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Code Issues Packages Projects Releases Wiki Activity

Detect pdf files on upload [Brad Chapman]. Resolves #357

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This commit is contained in:
Kanwei Li
2010-07-02 18:10:45 -04:00
parent 57521e88cf
commit 810c2291de
3 changed files with 22 additions and 2 deletions
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tools/data_source/upload.py
+7 -1
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@@ -10,6 +10,7 @@ from galaxy import eggs
import galaxy.model
from galaxy.datatypes import sniff
from galaxy.datatypes.binary import *
from galaxy.datatypes.images import Pdf
from galaxy.datatypes.registry import Registry
from galaxy import util
from galaxy.util.json import *
@@ -85,6 +86,8 @@ def check_bam( temp_name ):
return Bam().sniff( temp_name )
def check_sff( temp_name ):
return Sff().sniff( temp_name )
def check_pdf( temp_name ):
return Pdf().sniff( temp_name )
def check_gzip( temp_name ):
# This method returns a tuple of booleans representing ( is_gzipped, is_valid )
# Make sure we have a gzipped file
@@ -160,6 +163,9 @@ def add_file( dataset, json_file, output_path ):
elif check_sff( dataset.path ):
ext = 'sff'
data_type = 'sff'
elif check_pdf( dataset.path ):
ext = 'pdf'
data_type = 'pdf'
else:
# See if we have a gzipped file, which, if it passes our restrictions, we'll uncompress
is_gzipped, is_valid = check_gzip( dataset.path )
@@ -215,7 +221,7 @@ def add_file( dataset, json_file, output_path ):
return
if not data_type:
if check_binary( dataset.path ):
# We have a binary dataset, but it is not Bam or Sff
# We have a binary dataset, but it is not Bam, Sff or Pdf
data_type = 'binary'
#binary_ok = False
parts = dataset.name.split( "." )