nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2022-12-21T14:35:52Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/883Nexus examples downloads2022-12-21T14:35:52ZMarkus ScheidgenNexus examples downloadsI replaced the downloads in `generate_example_uplods.sh` with respective downloads that are done during processing. We are about to drastically reduce the size of our images and I do not want to loose these gains immediately. This also f...I replaced the downloads in `generate_example_uplods.sh` with respective downloads that are done during processing. We are about to drastically reduce the size of our images and I do not want to loose these gains immediately. This also fixes some of the issues in the examples and triggers `.nxs` processing while processing ELNs.Sherjeel ShabihSherjeel Shabihhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/882Resolve "Admin uploads cli is not showing empty uploads"2022-10-13T15:09:20ZMarkus ScheidgenResolve "Admin uploads cli is not showing empty uploads"Closes #1124Closes #1124https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/881Resolve "Instantiate a data file choosing among all inheriting sections"2022-10-13T08:22:41ZMarkus ScheidgenResolve "Instantiate a data file choosing among all inheriting sections"Closes #1116Closes #1116https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/880Allow creating archives from inside another archive's normalizer2022-10-13T12:25:29ZDavid SikterAllow creating archives from inside another archive's normalizerCloses #1118. Two methods are added to the `ServerContext` class:
- `raw_path_exists`, for determining if a file already exists
- `process_updated_raw_file`, which tells the processing framework that a file has been added or updated. Th...Closes #1118. Two methods are added to the `ServerContext` class:
- `raw_path_exists`, for determining if a file already exists
- `process_updated_raw_file`, which tells the processing framework that a file has been added or updated. This will cause the new/update file to be matched and processed (if a parser matches it). This method is intended to be used from the `normalize` or `parse` method.
Modifying existing files is allowed, but discouraged, as care needs to be taken so that we don't get infinite loops with files modifying each other. This is why I also added the `raw_path_exists` method, to make it easier to check this.
Technically, the solution works by allowing child processes to be non-blocking (this is to make it possible to modify existing files. An existing file might already be processing when the processing of another file causes it to be updated. What happens then is that the modified entry will be scheduled for reprocessing, and this time it should be guaranteed to see the modified version of the mainfile. This requires the child process to be non-blocking.).
I also changed the code of a failing gui test, and it _seems_ to have fixed the annoying problem we've had lately with seeing two "Save entry" buttons on the OverviewView page (though not entirely clear why the code fixes it).David SikterDavid Sikterhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/879Improved search UI and config2022-10-13T06:23:28ZLauri HimanenImproved search UI and configPart of #1113 that fixes the following:
- [x] The search results table does not support units at the moment.
- [x] An option to limit the number of significant digits in `config.py` displayed for a quantity would be good. (See the attac...Part of #1113 that fixes the following:
- [x] The search results table does not support units at the moment.
- [x] An option to limit the number of significant digits in `config.py` displayed for a quantity would be good. (See the attached screenshot as an example)
- [x] Pre-defined a search filter for looking only at a pre-filtered set of entries. i.e. results.material.functional_type=solar cell for looking at only Solar Cells in the solar cell app.Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/878Reference related issues.2022-10-13T05:51:55ZMarkus ScheidgenReference related issues.Fixes:
#985
#986
#1053
#1104Fixes:
#985
#986
#1053
#1104Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/877fixed duplicate log issue with gromacs parser2022-10-12T10:14:09ZJoseph Rudzinskifixed duplicate log issue with gromacs parserCloses #957Closes #957Alvin 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/875Add all inter-archive reference into archive metadata2022-10-12T06:10:37ZTheodore ChangAdd all inter-archive reference into archive metadata```
archive_references:
target_reference
target_entry_id
target_name
target_path
source_name
source_path
```
The detection of references is consistent with resolving in context.
Closes #999```
archive_references:
target_reference
target_entry_id
target_name
target_path
source_name
source_path
```
The detection of references is consistent with resolving in context.
Closes #999Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/874Resolve "Connecting with reference databases via celery"2022-12-05T13:56:23ZMarkus ScheidgenResolve "Connecting with reference databases via celery"Closes #789Closes #789https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/873Resolve "Add Wannier90 parser"2022-10-28T07:36:38ZJose PizarroResolve "Add Wannier90 parser"Closing #1115Closing #1115Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/872Add qe epw and phonon parsers #10342022-10-07T10:22:27ZAlvin Noe LadinesAdd qe epw and phonon parsers #1034Closes #1034Closes #1034Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/871Change to add doi to metadata reference only if it is not already there2022-10-07T07:45:54ZJose Marquez PrietoChange to add doi to metadata reference only if it is not already thereCloses #1105. Check if the reference is already in the metadata to avoid appending it again.Closes #1105. Check if the reference is already in the metadata to avoid appending it again.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/870Add support for identifying conventional cell from surfaces2022-10-07T09:59:39ZLauri HimanenAdd support for identifying conventional cell from surfacesCloses #909Closes #909Thea DenellThea Denellhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/869Resolve "Inherited subsections might break archive browser"2022-10-10T15:27:21ZMarkus ScheidgenResolve "Inherited subsections might break archive browser"Closes #1108Closes #1108https://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/867Draft: Ikz eln into develop2023-12-21T08:50:16ZSebastian BruecknerDraft: Ikz eln into developUpdate ikz_eln to 1.1.5Update ikz_eln to 1.1.5Sebastian BruecknerSebastian Bruecknerhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/866Nexus eln examples2022-12-21T14:50:27ZSherjeel ShabihNexus eln examplesSherjeel ShabihSherjeel Shabihhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/865Resolve "Workflow visualizer"2022-11-22T11:01:05ZAlvin Noe LadinesResolve "Workflow visualizer"Closes #1036Closes #1036https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/864Enabled materials search2022-10-04T09:49:23ZLauri HimanenEnabled materials searchCloses #1090Closes #1090