nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2021-05-03T11:07:42Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/326Implemented new wien2k parser2021-05-03T11:07:42ZAlvin Noe LadinesImplemented new wien2k parserMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/353Restructured spectrum data for XPS parser2021-06-09T13:37:00ZPrateek GoelRestructured spectrum data for XPS parserSupplemental channel data (those other than energy and count) are put together in a 2D array. Also fixed some test stuff.Supplemental channel data (those other than energy and count) are put together in a 2D array. Also fixed some test stuff.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/406Draft: Resolve "Exception in NOMAD parser when run from the files directory"2021-10-06T14:46:14ZMohammad NakhaeeDraft: Resolve "Exception in NOMAD parser when run from the files directory"Closes #537Closes #537v1.0.0-betaMohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/407Fix a bug concerning outcar parser2021-10-06T14:58:58ZMohammad NakhaeeFix a bug concerning outcar parserThis bug was discussed in issue #537
It returns an empty file name when we pass the file name as its argument
The problem was solved by using the absolute pathThis bug was discussed in issue #537
It returns an empty file name when we pass the file name as its argument
The problem was solved by using the absolute pathhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/410Rebased with v1.0.0 and added support for upload selection and launch token f...2021-10-08T06:57:30ZLauri HimanenRebased with v1.0.0 and added support for upload selection and launch token forwarding.- Rebased with v1.0.0 to get access to the improved Datatable used in upload selection for NORTH
- New layout for NORTH main page that includes the selection of an upload against which a tool is launched.
- Added the retrieval of a launc...- Rebased with v1.0.0 to get access to the improved Datatable used in upload selection for NORTH
- New layout for NORTH main page that includes the selection of an upload against which a tool is launched.
- Added the retrieval of a launch token for a selected upload, token gets added to the NORTH instance launch call.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/425Changing Calc.external_id to a list and rename it to external_ids2021-10-20T06:52:28ZDavid SikterChanging Calc.external_id to a list and rename it to external_idsAllows the user to store multiple external ids for the same entry by turning it into a list, rather than a single string.Allows the user to store multiple external ids for the same entry by turning it into a list, rather than a single string.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/437Adding support for automatic fixing of bad entry ids2021-10-29T07:59:09ZDavid SikterAdding support for automatic fixing of bad entry idsAdded checks that the entry's id matches the generated one (by examining the prod DB, I found two entries where this has happened). If amismatch is found, specifying --fix-problems will replace the id with the correct one during the conv...Added checks that the entry's id matches the generated one (by examining the prod DB, I found two entries where this has happened). If amismatch is found, specifying --fix-problems will replace the id with the correct one during the conversion.
Also fixed a typo and improved doc.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/442Froze most of the requirements.txt packages.2021-10-29T12:18:06ZMarkus ScheidgenFroze most of the requirements.txt packages.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/461Draft: remove owner key from the query2021-11-23T10:21:44ZLauri HimanenDraft: remove owner key from the query- All the functionality of the `EncyclopediaNormalizer` is now integrated into `ResultsNormalizer`.
- Updated `materia` to support visualizing 2D and 1D cells that may have zero-length basis vectors. With this update, the overview page n...- All the functionality of the `EncyclopediaNormalizer` is now integrated into `ResultsNormalizer`.
- Updated `materia` to support visualizing 2D and 1D cells that may have zero-length basis vectors. With this update, the overview page now also shows the conventional/primitive cell for 1D and 2D systems.
- Fixed issue with the ordering of basis vectors for conventional/primitive 1D and 2D structures. Now the order is fixed so that the periodic bases always come first.
- Migrated `test_encyclopedia.py` into `test_material.py`, `test_method.py` and `test_properties.py`. together with a few new tests.
- Removed the Encyclopedia GUI image dependency and docker build phase.
- Removed most Encyclopedia related config from nginx, helm and config.py. The only remaining config is `encyclopediaEnabled`, which activates/deactivates links to the material search and material-related links.
- Fixed issue where the optional `nmd`-prefixed Optimade data was not accepting data with unit information (`ureg.Quantity`) and was failiing when trying to serialize data set to `None`.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/436Added nexus parser2021-11-26T09:47:52ZSandor BrockhauserAdded nexus parserhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/466Draft: Adding the nexusparser2021-12-14T07:59:10ZMarkus ScheidgenDraft: Adding the nexusparserhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/510Refactor calc terminology2022-01-06T12:28:16ZDavid SikterRefactor calc terminologyChanges `calc_id` and `calc_hash` to `entry_id` and `entry_hash` in mongo and the archive. `calc_id` is still indexed in ES and works in the api, for legacy reasons. We do no longer use `calc_id` in our code, however. Also, variables, fu...Changes `calc_id` and `calc_hash` to `entry_id` and `entry_hash` in mongo and the archive. `calc_id` is still indexed in ES and works in the api, for legacy reasons. We do no longer use `calc_id` in our code, however. Also, variables, function names and doc using "calc-terminology" are updated to "entry-terminology", when appropriate.
The data migration script is also updated accordingly. Additionally cleaning up celery queue argument which does not seem to be used, and ordering the strings in `available_properties`.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/512Draft: Hotfix to worker_hostname handling.2022-01-06T12:38:00ZMarkus ScheidgenDraft: Hotfix to worker_hostname handling.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/516Draft: Publish fixes2022-01-11T12:39:34ZMohammad NakhaeeDraft: Publish fixesIssue #709 section 1Issue #709 section 1Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/525Draft: Resolve "Search suggestions improvement"2022-01-18T06:49:45ZLauri HimanenDraft: Resolve "Search suggestions improvement"Closes #718Closes #718Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/530Draft: Resolve "Workflow search"2022-01-19T15:59:25ZLauri HimanenDraft: Resolve "Workflow search"Closes #721Closes #721Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/532Resolve "Documentation review"2022-01-26T14:15:51ZThea DenellResolve "Documentation review"Closes #716Closes #716Thea DenellThea Denellhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/485adding nexus parser2022-01-27T13:07:56ZSandor Brockhauseradding nexus parser- nexus metainfo and parser as a submodule from github repo
- handling submodules recursively to support nexus definitions inside nexusparser
Closes #672- nexus metainfo and parser as a submodule from github repo
- handling submodules recursively to support nexus definitions inside nexusparser
Closes #672https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/554Resolve "GUI search fixes"2022-02-03T07:40:39ZLauri HimanenResolve "GUI search fixes"Closes #733Closes #733Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/550Draft: Section editor (#719)2022-02-19T12:57:39ZMohammad NakhaeeDraft: Section editor (#719)Mohammad NakhaeeMohammad Nakhaee