nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2022-10-20T05:57:45Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/891Resolve "DFT and ELN compatible search config"2022-10-20T05:57:45ZMarkus ScheidgenResolve "DFT and ELN compatible search config"Closes #1133Closes #1133Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/890Support for mounts and extra_hosts keyword in tools.json2022-10-20T06:54:46ZFlorian DobenerSupport for mounts and extra_hosts keyword in tools.jsonThis MR allows a mounts and extra_hosts keyword in the tools.json file to mount external directories and to pass additional hosts into the docker container.
See https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/blob/fhi-pcr...This MR allows a mounts and extra_hosts keyword in the tools.json file to mount external directories and to pass additional hosts into the docker container.
See https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/blob/fhi-pcr840/tools.json#L114 for an usage example.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/889Change style of references2022-10-19T07:55:48ZTheodore ChangChange style of referencesChange from `../entries/{entry_id}` to `../uploads/{upload_id}/archive/{entry_id}` style.
Closes #1120Change from `../entries/{entry_id}` to `../uploads/{upload_id}/archive/{entry_id}` style.
Closes #1120Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/888Resolve "Disable NORTH buttons on installations without NORTH"2022-10-18T15:02:19ZMarkus ScheidgenResolve "Disable NORTH buttons on installations without NORTH"Closes #1130Closes #1130Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/887Resolve "GW visualization"2022-10-27T12:42:19ZAlvin Noe LadinesResolve "GW visualization"addresses points 2 and 3 of #980addresses points 2 and 3 of #980Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/886Resolve "Problem with multiple quantities with only one to be read from Excel...2022-10-18T08:09:57ZAmir GolparvarResolve "Problem with multiple quantities with only one to be read from Excel file"Closes #1127Closes #1127Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/885Entry Search Dialog2022-12-02T15:33:49ZMohammad NakhaeeEntry Search DialogCloses #1020Closes #1020Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/884Resolve "Upload is stuck in status "Pending: process_upload""2022-10-19T13:57:16ZDavid SikterResolve "Upload is stuck in status "Pending: process_upload""Closes #1122. Uploads will get stuck in status PENDING if adding the celery task to the queue fails (for example if rabbitmq is down). This MR adds proper error handling (setting the `Proc` to status FAILED if the `@process`-task could n...Closes #1122. Uploads will get stuck in status PENDING if adding the celery task to the queue fails (for example if rabbitmq is down). This MR adds proper error handling (setting the `Proc` to status FAILED if the `@process`-task could not be added to the queue), and also updates the celery version to get more consistent behavior of the celery framework (the currently used version did not always raise an exception as expected).David SikterDavid Sikterhttps://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/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 Denell