Strip trailing whitespace from entrez.py.

diff --git a/posts/entrez/entrez.py b/posts/entrez/entrez.py
index 89b9da1d22781f2f038d6f011435bcc79235db12..73661b8574f59c07853c34588058459d15c4bdef 100755 (executable)
--- a/posts/entrez/entrez.py
+++ b/posts/entrez/entrez.py
@@ -16,7 +16,7 @@
 # You should have received a copy of the GNU General Public License
 # along with This program.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Code following John Vu's medline query code pybliographer/Pyblio/Query.py, 
+# Code following John Vu's medline query code pybliographer/Pyblio/Query.py,
 #
 # Python interface to the Entrez databases.
 # See http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
@@ -31,7 +31,7 @@
 #      NLM does not claim the copyright on the abstracts in PubMed; however, journal publishers or authors may.
 #      NLM provides no legal advice concerning distribution of copyrighted materials, consult your legal counsel.
 #
-# For a good Python-and-XML-DOM intro, see 
+# For a good Python-and-XML-DOM intro, see
 #  http://www.boddie.org.uk/python/XML_intro.html
 # for the official docs, see
 #  http://docs.python.org/lib/module-xml.dom.html
@@ -50,7 +50,7 @@ import urllib
 # supports Document Object Model (DOM) Level 1 Specification
 # http://docs.python.org/lib/module-xml.dom.minidom.html
 import xml.dom.minidom as dom
- 
+
 # For calling the bibutils conversion programs
 from subprocess import Popen, PIPE
 
@@ -106,7 +106,7 @@ def unique(seq, keepstr=True):
     Return the sequence (list, tuple, etc) without repeating entries
     by Paul Rubin and Jordan Callicoat.
     http://groups.google.com/group/comp.lang.python/browse_thread/thread/40c6c455f4fd5154/744a1a338afe1331?lnk=gst&rnum=7#744a1a338afe1331
-    
+
     for example [1,2,3,1,2] -> [1,2,3]
     """
     t = type(seq)
@@ -293,7 +293,7 @@ def field_dict(db='pubmed', page=None, parsed=None):
         field_info[field['Name']] = field
     clean_parsed_einfo(parsed,parsed_islocal)
     return (fields, tags, field_info)
-    
+
 def link_dict(db='pubmed', page=None, parsed=None):
     parsed,parsed_islocal = get_parsed_einfo(db, page, parsed)
     links = []
@@ -325,7 +325,7 @@ def database_info(db='pubmed', page=None, parsed=None):
     links,link_tags,link_info = link_dict(db=db, parsed=parsed)
     clean_parsed_einfo(parsed,parsed_islocal)
     return (fields, field_tags, field_info, links, link_tags, link_info)
- 
+
 def validate_field(field, fields):
     "Ensure that field is a valid field for the database db."
     try :
@@ -355,9 +355,9 @@ def validate_search_term(term, fields):
 
 ## Search an Entrez database
 
-def _query_esearch(term, db='pubmed', field=None, 
+def _query_esearch(term, db='pubmed', field=None,
                    reldate=None, daterange=None, datetype=None,
-                   retmax=None, rettype=None, sort=None, 
+                   retmax=None, rettype=None, sort=None,
                    validate=False, valid_fields=None, debug=False) :
     """
     Search an Entrez database.
@@ -391,7 +391,7 @@ def _query_esearch(term, db='pubmed', field=None,
      (implemented as mindate=2001&maxdate=2002/01/01)
 
     datetype:  Limit dates to a specific date field based on database.
-     For example: datetype=edat 
+     For example: datetype=edat
 
     retmax: Limit the number of items retrieved
      For example: retmax=100
@@ -453,7 +453,7 @@ def parse_esearch(page):
 
 ## Fetch records by Primary ID from an Entrez database
 
-def _query_efetch(id, db='pubmed', 
+def _query_efetch(id, db='pubmed',
                   retmax=None, retmode='xml', rettype='medline'):
     """
     Fetch records by primary ID from an Entrez database.
@@ -602,7 +602,7 @@ def _query_elink(id, term=None, db='all', dbfrom='pubmed',
      (implemented as mindate=2001&maxdate=2002/01/01)
 
     datetype:  Limit dates to a specific date field based on database.
-     For example: datetype=edat 
+     For example: datetype=edat
 
     retmode: Select the retrieval output format
      xml  (default)
@@ -649,14 +649,14 @@ def _query_elink(id, term=None, db='all', dbfrom='pubmed',
 
 def search_fetch_xml(term, db='pubmed', field=None,
                      reldate=None, daterange=None, datetype=None,
-                     retmax=None, sort=None, 
+                     retmax=None, sort=None,
                      validate=False, valid_fields=None,
                      retmode='xml', rettype='medline'):
     if validate and valid_fields == None:
         valid_fields,field_tags,field_info = field_dict(db)
     search_page = _query_esearch(term, db, field,
                                  reldate, daterange, datetype,
-                                 retmax, rettype='uilist', sort=sort, 
+                                 retmax, rettype='uilist', sort=sort,
                                  validate=validate, valid_fields=valid_fields)
     pid_list = parse_esearch(search_page)
     if not pid_list:
@@ -666,7 +666,7 @@ def search_fetch_xml(term, db='pubmed', field=None,
 
 def search_link(term, db='pubmed', field=None,
                 reldate=None, daterange=None, datetype=None,
-                retmax=None, sort=None, 
+                retmax=None, sort=None,
                 validate=False, valid_fields=None,
                 link_term=None, fromdb=None,
                 cmd=None, linkname=None, link_holding=None,
@@ -677,7 +677,7 @@ def search_link(term, db='pubmed', field=None,
         valid_fields,field_tags,field_info = field_dict(db)
     search_page = _query_esearch(term, db, field,
                                  reldate, daterange, datetype,
-                                 retmax, rettype='uilist', sort=sort, 
+                                 retmax, rettype='uilist', sort=sort,
                                  validate=validate, valid_fields=valid_fields)
     pid_list = parse_esearch(search_page)
     link_page = _query_elink(pid_list, term=link_term, db=db, dbfrom=fromdb,
@@ -963,7 +963,7 @@ free full text [sb]
 
 if __name__ == "__main__" :
     from optparse import OptionParser
-    
+
     usage_string = """%prog [options] SEARCH_TERM       (print medline xml matching search)
      | %prog -l [options] SEARCH_TERM    (print links to entries matching search)
      | %prog -L [-d DATABASE] [-f FILE]  (list databases)
@@ -1079,7 +1079,7 @@ for more details.
         databases = database_list()
         for db in databases:
             print >> outfile, "\t%s" % db
-    
+
     elif mode == 'explain':
         fields,tags,field_info = field_dict(db=options.database)
         if options.field == None :
@@ -1106,7 +1106,7 @@ for more details.
                 print >> outfile, "\t%*.*s\t%-*.*s" \
                     % (field_size[0], field_size[0], key,
                        field_size[1], field_size[1], field_info[options.field][key])
-            
+
     elif mode == 'search':
         search_term = args[0]
         LOG.debug('output %s' % output)
@@ -1154,6 +1154,6 @@ for more details.
                                    link_datetype=options.datetype,
                                    link_retmode=options.retmode,)
             print >> outfile, link_xml
-    
+
     if options.filename != None :
         outfile.close()