nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2022-07-22T13:57:02Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/753Resolve "Add Pandas object (datatype) support to NOMAD"2022-07-22T13:57:02ZAmir GolparvarResolve "Add Pandas object (datatype) support to NOMAD"Closes #501Closes #501Amir GolparvarAmir Golparvarhttps://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/751Resolve "Hash based ids for metainfo definitions"2022-07-18T15:20:52ZTheodore ChangResolve "Hash based ids for metainfo definitions"Closes #843Closes #843Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/750Draft: Sample ID ELn base class draft2022-07-14T13:34:08ZJose Marquez PrietoDraft: Sample ID ELn base class draftThis is a draft for having a Sample ID base class. Discussions about its content have been carried out within the frame of [Area A](https://github.com/FAIRmat-Experimental/Area_A_application_definitions/issues/1). At the moment, the Refe...This is a draft for having a Sample ID base class. Discussions about its content have been carried out within the frame of [Area A](https://github.com/FAIRmat-Experimental/Area_A_application_definitions/issues/1). At the moment, the Reference in children and parents' quantities does not seem to work. Additionally, `results.eln.lab_ids` does not seem to be populated, or at least I do not seem to be able to see it in search entries in the gui.
This is a good opportunity also to start discussing a strategy to start writing these base classes. I attach a yaml schema to test it.
[sample_id_test.schema.archive.yaml](/uploads/5df01a9f31deec43bfc4d009bfa6936d/sample_id_test.schema.archive.yaml)Jose Marquez PrietoJose Marquez Prietohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/749Perovskite Solar Cell database schema with ELN functionality2022-07-22T05:50:17ZJose Marquez PrietoPerovskite Solar Cell database schema with ELN functionalityThis draft contains a metainfo schema of the [Perovskite Database](https://www.perovskitedatabase.com/) with ELN annotations.
The schema contains several normalizers that populate quantities in `Results`. It also contains extra tools li...This draft contains a metainfo schema of the [Perovskite Database](https://www.perovskitedatabase.com/) with ELN annotations.
The schema contains several normalizers that populate quantities in `Results`. It also contains extra tools like:
1. `formula_converte.py` which converts formulas with soma abbreviations like `MA` to the chemical representation of the cations: CH3NH3.
2. `eqe_importer.py` which reads exemplary eqe files and does some parsing, and derivation of extra quantities.
3. `jv_reader.py` is a very specific reader of J-V data of a lab for demonstration purposes which is used to populate quantities in the schema.
4. `entry_writer.py` is a tool that was used to convert the entries in the .csv of the original database to archive.json type entries.
Additionally, an Optoelectronic subsection has been created in `Results` that also contains a more specific SolarCell generalized subsection. The goal of this subsection is to accommodate any solar cell data in the future regardless of the technology.
To discuss:
At the moment, I have doubts about whether or not we should display the PerovskiteSolarCell schema in ELN mode or not. The reason for it is that as we replicated the original schema of the database, some quantities are not ideal, e.g. many numeric quantities being `str` type because the database for this field contained numbers separated by `'|'` and so on.
An alternative would be to disable the ELN annotations in this schema and create solar cell base classes with ELN annotations that could be re-used in future versatile solar cell-based schemas.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/747Resolve "Docker image doesn't work"2022-07-05T09:22:07ZMarkus ScheidgenResolve "Docker image doesn't work"Closes #937Closes #937https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/746file preview (#873)2022-07-18T13:44:12ZMohammad Nakhaeefile preview (#873)Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/745Additional refactoring for #8282022-07-05T07:15:15ZDavid SikterAdditional refactoring for #828- Adds utilities for parsing and normalizing nomad urls
- renames `UploadContext` and `EntryContext` to the more descriptive `UploadPageContext` and `EntryPageContext`.- Adds utilities for parsing and normalizing nomad urls
- renames `UploadContext` and `EntryContext` to the more descriptive `UploadPageContext` and `EntryPageContext`.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/744Upgrade react to 17.0.22022-07-04T12:17:35ZDavid SikterUpgrade react to 17.0.2Upgrades react to 17.0.2.Upgrades react to 17.0.2.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/743Remove hyperlink from Email address2022-07-05T07:13:45ZMohammad NakhaeeRemove hyperlink from Email addressMohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/742Updating keycloak and other dependencies2022-07-04T07:06:54ZDavid SikterUpdating keycloak and other dependenciesContinuing the work to update old dependencies. This updates `react-keycloak` (deprecated) to `@react-keycloak/web`, and all other dependencies that seemed unproblematic to update (i.e. they don't require any changes and do not break any...Continuing the work to update old dependencies. This updates `react-keycloak` (deprecated) to `@react-keycloak/web`, and all other dependencies that seemed unproblematic to update (i.e. they don't require any changes and do not break any tests). Upgrading keycloak required only a few minor changes.
Also resolved some issues with outdated test snapshots, and configure the linter to report an error if using `let` instead of `const`.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/740Resolve "Migrating legacy helm 2 chart (v1) into helm 3 chart (v2)"2022-07-05T12:22:34ZAdam FeketeResolve "Migrating legacy helm 2 chart (v1) into helm 3 chart (v2)"Closes #915Closes #915https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/739Resolve "Improved support for complex structural topologies"2022-07-01T08:38:21ZMarkus ScheidgenResolve "Improved support for complex structural topologies"Closes #832Closes #832https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/738About page (#904)2022-06-30T06:32:01ZMohammad NakhaeeAbout page (#904)Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/737Resolve "Create ELN entry component shows only direct descendants of EntryData"2022-06-28T14:17:56ZAmir GolparvarResolve "Create ELN entry component shows only direct descendants of EntryData"Closes #885Closes #885Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/736Fixing linting warnings (using 'const' instead of 'let' when possible)2022-06-28T09:53:14ZDavid SikterFixing linting warnings (using 'const' instead of 'let' when possible)Fixes linting warnings introduced by the upgrade of the linter to a newer version. (These warnings were previously ignored).Fixes linting warnings introduced by the upgrade of the linter to a newer version. (These warnings were previously ignored).Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/735Resolve "Unexpected error: "Cannot read properties of undefined (reading 'fil...2022-06-27T15:20:28ZDavid SikterResolve "Unexpected error: "Cannot read properties of undefined (reading 'filter')"."Closes #912Closes #912Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/734Added support for nexusparser parameter files in h5web2022-06-28T09:54:13ZSherjeel ShabihAdded support for nexusparser parameter files in h5webSherjeel ShabihSherjeel Shabihhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/733Resolve "Hash based ids for metainfo definitions"2022-07-05T08:24:28ZTheodore ChangResolve "Hash based ids for metainfo definitions"- [x] Support exporting `m_def_id` with `m_def` controlled by the `with_def_id` flag.
- [x] Support exporting `definition_id` in schemas.
- [x] Add detection of `m_def_id`, in case of mismatch, retrieve the corresponding package via `Con...- [x] Support exporting `m_def_id` with `m_def` controlled by the `with_def_id` flag.
- [x] Support exporting `definition_id` in schemas.
- [x] Add detection of `m_def_id`, in case of mismatch, retrieve the corresponding package via `Context`
- [x] Add detection of definition id in plain reference, covering both python style (`nomad.metainfo.SampleSection@1a2b3c4d`) and url style (`http://my.domain#/path/to/definition@1a2b3c4d`).Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/732Resolve "Finetuning to nomad oasis' docker-compose"2022-08-25T06:51:30ZAdam FeketeResolve "Finetuning to nomad oasis' docker-compose"Closes #930Closes #930