nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2023-01-09T10:02:04Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1015Fix issue with serializing data from Ref_publication_date2023-01-09T10:02:04ZJose Marquez PrietoFix issue with serializing data from Ref_publication_dateCloses #1263Closes #1263https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/985Resolve "Optimization for the GUI test"2023-01-05T10:21:46ZMohammad NakhaeeResolve "Optimization for the GUI test"Closes #1233Closes #1233Mohammad NakhaeeMohammad Nakhaeehttps://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/1018Resolve "Hotfix: include Projection menu in the GUI"2023-01-02T11:49:12ZJose PizarroResolve "Hotfix: include Projection menu in the GUI"Closes #1266Closes #1266Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1003Include Projection filter menu2023-01-02T10:48:14ZJose PizarroInclude Projection filter menuCloses #1250Closes #1250https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1014Resolve "Empty ELN annotations are not possible anymore."2022-12-28T11:05:33ZMarkus ScheidgenResolve "Empty ELN annotations are not possible anymore."Closes #1262Closes #1262https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1011Fix to retain backwards compatibility with older GUI versions.2022-12-23T10:29:23ZMarkus ScheidgenFix to retain backwards compatibility with older GUI versions.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1009Improved documentation and handling of config classes2022-12-22T16:59:57ZDavid SikterImproved documentation and handling of config classesDid some minor improvements to the doc strings.
I also noted that if type annotation isn't added to the `NomadConfig` classes, the attributes might be listed in a strange order in the generated documentation, different from the order in...Did some minor improvements to the doc strings.
I also noted that if type annotation isn't added to the `NomadConfig` classes, the attributes might be listed in a strange order in the generated documentation, different from the order in which the attributes are defined, so I added some type annotations to make sure the logical order is preserved.
I also took myself the liberty to change the behaviour of the `customize` method so that it can take either a `NomadConfig` object or a dictionary as its sole argument (this meant I could simplify the code in some places, and I think it is cleaner. The important thing is that the dict is converted to an instance of the right `NomadConfig` class before we start accessing various settings, and I think this should be the responsibility of the `customize` method. This method also does all the checks in one place.) There was also a bug in the CLI commands relating to this (fixed now).David SikterDavid Sikterhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1005Resolve "Plot annotation gives parsing error"2022-12-22T12:28:30ZMarkus ScheidgenResolve "Plot annotation gives parsing error"Closes #1253Closes #1253https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/980New workflow normalizer2022-12-22T11:23:13ZAlvin Noe LadinesNew workflow normalizerImplement normalization of workflow2 in atomistic and electronic parsersImplement normalization of workflow2 in atomistic and electronic parsersMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1007Resolve "Incorrect aggregation size for structural_type"2022-12-22T11:22:41ZLauri HimanenResolve "Incorrect aggregation size for structural_type"Closes #1256Closes #1256https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1006Fixed missing uploads in north.2022-12-22T11:15:02ZMarkus ScheidgenFixed missing uploads in north.https://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/1004Resolve "The env.js has been "force" pushed"2022-12-21T14:37:35ZAdam FeketeResolve "The env.js has been "force" pushed"Closes #1254Closes #1254Adam FeketeAdam Feketehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/866Nexus eln examples2022-12-21T14:50:27ZSherjeel ShabihNexus eln examplesSherjeel ShabihSherjeel Shabihhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1002Resolve "New reference GUI element is not finding entries"2022-12-21T11:38:15ZMarkus ScheidgenResolve "New reference GUI element is not finding entries"Closes #1215Closes #1215https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1000Resolve "Entry not being shown due to upload processing issue"2022-12-20T20:00:21ZDavid SikterResolve "Entry not being shown due to upload processing issue"Closes #1218. The problem was due to failure to index the archive in ES. The old error handling attempts to catch errors and index only a minimal record in ES in case of failures, but the problem was that errors from the ES indexing step...Closes #1218. The problem was due to failure to index the archive in ES. The old error handling attempts to catch errors and index only a minimal record in ES in case of failures, but the problem was that errors from the ES indexing step itself were not caught. This merge extends the error handling to catch and handle also such errors.
One problem is that these errors may occur after the archive file has been written, so the error attributes might be set in ES but not in the archive file. To make sure that these errors can be viewed by the user, fixes are applied to the log view page in the UI, plus some improvements.David SikterDavid Sikterhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/990Resolve "Formal models, validation, and documentation for metainfo annotations"2023-02-22T10:04:52ZMarkus ScheidgenResolve "Formal models, validation, and documentation for metainfo annotations"Closes #1237Closes #1237https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1001Fix broken 404 app response.2022-12-20T15:53:28ZMarkus ScheidgenFix broken 404 app response.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/998Resolve "K8s doesn't work due to the missing rabbitmq chart"2022-12-20T21:53:41ZMarkus ScheidgenResolve "K8s doesn't work due to the missing rabbitmq chart"Closes #1247Closes #1247