nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2024-03-18T08:22:16Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1738Fixed typo.2024-03-18T08:22:16ZLauri HimanenFixed typo.Closes #1942Closes #1942Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1737Improving Install plugins docu2024-03-25T10:18:53ZJose PizarroImproving Install plugins docuCloses #1941
@aalbino would you mind reviewing these changes? I just wanted to improve a bit the description on how to add a plugin as a developer. I don't know whether the place for it is the best (because it is under How to > OASIS),...Closes #1941
@aalbino would you mind reviewing these changes? I just wanted to improve a bit the description on how to add a plugin as a developer. I don't know whether the place for it is the best (because it is under How to > OASIS), I just fixed the how to regarding us, developers :slight_smile:
Thanks!Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1736Fixed the keycloak image registry used by docker-compose example.2024-03-15T15:08:31ZMarkus ScheidgenFixed the keycloak image registry used by docker-compose example.The official keycloak images seem to be hosted on a different
registry now.
Changelog: FixedThe official keycloak images seem to be hosted on a different
registry now.
Changelog: Fixedhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1735Documentation update: added workaround needed for gui start on newer node.js ...2024-03-15T11:35:26ZFabian SchöppachDocumentation update: added workaround needed for gui start on newer node.js versionsCloses #1940Closes #1940https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1734Resolve "plotly config dictionary can't be fed in from normalize function"2024-03-15T10:59:52ZDinga WonankeResolve "plotly config dictionary can't be fed in from normalize function"We created a new function create_topology_porosity, which will enable users to easily populate the topology.
In addition, we moved most of the global functions from mof_deconstructor into atomutils, which will facilitate the implementat...We created a new function create_topology_porosity, which will enable users to easily populate the topology.
In addition, we moved most of the global functions from mof_deconstructor into atomutils, which will facilitate the implementation of the wrapping function in the future.https://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/1732Increased helm chart version.2024-03-15T11:19:44ZMarkus ScheidgenIncreased helm chart version.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1731Draft: Resolve "Parsing nexus files generates a lot of warnings and errors"2024-03-28T07:45:32ZMarkus ScheidgenDraft: Resolve "Parsing nexus files generates a lot of warnings and errors"Fixed some problems of #1934
- I fixed a bug in the attribute generation. Basically some attributes were missing. But this only solved a small portion of the problems.
- I fixed a bug in the MetainforNormalizer which tried to call thin...Fixed some problems of #1934
- I fixed a bug in the attribute generation. Basically some attributes were missing. But this only solved a small portion of the problems.
- I fixed a bug in the MetainforNormalizer which tried to call things called "normalize" in the schema, but where not actually normalize functions.
- I fixed the error handling a bit to better see what is actually causing the problems.
### The first error type mentioned in #1934
This is fixed with the MetainforNormalizer fix.
### The second error type mentioned in #1934
These are a few separate issues repeating. They are reported while setting an attribute, but they are caused because the parser could not find the quantity or section to put the attribute on. Therefore, they do not seem to be attribute problems. They are indicating a few mapping problems that I cannot resolve!
- string `unit` in `nxdl_path`, where the parser only expects instances of `ET.Element`. This maybe is a problem in `pynxtools.nexus.HandleNexus` which produces all the `nxdl_path`.
```
WARNING nomad.client 2024-03-14T13:46:17 Error while setting attribute.
- exception: Traceback (most recent call last):
File "/Users/markus/Documents/Projects/nomad-fairdi/nomad/parsing/nexus/nexus.py", line 167, in _populate_data
assert isinstance(
AssertionError: nx_path is not a list of ET.Element, one segment is "units:<class 'str'>"
```
- The parsre tries to set `version__attribute` to `nexus.NXentry.COLLECTION:SubSection`, but the nexus mapping does not define attributes on sub sections, I guess this is supposed to go to the section that the sub-section points to?
```
WARNING nomad.client 2024-03-14T13:46:17 Error while setting attribute.
- exception: Traceback (most recent call last):
File "/Users/markus/Documents/Projects/nomad-fairdi/nomad/parsing/nexus/nexus.py", line 194, in _populate_data
assert isinstance(
AssertionError: nexus.NXentry.COLLECTION:SubSection is not a Quantity
```
- `nexus.NXelectronanalyser.NXtransformations` has no suitable quantity for `depends_on__field`
```
WARNING nomad.client 2024-03-14T13:46:18 Error while setting attribute.
