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Fixes to imported EUtils to get it working happily with Bio:

* changed internal refs to import EUtils to Bio.EUtils
* modified setup.py so DTDs are installed
* modified MANIFEST.in to make sure DTDs get packaged
* got rid of the executable bit on all files
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commit b7761b6d9c4905dee75d92d909b1af65075c955b 1 parent 3221da0
chapmanb authored
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156 Bio/EUtils/DTDs/LinkOut.py
@@ -1,9 +1,9 @@
#!/usr/bin/python
# This file generated by a program. do not edit.
-import EUtils.POM
+import Bio.EUtils.POM
-# $Id: LinkOut.py,v 1.1 2003-06-13 00:49:37 dalke Exp $
+# $Id: LinkOut.py,v 1.2 2003-06-13 02:08:57 chapmanb Exp $
# LinkOut DTD version 1.1
#
# This document is still under revision and may change.
@@ -135,8 +135,8 @@
#
#
# internal DTD entities
-class SubjectType(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class SubjectType(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# can be one of the following; see LinkOut SubjectTypes and Attributes
@@ -204,8 +204,8 @@ class SubjectType(EUtils.POM.ElementNode):
# translation
#
#
-class Attribute(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Attribute(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# can be one of the following; see LinkOut SubjectTypes and Attributes
@@ -230,103 +230,103 @@ class Attribute(EUtils.POM.ElementNode):
#
#
# This is the top level element for Provider
-class Provider(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'ProviderId', ''), (u'Name', ''), (u'NameAbbr', ''), (u'SubjectType', u'*'), (u'Attribute', u'*'), (u'Url', u'*'), (u'IconUrl', u'*'), (u'Brief', u'?')], ''))
+class Provider(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'ProviderId', ''), (u'Name', ''), (u'NameAbbr', ''), (u'SubjectType', u'*'), (u'Attribute', u'*'), (u'Url', u'*'), (u'IconUrl', u'*'), (u'Brief', u'?')], ''))
-class ProviderId(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class ProviderId(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
-class Name(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Name(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
-class NameAbbr(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class NameAbbr(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
-class Url(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
- ATTLIST = EUtils.POM.AttributeList([EUtils.POM.XMLAttribute('LNG', ['DA', 'DE', 'EN', 'EL', 'ES', 'FR', 'IT', 'IW', 'JA', 'NL', 'NO', 'RU', 'SV', 'ZH'], 13, u'EN')])
+class Url(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+ ATTLIST = Bio.EUtils.POM.AttributeList([Bio.EUtils.POM.XMLAttribute('LNG', ['DA', 'DE', 'EN', 'EL', 'ES', 'FR', 'IT', 'IW', 'JA', 'NL', 'NO', 'RU', 'SV', 'ZH'], 13, u'EN')])
-class IconUrl(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
- ATTLIST = EUtils.POM.AttributeList([EUtils.POM.XMLAttribute('LNG', ['DA', 'DE', 'EN', 'EL', 'ES', 'FR', 'IT', 'IW', 'JA', 'NL', 'NO', 'RU', 'SV', 'ZH'], 13, u'EN')])
+class IconUrl(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+ ATTLIST = Bio.EUtils.POM.AttributeList([Bio.EUtils.POM.XMLAttribute('LNG', ['DA', 'DE', 'EN', 'EL', 'ES', 'FR', 'IT', 'IW', 'JA', 'NL', 'NO', 'RU', 'SV', 'ZH'], 13, u'EN')])
-class Brief(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Brief(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# End of Privider group
-class LinkSet(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [(u'Link', u'+')], ''))
+class LinkSet(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [(u'Link', u'+')], ''))
-class Link(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'LinkId', ''), (u'ProviderId', ''), (u'IconUrl', u'*'), (u'|', [(u'ObjectSelector', ''), (u'SubObjectSelector', '')], ''), (u'ObjectUrl', u'+')], ''))
+class Link(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'LinkId', ''), (u'ProviderId', ''), (u'IconUrl', u'*'), (u'|', [(u'ObjectSelector', ''), (u'SubObjectSelector', '')], ''), (u'ObjectUrl', u'+')], ''))
