nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2023-07-28T08:29:15Zhttps://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/1425Resolve "Small UX improvement for the upload page"2023-07-28T08:07:35ZLauri HimanenResolve "Small UX improvement for the upload page"Closes #1635Closes #1635Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1367Resolve "ELN for integration (elabFTW, labfolder, chemotion)"2023-07-27T12:17:13ZAmir GolparvarResolve "ELN for integration (elabFTW, labfolder, chemotion)"Related #896Related #896Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1409Resolve "A c library cannot be used in the nomad image"2023-07-26T08:57:59ZAdam FeketeResolve "A c library cannot be used in the nomad image"Closes #1597Closes #1597Adam FeketeAdam Feketehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1407Resolve "Keycloak client_id hardcoded in jupyterhub_config.py"2023-07-26T08:13:07ZJonas SchwabResolve "Keycloak client_id hardcoded in jupyterhub_config.py"Closes #1604Closes #1604Jonas SchwabJonas Schwabhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1422Updated plugin docker mounting docs.2023-07-25T10:33:35ZLauri HimanenUpdated plugin docker mounting docs.Closes #1615Closes #1615Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1421Resolve "Issue processing data with both schema + data"2023-07-25T10:10:29ZAmir GolparvarResolve "Issue processing data with both schema + data"Closes #1627Closes #1627Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1335Resolve "Additonal options for SectionSelectDialog"2023-07-24T05:02:21ZMohammad NakhaeeResolve "Additonal options for SectionSelectDialog"Closes #1529Closes #1529Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1420Resolve "Javascript error while searching through custom schema quantities"2023-07-23T10:48:06ZAhmed IlyasResolve "Javascript error while searching through custom schema quantities"Closes #1613Closes #1613Ahmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1419Resolve "Processing issue"2023-07-20T13:09:04ZLauri HimanenResolve "Processing issue"Closes #1611Closes #1611Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1339Don't index nans in ES2023-07-20T11:43:10ZFlorian DobenerDon't index nans in ESES does not process nan values leading to a failed processing. This fix removes nan values from indexing.ES does not process nan values leading to a failed processing. This fix removes nan values from indexing.https://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/1418Update parser ref2023-07-20T06:34:45ZAlvin Noe LadinesUpdate parser refImplement fix to orca parser.Implement fix to orca parser.Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1415Refactored periodic table using SVG.2023-07-20T06:19:34ZLauri HimanenRefactored periodic table using SVG.Closes #1252Closes #1252Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1417Resolve "Problem with removing archives generated with tabular parser entry m...2023-07-19T19:55:25ZAmir GolparvarResolve "Problem with removing archives generated with tabular parser entry mode"Closes #1612Closes #1612Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1377Resolve "Refactoring tabular parser"2023-07-19T12:43:09ZAmir GolparvarResolve "Refactoring tabular parser"Closes #1531
Closes #1583Closes #1531
Closes #1583Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1408Resolve "Create archive file from ReferenceEditQuantity choosing among the ch...2023-07-19T06:30:19ZMohammad NakhaeeResolve "Create archive file from ReferenceEditQuantity choosing among the children classes of the defined type"Closes #1578Closes #1578Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1411Draft: Resolve "Add ButtonEditQuantity"2023-07-18T11:23:42ZMichael GötteDraft: Resolve "Add ButtonEditQuantity"Closes #1607
- I copied ```BoolEditQuantity.js```to ```ButtonEditQuantity.js```
- I used ```@material-ui/core Button``` element
- I copied save functionality from ```.../archive/ArchiveBrowser.js``` not sure if this is correct.
This i...Closes #1607
- I copied ```BoolEditQuantity.js```to ```ButtonEditQuantity.js```
- I used ```@material-ui/core Button``` element
- I copied save functionality from ```.../archive/ArchiveBrowser.js``` not sure if this is correct.
This is how the button element looks like right now.
![grafik](/uploads/57879a5659780d8ca0ae27b2394540eb/grafik.png)Michael GötteMichael Göttehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1412Fixed issue with row action visuals.2023-07-18T07:05:00ZLauri HimanenFixed issue with row action visuals.Closes #1608Closes #1608Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1404small unit fix for ase atoms objects2023-07-17T09:23:23ZJames Darbysmall unit fix for ase atoms objectsCloses #1602.
As ase Atoms objects don't have attached units and expect Angstroms I think this should be the default behaviour.
@mscheidg please could you take a look at this?Closes #1602.
As ase Atoms objects don't have attached units and expect Angstroms I think this should be the default behaviour.
@mscheidg please could you take a look at this?