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Add mapping file functionality port to pyqi.

Creates the qiita_db pyqi structure and adds the command MappingFileAdder to qiita_db.
Fixes some issue in other files in order to be able to execute the code.
Centralizes database connection in a single file.
Adds an sql utils module that encapsulates most of the usual interactions with the postres database, reducing code replication.

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The alternative to this is to do from string import lower.

@josenavas
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This is right now almost functional.

I've added the MetadataMap object, which extends the QIIME's object with an _id attribute. However, when parsing the file, I get back a QIIME's MetadaMap obj, which does not have this attribute. Do you know any easy way to fix this issue without re-writing the static method parseMetadataMap?

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lod5sle

ElDeveloper added a commit that referenced this pull request Feb 18, 2014
@ElDeveloper ElDeveloper merged commit 8b8d4fb into qiita-spots:master Feb 18, 2014
@adamrp adamrp mentioned this pull request Feb 18, 2014
@josenavas josenavas deleted the pyqi branch February 19, 2014 00:01
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5 participants