-class LinkId(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class LinkId(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
-class ObjectSelector(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'Database', ''), (u'ObjectList', '')], ''))
+class ObjectSelector(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'Database', ''), (u'ObjectList', '')], ''))
-class Database(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Database(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# The databases available in LinkOut include the following:
# PubMed, Nucleotide, Protein, Genome, Structure, PopSet, Taxonomy and OMIM
-class ObjectList(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u'|', [(u'Query', ''), (u'ObjId', '')], u'+'))
+class ObjectList(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u'|', [(u'Query', ''), (u'ObjId', '')], u'+'))
-class Query(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Query(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
-class ObjId(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class ObjId(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# End of ObjectList group
# End of ObjectSelector group
# Libraries must use SubObjectSelector to refer to the sub providers
-class SubObjectSelector(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'Database', ''), (u'SubProvider', '')], ''))
+class SubObjectSelector(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'Database', ''), (u'SubProvider', '')], ''))
-class SubProvider(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'NameAbbr', ''), (u'|', [(u'InclQuery', ''), (u'ExclQuery', '')], u'*')], ''))
+class SubProvider(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'NameAbbr', ''), (u'|', [(u'InclQuery', ''), (u'ExclQuery', '')], u'*')], ''))
-class InclQuery(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class InclQuery(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
-class ExclQuery(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class ExclQuery(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# End of SubObjectSelector group
-class ObjectUrl(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'|', [(u',', [(u'Base', ''), (u'|', [(u'Rule', ''), (u'RuleToMany', '')], u'?')], ''), (u'|', [(u'Rule', ''), (u'RuleToMany', '')], '')], ''), (u'UrlName', u'?'), (u'SubjectType', u'*'), (u'Attribute', u'*')], ''))
- ATTLIST = EUtils.POM.AttributeList([EUtils.POM.XMLAttribute('LNG', ['DA', 'DE', 'EN', 'EL', 'ES', 'FR', 'IT', 'IW', 'JA', 'NL', 'NO', 'RU', 'SV', 'ZH'], 13, u'EN')])
+class ObjectUrl(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'|', [(u',', [(u'Base', ''), (u'|', [(u'Rule', ''), (u'RuleToMany', '')], u'?')], ''), (u'|', [(u'Rule', ''), (u'RuleToMany', '')], '')], ''), (u'UrlName', u'?'), (u'SubjectType', u'*'), (u'Attribute', u'*')], ''))
+ ATTLIST = Bio.EUtils.POM.AttributeList([Bio.EUtils.POM.XMLAttribute('LNG', ['DA', 'DE', 'EN', 'EL', 'ES', 'FR', 'IT', 'IW', 'JA', 'NL', 'NO', 'RU', 'SV', 'ZH'], 13, u'EN')])
-class Base(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Base(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
-class pad(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('|', [('#PCDATA', ''), (u'pad', ''), (u'apad', ''), (u'subs', ''), (u'toupper', ''), (u'tolower', ''), (u'strip', ''), (u'normalize', '')], '*'))
- ATTLIST = EUtils.POM.AttributeList([EUtils.POM.XMLAttribute('with', 1, 11, None), EUtils.POM.XMLAttribute('width', 1, 11, None), EUtils.POM.XMLAttribute('align', ['left', 'right'], 13, u'right')])
+class pad(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('|', [('#PCDATA', ''), (u'pad', ''), (u'apad', ''), (u'subs', ''), (u'toupper', ''), (u'tolower', ''), (u'strip', ''), (u'normalize', '')], '*'))
+ ATTLIST = Bio.EUtils.POM.AttributeList([Bio.EUtils.POM.XMLAttribute('with', 1, 11, None), Bio.EUtils.POM.XMLAttribute('width', 1, 11, None), Bio.EUtils.POM.XMLAttribute('align', ['left', 'right'], 13, u'right')])
# used to mark up strings that require padding to create fixed-length string
@@ -335,9 +335,9 @@ class pad(EUtils.POM.ElementNode):
