nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2022-01-04T10:51:17Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/507Remove old upload edit api2022-01-04T10:51:17ZDavid SikterRemove old upload edit apiRemoves old method for editing just the metadata on the upload level. Also removed "calc" terminology from the UI (#708).Removes old method for editing just the metadata on the upload level. Also removed "calc" terminology from the UI (#708).Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/506Workflow2022-01-03T14:11:16ZAlvin Noe LadinesWorkflowMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/505Remove calc terminology from documentation2022-01-03T14:11:54ZDavid SikterRemove calc terminology from documentationRemoves all usages of calc-terminology from the documentation (part of #708).Removes all usages of calc-terminology from the documentation (part of #708).Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/504Archive reference2022-01-03T08:37:48ZAlvin Noe LadinesArchive referenceAdded task in workflow.Added task in workflow.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/503Improve the Users/{user_id} route2021-12-23T09:28:48ZMohammad NakhaeeImprove the Users/{user_id} routeIssue #673Issue #673Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/502Resolve "Resolve cross archive references in ArchiveBrowser"2021-12-23T14:49:53ZMarkus ScheidgenResolve "Resolve cross archive references in ArchiveBrowser"Closes #706Closes #706Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/501Minor fixes of the migration cli2022-01-03T08:41:19ZDavid SikterMinor fixes of the migration cliSome minor fixes for the migration cli. Some legacy attributes (namely `upload_path`, `upload_time`, `temporary` and `joined` on upload and the `metadata` dict on the entries) were not removed by the migration scripts. This has been fixe...Some minor fixes for the migration cli. Some legacy attributes (namely `upload_path`, `upload_time`, `temporary` and `joined` on upload and the `metadata` dict on the entries) were not removed by the migration scripts. This has been fixed now, and also did some minor changes to make the logging more consistent.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/500Simplify processing logic2021-12-21T15:54:59ZDavid SikterSimplify processing logicSimplifies the logic by reducing the number of sync operations to 2 (instead of 3). Items are only added to the queue if a process is already running, and they are popped off the queue when the task finishes.
Also ensures that the proce...Simplifies the logic by reducing the number of sync operations to 2 (instead of 3). Items are only added to the queue if a process is already running, and they are popped off the queue when the task finishes.
Also ensures that the processing should work even if the mongo document does not have any `queue` or `sync_counter` attribute set (for example when they have been migrated from v0).
Also restricts the resetting of existing entries when reprocessing to only the ones that actually have status processing, as it should not be necessary to reset any other entries (this should anyway really only happen if something has gone wrong).Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/499Updated GUI search layout2021-12-21T15:54:41ZLauri HimanenUpdated GUI search layout- Reorganized the menus so that each property-panel first has a simple list of present quantities followed by a more detailed section for properties that have more options.
- Added search filter for polarized/non-polarized DOS and band s...- Reorganized the menus so that each property-panel first has a simple list of present quantities followed by a more detailed section for properties that have more options.
- Added search filter for polarized/non-polarized DOS and band structure.
- Added method type filter for energy-volume curves.
- The EELS search criteria are now shown in two different locations: method/eels and properties/spectroscopy/eels. If we can make a clear distinction between properties/method (e.g. is resolution set by the method, or is it determined from the result?) for EELS, we could modify the shown filters.
- Updated the look of `FilterSummary` that contains the chips for each present filter: now the targeted metainfo name is always shown above the chips. This makes it easier to see which metainfo is targeted and also makes the nested and non-nested filters look exactly the same.
- Added support for requesting aggregations for boolean fields (needed to show statistics for boolean search filters).
