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fix database download steps #5

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AldisiRana opened this issue Aug 10, 2019 · 5 comments
Open

fix database download steps #5

AldisiRana opened this issue Aug 10, 2019 · 5 comments

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@AldisiRana
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AldisiRana commented Aug 10, 2019

when the database file doesn't exist, bio2bel_drugbank asks the user to move the full database.xml to the .bio2bel/drugbank directory, but the code requires the zip file

  • even though the code has an option to parse the xml file, the parser is not able to find the xml file because of the PATH variable

UPDATE: I've tried to populate using the zip file but the process gets eliminated after 1%
bio2bel_drugbank

@AldisiRana AldisiRana changed the title update database download steps fix database download steps Aug 10, 2019
@cthoyt
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cthoyt commented Aug 10, 2019

Too much memory consumption?

@cthoyt
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cthoyt commented Aug 10, 2019

The newer file is definitely a lot bigger than before (like 1.4GB in release 5.1.4 vs .8GB in release 5.1.1)

@AldisiRana
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it doesn't actually say why it eliminates it. The process just stops after 1%.
I'm also using the old version (so the 0.8GB file), and it populated before so I don't know why it is not working now

@AldisiRana
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I've added a picture to clarify

@cthoyt
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cthoyt commented Aug 10, 2019

Add some more logging to bio2bel_drugbank then... it's hard to say where it's getting stuck

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