nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2022-07-12T11:23:54Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/752Improved metainfo browser GUI tests2022-07-12T11:23:54ZDavid SikterImproved metainfo browser GUI tests- Makes the gui tests in the CI pipeline run with the `--silent` flag, to reduce the noise.
- Changed the metainfo browser test to a pseudo-random walk. Rather than changing the timeout, in the future, we should adjust the probability de...- Makes the gui tests in the CI pipeline run with the `--silent` flag, to reduce the noise.
- Changed the metainfo browser test to a pseudo-random walk. Rather than changing the timeout, in the future, we should adjust the probability decay factor, which determines how many nodes will be visited.
- The test also computes a hash for the metainfo tree (the parts visited), to give the user a notice if the tree changes.
- If tree changes are expected, the user will have to update the test case with the new hash.
- Maybe requiring the user to update the hash in this way is a bit cumbersome, but let's test to see how it works.David SikterDavid Sikterhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/460Improved migrate cli2021-11-22T15:20:23ZDavid SikterImproved migrate cliA couple of small improvements of the migrate CLI command. Resolves #652 and #650.A couple of small improvements of the migrate CLI command. Resolves #652 and #650.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1075Improved overview UX2023-02-09T06:28:52ZLauri HimanenImproved overview UXImproved overview UX.
Closes #1312Improved overview UX.
Closes #1312Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/567Improved preview2022-02-22T07:49:02ZDavid SikterImproved previewSome minor fixes and improvements of the file browser and preview functionality:
- the `FilePreview` component is moved to a separate file
- code is refactored by introducing viewer objects, one for each file type we support. The viewer ...Some minor fixes and improvements of the file browser and preview functionality:
- the `FilePreview` component is moved to a separate file
- code is refactored by introducing viewer objects, one for each file type we support. The viewer object stores constant information, like matching file extensions, maxSizeAutoPreview etc, plus a `render` function.
- a viewer is introduced for json files (the same viewer used elsewhere).
- txt, yaml and yml files are automatically previewed with the text viewer
- error handling is added. If the viewer fails, we show a message and offers the user to view the file using the text viewer instead.
- optimizing the vertical file browser api calls, using the `include_entry_info` option instead of making a costly second api call.
- Highlighting the current entry mainfileMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/563Improved preview, including images and automatically previewing small files (...2022-02-16T07:43:48ZDavid SikterImproved preview, including images and automatically previewing small files (#738)Adds support for simple image preview, and paves the way for adding viewers for additional file types. Images are previewed automatically if they are small enough (<10 MB), otherwise the user has to request it by clicking on a preview bu...Adds support for simple image preview, and paves the way for adding viewers for additional file types. Images are previewed automatically if they are small enough (<10 MB), otherwise the user has to request it by clicking on a preview button. For text files (the fallback viewer) the user always has to press the button to open the viewer.
Also solves some issues with the text preview scrolling.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1306Improved resolution of system references in the visualizer, removed additiona...2023-05-23T10:07:01ZLauri HimanenImproved resolution of system references in the visualizer, removed additional comma.Closes #1508Closes #1508Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1266Improved searchability of systems2023-05-09T07:49:06ZLauri HimanenImproved searchability of systemsAdded atomic_fraction, mass_fraction to topologies, improved system_relation, exposed more topology quantities for search.
Closes #1474Added atomic_fraction, mass_fraction to topologies, improved system_relation, exposed more topology quantities for search.
Closes #1474Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1615Improved search bar2024-01-15T09:59:05ZLauri HimanenImproved search barCloses #1790, #1700Closes #1790, #1700Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/984Improved SearchBar customization and suggestions and added possibility to sel...2022-12-20T09:54:23ZLauri HimanenImproved SearchBar customization and suggestions and added possibility to select the active filters for each SearchContext.Closes #1224Closes #1224Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/202Improved search page layout, fixed issue in band structure plots not showing ...2020-11-02T13:39:13ZLauri HimanenImproved search page layout, fixed issue in band structure plots not showing all segment labels.You can check the changes in the beta deployment: https://nomad-lab.eu/prod/rae/beta/encyclopedia/#/searchYou can check the changes in the beta deployment: https://nomad-lab.eu/prod/rae/beta/encyclopedia/#/searchMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/201Improved search page layout, fixed issue in band structure plots not showing ...2020-11-02T13:01:53ZLauri HimanenImproved search page layout, fixed issue in band structure plots not showing all segment labels.You can check the changes in the beta deployment: https://nomad-lab.eu/prod/rae/beta/encyclopedia/#/searchYou can check the changes in the beta deployment: https://nomad-lab.eu/prod/rae/beta/encyclopedia/#/searchMarkus ScheidgenMarkus Scheidgenhttps://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/526Improved suggestions2022-01-19T10:49:38ZLauri HimanenImproved suggestionsFixes issue #718.Fixes issue #718.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/77Improved system_type detection2020-01-24T14:39:36ZLauri HimanenImproved system_type detectionAs per issue #257 I updated the system type detection to use the classifier implementation provided by MatID. It supports also a distinction between surfaces and 2D materials that cannot be made with just the periodicity check. I have in...As per issue #257 I updated the system type detection to use the classifier implementation provided by MatID. It supports also a distinction between surfaces and 2D materials that cannot be made with just the periodicity check. I have included a simple test case for all the supported types.
