nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2022-05-23T06:46:23Zhttps://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/683process table (#850)2022-05-23T06:45:50ZMohammad Nakhaeeprocess table (#850)Disable go to entry page if it is processingDisable go to entry page if it is processingMohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/686Reduced samping rate in fhiaims2022-05-23T06:45:23ZAlvin Noe LadinesReduced samping rate in fhiaimsMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/682Bugfix: track retry number2022-05-20T14:44:47ZTheodore ChangBugfix: track retry numberCloses #852Closes #852Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/684Resolve "ArchiveQuery retry number is not updated"2022-05-20T14:41:28ZTheodore ChangResolve "ArchiveQuery retry number is not updated"Closes #852Closes #852Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/677Resolve "Processing email text with unnamed upload"2022-05-20T07:21:45ZMarkus ScheidgenResolve "Processing email text with unnamed upload"Closes #809Closes #809https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/681Implement sampling of large traj in fhiaims2022-05-19T12:53:08ZAlvin Noe LadinesImplement sampling of large traj in fhiaimsMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/680Draft: Resolve "Support for inheriting sections"2022-05-19T09:17:11ZAmir GolparvarDraft: Resolve "Support for inheriting sections"Closes #834Closes #834Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/672GUI tests for uploadPage2022-05-19T06:29:42ZMohammad NakhaeeGUI tests for uploadPagecomplement uploadPage testscomplement uploadPage testsMohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/673Resolve "Optimade API is not working with v1.1.1"2022-05-18T14:39:15ZMarkus ScheidgenResolve "Optimade API is not working with v1.1.1"Closes #847Closes #847https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/674Resolve "Cannot resolve local m_def reference"2022-05-18T14:36:41ZMarkus ScheidgenResolve "Cannot resolve local m_def reference"Closes #849Closes #849https://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/594Resolve "ElasticSearch upgrade for v0.x"2022-05-17T14:06:13ZLauri HimanenResolve "ElasticSearch upgrade for v0.x"Closes #767
@mscheidg: I did not update any of the helm stuff, but otherwise this should now include all the necessary changes.Closes #767
@mscheidg: I did not update any of the helm stuff, but otherwise this should now include all the necessary changes.Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/620Resolve "Remove flask dependency"2022-05-17T12:37:21ZTheodore ChangResolve "Remove flask dependency"Closes #781Closes #781Theodore ChangTheodore Changhttps://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/667fix Markdown bug (#775)2022-05-13T08:08:42ZMohammad Nakhaeefix Markdown bug (#775)Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/668Test for the Example Uploads part2022-05-13T06:43:03ZAmir GolparvarTest for the Example Uploads partBranch is checked out from branch 826. I made changes only to gui/src/components/uploads/UploadsPage.spec.js
Test for the ExampleUploads is added.
Closes #822Branch is checked out from branch 826. I made changes only to gui/src/components/uploads/UploadsPage.spec.js
Test for the ExampleUploads is added.
Closes #822https://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/654Resolve "Custom schema eln issues"2022-05-11T12:07:52ZMarkus ScheidgenResolve "Custom schema eln issues"Closes #826Closes #826Markus ScheidgenMarkus Scheidgen