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DEIB-GECO / GMQL

GMQL - GenoMetric Query Language
http://www.bioinformatics.deib.polimi.it/geco/
Apache License 2.0
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Standardization of names in datasets created by API and web services #87

Closed marcomass closed 6 years ago

marcomass commented 6 years ago

Datasets created by web include a schema file named "schema.xml" and a subdirectory named "files". Conversely, datasets created by API include a schema file named "test.xml" and a subdirectory named "exp". The two output has to be standardized setting the names created by the API as the ones (more intuitive) created by the web. This is due to avoid possible conflicts in pyGMQL / RGMQL which manage both files created (remotely) by web and file created locally by API

lucananni93 commented 6 years ago

From the point of view of PyGMQL this is not a serious problem and, for the moment, I can handle this behavior from my side. If there are more serious issues, please address them before.

marcomass commented 6 years ago

This can be an issue in RGMQL (I'm glad it is not in pyGMQL ;-) )

lucananni93 commented 6 years ago

I would propose to leave this as an enhancement for the moment since there are more important issues to solve.

marcomass commented 6 years ago

@akaitoua Could you please change the name of the schema file of a dataset generated by the API from "test.schema" to "schema.xml" and make the read dataset API reading such schema.xml file when using CustomParser? This is affecting RGMQL usage: datasets created and downloaded trough web services cannot be read by API.

Also, please standardize name of subdirectory, changing the name of the subdirectory generated by the API from "exp" to "files"

acanakoglu commented 6 years ago

The exp folder will be changed into files as discussed in the GitHub issue: https://github.com/DEIB-GECO/PyGMQL/issues/13

The name of the schema is a bit difficult because of the back-compatibility problem. The schema names should be changed for currently available DSs. I would resolve this as a later correction.

marcomass commented 6 years ago

Thanks @acanakoglu The issue of the schema file name is currently preventing the API from reading any dataset regardless where it was created, affecting particularly RGMQL. Could this fix not delayed, making the API able to read with CustomParser schema file named schema.xml?

marcomass commented 6 years ago

@acanakoglu (cc. @Sim1Pall8a ) The issue is in the function setSchema() of the API for custom parser, which check if a XML .schema file exist; if not it generates error. It should be managed also the possibility to find a schema file named .xml instead. Could you please do it?

acanakoglu commented 6 years ago

DONE