nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2024-03-09T03:03:52Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1692Changed config to use the new archive writer by default.2024-03-09T03:03:52ZMarkus ScheidgenChanged config to use the new archive writer by default.Changelog: AddedChangelog: AddedMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1714Fixed gui data etag.2024-03-11T20:10:22ZMarkus ScheidgenFixed gui data etag.Changelog: FixedChangelog: Fixedhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1712copy local path to temp directory2024-03-07T12:54:20ZAhmed Ilyascopy local path to temp directoryIf a local path is provided, copy it to a temp dir before importing. Otherwise when the upload is deleted, the original local path file ends up getting deleted too.If a local path is provided, copy it to a temp dir before importing. Otherwise when the upload is deleted, the original local path file ends up getting deleted too.Ahmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1695Resolve "conversion of ArchiveQuery to dataframe works only for the last call...2024-03-07T12:40:21ZAmir GolparvarResolve "conversion of ArchiveQuery to dataframe works only for the last call of the downloaded entries"Closes #1909Closes #1909Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1708Resolve "Reloading link bugs out"2024-03-07T10:07:30ZLauri HimanenResolve "Reloading link bugs out"Closes #1918Closes #1918Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1711Add raw_path_exists method to ClientContext2024-03-06T14:23:57ZSarthak KapoorAdd raw_path_exists method to ClientContext`nomad.datamodel.Context` has a `raw_path_exists` method which needs to implemented in it's child classes. But this implementation is missing in one of the child classes `ClientContext`. The current MR fixes it.
_Why is this needed?_ Wh...`nomad.datamodel.Context` has a `raw_path_exists` method which needs to implemented in it's child classes. But this implementation is missing in one of the child classes `ClientContext`. The current MR fixes it.
_Why is this needed?_ When testing a schema class locally using pytest, the context associated with the archive is of class `ClientContext`. If the schema uses `archive.m_context.raw_path_exists(filepath)` in normalize, the test fails as the method is not implemented.Sarthak KapoorSarthak Kapoorhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1709updated submodules and gui artifacts2024-03-05T14:30:33ZJoseph Rudzinskiupdated submodules and gui artifactsCloses #1921Closes #1921Joseph RudzinskiJoseph Rudzinskihttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1707Resolve "CP2K parser failure"2024-03-05T11:52:22ZNathan DaelmanResolve "CP2K parser failure"- Update `CP2K` parser with header patch
- Update `Phonopy` parser with non-canonical hexagonal cell patch
Closes #1919- Update `CP2K` parser with header patch
- Update `Phonopy` parser with non-canonical hexagonal cell patch
Closes #1919Nathan DaelmanNathan Daelmanhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1703Reverted automated re-lableing of sub sections in archive browser and ELN.2024-03-04T16:33:41ZMarkus ScheidgenReverted automated re-lableing of sub sections in archive browser and ELN.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1702Resolve "errors in the gui whenquantitities are of type=np.float64 and no uni...2024-03-04T15:04:11ZMarkus ScheidgenResolve "errors in the gui whenquantitities are of type=np.float64 and no unit given"Closes #1913Closes #1913https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1694Resolve "ArchiveQuery sends to many requests."2024-03-04T13:01:35ZTheodore ChangResolve "ArchiveQuery sends to many requests."Closes #1905Closes #1905Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1674Remove CAS image after test2024-03-01T12:04:41ZSascha KlawohnRemove CAS image after testThe test `tests/datamodel/metainfo/eln/test_system.py::test_substance` left an SVG file (`cas_10101-63-0_image.svg`) after processing.
This MR removes the image at the end of the test, thereby also checking if it existed.The test `tests/datamodel/metainfo/eln/test_system.py::test_substance` left an SVG file (`cas_10101-63-0_image.svg`) after processing.
This MR removes the image at the end of the test, thereby also checking if it existed.Sascha KlawohnSascha Klawohnhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1697Changed loader type.2024-03-01T11:53:24ZLauri HimanenChanged loader type.Closes #1911Closes #1911Lauri 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/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/1689saving and loading nexus schema instead of building it from NXDL to save abou...2024-03-01T17:42:48ZSandor Brockhausersaving and loading nexus schema instead of building it from NXDL to save about 50%https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1691Fixed issue with file preview using incorrect content length for deciding whe...2024-02-28T09:23:10ZLauri HimanenFixed issue with file preview using incorrect content length for deciding when to stop streaming.Closes #1904Closes #1904Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1690Loop elastic check2024-02-27T18:39:13ZTheodore ChangLoop elastic checkTheodore ChangTheodore Changhttps://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/1688Resolve "Update pymatgen dependency and make float128 optional"2024-02-27T15:44:46ZLauri HimanenResolve "Update pymatgen dependency and make float128 optional"Closes #1902Closes #1902Lauri HimanenLauri Himanen