# width result string size (required) (integer)
# align the text should align to (left|right) (default:right)
#
-class apad(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('|', [('#PCDATA', ''), (u'pad', ''), (u'apad', ''), (u'subs', ''), (u'toupper', ''), (u'tolower', ''), (u'strip', ''), (u'normalize', '')], '*'))
- ATTLIST = EUtils.POM.AttributeList([EUtils.POM.XMLAttribute('with', 1, 11, None), EUtils.POM.XMLAttribute('width', 1, 11, None), EUtils.POM.XMLAttribute('align', ['left', 'right'], 13, u'right')])
+class apad(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('|', [('#PCDATA', ''), (u'pad', ''), (u'apad', ''), (u'subs', ''), (u'toupper', ''), (u'tolower', ''), (u'strip', ''), (u'normalize', '')], '*'))
+ ATTLIST = Bio.EUtils.POM.AttributeList([Bio.EUtils.POM.XMLAttribute('with', 1, 11, None), Bio.EUtils.POM.XMLAttribute('width', 1, 11, None), Bio.EUtils.POM.XMLAttribute('align', ['left', 'right'], 13, u'right')])
# used to mark up strings that require padding to create fixed-length string
@@ -349,9 +349,9 @@ class apad(EUtils.POM.ElementNode):
# <apad with = "0" width = "6">E32</apad> => "E00032"
# <apad with = "0" width = "6">640</apad> => "000640"
#
-class subs(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('|', [('#PCDATA', ''), (u'pad', ''), (u'apad', ''), (u'subs', ''), (u'toupper', ''), (u'tolower', ''), (u'strip', ''), (u'normalize', '')], '*'))
- ATTLIST = EUtils.POM.AttributeList([EUtils.POM.XMLAttribute('for', 1, 11, None), EUtils.POM.XMLAttribute('with', 1, 11, None)])
+class subs(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('|', [('#PCDATA', ''), (u'pad', ''), (u'apad', ''), (u'subs', ''), (u'toupper', ''), (u'tolower', ''), (u'strip', ''), (u'normalize', '')], '*'))
+ ATTLIST = Bio.EUtils.POM.AttributeList([Bio.EUtils.POM.XMLAttribute('for', 1, 11, None), Bio.EUtils.POM.XMLAttribute('with', 1, 11, None)])
# substitute one string for another in the element's content
@@ -359,25 +359,25 @@ class subs(EUtils.POM.ElementNode):
# for the string to replace
# with the string to substitute
#
-class toupper(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('|', [('#PCDATA', ''), (u'pad', ''), (u'apad', ''), (u'subs', ''), (u'toupper', ''), (u'tolower', ''), (u'strip', ''), (u'normalize', '')], '*'))
+class toupper(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('|', [('#PCDATA', ''), (u'pad', ''), (u'apad', ''), (u'subs', ''), (u'toupper', ''), (u'tolower', ''), (u'strip', ''), (u'normalize', '')], '*'))
# convert element content into upper case
-class tolower(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('|', [('#PCDATA', ''), (u'pad', ''), (u'apad', ''), (u'subs', ''), (u'toupper', ''), (u'tolower', ''), (u'strip', ''), (u'normalize', '')], '*'))
+class tolower(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('|', [('#PCDATA', ''), (u'pad', ''), (u'apad', ''), (u'subs', ''), (u'toupper', ''), (u'tolower', ''), (u'strip', ''), (u'normalize', '')], '*'))
# convert element content into lower case
-class strip(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('|', [('#PCDATA', ''), (u'pad', ''), (u'apad', ''), (u'subs', ''), (u'toupper', ''), (u'tolower', ''), (u'strip', ''), (u'normalize', '')], '*'))
- ATTLIST = EUtils.POM.AttributeList([EUtils.POM.XMLAttribute('what', ['spaces', 'letters', 'nondigits', 'digits'], 11, None)])
+class strip(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('|', [('#PCDATA', ''), (u'pad', ''), (u'apad', ''), (u'subs', ''), (u'toupper', ''), (u'tolower', ''), (u'strip', ''), (u'normalize', '')], '*'))
+ ATTLIST = Bio.EUtils.POM.AttributeList([Bio.EUtils.POM.XMLAttribute('what', ['spaces', 'letters', 'nondigits', 'digits'], 11, None)])
# strip off spaces/letters/digits in the element's content
#
-class normalize(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('|', [('#PCDATA', ''), (u'pad', ''), (u'apad', ''), (u'subs', ''), (u'toupper', ''), (u'tolower', ''), (u'strip', ''), (u'normalize', '')], '*'))
+class normalize(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('|', [('#PCDATA', ''), (u'pad', ''), (u'apad', ''), (u'subs', ''), (u'toupper', ''), (u'tolower', ''), (u'strip', ''), (u'normalize', '')], '*'))
