json into a pandas dataframe
- [x] reconstruct dataframe to json
- [x] options: depth of the json to flatten
- [x] options: order resultant dataframe alphabetically or by a list of strings
Closes #1849Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1625Resolve "Attribute inheritance"2024-02-29T11:46:43ZMarkus ScheidgenResolve "Attribute inheritance"Closes #1845Closes #1845Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1615Improved search bar2024-01-15T09:59:05ZLauri HimanenImproved search barCloses #1790, #1700Closes #1790, #1700Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1576Added wrap mode option to the API endpoint for retrieving system geometries.2023-12-04T08:10:24ZLauri HimanenAdded wrap mode option to the API endpoint for retrieving system geometries.Closes #1804Closes #1804Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1553Add computational core-hole metadata2023-12-20T06:12:10ZNathan DaelmanAdd computational core-hole metadataAdd `CoreHole` under `AtomParameters`, but with an interface to `AtomsGroup` and by extension topology.Add `CoreHole` under `AtomParameters`, but with an interface to `AtomsGroup` and by extension topology.Nathan DaelmanNathan Daelmanhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1543Resolve "OpenBIS Integration"2023-12-07T09:17:36ZAmir GolparvarResolve "OpenBIS Integration"Closes #1768Closes #1768Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1542Resolve "Unit selection component"2023-12-01T06:01:20ZLauri HimanenResolve "Unit selection component"Closes #1758, #960Closes #1758, #960Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1510Resolve "Search interface improvements"2023-11-01T06:55:21ZLauri HimanenResolve "Search interface improvements"Closes #1740Closes #1740Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1502Resolve "Workflow for chemical reaction steps"2023-10-23T16:51:59ZAlvin Noe LadinesResolve "Workflow for chemical reaction steps"Closes #1430Closes #1430Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1482Exposed upload_name in the search, added suggestions for upload_name.2023-10-03T05:34:16ZLauri HimanenExposed upload_name in the search, added suggestions for upload_name.Closes #1708Closes #1708Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1472Add AppTokenForm to APIs page2023-10-02T15:28:18ZSascha KlawohnAdd AppTokenForm to APIs pageCloses #1681
TODO: Fix typo when squashing (AppFormToken -> AppTokenForm)Closes #1681
TODO: Fix typo when squashing (AppFormToken -> AppTokenForm)Sascha KlawohnSascha Klawohnhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1471Add presence regex2023-09-26T12:32:23ZNathan DaelmanAdd presence regexCloses #1687Closes #1687Nathan DaelmanNathan Daelmanhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1469Resolve "Apps for python schemas"2023-09-21T13:07:11ZLauri HimanenResolve "Apps for python schemas"Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1460Resolve "Application Token"2023-09-19T14:01:54ZSascha KlawohnResolve "Application Token"Closes #1654
Implements endpoint `/app_token?expires_in=<int>` for simple tokens like the signature token to access every endpoint available with the Keycloak access token via the `Authorization: Bearer <app token>` header. Adds tests ...Closes #1654
Implements endpoint `/app_token?expires_in=<int>` for simple tokens like the signature token to access every endpoint available with the Keycloak access token via the `Authorization: Bearer <app token>` header. Adds tests for requesting the both app and signature token with and without authorization. Adds a single test to access a restricted endpoint (`/users/me`) with the app token.