nomad-FAIR issueshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues2024-03-12T12:37:33Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1928data structure of the .eln file format has changed2024-03-12T12:37:33ZAmir Golparvardata structure of the .eln file format has changedElabftw provides this .eln file format for the exported files but the data model is changed. Elabftw parser needs to be updatedElabftw provides this .eln file format for the exported files but the data model is changed. Elabftw parser needs to be updatedAmir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1909conversion of ArchiveQuery to dataframe works only for the last call of the d...2024-03-07T12:40:20ZAmir Golparvarconversion of ArchiveQuery to dataframe works only for the last call of the downloaded entriesAmir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1612Problem with removing archives generated with tabular parser entry mode2023-07-19T19:55:26ZAmir GolparvarProblem with removing archives generated with tabular parser entry modeTabular parser is producing errors while removing generated child archivesTabular parser is producing errors while removing generated child archivesAmir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1583Refactoring tabular parser2023-07-19T12:43:08ZAmir GolparvarRefactoring tabular parserRefactoring tabular parser:
- [x] improving tabular annotations
- [x] fixing tests
- [x] writing docsRefactoring tabular parser:
- [x] improving tabular annotations
- [x] fixing tests
- [x] writing docsAmir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1513Consider MEnum as key quantity2023-05-24T19:15:18ZTheodore ChangConsider MEnum as key quantityTheodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1410Tabular parsing: bug in datetime quantities read from spreadsheet files2023-03-25T14:21:19ZAndrea AlbinoTabular parsing: bug in datetime quantities read from spreadsheet filesIf the excel file contains a cell whose format has been set to Date, then our metainfo is reading it as a Timestamp type, it used to read it as a string but some recent update changed the things.
This need a fix in the TableData class a...If the excel file contains a cell whose format has been set to Date, then our metainfo is reading it as a Timestamp type, it used to read it as a string but some recent update changed the things.
This need a fix in the TableData class and @amgo is already informedAmir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1351POTCARs are being published2023-02-17T19:26:13ZNathan DaelmanPOTCARs are being published`POTCAR` files are still visible in the `FILES` overview, along with POTCAR.stripped`POTCAR` files are still visible in the `FILES` overview, along with POTCAR.strippedNathan DaelmanNathan Daelmanhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1266Hotfix: include Projection menu in the GUI2023-01-02T11:49:11ZJose PizarroHotfix: include Projection menu in the GUII want to include a Menu in the GUI for `Projection`, as shown in the following picture:
![Screenshot_from_2023-01-02_11-02-52](/uploads/d1337d79f7c95dd6f5024c6368174142/Screenshot_from_2023-01-02_11-02-52.png)
This is a hotfix on [#12...I want to include a Menu in the GUI for `Projection`, as shown in the following picture:
![Screenshot_from_2023-01-02_11-02-52](/uploads/d1337d79f7c95dd6f5024c6368174142/Screenshot_from_2023-01-02_11-02-52.png)
This is a hotfix on [#1250](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1250); it should have been included in there.Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1117GUI tests failing on develop2022-10-19T19:12:32ZMichael GötteGUI tests failing on developHey Nomad,
i get the following CI error: https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/jobs/1869159
although i have never touched any of the gui code.
Best MichaHey Nomad,
i get the following CI error: https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/jobs/1869159
although i have never touched any of the gui code.
Best MichaLauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1098Dataset page raises a javascript error2022-09-29T14:07:37ZMarkus ScheidgenDataset page raises a javascript errorFor example here: https://nomad-lab.eu/prod/v1/staging/gui/dataset/id/ly5xV6JXRpuwa9ByWP-a4w
But it seems to happen with any dataset.For example here: https://nomad-lab.eu/prod/v1/staging/gui/dataset/id/ly5xV6JXRpuwa9ByWP-a4w
But it seems to happen with any dataset.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1089EnumEditQuantity is broken or changed?2022-10-04T10:44:05ZMichael GötteEnumEditQuantity is broken or changed?Dear Nomad,
I just merge develop and the EnumEditQuantities break the GUI. So my ld code does not work anymore. Did you change the syntax for these?