# are used for normalization of &lo.voll , &lo.iss; elements.
@@ -388,22 +388,22 @@ class normalize(EUtils.POM.ElementNode):
# "10 Suppl 2 Pt 1" ==> "10"
# "2/3" ==> "2/3"
#
-class Rule(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('|', [('#PCDATA', ''), (u'pad', ''), (u'apad', ''), (u'subs', ''), (u'toupper', ''), (u'tolower', ''), (u'strip', ''), (u'normalize', '')], '*'))
+class Rule(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('|', [('#PCDATA', ''), (u'pad', ''), (u'apad', ''), (u'subs', ''), (u'toupper', ''), (u'tolower', ''), (u'strip', ''), (u'normalize', '')], '*'))
-class UrlName(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class UrlName(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
-class RuleToMany(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'Rule', ''), (u'Separator', '')], ''))
+class RuleToMany(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'Rule', ''), (u'Separator', '')], ''))
-class Separator(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Separator(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# End of ObjectUrl group
# End of Link group
-# End of LinkSet group
+# End of LinkSet group
View
84 Bio/EUtils/DTDs/eInfo_020511.py
@@ -1,102 +1,102 @@
#!/usr/bin/python
# This file generated by a program. do not edit.
-import EUtils.POM
+import Bio.EUtils.POM
#
# This is the Current DTD for Entrez eInfo
-# $Id: eInfo_020511.py,v 1.1 2003-06-13 00:49:37 dalke Exp $
+# $Id: eInfo_020511.py,v 1.2 2003-06-13 02:08:57 chapmanb Exp $
#
# =================================================================
-class DbName(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class DbName(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \S+
-class Name(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Name(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class Descriptor(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Descriptor(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class TermCount(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class TermCount(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \d+
-class Menu(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Menu(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class DbTo(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class DbTo(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \S+
-class MenuName(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class MenuName(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class Count(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Count(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \d+
-class ERROR(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class ERROR(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class IsDate(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class IsDate(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# (Y|N)
-class IsNumerical(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class IsNumerical(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# (Y|N)
-class SingleToken(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class SingleToken(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# (Y|N)
-class Hierarchy(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Hierarchy(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# (Y|N)
-class DbList(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [(u'DbName', u'+')], ''))
+class DbList(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [(u'DbName', u'+')], ''))
-class Field(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'Name', ''), (u'Descriptor', ''), (u'TermCount', ''), (u'IsDate', ''), (u'IsNumerical', ''), (u'SingleToken', ''), (u'Hierarchy', '')], ''))
+class Field(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'Name', ''), (u'Descriptor', ''), (u'TermCount', ''), (u'IsDate', ''), (u'IsNumerical', ''), (u'SingleToken', ''), (u'Hierarchy', '')], ''))
-class Link(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'Name', ''), (u'Menu', ''), (u'Descriptor', ''), (u'DbTo', '')], ''))
+class Link(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'Name', ''), (u'Menu', ''), (u'Descriptor', ''), (u'DbTo', '')], ''))
-class LinkList(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [(u'Link', u'*')], ''))
+class LinkList(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [(u'Link', u'*')], ''))
-class FiledList(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [(u'Filed', u'*')], ''))
+class FiledList(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [(u'Filed', u'*')], ''))
-class DbInfo(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'DbName', ''), (u'MenuName', ''), (u'Descriptor', ''), (u'Count', ''), (u'FieldList', ''), (u'LinkList', u'?')], ''))
+class DbInfo(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'DbName', ''), (u'MenuName', ''), (u'Descriptor', ''), (u'Count', ''), (u'FieldList', ''), (u'LinkList', u'?')], ''))
-class eInfoResult(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u'|', [(u'DbList', ''), (u'DbInfo', ''), (u'ERROR', '')], ''))
+class eInfoResult(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u'|', [(u'DbList', ''), (u'DbInfo', ''), (u'ERROR', '')], ''))
