Add my script to convert Caltech's made_for field to htsworkflow 0.2's affiliation...

This could be used as an example for other sites.

diff --git a/docs/conv_caltech_v0.1_made_for.py b/docs/conv_caltech_v0.1_made_for.py
new file mode 100644 (file)
index 0000000..b8ed382
--- /dev/null
+++ b/docs/conv_caltech_v0.1_made_for.py
@@ -0,0 +1,105 @@
+"""
+Read the made-for field and split them up into different affiliations
+while fixing the different spellings for some of our users
+"""
+import os
+
+script_dir = os.path.split(__file__)[0]
+settings_path = os.path.join(script_dir, 'htsworkflow','frontend')
+os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.frontend.settings'
+
+from htsworkflow.frontend.samples import models as samples
+
+def main():
+    # names  ( {'target name': ('current name', 'current name') )
+    names = [
+      'Unknown',
+      'Adam Rosenthal',
+      'Adler Dillman',
+      'Ali',
+      'Ali/EHD',
+      'Ali/PWS',
+      'Andrew Medina-Marino',
+      'Brian Williams',
+      'Davidson',
+      'Elowitz',
+      'Erich Schwarz',
+      'Georgi Warinov',
+      'Gilberto Desalvo',
+      'Gigio',
+      'Gordon Kwan',
+      'Hudson-Alpha',
+      'James Puckett',
+      'Jingli Zhang',
+      'Ellen Rothenberg',
+      'Jose Luis',
+      'Katherine Fisher',
+      'Meyerowitz',
+      'Ryan',
+      'Demo',
+      'Angela Stathopoulos',
+      'Steven Kuntz',
+      'Tony',
+      'Tristan',
+      'Yuling Jiao',
+    ]
+
+    name_map = {
+      '': ('Unknown',) ,
+      'Adam Rosenthal': ('Adam Rosenthal',),
+      'Adler Dillman': ('Adler Dillman',),
+      'Ali': ('Ali',),
+      'Ali/EHD': ('Ali/EHD',),
+      'Ali/PWS': ('Ali/PWS',),
+      'Andrew Medina-Marina': ('Andrew Medina-Marino',),
+      'Andrew Medina-Marino': ('Andrew Medina-Marino',),
+      'Brian': ('Brian Williams',),
+      'Brian Williams': ('Brian Williams',),
+      'Davidson': ('Davidson',),
+      'Elowitz': ('Elowitz',),
+      'Erich Schwarz': ('Erich Schwarz',),
+      'Erich Schwartz': ('Erich Schwarz',),
+      'Georgi Warinov': ('Georgi Warinov',),
+      'Gilberto Desalvo': ('Gilberto Desalvo',),
+      'Gordon Kwan': ('Gordon Kwan',),
+      'Gordon': ('Gordon Kwan',),
+      'Alpha-Hudson': ('Hudson-Alpha',),
+      'Hudson-Alpha': ('Hudson-Alpha',),
+      'James Puckett': ('James Puckett',),
+      'Jingli Zhang, Rothenberg': ('Jingli Zhang', 'Ellen Rothenberg',),
+      'Jingli Zhang': ('Jingli Zhang',),
+      'Jose Luis': ('Jose Luis',),
+      'Katherine Fisher': ('Katherine Fisher',),
+      'Katherine, Gigio': ('Katherine Fisher', 'Gigio',),
+      'Meyerowitz': ('Meyerowitz',),
+      'Ryan, Demo': ('Ryan', 'Demo',),
+      'Stathopoulos': ('Angela Stathopoulos',),
+      'Steve Kuntz': ('Steven Kuntz',),
+      'Steven Kuntz': ('Steven Kuntz',),
+      'Tony': ('Tony',),
+      'Tristan': ('Tristan',),
+      'Yuling Jiao': ('Yuling Jiao',),
+    }
+
+    affiliations = {}
+    for name in names:
+      aff = samples.Affiliation(name=name)
+      affiliations[name] = aff
+      aff.save()
+
+    for lib in samples.Library.objects.all():
+      made_list = name_map[lib.made_for]
+      assert type(made_list) == type((None,))
+      affiliation_list = []
+      for n in made_list:
+        lib.affiliations.add(affiliations[n])
+      lib.save()
+
+if __name__ == "__main__":
+  print "don't run this unless you know what its for"
+  print "it converts the caltech 'made_for' field into a set of"
+  print "affiliations."
+  print ""
+  print "The user lists are hard coded and exist mostly for my"
+  print "convienence."
+  #main()