nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2021-10-15T07:00:49Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/422Refactor permissions2021-10-15T07:00:49ZDavid SikterRefactor permissionsRefactoring the permission-related fields as discussed in #580
- `Upload.user_id` and `EntryMetadata.uploader` are renamed to `main_author`
- It becomes possible to set coauthors on both the upload and the entry level. The fields are na...Refactoring the permission-related fields as discussed in #580
- `Upload.user_id` and `EntryMetadata.uploader` are renamed to `main_author`
- It becomes possible to set coauthors on both the upload and the entry level. The fields are named `coauthors` and `entry_coauthors`, respectively.
- **NOTE 1**: The field `coauthors` was previously defined on the entry level, but now it is set on the upload level.
- **NOTE 2**: we prefer users to use the field `coauthors` on the upload level, and if possible it would be nice to get rid of the `entry_coauthor` field eventually.
- The field `Calc.shared_with` is renamed and moved to `Upload.reviewers` (the name change is to make it more clear that they only have read permissions, now that there will potentially be multiple readers and writers)
- The derived field `EntryMetadata.owners` is renamed to `viewers` (also to make it clearer that these are the users who can _read_ the data). The field is defined as `main_author` + `coauthors` + `reviewers`.
- Introduces a new derived field `EntryMetadata.writers` to denote users who can write to the upload. Defined as `main_author` + `coauthors`
- The derived field `EntryMetadata.authors` is defined as `main_author` + `coauthors` + `entry_coauthors`
- **NOTE**: being in the `entry_coauthors` doesn't give you any permissions, neither to read from or to write to the upload. It only means you're listed as an author in the search index. This is the point, because we want the permissions to be determined at the upload level, so you either have read/write access to the _whole_ upload or not (would be messy to have different permissions to different entries within the same upload)Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/424Additional cleanup of processing related Mongo fields2021-10-15T13:57:28ZDavid SikterAdditional cleanup of processing related Mongo fields- Removes the field `Proc.current_process_step` and instead use `last_status_message`
- Removes the "hacky" solution with the field `Upload.pending_operations` and use process arguments instead- Removes the field `Proc.current_process_step` and instead use `last_status_message`
- Removes the "hacky" solution with the field `Upload.pending_operations` and use process arguments insteadMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/425Changing Calc.external_id to a list and rename it to external_ids2021-10-20T06:52:28ZDavid SikterChanging Calc.external_id to a list and rename it to external_idsAllows the user to store multiple external ids for the same entry by turning it into a list, rather than a single string.Allows the user to store multiple external ids for the same entry by turning it into a list, rather than a single string.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/426add some changes in uploads page and upload page2021-10-20T09:04:18ZMohammad Nakhaeeadd some changes in uploads page and upload pageReprocess button was added to the upload page and a reload button was added to the table of uploads.
Additionally, the NewUploadButton would be disabled when we reach the maximum number of unpublished uploads.Reprocess button was added to the upload page and a reload button was added to the table of uploads.
Additionally, the NewUploadButton would be disabled when we reach the maximum number of unpublished uploads.Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/427Set a maximum width for all browser tabs2021-10-20T09:15:48ZMohammad NakhaeeSet a maximum width for all browser tabsConcerning issue #599
I set the maximum width = 340
In my browser, it looks like this
![Screenshot](/uploads/fa64d2725240d978ec523d8b616e0e07/Screenshot.png)
It can be smaller, but I am afraid of masking the keys.Concerning issue #599
I set the maximum width = 340
In my browser, it looks like this
![Screenshot](/uploads/fa64d2725240d978ec523d8b616e0e07/Screenshot.png)
It can be smaller, but I am afraid of masking the keys.Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/428Add OpenMX to the list of supported parsers2021-10-20T13:40:55ZMohammad NakhaeeAdd OpenMX to the list of supported parsersIssue #635
Not sure about the followings
"parserSpecific": "",
"tableOfFiles": ""
Where can I check them?Issue #635
Not sure about the followings
"parserSpecific": "",
"tableOfFiles": ""
Where can I check them?Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/430Use the real mongo for the tests2021-10-22T15:29:51ZMohammad NakhaeeUse the real mongo for the testsConcerning issue #579Concerning issue #579Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/431Fixes to nginx-config (and other deployment related issues) #6382021-10-22T16:27:49ZMarkus ScheidgenFixes to nginx-config (and other deployment related issues) #638v1.0.0-betahttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/432Fixed parser metadata generation2021-10-25T11:22:26ZMarkus ScheidgenFixed parser metadata generationhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/429remove preview functionality2021-10-26T10:22:20ZMohammad Nakhaeeremove preview functionalityThe preview button has been removed in this branch.The preview button has been removed in this branch.Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/434Introduce CLI for upgrading and migrating mongo data2021-10-26T10:22:29ZDavid SikterIntroduce CLI for upgrading and migrating mongo dataFirst version of CLI command for migrating data from one mongodb to another. The data transformations needed are kept track of by #578 (all requirements concerning mongo specified in this issue until now are handled by the CLI).