View
98 Bio/EUtils/DTDs/eLink_020511.py
@@ -1,119 +1,119 @@
#!/usr/bin/python
# This file generated by a program. do not edit.
-import EUtils.POM
+import Bio.EUtils.POM
#
# This is the Current DTD for Entrez eLink
-# $Id: eLink_020511.py,v 1.1 2003-06-13 00:49:37 dalke Exp $
+# $Id: eLink_020511.py,v 1.2 2003-06-13 02:08:57 chapmanb Exp $
#
# =================================================================
-class ERROR(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class ERROR(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class Info(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Info(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class Id(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
- ATTLIST = EUtils.POM.AttributeList([EUtils.POM.XMLAttribute('HasLinkOut', ['Y', 'N'], 12, None), EUtils.POM.XMLAttribute('HasNeighbor', ['Y', 'N'], 12, None)])
+class Id(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+ ATTLIST = Bio.EUtils.POM.AttributeList([Bio.EUtils.POM.XMLAttribute('HasLinkOut', ['Y', 'N'], 12, None), Bio.EUtils.POM.XMLAttribute('HasNeighbor', ['Y', 'N'], 12, None)])
# \d+
-class Score(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Score(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \d+
-class DbFrom(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class DbFrom(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \S+
-class DbTo(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class DbTo(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \S+
-class LinkName(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class LinkName(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \S+
-class IdList(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [(u'Id', u'*')], ''))
+class IdList(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [(u'Id', u'*')], ''))
# cmd=neighbor
-class Link(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'Id', ''), (u'Score', u'?')], ''))
+class Link(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'Id', ''), (u'Score', u'?')], ''))
-class LinkSetDb(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'DbTo', ''), (u'LinkName', ''), (u'|', [(u'Link', u'*'), (u'Info', '')], ''), (u'ERROR', u'?')], ''))
+class LinkSetDb(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'DbTo', ''), (u'LinkName', ''), (u'|', [(u'Link', u'*'), (u'Info', '')], ''), (u'ERROR', u'?')], ''))
# cmd=links
-class Url(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Url(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \S+
-class IconUrl(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class IconUrl(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \S+
-class SubjectType(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class SubjectType(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class Attribute(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Attribute(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class Name(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Name(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class NameAbbr(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class NameAbbr(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \S+
-class Provider(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'Name', ''), (u'NameAbbr', ''), (u'Id', ''), (u'Url', ''), (u'IconUrl', u'?')], ''))
