nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2022-05-11T15:39:57Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/666Fix docs artifacts build.2022-05-11T15:39:57ZMarkus ScheidgenFix docs artifacts build.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/665Fix docs artifacts build.2022-05-11T12:59:24ZMarkus ScheidgenFix docs artifacts build.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/664Merge v1.0.8 for release2022-05-10T13:16:39ZMarkus ScheidgenMerge v1.0.8 for releasehttps://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/660Resolve "Brillouin Zone viewer issue"2022-05-10T09:55:42ZLauri HimanenResolve "Brillouin Zone viewer issue"Closes #829Closes #829Markus 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/658Section plots (#812)2022-05-25T08:22:05ZMohammad NakhaeeSection plots (#812)Mohammad NakhaeeMohammad Nakhaeehttps://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/656Parser fixes v1.0.82022-05-06T07:49:32ZAlvin Noe LadinesParser fixes v1.0.8Rename mp workflow parser to atomate.Rename mp workflow parser to atomate.https://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/654Resolve "Custom schema eln issues"2022-05-11T12:07:52ZMarkus ScheidgenResolve "Custom schema eln issues"Closes #826Closes #826Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/653New parsers v1.0.82022-05-04T06:19:29ZAlvin Noe LadinesNew parsers v1.0.8New parsers bopfox and xtbNew parsers bopfox and xtbMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/652Fix EnumEditQuantity with suggestions2022-05-04T06:19:47ZMohammad NakhaeeFix EnumEditQuantity with suggestionsMohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/650Resolve "Gui tests fail after latest merge"2022-05-03T06:16:29ZDavid SikterResolve "Gui tests fail after latest merge"Closes #824. The reason was a left-over debug print statement in a react component (the recursive browser render test raise exceptions if anything is written to the console).Closes #824. The reason was a left-over debug print statement in a react component (the recursive browser render test raise exceptions if anything is written to the console).Markus ScheidgenMarkus Scheidgenhttps://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/648EnumWithSuggestions (#774)2022-05-02T07:05:14ZMohammad NakhaeeEnumWithSuggestions (#774)Complementing EnumQuantity to act as a string field with suggestionsComplementing EnumQuantity to act as a string field with suggestionsMohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/647Additional Gui test for edit quantity2022-05-02T07:08:51ZMohammad NakhaeeAdditional Gui test for edit quantityMohammad NakhaeeMohammad Nakhaeehttps://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/645Add test for processing empty section2022-05-02T07:05:44ZMohammad NakhaeeAdd test for processing empty sectionMohammad NakhaeeMohammad Nakhaee