- Fixed issue with InputSlider not being full-width.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/498Parser fixes issue #7012021-12-21T07:19:20ZAlvin Noe LadinesParser fixes issue #701Various parser fixes.Various parser fixes.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/497Merge for release v0.10.112021-12-20T16:08:53ZMarkus ScheidgenMerge for release v0.10.11https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/496Various metainfo related fixes and improvements.2021-12-20T15:39:15ZMarkus ScheidgenVarious metainfo related fixes and improvements.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/495Improved incremental processing and upload API2021-12-21T15:16:19ZDavid SikterImproved incremental processing and upload APICloses #587. Introduces an additional `path_filter` argument to the `process_upload` that enables limiting the processing to a specific path. This is used to optimize the API calls to put and delete individual files and folders at the sp...Closes #587. Introduces an additional `path_filter` argument to the `process_upload` that enables limiting the processing to a specific path. This is used to optimize the API calls to put and delete individual files and folders at the specified raw path.David SikterDavid Sikterhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/494Set gromacs parser to master.2021-12-20T10:03:41ZMarkus ScheidgenSet gromacs parser to master.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/493Clean API user metadata.2021-12-17T18:15:37ZMarkus ScheidgenClean API user metadata.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/492Clean API user metadata.2021-12-17T18:16:03ZMarkus ScheidgenClean API user metadata.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/491GUI improvement2021-12-17T11:05:35ZLauri HimanenGUI improvement- The suggestion list in the search bar now supports custom prioritization of items. I bumped up the priority of certain metainfo (elements, formulas, program name, author etc.)
- Improved the layout for `EntryDetails`: still not perfec...- The suggestion list in the search bar now supports custom prioritization of items. I bumped up the priority of certain metainfo (elements, formulas, program name, author etc.)
- Improved the layout for `EntryDetails`: still not perfect but better.
- Added number formatting (=separators) for the number of results.
- Improved the `Quantity`-component: now it automatically loads a preset based on the quantity name (this preset can still be overridden). This makes sure that quantities look identical no matter where they are used in the app. E.g. the quantities shown by `EntryDetails` and `OverviewView` were slightly different before, now they are identical and require less config.
- Added formatting for timestamps in the results list.
- Completely redesigned filter menu headers (see screenshot):
- The new headers are separated into two "levels": There is a topmost level that shows the common filter panel actions and can also show an overline title text. The second level is reserved for information and actions that are specific to the currently shown menu: it shows the menu title and can also show a list of actions.
- The resource (entries or materials) targeted by the currently active search context is now shown in the overline text of the main filter menu. This resource was not shown explicitly before e.g. in "Search your own data" or the dataset search page. If we want to enable materials search for these pages, it would be natural to make this simple title into a dropdown menu.
- The overline text in the submenu now shows the number of results. This allows the user to directly see the number of results when the submenu is open, but the number of results is never visible twice.
- I added a checkbox for directly filtering for `method_name` in the DFT, GW and EELS menus. With the new layout, there is now space for adding this checkbox along with other actions if needed.
- The filter header is now "sticky": it will not scroll along with the options. This ensures that the actions and the number of results are always shown.
- Added better scaling defaults for statistics.
- Now the "show more" button tracks the aggregation call and will be disabled when the items are loading (previously it was just disappearing incorrectly and there was no way to track the status of an individual aggregation request).
- Fixed issues in the statistics item sizing: `InputList` was sometimes loading an incorrect number of items and the title was overflowing in some extreme cases.
- I added `quantities` also to the materials index because the new Archive search panel was broken for materials search. If this causes ES space issues we could consider removing this data and then disabling the Archive search in materials search.
- Fixed issue with handling value changes in `InputRadio`.
- Added caching for dataset search page.
![example](/uploads/2276d8e0d967fa8b98aa42bb764b7f5b/example.jpg)Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/490Unify logic for setting metadata via files and via the api/process2021-12-17T10:51:03ZDavid SikterUnify logic for setting metadata via files and via the api/processCloses #694. With these changes, `MetadataEditRequestHandler` handles both metadata files and requests to edit metadata through the api/by calling `Upload.edit_upload_metadata`, and we thus have the same validation and json format in bot...Closes #694. With these changes, `MetadataEditRequestHandler` handles both metadata files and requests to edit metadata through the api/by calling `Upload.edit_upload_metadata`, and we thus have the same validation and json format in both cases. Setting metadata via the ArchiveParser is also disallowed, at least for now (if this should be allowed, we should probably use the same class also in this case). Also refactored `MetadataEditRequestHandler` a bit to make it use a simpler and more consistent terminology.David SikterDavid Sikterhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/489Resolve "v1 GUI raw files"2021-12-16T15:44:06ZMarkus ScheidgenResolve "v1 GUI raw files"Closes #692Closes #692Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/487Fixes after reprocessing #689 #6902021-12-16T12:16:39ZAlvin Noe LadinesFixes after reprocessing #689 #690Provided fixes for the list indicated in issues #689 #690Provided fixes for the list indicated in issues #689 #690Markus ScheidgenMarkus Scheidgen