+class Provider(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'Name', ''), (u'NameAbbr', ''), (u'Id', ''), (u'Url', ''), (u'IconUrl', u'?')], ''))
-class ObjUrl(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'Url', ''), (u'LinkName', u'?'), (u'SubjectType', u'*'), (u'Attribute', u'*'), (u'Provider', '')], ''))
+class ObjUrl(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'Url', ''), (u'LinkName', u'?'), (u'SubjectType', u'*'), (u'Attribute', u'*'), (u'Provider', '')], ''))
-class IdUrlSet(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'Id', ''), (u'|', [(u'ObjUrl', u'+'), (u'Info', '')], '')], ''))
+class IdUrlSet(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'Id', ''), (u'|', [(u'ObjUrl', u'+'), (u'Info', '')], '')], ''))
-class IdUrlList(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'IdUrlSet', u'*'), (u'ERROR', u'?')], ''))
+class IdUrlList(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'IdUrlSet', u'*'), (u'ERROR', u'?')], ''))
# cmd=ncheck & lcheck
-class IdCheckList(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'Id', u'*'), (u'ERROR', u'?')], ''))
+class IdCheckList(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'Id', u'*'), (u'ERROR', u'?')], ''))
# Common
-class LinkSet(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'DbFrom', ''), (u'|', [(u',', [(u'IdList', u'?'), (u'LinkSetDb', u'*')], ''), (u'IdUrlList', ''), (u'IdCheckList', ''), (u'ERROR', '')], '')], ''))
+class LinkSet(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'DbFrom', ''), (u'|', [(u',', [(u'IdList', u'?'), (u'LinkSetDb', u'*')], ''), (u'IdUrlList', ''), (u'IdCheckList', ''), (u'ERROR', '')], '')], ''))
-class eLinkResult(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'LinkSet', u'+'), (u'ERROR', u'?')], ''))
+class eLinkResult(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'LinkSet', u'+'), (u'ERROR', u'?')], ''))
View
28 Bio/EUtils/DTDs/ePost_020511.py
@@ -1,40 +1,40 @@
#!/usr/bin/python
# This file generated by a program. do not edit.
-import EUtils.POM
+import Bio.EUtils.POM
#
# This is the Current DTD for Entrez ePost
-# $Id: ePost_020511.py,v 1.1 2003-06-13 00:49:37 dalke Exp $
+# $Id: ePost_020511.py,v 1.2 2003-06-13 02:08:57 chapmanb Exp $
#
#
# =================================================================
-class QueryKey(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class QueryKey(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \d+
-class WebEnv(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class WebEnv(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \S+
-class ERROR(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class ERROR(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
# Added by Andrew Dalke (dalke@dalkescientific.com) to support
# the new InvalidIdList interface
-class Id(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Id(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class InvalidIdList(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [(u'Id', u'*')], ''))
+class InvalidIdList(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [(u'Id', u'*')], ''))
-class ePostResult(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u'|', [(u',', [(u'QueryKey', ''), (u'InvalidIdList', u'?'), (u'WebEnv', '')], ''), (u'ERROR', '')], ''))
+class ePostResult(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u'|', [(u',', [(u'QueryKey', ''), (u'InvalidIdList', u'?'), (u'WebEnv', '')], ''), (u'ERROR', '')], ''))