The change effectively splits the system type `"surface / 2D"` into `"surface"` and `"2D"`. This change is only tested at the normalization level, the changes in the GUI have not been checked.
The old system detection code was also using the periodic dimensions as a backup if the dimensionality check failed. This is now removed because the periodic dimensions do not reveal the correct system type (for computational reasons pretty much all calculations are made with fully periodic simulation cell. In reality the simulated system can however be isolated from periodic copies by vacuum). Thus if the system_check fails, the value is left as `unavailable`.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/214Improved the Encyclopedia API documentation, made the API input for chemical ...2020-11-20T06:15:46ZLauri HimanenImproved the Encyclopedia API documentation, made the API input for chemical elements into a list instead of a comma-separated string, added license boilerplate to the CLI command that generates the units.js file.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/444Improved the suggestion feature2021-11-04T08:08:57ZLauri HimanenImproved the suggestion featureIn the GUI we offer suggestions for certain index fields. These are implemented using the [ES Completion suggester feature](https://www.elastic.co/guide/en/elasticsearch/reference/6.8/search-suggesters-completion.html) which is a special...In the GUI we offer suggestions for certain index fields. These are implemented using the [ES Completion suggester feature](https://www.elastic.co/guide/en/elasticsearch/reference/6.8/search-suggesters-completion.html) which is a special feature built exactly for this kind of task.
Previously we were defining a new [ES field](https://www.elastic.co/guide/en/elasticsearch/reference/current/multi-fields.html) with the `completion` type in order to create these suggestions. This way the indexing of suggestion values comes pretty much for free and the index size is not affected too much. This means, however, that only one suggestion value was supported per quantity, which makes it impossible to make autocompletion suggestions if the user types e.g. a word in the middle of a keyword or string: e.g. typing `salt` would not create a suggestion for `rock salt`. Technically this is because the Completion suggester is based on a special graph data structure that can only start suggesting values from the beginning of a string.
To overcome this limitation, the default approach is to augment the suggestion values by adding several suggestion values at index time (examples of this discussion [here](https://discuss.elastic.co/t/completion-suggester-and-analyzer/13867), [here](https://www.elastic.co/blog/you-complete-me) and [here](https://taranjeet.medium.com/elasticsearch-using-completion-suggester-to-build-autocomplete-e9c120cf6d87)). **This merge request implements this mechanism by storing suggestions under `<quantity name>__suggestion` when the values need to be tokenized.**
The suggestion mechanism is selected by specifying a predefined string option (`suggestion="simple"`: the old behaviour, `suggestion="default"`: tokenization using whitespaces and underscores, `suggestion="formula"`: tokenization using formula fragments, `suggestion=<function>`: custom tokenization function). The old mechanism of storing a single suggestion string under a field is used when `suggestion="simple"`.
The downside of using a new index attribute instead of a field for each suggestion is that the index size becomes bigger and that the source documents look quite busy with all this new suggestion data. By default, the suggestion values are completely excluded from the source documents in all metadata searches. Depending on our experience with the index size, we can think about limiting suggestions, using a separate index for suggestions (really nasty), or experimenting with other suggestion mechanisms ([here is a really good article about all reasonable options](https://medium.com/@mourjo_sen/a-detailed-comparison-between-autocompletion-strategies-in-elasticsearch-66cb9e9c62c4)).Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/930Improvement definition id generation2022-11-08T12:44:33ZTheodore ChangImprovement definition id generationTheodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1539Improvement excited state workflows MethodNormalizer2023-11-07T10:28:48ZJose PizarroImprovement excited state workflows MethodNormalizerIn a recent merge for the `SimulationWorkflow.normalize()`, a different ordering was introduced for writting the inputs. I then adapted the MethodNormalizer part handling GW, BSE, XS workflows to handle these potential issues, such that ...In a recent merge for the `SimulationWorkflow.normalize()`, a different ordering was introduced for writting the inputs. I then adapted the MethodNormalizer part handling GW, BSE, XS workflows to handle these potential issues, such that now it scans the inputs and searches for one having the keyword `'method'` in the name.Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/960Improve parsing of trajectory in cpmd2022-12-07T15:56:46ZAlvin Noe LadinesImprove parsing of trajectory in cpmdCloses #1196Closes #1196https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/991Improve Projection methods2022-12-19T10:47:56ZJose PizarroImprove Projection methodsMoved HoppingMatrix to Method, while importing it in Calculation
Added Projection.orbitals_angular_momentum metainfo
New tests for Projection method
Closes #1238Moved HoppingMatrix to Method, while importing it in Calculation
Added Projection.orbitals_angular_momentum metainfo
New tests for Projection method
Closes #1238Jose PizarroJose Pizarro