nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2022-04-06T15:57:59Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/622Resolve "ELN tests, documentation, and examples"2022-04-06T15:57:59ZMarkus ScheidgenResolve "ELN tests, documentation, and examples"Closes #796Closes #796https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/632Resolve "Section references should use names"2022-04-08T08:35:17ZMarkus ScheidgenResolve "Section references should use names"Closes #800Closes #800Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/608Added metainfo references and context support in the GUI. #7052022-04-21T17:47:39ZMarkus ScheidgenAdded metainfo references and context support in the GUI. #705Closes #705
- refactored metainfo.js: there is a Metainfo class. Metainfo instances can build on each other, i.e. the global metainfo can be extended by more local and temporary Metainfo instances
- refactored the use of "context" in t...Closes #705
- refactored metainfo.js: there is a Metainfo class. Metainfo instances can build on each other, i.e. the global metainfo can be extended by more local and temporary Metainfo instances
- refactored the use of "context" in the browser. All adaptors now have a `context` memberMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/597Resolve "Range picker histograms"2022-04-22T09:59:38ZLauri HimanenResolve "Range picker histograms"Closes #656Closes #656Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/646Resolve "Upload overview should show an optional README.md"2022-05-02T07:06:50ZMarkus ScheidgenResolve "Upload overview should show an optional README.md"Closes #783Closes #783https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/643Implement client side context2022-05-04T06:22:17ZTheodore ChangImplement client side contextTheodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/649Resolve "Oasis installation and registration"2022-05-04T10:04:45ZMarkus ScheidgenResolve "Oasis installation and registration"Closes #820Closes #820https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/655Add support for upload of multiple files2022-05-05T06:16:49ZDavid SikterAdd support for upload of multiple filesSupport simultaneous upload of multiple files, as required by #819Support simultaneous upload of multiple files, as required by #819Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/624Resolve "More scalable entry logs view"2022-05-06T07:52:00ZAmir GolparvarResolve "More scalable entry logs view"Closes #777Closes #777Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/657Resolve "Unit prefixes and complex units in the GUI"2022-05-06T20:13:46ZLauri HimanenResolve "Unit prefixes and complex units in the GUI"Closes #802Closes #802https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/663Add entry delete buttons2022-05-10T09:55:31ZDavid SikterAdd entry delete buttonsAdds entry delete buttons as requested in #819. Entries can be removed either from the table on the upload overview page or from the entry overview page. A new endpoint was created: `uploads/{upload_id}/action/delete-entry-files`, which ...Adds entry delete buttons as requested in #819. Entries can be removed either from the table on the upload overview page or from the entry overview page. A new endpoint was created: `uploads/{upload_id}/action/delete-entry-files`, which allows the deletion of entry files based on a query (restricted to a single upload). When clicking the delete buttons, a dialog is opened, asking the user to confirm, and to specify if we should delete only the mainfiles or the mainfiles + their folders.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/662Resolve "Molecular Dynamics support"2022-05-16T09:04:28ZLauri HimanenResolve "Molecular Dynamics support"Closes #677Closes #677Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/659Resolve "Inter-entry reference resolution in client, cli, and archive reader"2022-05-17T16:05:52ZTheodore ChangResolve "Inter-entry reference resolution in client, cli, and archive reader"- [x] add functionality to resolve references to different archives on the **same** server, using the provided user credentials
- [x] add a simple test which involves references to both the same and a different archive
A few points:
1....- [x] add functionality to resolve references to different archives on the **same** server, using the provided user credentials
- [x] add a simple test which involves references to both the same and a different archive
A few points:
1. References to another installation (a remote url such as: `https://his.oasis/uploads/some_upload/archive/some_archive#path/relative/to/entry`) will not be resolved accounting for the fact that there may not be access to that installation, even with the provided user credentials.
2. All references to another entry are resolved by:
- Retrieve the plain json data from the public API `answer_entry_archive_request`
- Apply the same `required` to extract relavent data.
At this stage, there is no need to distingush whether another entry is in the same upload or another upload. Using `answer_entry_archive_request` handles both case uniformly.
3. In the case of references need to be resolved but not in-place, the current implementation adds the same data structure to the result json, this leads to data overlapping for references like `entry_a#/run/0/system/0` and `entry_b#/run/0/system/0`. All references to another entry are prefixed by the corresponding entry id to avoid data overlapping. See the example for comparision.
The example archive has a reference to `XUlSxqEvec0LvPQbSLWeysB1Ksns`,
```json
{"workflow":[{"calculation_result_ref":"../uploads/examples_template/archive/XUlSxqEvec0LvPQbSLWeysB1Ksns#/run/0/calculation/0"}]}
```
which further has references to itself.
```json
{"run":[{"calculation":[{"system_ref":"/run/0/system/0","method_ref":"/run/0/method/0","energy":{"total":{"value":-1.5935696296699573e-18},"free":{"value":-1.5936767191492225e-18},"total_t0":{"value":-3.2126683561907e-22}}}]}]}
```
After resolving all references, it becomes (other associated data is removed here for clearer presentation):
```json
{
"XUlSxqEvec0LvPQbSLWeysB1Ksns":{
"run":[
{
"calculation":[
{
"system_ref":"/XUlSxqEvec0LvPQbSLWeysB1Ksns/run/0/system/0",
"method_ref":"/XUlSxqEvec0LvPQbSLWeysB1Ksns/run/0/method/0",
"energy":{
"total":{
"value":-1.5935696296699573e-18
},
"free":{
"value":-1.5936767191492225e-18
},
"total_t0":{
"value":-3.2126683561907e-22
}
}
}
]
}
]
},
"workflow":[
{
"calculation_result_ref":"/XUlSxqEvec0LvPQbSLWeysB1Ksns/run/0/calculation/0"
}
]
}
```Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/671Unify reference url handling2022-05-23T06:46:23ZTheodore ChangUnify reference url handlingCloses #806
- [x] Use the same function to handle references.
- [x] Add user authentication to client side context, add parameters to parser CLI.Closes #806
- [x] Use the same function to handle references.
- [x] Add user authentication to client side context, add parameters to parser CLI.Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/700Relocate additional archives2022-06-10T06:13:56ZTheodore ChangRelocate additional archivesCloses #806Closes #806Theodore ChangTheodore Changhttps://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/708Resolve "Deploy jupyterhub using nomad helm chart"2022-06-30T13:33:14ZAdam FeketeResolve "Deploy jupyterhub using nomad helm chart"Closes #893Closes #893Adam FeketeAdam Feketehttps://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/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/732Resolve "Finetuning to nomad oasis' docker-compose"2022-08-25T06:51:30ZAdam FeketeResolve "Finetuning to nomad oasis' docker-compose"Closes #930Closes #930