nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2022-08-16T09:08:46Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/766Resolve "Support names instead of indices in metainfo definition references"2022-08-16T09:08:46ZAmir GolparvarResolve "Support names instead of indices in metainfo definition references"Closes #925Closes #925Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/765Resolve "ArchiveBrowser hash test"2022-07-27T07:59:19ZLauri HimanenResolve "ArchiveBrowser hash test"Closes #963Closes #963Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/764Use urls for uploads in the store and file browser2022-08-01T09:05:42ZDavid SikterUse urls for uploads in the store and file browserA part of the refactoring for #828. The store is updated to use installationUrl + uploadId, rather than just uploadId to manage uploads, and the file browser adaptors are updated so they take absolute upload urls as the main argument (co...A part of the refactoring for #828. The store is updated to use installationUrl + uploadId, rather than just uploadId to manage uploads, and the file browser adaptors are updated so they take absolute upload urls as the main argument (containing information about installationUrl + uploadId + rawPath), rather than just uploadId + rawPath. Some additional work still needs to be done before we can actually fetch data from external installations, though, so only urls pointing to the local installations work for now.David SikterDavid Sikterhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/763Eln user author (#918)2022-07-22T16:31:51ZMohammad NakhaeeEln user author (#918)Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/762Improved/corrected url parsing utils and documentation2022-08-03T05:58:26ZDavid SikterImproved/corrected url parsing utils and documentationImprovement of documentation and utilities for handling a harmonized "nomad url" concept. Part of the work with #828.Improvement of documentation and utilities for handling a harmonized "nomad url" concept. Part of the work with #828.David SikterDavid Sikterhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/761Remove the cdf file from text viewer since it is not ascii2022-07-19T13:27:02ZMohammad NakhaeeRemove the cdf file from text viewer since it is not asciiRelated to #916Related to #916Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/760Validate eln annotations (#941)2022-08-01T09:22:03ZMohammad NakhaeeValidate eln annotations (#941)Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/759print traceback appworker (#952)2022-07-20T07:14:35ZMohammad Nakhaeeprint traceback appworker (#952)Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/758Resolve "GUI error when clicking in "+" in filters in entries search."2022-07-29T14:11:48ZLauri HimanenResolve "GUI error when clicking in "+" in filters in entries search."Closes #950Closes #950Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/756Resolve "Copy function for files/mainfiles"2022-09-02T08:02:33ZAmir GolparvarResolve "Copy function for files/mainfiles"Closes #840Closes #840Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/755Sample id baseclass (#945)2022-07-14T13:34:08ZMohammad NakhaeeSample id baseclass (#945)The problem is that the SampleID which references to itself has a the qualifiedName 'nomad.bla.bla.SampleID', but the sections which are inherited from this section has a different qualifiedName. The qualified name is needed for creating...The problem is that the SampleID which references to itself has a the qualifiedName 'nomad.bla.bla.SampleID', but the sections which are inherited from this section has a different qualifiedName. The qualified name is needed for creating a Reference(), the reference is searching for 'nomad.bla.bla.SampleID'. Now I am also searching for the sections which have the base section with the qualifiedName 'nomad.bla.bla.SampleID'.Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/754Optimade search quantity (#848)2022-07-14T07:19:50ZMohammad NakhaeeOptimade search quantity (#848)Mohammad NakhaeeMohammad Nakhaeehttps://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 Scheidgen