nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2022-06-28T09:53:14Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/736Fixing linting warnings (using 'const' instead of 'let' when possible)2022-06-28T09:53:14ZDavid SikterFixing linting warnings (using 'const' instead of 'let' when possible)Fixes linting warnings introduced by the upgrade of the linter to a newer version. (These warnings were previously ignored).Fixes linting warnings introduced by the upgrade of the linter to a newer version. (These warnings were previously ignored).Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/735Resolve "Unexpected error: "Cannot read properties of undefined (reading 'fil...2022-06-27T15:20:28ZDavid SikterResolve "Unexpected error: "Cannot read properties of undefined (reading 'filter')"."Closes #912Closes #912Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/734Added support for nexusparser parameter files in h5web2022-06-28T09:54:13ZSherjeel ShabihAdded support for nexusparser parameter files in h5webSherjeel ShabihSherjeel Shabihhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/733Resolve "Hash based ids for metainfo definitions"2022-07-05T08:24:28ZTheodore ChangResolve "Hash based ids for metainfo definitions"- [x] Support exporting `m_def_id` with `m_def` controlled by the `with_def_id` flag.
- [x] Support exporting `definition_id` in schemas.
- [x] Add detection of `m_def_id`, in case of mismatch, retrieve the corresponding package via `Con...- [x] Support exporting `m_def_id` with `m_def` controlled by the `with_def_id` flag.
- [x] Support exporting `definition_id` in schemas.
- [x] Add detection of `m_def_id`, in case of mismatch, retrieve the corresponding package via `Context`
- [x] Add detection of definition id in plain reference, covering both python style (`nomad.metainfo.SampleSection@1a2b3c4d`) and url style (`http://my.domain#/path/to/definition@1a2b3c4d`).Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/732Resolve "Finetuning to nomad oasis' docker-compose"2022-08-25T06:51:30ZAdam FeketeResolve "Finetuning to nomad oasis' docker-compose"Closes #930Closes #930https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/731Update various dependencies to newer versions, including h5web.2022-06-27T09:40:34ZDavid SikterUpdate various dependencies to newer versions, including h5web.Updates a couple of the core dependencies, notably `react-scripts` and h5web (#900), to a newer version. Almost all dev dependencies are also upgraded. This makes the linting more sensitive/accurate, so various linting errors needed to b...Updates a couple of the core dependencies, notably `react-scripts` and h5web (#900), to a newer version. Almost all dev dependencies are also upgraded. This makes the linting more sensitive/accurate, so various linting errors needed to be fixed, and some less relevant warnings have been disabled. These changes should pave the way for an upgrade of the react library.
Note, requires a more recent version of node than previously used in the CI docker, and also more recent than what comes with the current standard installation of e.g. Ubuntu.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/730Concurrent editing (#841)2022-07-01T06:11:07ZMohammad NakhaeeConcurrent editing (#841)Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/729Resolve "Encyclopedia 2D and 1D visualization improvement"2022-06-24T09:40:50ZLauri HimanenResolve "Encyclopedia 2D and 1D visualization improvement"Closes #923Closes #923Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/728Editable Archive2022-06-23T06:33:29ZMohammad NakhaeeEditable ArchiveMohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/727Draft: Nomad link to send installation information from local to central2022-10-19T14:22:24ZDaniel LehmbergDraft: Nomad link to send installation information from local to centralRelates to #820 and #886 (substitues MR !697)
### There is also an alternative implementation which overcomes some of the issues raised in the code review -- !784
So far I set up the following structure with stub methods/classes:
...Relates to #820 and #886 (substitues MR !697)
### There is also an alternative implementation which overcomes some of the issues raised in the code review -- !784
So far I set up the following structure with stub methods/classes:
* `SubmitInstallationInfoToCentral` is currently the class to frequently send data from local to central (it is used in the FastAPI middleware `submit_installation_info`)
* The module (/ FastAPI router) `federation.py` contains the REST/POST where the local Nomad installation sends the data to / central Nomad receives the data.
* The `InstallationInfo` class specifies the content and format that is sent from local to central.
* in `test_federation.py` there are two tests and conftest.py (at same level) includes fixtures to set up the testing for federation
To clarify (for myself to keep track, but also happy to get comments/hints on these issues):
* [x] ~~Could there be a race condition on the "last_timestamp" in `SubmitInstallationInfoToCentral`?~~
* [x] Is there a flag to distinguish between the local and central OASIS? This way I would only provide the landscape/POST on the central oasis. (not yet, for now also provide the federation API on local installations)
* [ ] How to get all of the data to submit? oasis id [OK], oasis url [OK], oasis maintainer [OK], nomad version [OK], and a few "telemetry" data [OPEN]
* [x] How to use mongodb (to be used within `federation.py`) to store the data at central Nomad?
* [ ] `RuntimeError('This event loop is already running')` still appears when not using the `nest_asyncio` package (the import is limited to `test_federation.py` only though)
* [ ] option to turn feature on/off?
* [ ] What if the frequency to submit data is set to very low in the configuration? Set a minimum value in the source code and make a warning?Daniel LehmbergDaniel Lehmberghttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/726Resolve "Encyclopedia GUI update"2022-06-22T06:06:25ZLauri HimanenResolve "Encyclopedia GUI update"Closes #917Closes #917Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/725Partially selected entries in edit meta dialog (#859)2022-06-21T06:13:57ZMohammad NakhaeePartially selected entries in edit meta dialog (#859)Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/724Fixed docker-compose oasis to support north.2022-06-20T13:57:11ZMarkus ScheidgenFixed docker-compose oasis to support north.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/723Unit Conversion (#882)2022-07-04T07:03:51ZMohammad NakhaeeUnit Conversion (#882)Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/722Use joblib2022-06-21T06:13:09ZTheodore ChangUse joblibCloses #898Closes #898Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/721Resolve "Not all normalize functions are called with multiple base sections"2022-06-16T12:47:17ZMarkus ScheidgenResolve "Not all normalize functions are called with multiple base sections"Closes #907Closes #907https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/720Resolve "Parsing .xlsx files from yaml schema"2022-07-18T09:37:48ZAmir GolparvarResolve "Parsing .xlsx files from yaml schema"Closes #899Closes #899https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/719Resolve "Datetime is not correctly parsed from the tabular file"2022-06-16T10:05:57ZAmir GolparvarResolve "Datetime is not correctly parsed from the tabular file"Closes #901Closes #901https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/718axis with no unit (#881)2022-06-16T06:29:14ZMohammad Nakhaeeaxis with no unit (#881)Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/717Resolve "Encyclopedia GUI is not authenticating with the API (even if the use...2022-06-16T06:29:46ZLauri HimanenResolve "Encyclopedia GUI is not authenticating with the API (even if the user is logged in)"Closes #750Closes #750Markus ScheidgenMarkus Scheidgen