nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2022-09-26T11:05:22Zhttps://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/837Fixed issue with converting units that start with a number2022-09-19T12:00:20ZLauri HimanenFixed issue with converting units that start with a numberCloses #1062Closes #1062Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/836Resolve "JS error in structure viewer is not caught"2022-09-20T08:00:23ZLauri HimanenResolve "JS error in structure viewer is not caught"Closes #1039Closes #1039Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/835Resolve "Error in gromacs parser pruning thermo data"2022-09-19T07:32:30ZLauri HimanenResolve "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/834Resolve "hotfix: blocked pipelline"2022-09-19T09:41:50ZAdam FeketeResolve "hotfix: blocked pipelline"Closes #1065Closes #1065Adam FeketeAdam Feketehttps://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/832Resolve "Fuse together User and Author eln annotations"2022-09-30T13:38:54ZMohammad NakhaeeResolve "Fuse together User and Author eln annotations"Closes #1057Closes #1057Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/831Archive browser full storage quantities2022-09-16T10:51:46ZMarkus ScheidgenArchive browser full storage quantitiesMarkus ScheidgenMarkus Scheidgenhttps://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/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/828Draft: Bring in latest Nexus features and corresponding ELNs2022-12-21T14:50:26ZSherjeel ShabihDraft: Bring in latest Nexus features and corresponding ELNsThis still does not have the IV_temp example. But I have tested it to work in a new nomad install.
TODOs:
- [ ] MPES container doesn't launch
- [x] Add IV temp example
- [x] Resolve dependency issues
- [ ] Make sure nexusparser function...This still does not have the IV_temp example. But I have tested it to work in a new nomad install.
TODOs:
- [ ] MPES container doesn't launch
- [x] Add IV temp example
- [x] Resolve dependency issues
- [ ] Make sure nexusparser functionality works on commit deployment
- [ ] Review by @kuehbachm
- [x] Review by @dflor
- [ ] Review by @ecaro
- [x] Update submodule for nomad-remote-tools
- [x] Update submodule for nomad-parser-nexus
- [x] Make issue for MetainfoError: Cannot serialize float64 quantitySherjeel ShabihSherjeel Shabihhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/827Updating api crossref gets to have timeouts and response handling2022-09-15T16:03:39ZJose Marquez PrietoUpdating api crossref gets to have timeouts and response handlingThe ELN base class `PublicationReference` has calls to retrieve data from the `crossref` API. This merge request set timeouts and a mailto within the `request.get` to fall into `polite` pool. This was necessary because the external API h...The ELN base class `PublicationReference` has calls to retrieve data from the `crossref` API. This merge request set timeouts and a mailto within the `request.get` to fall into `polite` pool. This was necessary because the external API has ofter some downtime that gets the processing of the uploads stuck.Jose Marquez PrietoJose Marquez Prietohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/826Resolve "Refactor the relationship between FileBrowser, various entry/upload ...2022-09-15T10:04:47ZDavid SikterResolve "Refactor the relationship between FileBrowser, various entry/upload views and their contexts"Final part of the refactor #828. The main idea is that instead of passing around changing context parameters in the browser, we use the data store, which acts like a kind of central cache/context, and we make sure that components keep tr...Final part of the refactor #828. The main idea is that instead of passing around changing context parameters in the browser, we use the data store, which acts like a kind of central cache/context, and we make sure that components keep track of urls indicating "where they are", and use these when they need to resolve any references etc. The resolving logic is also made more explicit, by instead of methods like `resolveRef` and `resolveRefAsync` using methods with a bit more narrow functionality and clearer and well-documented interface. Usually resolving a reference is now a two-stage process, first using `resolveNomadUrl` to calculate a url and then using the store to fetch the data, which forces the code to be very specific/explicit. Also fixes some sporadically failing gui and python tests.David SikterDavid Sikterhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/825Resolve "Align metainfo with nexus even more"2022-09-30T10:06:21ZTheodore ChangResolve "Align metainfo with nexus even more"Closes #1037
Closes #1050
Closes #1086Closes #1037
Closes #1050
Closes #1086Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/824Resolve "quantity type "string" failing in yaml schema"2022-09-23T10:25:37ZMohammad NakhaeeResolve "quantity type "string" failing in yaml schema"Closes #1001Closes #1001Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/823Added tests for custom schema with Solar cell base section and parsing2022-09-12T12:42:23ZJose Marquez PrietoAdded tests for custom schema with Solar cell base section and parsingCloses #1023
Test coverage for the parsing and normalizing of the Solar Cell ELN base classes.
@himanel1 could you look at this or suggest somebody that could? Thanks a lot and sorry for asking too much!Closes #1023
Test coverage for the parsing and normalizing of the Solar Cell ELN base classes.
@himanel1 could you look at this or suggest somebody that could? Thanks a lot and sorry for asking too much!Jose Marquez PrietoJose Marquez Prietohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/822Resolve "Beta deployment (staging) getting stuck in nomad loading logo in som...2022-09-13T09:50:05ZMohammad NakhaeeResolve "Beta deployment (staging) getting stuck in nomad loading logo in some devices"Closes #1042Closes #1042Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/821Draft: Base section for crystal structure file parsing into the metainfo2023-02-15T10:02:00ZJose Marquez PrietoDraft: Base section for crystal structure file parsing into the metainfoA nomad User asked about how he could deposit crystal structure files from a structure generative ML model into nomad. Whilst the general discussion about how we are going to design a workflow for ML-generated data is gonna take some tim...A nomad User asked about how he could deposit crystal structure files from a structure generative ML model into nomad. Whilst the general discussion about how we are going to design a workflow for ML-generated data is gonna take some time, I have created a base class to parse structure files into the nomad metainfo. At the moment, it writes the `run.system` section, but I understand from the discussion in #1038 that the section run is reserved for DFT codes. Should it be ok to put a System section in `data` and the parse this to Results?
@mscheidg @himanel1, any advice on how would you approach this?
Thanks!Jose Marquez PrietoJose Marquez Prietohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/820Reinstated the delta unit check, fixed issue in delta unit serialization and...2022-09-09T08:05:14ZLauri HimanenReinstated the delta unit check, fixed issue in delta unit serialization and...Reinstated the delta unit check, fixed issue in delta unit serialization and deserialization, extended tests.
Closes #1043Reinstated the delta unit check, fixed issue in delta unit serialization and deserialization, extended tests.
Closes #1043Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/819Resolve "Show working references in ELNs"2022-09-22T07:28:28ZMarkus ScheidgenResolve "Show working references in ELNs"Closes #1015Closes #1015Markus ScheidgenMarkus Scheidgen