- exception: Traceback (most recent call last):
File "/Users/markus/Documents/Projects/nomad-fairdi/nomad/parsing/nexus/nexus.py", line 182, in _populate_data
assert metainfo_def, f'{current.m_def} has no suitable property for {parent_field_name}'
AssertionError: nexus.NXelectronanalyser.NXtransformations:Section has no suitable property for depends_on__field
```
- `nexus.NXelectronanalyser.NXtransformations` has no suitable quantity for `transformation_type__field`
```
WARNING nomad.client 2024-03-14T13:46:18 Error while setting attribute.
- exception: Traceback (most recent call last):
File "/Users/markus/Documents/Projects/nomad-fairdi/nomad/parsing/nexus/nexus.py", line 182, in _populate_data
assert metainfo_def, f'{current.m_def} has no suitable property for {parent_field_name}'
AssertionError: nexus.NXelectronanalyser.NXtransformations:Section has no suitable property for transformation_type__field
```
Then there are a few less frequent things:
- The value "HHG laser" is not an enum value for `nexus.NXsource.type__field`.
- NaN value is not set for field on `size__field[size__field]`
# The third error mentioned in #1934
These errors are caused because we try to interpret enum values as floats. This is all for this `nexus.NXtransformations.AXISNAME__field`, which is defined as a float in the schema. I guess it should not be a float?https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1730Add pytest options for faster local testing2024-03-18T10:05:01ZSascha KlawohnAdd pytest options for faster local testingThe `celery.inspect.().active()` broadcast used in the cleanup of fixture `worker` waits until timeout (default 1 s) is reached, which accumulates for each test with this fixture, e.g. about 14 min instead of 7 min on a laptop. Removal m...The `celery.inspect.().active()` broadcast used in the cleanup of fixture `worker` waits until timeout (default 1 s) is reached, which accumulates for each test with this fixture, e.g. about 14 min instead of 7 min on a laptop. Removal may lead to tasks still running during the next test.
This MR adds the pytest option `--celery-inspect-timeout`, which can be used to decrease the timeout for faster local testing.
It further adds the option `--fixture-filters` to run only tests that depend (directly or indirectly) on a list of fixtures and do not depend on fixtures prefixed with '!'.Sascha KlawohnSascha Klawohnhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1729Resolve "Config refactor"2024-03-15T09:20:46ZLauri HimanenResolve "Config refactor"Closes #1917Closes #1917Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1728Revert "Merge branch '1917-delay-config-validation' into 'develop'"2024-03-14T10:23:55ZLauri HimanenRevert "Merge branch '1917-delay-config-validation' into 'develop'"This reverts merge request !1716This reverts merge request !1716https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1727Fixed broken error handling on datacite errors.2024-03-13T21:02:00ZMarkus ScheidgenFixed broken error handling on datacite errors.Changelog: FixedChangelog: FixedMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1726Integrity check2024-03-20T23:12:44ZTheodore ChangIntegrity checkTheodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1725Added entry create time as an available search filter.2024-03-13T08:15:28ZLauri HimanenAdded entry create time as an available search filter.Closes #1931Closes #1931Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1724Archive converter refinement2024-03-15T10:06:20ZTheodore ChangArchive converter refinementTheodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1722Added new troubleshooting section to OASIS installation.2024-03-12T12:21:58ZLauri HimanenAdded new troubleshooting section to OASIS installation.Closes #1927Closes #1927Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1721Remove cache2024-03-21T15:05:25ZTheodore ChangRemove cacheTheodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1720Resolve "data structure of the .eln file format has changed"2024-03-12T12:37:34ZAmir GolparvarResolve "data structure of the .eln file format has changed"Closes #1928Closes #1928Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1719Draft: bump dependencies for pandas and scipy2024-03-11T14:04:41ZAhmed IlyasDraft: bump dependencies for pandas and scipyAhmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1718Documentation: Tiny improvement and typo fix2024-03-11T13:14:18ZFabian SchöppachDocumentation: Tiny improvement and typo fix