nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2020-08-20T06:23:23Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/151V0.8.62020-08-20T06:23:23ZMarkus ScheidgenV0.8.6https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/154V0.8.72020-08-20T16:42:31ZMarkus ScheidgenV0.8.7https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/153Complex query2020-08-20T18:12:28ZAlvin Noe LadinesComplex queryImplemented complex query to archive, repo and raw api endpoints.Implemented complex query to archive, repo and raw api endpoints.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/152Structure.js component2020-08-21T06:34:27ZLauri HimanenStructure.js componentI created a React Structure.js component that supports viewing atomistic structures. It is now initially integrated into the ArchiveBrowser where it will show the structure for any `section_system` below the title.
You can check it in...I created a React Structure.js component that supports viewing atomistic structures. It is now initially integrated into the ArchiveBrowser where it will show the structure for any `section_system` below the title.
You can check it in action at the development cluster, e.g. [here](http://labdev-nomad.esc.rzg.mpg.de/dev/nomad/encyclopedia-gui-integration/gui/entry/id/6puvhxedSYyTjG0l6ck43g/GTZi4-q5ZcyG6B2u3j6XJ_16dSxd/archive/section_run/section_system:0) In the context of the ArchiveBrowser the viewer tries to intelligently load new data:
- There is only one shared instance of StructureViewer object from the [materia-library](https://lauri-codes.github.io/materia/).
- If a new structure is loaded from the same archive, only the positions are updated. This is much faster than reloading the entire structure and should be a valid assumption since the number of atoms or their species should not change within an archive.
- If more than 300 atoms (this is configurable) are present, the visualization is disabled and a message is displayed.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/156About2020-08-21T07:16:37ZMarkus ScheidgenAboutImproved the about page with actual encyclopedia and ai toolkit info.Improved the about page with actual encyclopedia and ai toolkit info.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/155Backend refactor2020-08-21T07:16:44ZMarkus ScheidgenBackend refactorRefactored the CLI, processing and test code to rely on EntryArchive instead of Backend.Refactored the CLI, processing and test code to rely on EntryArchive instead of Backend.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/157Parallel archive client2020-08-21T18:48:58ZMarkus ScheidgenParallel archive clientFixed parallel archive access issues. #350Fixed parallel archive access issues. #350https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/158Added authentication support to all encyclopedia API routes and added links f...2020-08-26T06:35:27ZLauri HimanenAdded authentication support to all encyclopedia API routes and added links from encyclopedia back to the individual entries.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/159Alvin read metadata2020-08-26T15:17:24ZAlvin Noe LadinesAlvin read metadataRead and use upload user-metadata (nomad.yaml). #390Read and use upload user-metadata (nomad.yaml). #390Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/160V0.8.82020-08-26T19:32:48ZMarkus ScheidgenV0.8.8https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/161Phonon workflow2020-08-28T09:01:38ZAlvin Noe LadinesPhonon workflowImplemented phonon workflow and fixed the phonopy parser to include phonopy database.Implemented phonon workflow and fixed the phonopy parser to include phonopy database.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/162Added support for ingesting/displaying DOS similarity data in Encyclopedia GU...2020-08-31T06:58:42ZLauri HimanenAdded support for ingesting/displaying DOS similarity data in Encyclopedia GUI. Additionally, the MongoDB metainfo extension now can handle nested sections.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/163Alvin workflow fix2020-09-02T17:47:55ZAlvin Noe LadinesAlvin workflow fixFixed unit conversion warning in workflow normalizer issue #411 and introduction of
references to calculations in Relaxation metainfo.Fixed unit conversion warning in workflow normalizer issue #411 and introduction of
references to calculations in Relaxation metainfo.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/164Mongo archive2020-12-18T16:07:59ZMarkus ScheidgenMongo archiveAdded partial archives stored in new mongodb collection and archive API and client that make use of it. Some complex search API fixes. #401Added partial archives stored in new mongodb collection and archive API and client that make use of it. Some complex search API fixes. #401https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/165Elastic workflow2020-09-04T18:45:33ZAlvin Noe LadinesElastic workflowImplementation of the elastic workflow and elastic parser update.Implementation of the elastic workflow and elastic parser update.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/166Experimental2020-09-05T20:58:22ZMarkus ScheidgenExperimentalUpdated the experimental metadata, parsers, and gui. Added support for non NOMAD user authors and external databases. #403 #330Updated the experimental metadata, parsers, and gui. Added support for non NOMAD user authors and external databases. #403 #330https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/167Refactored the properties tab to use a different set of properties, modified ...2020-09-08T11:00:40ZLauri HimanenRefactored the properties tab to use a different set of properties, modified the properties tab layout, added support for choosing multiple histogram values with the 'multiple'-flag.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/168Search relabeling2020-09-10T21:45:47ZMarkus ScheidgenSearch relabelingOverhaul of the properties search tab. #392Overhaul of the properties search tab. #392https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/169Added new components for plotting: Plot, DOS and BandStructure. The DOS and B...2020-09-11T13:24:38ZLauri HimanenAdded new components for plotting: Plot, DOS and BandStructure. The DOS and BS plots are now also integrated to the ArchiveBrowser where they are shown in the overview.The plotting is based on the Plotly.js library and a custom React component built around it. The plots can be reset, 'floated' and captured. The preset for capturing probably needs some tweaking: currently the plots are exported as SVG f...The plotting is based on the Plotly.js library and a custom React component built around it. The plots can be reset, 'floated' and captured. The preset for capturing probably needs some tweaking: currently the plots are exported as SVG files with fixed width.
The Brillouin zone viewer still needs some work, so I did not include it yet.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/171Parser metadata2020-09-14T09:09:17ZMarkus ScheidgenParser metadataAdded a new code list and dialog with detailed upload information to the GUI.Added a new code list and dialog with detailed upload information to the GUI.