nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2023-05-30T17:34:34Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1328Update parsers ref2023-05-30T17:34:34ZAlvin Noe LadinesUpdate parsers refAlvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1327Resolve "ReferenceEditQuantity does not allow navigation to entries with proc...2023-06-23T10:21:12ZAhmed IlyasResolve "ReferenceEditQuantity does not allow navigation to entries with processing errors"Closes #1519Closes #1519Ahmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1326Fixed the name of the fhi parser.2023-05-31T07:17:42ZMarkus ScheidgenFixed the name of the fhi parser.The name was accidentally changed, presumably when adding the
plugins. It is now changed back. It is important that the
name does not change, because of existing entries.
Changelog: FixedThe name was accidentally changed, presumably when adding the
plugins. It is now changed back. It is important that the
name does not change, because of existing entries.
Changelog: Fixedhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1324Resolve "Staging deployment constantly breaks"2023-05-31T08:54:58ZMarkus ScheidgenResolve "Staging deployment constantly breaks"Closes #1522Closes #1522https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1322Updates north + pynxtools apm test branch2023-09-05T19:48:22ZFlorian DobenerUpdates north + pynxtools apm test branchhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1321Resolve "Labfolder parser should query the entries in a project"2023-05-30T11:53:41ZAmir GolparvarResolve "Labfolder parser should query the entries in a project"Closes #1518Closes #1518Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1320Fix creation of d3 elements2023-05-30T10:00:31ZAlvin Noe LadinesFix creation of d3 elementsAlvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1319Implement eos fit normalization #14392023-06-08T19:20:53ZAlvin Noe LadinesImplement eos fit normalization #1439Closes #1439Closes #1439Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1318Resolve "Visually indicate entries with processing errors"2023-06-02T09:19:11ZAhmed IlyasResolve "Visually indicate entries with processing errors"Closes #1517Closes #1517Ahmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1316Spectra normalizer2023-07-28T08:29:15ZJose PizarroSpectra normalizerList of changes #1506:
- Changed `ParticleHoleExcitations` to `XS` workflow name.
- Added `methodology` in `ElectronicStructureProvenance`.
- Added `intensities_units` for `Spectra`.
- Added `SpectraNormalizer`.
- Added provenance fo...List of changes #1506:
- Changed `ParticleHoleExcitations` to `XS` workflow name.
- Added `methodology` in `ElectronicStructureProvenance`.
- Added `intensities_units` for `Spectra`.
- Added `SpectraNormalizer`.
- Added provenance for spectra pointing to the specific `method.photon` section.
- Added provenance for spectra in case of being in an XS workflow pointing to `method.bse` section of each corresponding task.
- New result class for `results.properties.spectroscopic.Spectra`. This contains:
- `type` to identify the type of spectra obtained.
- `label` to differentiate between experiment or computation.
- `n_energies`, `energies`, `intensities`, `intensities_units` as the axes of the data.
- `provenance` pointing to `SpectraProvenance(ProvenanceTracker)`. This contains two sub sections, `eels`, `electronic_structure`. The idea would be to extend this.
- Moved certain definitions and normalization from the EELSDB parser to here (https://github.com/nomad-coe/nomad-parser-eelsdb/pull/7).
- Added `resolve_spectra` and `xs_workflow_properties` in ResultsNormalizer.
- Modified the visualization side to get the new `results.properties.spectroscopic.spectra` data. Also modified names from EELS to Spectroscopic.
This MR is dependent on the merge of !1261.
The current `SpectraNormalizer` looks a bit empty right now, but my plan is to extend it soon.
Should I move the EELSDB normalization to there?
In any case, let me know what you think; maybe there is a better / more convenient solution for this.
TODO:
- [x] Fix testing and clean up.
- [x] Define a normalization similar to the plot for DOS.
- [x] ~~Move `label` inside provenance.~~ No, `provenance.label` contains other information that cannot be overwritten.
- [x] Use `label` to identify each line or plot: `comp. 1` or `exp. 1`.
- [x] Use `type` to title each plot.
- [x] ~~Populate `results.properties.X` where `X=electronic, vibrational, structural` according to the `type` of spectra (e.g., `XAS` should be repeated in `electronic`, `XRD` in `structural`, etc.). This is something I talked with Luca.~~ TODO in another merge request.
- [x] ~~Define FilterMenu `Spectroscopic` and move `EELS` below it. `Spectroscopic` will be clickable and contain `label` inside. I need some feedback here.~~ TODO in another merge request.
- [x] ~~Develop ref for plot labels pointing to the specific provenance of the property (if available).~~ TODO in another merge request.Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1314Resolve "Consider MEnum as key quantity"2023-05-24T19:15:19ZTheodore ChangResolve "Consider MEnum as key quantity"Closes #1513Closes #1513Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1313Resolve "In the GUI, in Uploads Page, delete button is disabled when selectin...2023-05-31T11:00:22ZAhmed IlyasResolve "In the GUI, in Uploads Page, delete button is disabled when selecting all uploads"Closes #1510Closes #1510Ahmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1312Resolve "Duplicate functionality for entries."2023-06-08T09:43:32ZAhmed IlyasResolve "Duplicate functionality for entries."Closes #1511Closes #1511Ahmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1310Fix method normalizer2023-05-24T14:11:34ZJose PizarroFix method normalizer@ndaelman I fixed this.@ndaelman I fixed this.Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1309Fixed ref to electronicparsers submodule2023-05-24T08:37:32ZJose PizarroFixed ref to electronicparsers submodulehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1308Resolve "OverviewView.spec.js failed occasionally"2023-05-24T10:21:34ZMohammad NakhaeeResolve "OverviewView.spec.js failed occasionally"Closes #1478Closes #1478Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1306Improved resolution of system references in the visualizer, removed additiona...2023-05-23T10:07:01ZLauri HimanenImproved resolution of system references in the visualizer, removed additional comma.Closes #1508Closes #1508Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1305Resolve "When uploading a file with the FileEditQuantity, no upload progress ...2023-05-25T07:43:37ZAhmed IlyasResolve "When uploading a file with the FileEditQuantity, no upload progress is shown"Closes #1507Closes #1507Ahmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1304DMFT workflow2023-07-20T09:45:59ZJose PizarroDMFT workflowCloses #1445Closes #1445Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1303Resolve "Indicate that there are co-authors in the uploads list"2023-05-30T07:33:41ZAhmed IlyasResolve "Indicate that there are co-authors in the uploads list"Closes #1505Closes #1505Ahmed IlyasAhmed Ilyas