nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2022-12-09T08:15:20Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/958Add section defs2022-12-09T08:15:20ZTheodore ChangAdd section defsCloses #1190Closes #1190Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/957New workflow visualizer2023-02-11T00:06:53ZAlvin Noe LadinesNew workflow visualizerImplementation of visualizer following the new workflow schema.Implementation of visualizer following the new workflow schema.Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/956Refactor: change terminology from installationUrl to deploymentUrl, and2022-11-22T09:21:23ZDavid SikterRefactor: change terminology from installationUrl to deploymentUrl, andRefactor: change terminology from installationUrl to deploymentUrl, and deployment_id -> deployment_url, etc.Refactor: change terminology from installationUrl to deploymentUrl, and deployment_id -> deployment_url, etc.David SikterDavid Sikterhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/955Refactor bundle functionality2022-12-14T09:56:47ZDavid SikterRefactor bundle functionalityRefactoring and improvements related to bundle functionality, part of #1181.
The bundle functionality is modularized, broken out into a new module `bundles.py`, and CLI commands are introduced for import and exporting bundles. The setti...Refactoring and improvements related to bundle functionality, part of #1181.
The bundle functionality is modularized, broken out into a new module `bundles.py`, and CLI commands are introduced for import and exporting bundles. The settings are reorganized, and importing bundles through the api is by default disabled for now (previously, it was enabled by default). The bundle file format is essentially unchanged, except for renaming `export_options` to `export_settings` for more consistency. Also made some improvements to related code, to make sure the GUI doesn't crash and that the user can always delete uploads where the import failed.
As before, importing is done by first creating a "skeleton upload" and then running a process (locally or on the worker) on this upload to do the main part of the work. Unlike before, the process is now focused on importing the parsed archive files, not reprocessing the raw files (reprocessing is still possible, but disabled by default).David SikterDavid Sikterhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/954Resolve "Add Rg plots to overview GUI page for molecular dynamics trajectories"2022-12-13T13:44:54ZJoseph RudzinskiResolve "Add Rg plots to overview GUI page for molecular dynamics trajectories"Closes #1157Closes #1157Joseph RudzinskiJoseph Rudzinskihttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/953Draft: Resolve "Error in rendering ReferenceEditQuantity"2022-11-18T14:40:40ZMohammad NakhaeeDraft: Resolve "Error in rendering ReferenceEditQuantity"Closes #1149Closes #1149Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/952Resolve "Add RFC 3161 timestamps to entry metadata"2022-12-03T01:00:02ZTheodore ChangResolve "Add RFC 3161 timestamps to entry metadata"Closes #1179Closes #1179Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/951Added if statement to include the right prefix for the DOIs2022-11-18T10:28:50ZJose Marquez PrietoAdded if statement to include the right prefix for the DOIsCloses #1183Closes #1183https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/950Archive browser data links2022-11-18T08:56:02ZTheodore ChangArchive browser data linksCloses #999Closes #999Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/949Resolve "GW metainfo and parsing for exciting and FHIaims"2022-12-15T12:56:41ZJose PizarroResolve "GW metainfo and parsing for exciting and FHIaims"Closes #1131Closes #1131Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/948Resolve "Survey 3rd-party ELNs for integration"2023-01-03T10:37:08ZAmir GolparvarResolve "Survey 3rd-party ELNs for integration"Related #896Related #896Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/947Draft: Resolve "GW metainfo and parsing for exciting and FHIaims"2022-11-14T11:01:27ZJose PizarroDraft: Resolve "GW metainfo and parsing for exciting and FHIaims"Closes #1131Closes #1131https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/946Adds test for nexus parsing error2022-11-16T05:56:40ZFlorian DobenerAdds test for nexus parsing errorhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/945DOS normalization (FHIaims, VASP, exciting)2022-12-22T09:55:49ZNathan DaelmanDOS normalization (FHIaims, VASP, exciting)This MR resolves https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/728 and https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/868.
It is accompanied by https://github.com/nomad-coe/electronic-parsers/pull/16 on the parser ...This MR resolves https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/728 and https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/868.
It is accompanied by https://github.com/nomad-coe/electronic-parsers/pull/16 on the parser side.
Basically, the DOS in FHIaims, VASP, exciting were incorrectly scaled at the parser side:
they no longer lead to integer electrons when integrating over a band.
Moreover, the total DOS in older FHIaims versions was off by a factor of 2 (regardless of spin).
Projected DOS or bands were not affected.
This MR updates the parsers and adds the new metadata entry `raw_data_normalization_factor`, to store the original FHIaims DOS without any correction.
Up to now, this metadata only applies to FHIaims, so I could also move it to that parser's specific metadata.Nathan DaelmanNathan Daelmanhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/944Decreased the size limit for processing topology, skipped topology tests2022-11-11T14:05:49ZLauri HimanenDecreased the size limit for processing topology, skipped topology testsA hotfix for #1174.A hotfix for #1174.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/943Switched to updated matid version with fix for empty prototype cell.2022-11-11T12:51:33ZLauri HimanenSwitched to updated matid version with fix for empty prototype cell.Closes #1173Closes #1173Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/942Resolve "Reprocessing fails without add_matched_entries_to_published"2022-11-11T08:37:18ZMarkus ScheidgenResolve "Reprocessing fails without add_matched_entries_to_published"Closes #1175Closes #1175https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/941Update README.md2022-11-11T16:15:55ZMarkus ScheidgenUpdate README.mdhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/940Draft: Resolve "Integrating Labfolder"2023-01-24T11:29:02ZAmir GolparvarDraft: Resolve "Integrating Labfolder"https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/939Resolve "Quantity with float value "0" is not shown in gui"2022-11-17T08:19:42ZDavid SikterResolve "Quantity with float value "0" is not shown in gui"Closes #1170. The reason for the problem was that falsey values were treated as empty values. The fix makes sure to test for if a value is undefined rather than falsey in a couple of places.
Also added fixes for three test problems (inc...Closes #1170. The reason for the problem was that falsey values were treated as empty values. The fix makes sure to test for if a value is undefined rather than falsey in a couple of places.
Also added fixes for three test problems (including the two most common reasons for GUI and python test failures).David SikterDavid Sikter