View
108 Bio/EUtils/DTDs/eSearch_020511.py
@@ -1,133 +1,133 @@
#!/usr/bin/python
# This file generated by a program. do not edit.
-import EUtils.POM
+import Bio.EUtils.POM
#
# This is the Current DTD for Entrez eSearch
-# $Id: eSearch_020511.py,v 1.1 2003-06-13 00:49:37 dalke Exp $
+# $Id: eSearch_020511.py,v 1.2 2003-06-13 02:08:57 chapmanb Exp $
#
# =================================================================
-class Count(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Count(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \d+
-class RetMax(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class RetMax(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \d+
-class RetStart(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class RetStart(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \d+
-class Id(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Id(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \d+
-class From(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class From(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class To(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class To(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class Term(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Term(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class Field(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Field(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class QueryKey(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class QueryKey(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \d+
-class WebEnv(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class WebEnv(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \S+
-class Explode(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Explode(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# (Y|N)
-class OP(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class OP(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# (AND|OR|NOT|RANGE)
-class IdList(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [(u'Id', u'*')], ''))
+class IdList(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [(u'Id', u'*')], ''))
-class Translation(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'From', ''), (u'To', '')], ''))
+class Translation(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'From', ''), (u'To', '')], ''))
-class TranslationSet(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [(u'Translation', u'*')], ''))
+class TranslationSet(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [(u'Translation', u'*')], ''))
-class TermSet(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'Term', ''), (u'Field', ''), (u'Count', ''), (u'Explode', '')], ''))
+class TermSet(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'Term', ''), (u'Field', ''), (u'Count', ''), (u'Explode', '')], ''))
-class TranslationStack(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [(u'|', [(u'TermSet', ''), (u'OP', '')], u'*')], ''))
+class TranslationStack(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [(u'|', [(u'TermSet', ''), (u'OP', '')], u'*')], ''))
# Error message tags
-class ERROR(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class ERROR(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class OutputMessage(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class OutputMessage(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class QuotedPhraseNotFound(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class QuotedPhraseNotFound(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class PhraseIgnored(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class PhraseIgnored(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class FieldNotFound(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class FieldNotFound(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class PhraseNotFound(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class PhraseNotFound(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class ErrorList(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'PhraseNotFound', u'*'), (u'FieldNotFound', u'*')], ''))
+class ErrorList(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'PhraseNotFound', u'*'), (u'FieldNotFound', u'*')], ''))
-class WarningList(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'PhraseIgnored', u'*'), (u'QuotedPhraseNotFound', u'*'), (u'OutputMessage', u'*')], ''))
+class WarningList(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'PhraseIgnored', u'*'), (u'QuotedPhraseNotFound', u'*'), (u'OutputMessage', u'*')], ''))
# Response tags
-class eSearchResult(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'|', [(u',', [(u'Count', ''), (u',', [(u'RetMax', ''), (u'RetStart', ''), (u'QueryKey', u'?'), (u'WebEnv', u'?'), (u'IdList', ''), (u'TranslationSet', ''), (u'TranslationStack', u'?')], u'?')], ''), (u'ERROR', '')], ''), (u'ErrorList', u'?'), (u'WarningList', u'?')], ''))