just go to the beta (nomad-lab.eu), create a perovscite archive, add cell and click sol...Dear Nomad,
I just merge develop and the EnumEditQuantities break the GUI. So my ld code does not work anymore. Did you change the syntax for these?
just go to the beta (nomad-lab.eu), create a perovscite archive, add cell and click solar cell architecture to reproduce this
Best MichaMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1087Archive browser only shows default value2022-10-12T13:33:58ZMarkus ScheidgenArchive browser only shows default valueThe archive browser only shows the default value for all quantities that have a default value.The archive browser only shows the default value for all quantities that have a default value.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1066Archive API fails on many archives with "could not resolve reference"2022-09-22T07:04:35ZMohammad NakhaeeArchive API fails on many archives with "could not resolve reference"This happens with 1.1 and 1.0. Quite a lot of entries seem effected. See links below.
It looks like an UI error, but its caused by API returning 500 due to exception.
--
Original post
The following entry has an unexpected error
[ent...This happens with 1.1 and 1.0. Quite a lot of entries seem effected. See links below.
It looks like an UI error, but its caused by API returning 500 due to exception.
--
Original post
The following entry has an unexpected error
[entry link](https://nomad-lab.eu/prod/v1/staging/gui/search/entries/entry/id/i1XuvK8G1FKGNha__lOdvQKsHaIY)
actually this is the case for all the entries that I searched [here](https://nomad-lab.eu/prod/v1/staging/gui/search/entries?structural_type=2D&elements=C&electronic_properties=band_structure_electronic)
Maybe te GUI tests should be much stricter?Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1042Beta deployment (staging) getting stuck in nomad loading logo in some devices2022-09-13T09:50:04ZJose Marquez PrietoBeta deployment (staging) getting stuck in nomad loading logo in some devicesWhen opening the beta deployment on some devices the page does not load in and gets stuck in the nomad logo. I had no problems on my laptop, but it does not work on an iPhone nor on an iPad tested on Safari and Chrome. The page gets dete...When opening the beta deployment on some devices the page does not load in and gets stuck in the nomad logo. I had no problems on my laptop, but it does not work on an iPhone nor on an iPad tested on Safari and Chrome. The page gets detected as "non-secure". @mscheidg any idea what could be the issue with this?
This did not happen in the *Test* version or the *Legacy 0.10* version.Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1029Assign dataset DOI does not update index2023-12-21T15:38:44ZMarkus ScheidgenAssign dataset DOI does not update indexWhen we assign a DOI the DOI should also be added to the ES index. Similar to when we edit other metadata on entries (e.g. datasets themselves).When we assign a DOI the DOI should also be added to the ES index. Similar to when we edit other metadata on entries (e.g. datasets themselves).https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/937Docker image doesn't work2022-09-13T08:22:28ZAdam FeketeDocker image doesn't work`kubectl logs pod/dev-develop-vgkp4l-nomad-app-6c97875c77-m4b78`:
```
...
2022-07-01 11:18:25 [14] [INFO] Started server process [14]
2022-07-01 11:18:25 [14] [INFO] Waiting for application startup.
...
2022-07-01 11:18:44 [15] [ERROR] ...`kubectl logs pod/dev-develop-vgkp4l-nomad-app-6c97875c77-m4b78`:
```
...
2022-07-01 11:18:25 [14] [INFO] Started server process [14]
2022-07-01 11:18:25 [14] [INFO] Waiting for application startup.
...
