nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2022-11-16T05:56:40Zhttps://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/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 Sikterhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/938Hall schema for IKZ2023-03-01T08:10:03ZAndrea AlbinoHall schema for IKZhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/937Resolve "Drag and drop uses the old uploaded data"2022-11-10T16:22:08ZDavid SikterResolve "Drag and drop uses the old uploaded data"Closes #1103. The problem was that even though the `CreateEntry` button does try to refresh the options in the list whenever the upload is reprocessed, it did so without clearing the DataStore caches. This caused it to still show old dat...Closes #1103. The problem was that even though the `CreateEntry` button does try to refresh the options in the list whenever the upload is reprocessed, it did so without clearing the DataStore caches. This caused it to still show old data in the drop down.David SikterDavid Sikterhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/936> Fixed regex fermi_level in FHIaims2022-11-10T12:33:21ZJose Pizarro> Fixed regex fermi_level in FHIaimsCloses #939Closes #939https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/934Fixes in eqe parser2022-11-17T14:35:08ZJose Marquez PrietoFixes in eqe parserIncludes some fixes in the EQE parsers:
- It does not allow to return of an Urbach energy of it is negative or larger than 0.5 eV.
- The EQE LN base class logs the error of the fit of the Urbach energy.Includes some fixes in the EQE parsers:
- It does not allow to return of an Urbach energy of it is negative or larger than 0.5 eV.
- The EQE LN base class logs the error of the fit of the Urbach energy.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/933Overview reference card2022-11-14T14:20:08ZTheodore ChangOverview reference cardTheodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/932Add missing information2022-11-17T13:27:28ZTheodore ChangAdd missing informationClose #1168Close #1168Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/931Keep track of exact data path in the archive browser2022-11-08T12:37:52ZDavid SikterKeep track of exact data path in the archive browserCloses #1166. Until now, it hasn't been necessary to keep track of the exact path in the browser, but for handling bi-directional references etc, having the exact path is necessary. Changes the Adaptor code to use the exact url of obj, r...Closes #1166. Until now, it hasn't been necessary to keep track of the exact path in the browser, but for handling bi-directional references etc, having the exact path is necessary. Changes the Adaptor code to use the exact url of obj, rather than just providing a baseUrl that enables us to resolve references. Also fixes the recursive browsing gui tests so they expand collapsed compartments.David SikterDavid Sikterhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/930Improvement definition id generation2022-11-08T12:44:33ZTheodore ChangImprovement definition id generationTheodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/929Added plot actions2022-11-14T07:46:20ZMohammad NakhaeeAdded plot actionsAdded plot actions together with widget actions
Related to #961Added plot actions together with widget actions
Related to #961Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/927Resolve "ELN: Overwriting exsiting archives"2022-11-10T09:54:42ZDavid SikterResolve "ELN: Overwriting exsiting archives"Closes #1069. The button for creating new ELN archives does not allow the creation if a file by the same name already exists. Also fixed proper error messages when moving or copying files cannot be carried out because the target already ...Closes #1069. The button for creating new ELN archives does not allow the creation if a file by the same name already exists. Also fixed proper error messages when moving or copying files cannot be carried out because the target already exists. Also extended the timeout for two long-running gui tests that often fail the CI.David SikterDavid Sikterhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/924Resolve "Items lists in results table do not display correctly"2022-11-03T12:50:34ZLauri HimanenResolve "Items lists in results table do not display correctly"Closes #1158Closes #1158https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/923Updated materia submodule.2022-11-03T13:44:22ZLauri HimanenUpdated materia submodule.Closes #1163Closes #1163https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/922Enable metainfo version hashes in the GUI2022-11-17T20:28:34ZDavid SikterEnable metainfo version hashes in the GUICloses #1135. Enables the GUI to handle schema urls that have version hashes in them ("frozen schemas"). Frozen schemas are fetched using a special api endpoint, which fetches an entire frozen version of a package containing the versionH...Closes #1135. Enables the GUI to handle schema urls that have version hashes in them ("frozen schemas"). Frozen schemas are fetched using a special api endpoint, which fetches an entire frozen version of a package containing the versionHash requested. During parsing, all loaded frozen definitions are stored in a cache, indexed by the version hash, which is used when resolving references. For now, this cache just accumulates definitions, and is never cleared (as the frozen schemas should be static, the only reason we might want to clear the cache is if we want to save memory, but the schemas should hopefully not take up much memory). The reason for not clearing the cache is that we want to keep the current python schema hashes in the cache.
The merge has no real effect unless the version hash functionality is enabled in `config.py`.David SikterDavid Sikter