+class eSearchResult(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'|', [(u',', [(u'Count', ''), (u',', [(u'RetMax', ''), (u'RetStart', ''), (u'QueryKey', u'?'), (u'WebEnv', u'?'), (u'IdList', ''), (u'TranslationSet', ''), (u'TranslationStack', u'?')], u'?')], ''), (u'ERROR', '')], ''), (u'ErrorList', u'?'), (u'WarningList', u'?')], ''))
View
26 Bio/EUtils/DTDs/eSummary_020511.py
@@ -1,33 +1,33 @@
#!/usr/bin/python
# This file generated by a program. do not edit.
-import EUtils.POM
+import Bio.EUtils.POM
#
# This is the Current DTD for Entrez eSummary
-# $Id: eSummary_020511.py,v 1.1 2003-06-13 00:49:37 dalke Exp $
+# $Id: eSummary_020511.py,v 1.2 2003-06-13 02:08:57 chapmanb Exp $
#
# =================================================================
-class Id(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class Id(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# \d+
-class Item(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('|', [('#PCDATA', ''), (u'Item', '')], '*'))
- ATTLIST = EUtils.POM.AttributeList([EUtils.POM.XMLAttribute('Name', 1, 11, None), EUtils.POM.XMLAttribute('Type', ['Integer', 'Date', 'String', 'List', 'Unknown'], 11, None)])
+class Item(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('|', [('#PCDATA', ''), (u'Item', '')], '*'))
+ ATTLIST = Bio.EUtils.POM.AttributeList([Bio.EUtils.POM.XMLAttribute('Name', 1, 11, None), Bio.EUtils.POM.XMLAttribute('Type', ['Integer', 'Date', 'String', 'List', 'Unknown'], 11, None)])
# .+
-class ERROR(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
+class ERROR(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel(('', [('#PCDATA', '')], ''))
# .+
-class DocSum(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u',', [(u'Id', ''), (u'Item', u'+')], ''))
+class DocSum(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u',', [(u'Id', ''), (u'Item', u'+')], ''))
-class eSummaryResult(EUtils.POM.ElementNode):
- CONTENTMODEL = EUtils.POM.ContentModel((u'|', [(u'DocSum', u'*'), (u'ERROR', u'?')], ''))
+class eSummaryResult(Bio.EUtils.POM.ElementNode):
+ CONTENTMODEL = Bio.EUtils.POM.ContentModel((u'|', [(u'DocSum', u'*'), (u'ERROR', u'?')], ''))
View
2  Bio/EUtils/dtd2py.py
@@ -21,7 +21,7 @@
import sys, os
import getopt
-from EUtils import POM
+from Bio.EUtils import POM
def compile_file(dtdfile, mixin, toupper):
outfilename = POM.get_mod_file(dtdfile)
View
2  Bio/EUtils/parse.py
@@ -33,7 +33,7 @@ def __call__(self, obj):
class UsePOMParser:
def __init__(self, module_name):
- self.module_name = "EUtils.DTDs." + module_name
+ self.module_name = "Bio.EUtils.DTDs." + module_name
def parse_using_dtd(self, file):
module = _load_module(self.module_name)
View
1  MANIFEST.in
@@ -20,6 +20,7 @@ include Bio/KDTree/Makefile # Include files for building KDTree.
include Bio/KDTree/_KDTree.i
include Bio/KDTree/README
include Bio/SCOP/tests/*.txt # Include files for testing SCOP.
+include Bio/EUtils/DTDs/*.dtd # Include DTD files for EUtils
exclude Tests/Graphics/*.pdf # Exclude test files generated by reportlab.
exclude Tests/Graphics/*.eps
View
26 setup.py
@@ -9,7 +9,7 @@
For more in-depth instructions, see the installation section of the
biopython manual, linked to from:
-http://biopython.org/wiki/html/BioPython/BiopythonCode.html
+http://www.biopython.org/documentation/
Or for more details about the options available from distutils, look at
the 'Installing Python Modules' distutils documentation, available from:
@@ -18,10 +18,10 @@
Or, if all else fails, feel free to write to the biopython list at
biopython@biopython.org and ask for help.
-
"""
import sys
import os
+import shutil
# Make sure I have the right Python version.
if sys.version_info[:2] < (2, 2):
@@ -58,7 +58,10 @@ class install_biopython(install):
This will just run the normal install, and then print warning messages
if packages are missing.
-
+
+ This also has a hack to install DTDs needed for EUtils into
+ Bio.EUtils.DTDs. This is not a pretty thing since we should
+ really only have pure python modules installed.
"""
def check_dependencies(self):
"""S.check_dependencies() -> boolean
@@ -109,11 +112,26 @@ def check_dependencies(self):
"Do you want to continue this installation?", default):
return 0
return 1
+
+ def install_eutils_dtds(self):
+ """This is a hack to install DTDs needed for EUtils into Bio.
+ """
+ dtds_dir = os.path.join(os.getcwd(), "Bio", "EUtils", "DTDs")
+ install_dir = os.path.join(self.install_purelib, "Bio", "EUtils",
+ "DTDs")
+ potential_dtds = os.listdir(dtds_dir)
+ for potential_dtd in potential_dtds:
+ name, ext = os.path.splitext(potential_dtd)
+ if ext == ".dtd":
+ shutil.copy(os.path.join(dtds_dir, potential_dtd),
+ install_dir)
+
def run(self):
if self.check_dependencies():
# Run the normal install.
install.run(self)
+ self.install_eutils_dtds()
class build_py_biopython(build_py):
def run(self):
@@ -234,6 +252,8 @@ def is_reportlab_installed():
'Bio.expressions.blast',
'Bio.expressions.embl',
'Bio.expressions.swissprot',
+ 'Bio.EUtils',
+ 'Bio.EUtils.DTDs',
'Bio.Fasta',
'Bio.formatdefs',
'Bio.FSSP',
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