The com...First version of CLI command for migrating data from one mongodb to another. The data transformations needed are kept track of by #578 (all requirements concerning mongo specified in this issue until now are handled by the CLI).
The command takes options for specifying a source and a destination mongo DB, and it offers a dry run mode. It migrates selected uploads and all records related to them (entries and datasets). It currently just overwrites any existing records in the destination DB, but it may be a good idea to add some customizable smartness (for example a "don't overwrite" or "overwrite only if newer" mode, etc).
Uploads can be selected by a query or by a file listing upload IDs. Uploads that have a status saying that they are currently processing are ignored. If an entry is marked as processing though the upload is not (or at least was not at the moment when we read it), that particular upload will be reported as failed (neither the upload nor its entries will be updated). The script also performs various validation checks.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/433Added nexus parser2021-10-27T08:26:23ZSandor BrockhauserAdded nexus parserhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/439Freeze pymongo version.2021-10-27T12:54:26ZMarkus ScheidgenFreeze pymongo version.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/440Froze most of the requirements.txt packages.2021-10-28T06:26:15ZMarkus ScheidgenFroze most of the requirements.txt packages.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/438Support for mechanical properties, better nested query support + GUI refactoring2021-10-28T07:19:17ZLauri HimanenSupport for mechanical properties, better nested query support + GUI refactoringThe main goal of this merge was to add support for mechanical properties. This includes:
- Adding metadata and normalizer functionality for storing mechanical properties under `results.properties.mechanical`
- New GUI filters for `bulk_...The main goal of this merge was to add support for mechanical properties. This includes:
- Adding metadata and normalizer functionality for storing mechanical properties under `results.properties.mechanical`
- New GUI filters for `bulk_modulus`, `shear_modulus` and available `mechanical_properties`.
- GUI support for defining nested queries. The current mechanism works so that if you wrap input filter components within `InputSection`, they automatically become nested. Currently, only one nested query per section is supported, might change in the future. Also, there is not yet any syntax for defining nested properties through the search bar.
- GUI support for showing active nested properties. Added a new component for grouping `FilterChips` so that they differ from the "flat" filters.
- Support for the serialization of nested filter in the URL and in the API queries.
- Added GUI support for pressure units (needed for bulk/shear modulus).
- Normalizer + GUI tests
As a side effect, the following changes were made:
- The layout of property cards was simplified and unified. One no longer has to manually specify an aspect ratio and the layout is fully grid-based.
- Small restyling of the filter menus: Added vertical separators in order to better distinguish between different filters, especially important for the new nested filter sections.
- The new nested filters were enabled for band gap search (one task in #569). This introduced a small rename for the metainfo related to band gaps.
- Restyling of the `SectionTable` component. Now looks like the default table from MUI.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/437Adding support for automatic fixing of bad entry ids2021-10-29T07:59:09ZDavid SikterAdding support for automatic fixing of bad entry idsAdded checks that the entry's id matches the generated one (by examining the prod DB, I found two entries where this has happened). If amismatch is found, specifying --fix-problems will replace the id with the correct one during the conv...Added checks that the entry's id matches the generated one (by examining the prod DB, I found two entries where this has happened). If amismatch is found, specifying --fix-problems will replace the id with the correct one during the conversion.
Also fixed a typo and improved doc.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/441Migration fix cli imports2021-10-29T07:59:41ZMarkus ScheidgenMigration fix cli imports@dsikter This is what I tried to explain with my last comments in !437. Let me know, if this is acceptable.
This MR contains the commits of !437@dsikter This is what I tried to explain with my last comments in !437. Let me know, if this is acceptable.
This MR contains the commits of !437David SikterDavid Sikterhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/421New GUI for AI toolkit2021-10-29T08:55:46ZLuigi SbailoNew GUI for AI toolkitThe GUI of the AI toolkit comprises three different pages. A landing page and two tutorials lists.The GUI of the AI toolkit comprises three different pages. A landing page and two tutorials lists.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/442Froze most of the requirements.txt packages.2021-10-29T12:18:06ZMarkus ScheidgenFroze most of the requirements.txt packages.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/443Release v0.10.82021-10-29T12:47:37ZMarkus ScheidgenRelease v0.10.8Add explanation to increase the virtual memory for Elasticsearch. (At least for Linux users)Add explanation to increase the virtual memory for Elasticsearch. (At least for Linux users)