nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2022-08-30T08:41:43Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/768Draft: Resolve "Improving the handling of numeric datatypes in the metainfo"2022-08-30T08:41:43ZLauri HimanenDraft: Resolve "Improving the handling of numeric datatypes in the metainfo"Closes #965Closes #965Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/794Draft: Resolve "Improve on gitlab ci/cd script"2022-08-30T09:18:24ZAdam FeketeDraft: Resolve "Improve on gitlab ci/cd script"Closes #935
- [ ] define environments for `staging` (aka `develop`) similarly to `dev`
- [ ] checking the rules because some of them does not make sense anymore (like: `$CI_COMMIT_REF_NAME =~ /^dev-.*$/`)
- [ ] checking the way how ini...Closes #935
- [ ] define environments for `staging` (aka `develop`) similarly to `dev`
- [ ] checking the rules because some of them does not make sense anymore (like: `$CI_COMMIT_REF_NAME =~ /^dev-.*$/`)
- [ ] checking the way how initialisation of submodules works
- [ ] get rid of docker login waning (`echo $CI_BUILD_TOKEN | docker login --username foo --password-stdin`)
- [ ] cleanup (eg. using `before_script` more often)
- [ ] regularly rebuild the image from scratch to avoid issues like #937 (--no-cache)Adam FeketeAdam Feketehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/788Draft: Plotly multi xaxies (#897)2022-09-02T13:35:43ZMohammad NakhaeeDraft: Plotly multi xaxies (#897)Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/675External references v1.1.02022-09-15T16:07:30ZAlvin Noe LadinesExternal references v1.1.0Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/833Fixes replacement of .nxdl at the end of the definition file2022-09-16T14:42:32ZFlorian DobenerFixes replacement of .nxdl at the end of the definition fileChange logic of ordering the replacement of cations in formulas to start with the shortest abbreviations firstChange logic of ordering the replacement of cations in formulas to start with the shortest abbreviations firstFlorian DobenerFlorian Dobenerhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/829Draft: Resolve "Error in gromacs parser pruning thermo data"2022-09-19T05:52:00ZJoseph RudzinskiDraft: Resolve "Error in gromacs parser pruning thermo data"Closes #1060
@himanel1 : You have to also merge the corresponding parser branch in atomistic. Wasn't sure if I needed to put in a merge request there as well.Closes #1060
@himanel1 : You have to also merge the corresponding parser branch in atomistic. Wasn't sure if I needed to put in a merge request there as well.Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/849Resolve "Docker image version tags are wrong"2022-09-26T10:36:58ZAdam FeketeResolve "Docker image version tags are wrong"Closes #1079Closes #1079Adam FeketeAdam Feketehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/838Draft: Resolve "Improve on python setup process"2022-09-26T11:05:22ZAdam FeketeDraft: Resolve "Improve on python setup process"Closes #1048Closes #1048Adam FeketeAdam Feketehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/854Draft: Resolve "Extended topology tests"2022-09-28T07:16:32ZThea DenellDraft: Resolve "Extended topology tests"Closes #1077Closes #1077Thea DenellThea Denellhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/855Draft: Resolve "Extended topology tests"2022-09-28T07:19:08ZThea DenellDraft: Resolve "Extended topology tests"Closes #1077Closes #1077Thea DenellThea Denellhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/868Draft: Resolve "Inherited subsections might break archive browser"2022-10-06T08:22:14ZMarkus ScheidgenDraft: Resolve "Inherited subsections might break archive browser"Closes #1108Closes #1108https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/779Resolve "Add support for identifying conventional cell from surfaces"2022-10-07T09:44:16ZThea DenellResolve "Add support for identifying conventional cell from surfaces"Closes #909Closes #909Thea DenellThea Denellhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/830Resolve "Connecting with reference databases"2022-10-07T14:29:56ZAlvin Noe LadinesResolve "Connecting with reference databases"Implement #789Implement #789Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/876Draft: Resolve "Standard output / Log file "duplication" for Molecular Dynami...2022-10-11T12:10:00ZJoseph RudzinskiDraft: Resolve "Standard output / Log file "duplication" for Molecular Dynamics data from Gromacs"Closes #957
issue fixed by adjusting regex mainfile command for gromacsCloses #957
issue fixed by adjusting regex mainfile command for gromacsAlvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/697Draft: Oasis link from local to central2022-10-19T14:22:24ZDaniel LehmbergDraft: Oasis link from local to centralRelates to #820 and #886
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...Relates to #820 and #886
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)Daniel LehmbergDaniel Lehmberghttps://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/784Draft: 820 nomad link (alternative implementation using asyncio)2022-10-19T14:22:57ZDaniel LehmbergDraft: 820 nomad link (alternative implementation using asyncio)Alternative implementation to !727
Here I add an asyncio task during the startup of the FastAPI (note: as of my knowledge it is mandatory to attach this to the main `app`, not to mounted ones).
#### Aspects:
* this solution sends the...Alternative implementation to !727
Here I add an asyncio task during the startup of the FastAPI (note: as of my knowledge it is mandatory to attach this to the main `app`, not to mounted ones).
#### Aspects:
* this solution sends the telemetry data at fixed intervals (for the middleware we need an API interaction to actually send again)
* ~~this requires a new package `fastapi_utils` with the `repeat_task` decorator~~ -- I implemented my own mechanism using only native functionality (from asyncio). So in the current implementation there is no py-package dependency (except the nest_asyncio within for testing coroutines)
See https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/727#note_140922 on what we agreed to collect and submit log entries.Daniel LehmbergDaniel Lehmberghttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/906Draft: Resolve "Add MSD plot to overview page for MD"2022-10-26T07:38:07ZJoseph RudzinskiDraft: Resolve "Add MSD plot to overview page for MD"Closes #1144Closes #1144Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/925Draft: Added possibility to add new widgets, started adding edit dialog valia...2022-11-04T14:04:47ZMohammad NakhaeeDraft: Added possibility to add new widgets, started adding edit dialog valiation,...Added possibility to add new widgets, started adding edit dialog valiation, fixed issue with D3 plot ids.
Related #961Added possibility to add new widgets, started adding edit dialog valiation, fixed issue with D3 plot ids.
Related #961Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/926Draft: ALF parser2022-11-08T12:56:37ZJose PizarroDraft: ALF parserCloses #1155Closes #1155Jose PizarroJose Pizarro