2022-07-01 11:18:44 [15] [ERROR] Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/mongoengine/connection.py", line 319, in _create_connection
return connection_class(**connection_settings)
File "/usr/local/lib/python3.7/site-packages/pymongo/mongo_client.py", line 672, in __init__
connect_timeout=timeout)
File "/usr/local/lib/python3.7/site-packages/pymongo/uri_parser.py", line 458, in parse_uri
"begin with '%s' or '%s'" % (SCHEME, SRV_SCHEME))
pymongo.errors.InvalidURI: Invalid URI scheme: URI must begin with 'mongodb://' or 'mongodb+srv://'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "./nomad/infrastructure.py", line 85, in setup_mongo
mongo_client = connect(db=config.mongo.db_name, host=config.mongo.host, port=config.mongo.port)
File "/usr/local/lib/python3.7/site-packages/mongoengine/connection.py", line 406, in connect
return get_connection(alias)
File "/usr/local/lib/python3.7/site-packages/mongoengine/connection.py", line 307, in get_connection
alias=alias, connection_class=connection_class, **conn_settings
File "/usr/local/lib/python3.7/site-packages/mongoengine/connection.py", line 321, in _create_connection
raise ConnectionFailure("Cannot connect to database %s :\n%s" % (alias, e))
mongoengine.connection.ConnectionFailure: Cannot connect to database default :
Invalid URI scheme: URI must begin with 'mongodb://' or 'mongodb+srv://'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/mongoengine/connection.py", line 319, in _create_connection
return connection_class(**connection_settings)
File "/usr/local/lib/python3.7/site-packages/pymongo/mongo_client.py", line 672, in __init__
connect_timeout=timeout)
File "/usr/local/lib/python3.7/site-packages/pymongo/uri_parser.py", line 458, in parse_uri
"begin with '%s' or '%s'" % (SCHEME, SRV_SCHEME))
pymongo.errors.InvalidURI: Invalid URI scheme: URI must begin with 'mongodb://' or 'mongodb+srv://'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/starlette/routing.py", line 540, in lifespan
async for item in self.lifespan_context(app):
File "/usr/local/lib/python3.7/site-packages/starlette/routing.py", line 481, in default_lifespan
await self.startup()
File "/usr/local/lib/python3.7/site-packages/starlette/routing.py", line 516, in startup
await handler()
File "./nomad/app/main.py", line 96, in startup_event
infrastructure.setup()
File "./nomad/infrastructure.py", line 71, in setup
setup_mongo()
File "./nomad/infrastructure.py", line 88, in setup_mongo
mongo_client = connect(db=config.mongo.db_name, host=config.mongo.host, port=config.mongo.port)
File "/usr/local/lib/python3.7/site-packages/mongoengine/connection.py", line 406, in connect
return get_connection(alias)
File "/usr/local/lib/python3.7/site-packages/mongoengine/connection.py", line 307, in get_connection
alias=alias, connection_class=connection_class, **conn_settings
File "/usr/local/lib/python3.7/site-packages/mongoengine/connection.py", line 321, in _create_connection
raise ConnectionFailure("Cannot connect to database %s :\n%s" % (alias, e))
mongoengine.connection.ConnectionFailure: Cannot connect to database default :
Invalid URI scheme: URI must begin with 'mongodb://' or 'mongodb+srv://'
2022-07-01 11:18:44 [15] [ERROR] Application startup failed. Exiting.
....
```Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/930Finetuning to nomad oasis' docker-compose2022-07-07T07:25:04ZAdam FeketeFinetuning to nomad oasis' docker-composehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/903Current NORTH docker-compose installation2022-06-21T07:15:06ZMarkus ScheidgenCurrent NORTH docker-compose installationThere are a few problems to fix
- on linux all created .volumes/ directories belong to the wrong user (root)
- the nginx config has a bug (location hub instead of north)
- the tools bind mount the wrong directories. They use the path fro...There are a few problems to fix
- on linux all created .volumes/ directories belong to the wrong user (root)
- the nginx config has a bug (location hub instead of north)
- the tools bind mount the wrong directories. They use the path from the hub container not from the host
Here are more details:
https://matsci.org/t/nomad-remote-tools-hub-north/42861https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/889Cannot download data from search results table2022-06-10T06:42:21ZMarkus ScheidgenCannot download data from search results tableYou are always getting a json docuemnt with not found error. The signature token is not used.You are always getting a json docuemnt with not found error. The signature token is not used.Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/859Wrong datasets in edit-meta-data dialog2022-06-21T10:35:41ZMohammad NakhaeeWrong datasets in edit-meta-data dialogWrong datasets in edit-meta-data dialog when the entries are selectedWrong datasets in edit-meta-data dialog when the entries are selectedMohammad NakhaeeMohammad Nakhaee