Parsing bug for GEO dataset summary and newlines

[JTFouquier]

When loading GEO datasets, the "summary" field should be imported into the metadata. There was a bug importing the summary for GSE18842. The summary right now only reads "PURPOSE", presumably because it was truncated at the first newline in the GEO entry (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18842). If this diagnosis is correct, then the GEO data importer should be fixed to import the entire summary field.

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• Bitbucket: https://bitbucket.org/sulab/biogps_core/issue/36
• Originally reported by: Andrew Su
• Originally created at: 2013-11-16T02:00:11.485

[JTFouquier]

confirmed that "ParseGSEFiles.py" script takes only the first paragraph of the summary text. The logic should be fixed at here.

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Original comment by: Chunlei Wu

[JTFouquier]

Re-uploading GEO datasets requires a revamp of the original "ParseGSEFiles.py" script, as the original insilicodb api doesn't work any more. Their new api is here:

https://insilicodb.org/api/class-interface-controller.html

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Original comment by: Chunlei Wu

[JTFouquier]

instead of fixing this bug, we will make a new dataset-loading pipeline at #37

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Original comment by: Chunlei Wu