Comments (2)
Temporary workaround
Open the cif_core.dic
file and do the following changes:
- Line 8: "data_CIF_CORE" => data_CIF_CORE_DIC
- Line 10: " _dictionary.title CIF_CORE" -> "_dictionary.title CIF_CORE_DIC"
- Line 35: " _name.category_id CIF_CORE" -> "_name.category_id CIF_CORE_DIC"
After this, running dic2owl cif_core.dic
should successfully build the cif_core.tll
file.
The problem
Recently, the CIF_CORE
dictionary was internally renamed from CORE_DIC
to CIF_CORE
to adhere to the newly agreed upon conventions. However, this also resulted in a CIF file in which the data block (top level container) and a save frame (lower level container) both have the same name (CORE_DIC
). While this is perfectly valid in CIF, the dic2owl
script seems to not process this very well. At least that is my educated guess.
Long term solution
There have been discussions in the CIF_CORE repository to also change the name of the save frame so the issue might just go away on its own. However, it would still make sense to also update the dic2owl
script to properly process such valid CIF dictionary files.
from cif-ontology.
@stuchalk Ok, so with the recent changes to the CIF_CORE
dictionary (COMCIFS/cif_core#492), this bug no longer manifests. Just remove all of the ignored/generated files and rerun the ttl file build command.
While the underlying issue in the software is still present, it is unlikely to manifest again with the IUCr CIF dictionaries given the recently agreed upon naming conventions (COMCIFS/cif_core#488). Patching the bug would be nice, but the issue should be viewed as having a much lower priority.
from cif-ontology.
Related Issues (20)
- Readme in Master Branch out of data or files missing
- RDFLib vulnerability
- Support imported dictionaries
- Comply with PEP 484 HOT 1
- Support python version range for pre-commit
- Consider using SINTEF/ci-cd
- Running dic2owl on the latest ddlm version of cif core I get an error HOT 2
- CIF ontology file needs to be updated HOT 1
- Possibly replace Generator 'comment' parameter
- Special cases for ddl_name
- Extract extra metadata from a 'dic' object HOT 1
- Use ruff instead of pylint
- Move to 'flit' build system
- Upgrade to min. Python 3.8
- Handle non-ASCII Unicode symbols in CIF dictionary files HOT 3
- Update DDL ontology
- Add support for the new `Word` DDLm content type
- GH GraphQL variable type to be fixed
- Ignore NumPy safety issue
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from cif-ontology.