nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2022-02-23T07:22:20Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/565Optimize ArchiveReader read disk performance2022-02-23T07:22:20ZTheodore ChangOptimize ArchiveReader read disk performanceCloses #751Closes #751Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/566H5web north2022-02-21T07:59:37ZSandor BrockhauserH5web northhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/567Improved preview2022-02-22T07:49:02ZDavid SikterImproved previewSome minor fixes and improvements of the file browser and preview functionality:
- the `FilePreview` component is moved to a separate file
- code is refactored by introducing viewer objects, one for each file type we support. The viewer ...Some minor fixes and improvements of the file browser and preview functionality:
- the `FilePreview` component is moved to a separate file
- code is refactored by introducing viewer objects, one for each file type we support. The viewer object stores constant information, like matching file extensions, maxSizeAutoPreview etc, plus a `render` function.
- a viewer is introduced for json files (the same viewer used elsewhere).
- txt, yaml and yml files are automatically previewed with the text viewer
- error handling is added. If the viewer fails, we show a message and offers the user to view the file using the text viewer instead.
- optimizing the vertical file browser api calls, using the `include_entry_info` option instead of making a costly second api call.
- Highlighting the current entry mainfileMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/568Parsers2022-03-15T12:32:30ZAlvin Noe LadinesParsers1. Implemented new full parsers: gamess, tinker, qbox, onetep, dftbplus, fleur, siesta
2. Group parsers into: electronic, atomistic, workflow
3. Move parser initialization to nomad
4. Move gw results to calculation
5. Various minor fixes1. Implemented new full parsers: gamess, tinker, qbox, onetep, dftbplus, fleur, siesta
2. Group parsers into: electronic, atomistic, workflow
3. Move parser initialization to nomad
4. Move gw results to calculation
5. Various minor fixesMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/569Moved dcat to fastapi. Added dois to dcat. Removed flask_restplus.2022-02-22T07:22:44ZMarkus ScheidgenMoved dcat to fastapi. Added dois to dcat. Removed flask_restplus.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/570Draft: Resolve "Material UI"2023-12-21T08:49:47ZLauri HimanenDraft: Resolve "Material UI"Closes #753Closes #753Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/571Draft: edit Quantity (#740)2022-02-24T13:31:04ZMohammad NakhaeeDraft: edit Quantity (#740)Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/572Resolve "Archive API raised 500 if NaN values are present"2022-02-25T07:21:16ZMarkus ScheidgenResolve "Archive API raised 500 if NaN values are present"Closes #754Closes #754Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/573Making file browser editable2022-02-25T07:25:50ZDavid SikterMaking file browser editableExtending the browser with basic edit functionality. For now, when a something is added or deleted, a dialog shows up and blocks further actions until processing is complete. This "modal" dialog is defined in `Browser.js`, and some codec...Extending the browser with basic edit functionality. For now, when a something is added or deleted, a dialog shows up and blocks further actions until processing is complete. This "modal" dialog is defined in `Browser.js`, and some codechanges have also been made to allow rerendering (and possibly re-fetching data via the api) of adaptors/lanes even when the path is the same. This part needs more work, though.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/574Resolve "Metainfo search is broken in v1"2022-03-01T12:57:13ZMarkus ScheidgenResolve "Metainfo search is broken in v1"Closes #752Closes #752Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/575Add support for dropping files for file reference quantities2022-03-02T08:26:25ZDavid SikterAdd support for dropping files for file reference quantitiesAdds an EditQuantity-component for file reference quantities. The component allows the user to select/drop local files and upload them.Adds an EditQuantity-component for file reference quantities. The component allows the user to select/drop local files and upload them.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/576Resolve "NOMAD Oasis with keycloak"2022-03-01T13:21:08ZMarkus ScheidgenResolve "NOMAD Oasis with keycloak"Closes #758Closes #758Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/577EditQuantity components (#740)2022-03-14T10:15:12ZMohammad NakhaeeEditQuantity components (#740)Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/578TinyMCE as a rich text edit2022-03-02T08:26:24ZSherjeel ShabihTinyMCE as a rich text editCurrently, we save the images dropped as base64 strings. This should be replaced with URLs to binary files once other things are sorted that can allow that.
I have also added a Nomad skin to TinyMCE. All of this can be moved in a better...Currently, we save the images dropped as base64 strings. This should be replaced with URLs to binary files once other things are sorted that can allow that.
I have also added a Nomad skin to TinyMCE. All of this can be moved in a better build routine as you feel it fits better.Sherjeel ShabihSherjeel Shabihhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/579Add pdf preview and improved memoizing2022-03-04T09:35:30ZDavid SikterAdd pdf preview and improved memoizingAdds viewer for pdf files.Adds viewer for pdf files.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/580Merge for release v1.0.32022-03-03T08:21:14ZMarkus ScheidgenMerge for release v1.0.3https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/581edit quantity components (#719)2022-03-04T13:54:24ZMohammad Nakhaeeedit quantity components (#719)Modules have been splitted to separate filesModules have been splitted to separate filesMohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/582Edit Quantity Components (#740)2022-03-05T08:50:17ZMohammad NakhaeeEdit Quantity Components (#740)Origin: #719Origin: #719Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/583Resolve "Improve ArchiveReader performance"2022-03-20T23:10:59ZTheodore ChangResolve "Improve ArchiveReader performance"Closes #747
Use anyio to implement async file I/O.
anyio handles nested event loops well (celery + asyncio).Closes #747
Use anyio to implement async file I/O.
anyio handles nested event loops well (celery + asyncio).Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/584Resolve "ElasticSearch upgrade for v1.x"2022-03-18T13:22:27ZLauri HimanenResolve "ElasticSearch upgrade for v1.x"Closes #760
@mscheidg: Luckily I did not have to change that much, see the issue for the changes I did. How do we go from here? Will you just merge and then we deploy this to beta? The old indices should work, at least that's what [ES s...Closes #760
@mscheidg: Luckily I did not have to change that much, see the issue for the changes I did. How do we go from here? Will you just merge and then we deploy this to beta? The old indices should work, at least that's what [ES says in their docs](https://www.elastic.co/guide/en/elasticsearch/reference/7.17/breaking-changes-7.0.html#_indices_created_before_7_0).Lauri HimanenLauri Himanen