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1 import json
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2 from galaxy.datatypes.data import Text
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3 from galaxy.datatypes.images import Html
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4
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5 class Jplace(Text):
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6 file_ext = "jplace"
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7
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8 def sniff(self, filename):
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9 try:
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10 with open(filename, "r") as f:
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11 data = json.load(f)
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12 if all (k in data for k in ("version", "tree", "placements", "fields")):
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13 return True
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14 except:
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15 pass
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16
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17 return False
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18
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19 def get_mime(self):
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20 return "application/json"
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21
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22 class AutoPrimaryComposite(Html):
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23 composite_type = "auto_primary_file"
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24
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25 def __init__(self, **kwd):
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26 Html.__init__(self, **kwd)
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27
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28 def regenerate_primary_file(self,dataset):
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29 """
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30 cannot do this until we are setting metadata
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31 """
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32 bn = dataset.metadata.base_name
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33 efp = dataset.extra_files_path
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34 flist = os.listdir(efp)
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35 rval = ['<html><head><title>Files for Composite Dataset %s</title></head><body><p/>Composite %s contains:<p/><ul>' % (dataset.name,dataset.name)]
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36 for i,fname in enumerate(flist):
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37 sfname = os.path.split(fname)[-1]
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38 f,e = os.path.splitext(fname)
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39 rval.append( '<li><a href="%s">%s</a></li>' % ( sfname, sfname) )
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40 rval.append( '</ul></body></html>' )
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41 f = file(dataset.file_name,'w')
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42 f.write("\n".join( rval ))
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43 f.write('\n')
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44 f.close()
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45
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46 def set_meta(self, dataset, **kwd):
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47 Html.set_meta(self, dataset, **kwd)
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48 self.regenerate_primary_file(dataset)
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49
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50 def get_mime(self):
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51 return "text/html"
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52
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53 class BasicHtmlComposite(Html):
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54 composite_type = "basic"
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