[Blends-commit] [SCM] website branch, master, updated. 89c601c11eb22ba6b62a0c62f1f6e255ac7b9803
Ole Streicher
olebole at debian.org
Wed Mar 23 20:00:00 UTC 2016
The following commit has been merged in the master branch:
commit 8a4a6e8e3668a223b4d6e785f1d5643bdf1a3bb4
Author: Ole Streicher <olebole at debian.org>
Date: Tue Mar 22 08:47:55 2016 +0100
Change DependantPackage.SetPublications to a function.
Since this was the only method of DependantPackage, this class can now replaced
by a dict.
diff --git a/webtools/blendstasktools.py b/webtools/blendstasktools.py
index 3487843..d6c1c18 100644
--- a/webtools/blendstasktools.py
+++ b/webtools/blendstasktools.py
@@ -748,60 +748,60 @@ class DependantPackage:
# ret += ", desc['en']:" + str(self.desc['en'])
return ret
- def SetPublications(self, taskname, row):
- for pub in ("year", "title", "authors", "doi", "pubmed", "url",
- "journal", "volume", "number", "pages", "eprint"):
- if row[pub]:
- if pub == "pages":
- row[pub] = re.sub("--", "-", row[pub])
- if (pub == "authors" and row[pub].count(" and ") or row[pub].count(" AND ")):
- # assume "authors" string is a regular BibTeX "and" separated list of authors
- row[pub] = re.sub("AND", "and", row[pub].strip())
- authors_list = row[pub].split(" and ")
- # normalize several BibTeX styles to "First Last, First Last and First Last":
- # 1. "First Last and First Last and First Last"
- # 2. "Last, First and Last, First and Last, First"
- # 3. "First Last, First Last and First Last"
- authors_string = ""
- while (authors_list):
- author = authors_list.pop(0)
- if (author.count(",") > 1):
- # 3. "First Last, First Last and First Last"
- # authors string is already in desired format, keep it
- authors_string = row[pub].strip()
- break
- elif (row[pub].count(",") == row[pub].count(" and ") + 1):
- # 2. "Last, First and Last, First and Last, First"
- # reverse last and first name
- (last, first) = author.split(", ")
- full_author = first + " " + last
- else:
- # 1. "First Last and First Last and First Last"
- full_author = author
- if (len(authors_list) > 1):
- authors_string += full_author + ", "
- elif (len(authors_list) > 0):
- authors_string += full_author + " and "
- else:
- authors_string += full_author
- if row[pub] != authors_string:
- # emergency brake if algorithm fails to detect non-names like '1000 Genome Project Data Processing Subgroup'
- if authors_string.count(',') > row[pub].count(' and '):
- logger.warning("Refuse to change Author string in %s: '%s'(%i) -> '%s'(%i)"
- % (self.properties['name'], row[pub], row[pub].count(' and '), authors_string, authors_string.count(',')))
- else:
- logger.debug("Author string changed in %s: '%s' -> '%s'"
- % (self.properties['name'], row[pub], authors_string))
- row[pub] = authors_string
- if 'published' not in self.properties:
- self.properties['published'] = {}
- if pub in self.properties['published']:
- if self.properties['published'][pub] == row[pub]:
- rmpub.write("%s: %s: Published-%s: %s" % (taskname, self.properties['name'], pub, row[pub]))
- logger.info("%s/%s: Publication-%s = %s can be removed" % (taskname, self.properties['name'], pub, row[pub]))
+def setPublications(dep, taskname, row):
+ for pub in ("year", "title", "authors", "doi", "pubmed", "url",
+ "journal", "volume", "number", "pages", "eprint"):
+ if row[pub]:
+ if pub == "pages":
+ row[pub] = re.sub("--", "-", row[pub])
+ if (pub == "authors" and row[pub].count(" and ") or row[pub].count(" AND ")):
+ # assume "authors" string is a regular BibTeX "and" separated list of authors
+ row[pub] = re.sub("AND", "and", row[pub].strip())
+ authors_list = row[pub].split(" and ")
+ # normalize several BibTeX styles to "First Last, First Last and First Last":
+ # 1. "First Last and First Last and First Last"
+ # 2. "Last, First and Last, First and Last, First"
+ # 3. "First Last, First Last and First Last"
+ authors_string = ""
+ while (authors_list):
+ author = authors_list.pop(0)
+ if (author.count(",") > 1):
+ # 3. "First Last, First Last and First Last"
+ # authors string is already in desired format, keep it
+ authors_string = row[pub].strip()
+ break
+ elif (row[pub].count(",") == row[pub].count(" and ") + 1):
+ # 2. "Last, First and Last, First and Last, First"
+ # reverse last and first name
+ (last, first) = author.split(", ")
+ full_author = first + " " + last
+ else:
+ # 1. "First Last and First Last and First Last"
+ full_author = author
+ if (len(authors_list) > 1):
+ authors_string += full_author + ", "
+ elif (len(authors_list) > 0):
+ authors_string += full_author + " and "
else:
- logger.info("%s conflicting fields Publication-%s in tasks file with value '%s' and in UDD with value '%s'" % (self.properties['name'], pub, self.properties['published'][pub], row[pub]))
- self.properties['published'][pub] = row[pub]
+ authors_string += full_author
+ if row[pub] != authors_string:
+ # emergency brake if algorithm fails to detect non-names like '1000 Genome Project Data Processing Subgroup'
+ if authors_string.count(',') > row[pub].count(' and '):
+ logger.warning("Refuse to change Author string in %s: '%s'(%i) -> '%s'(%i)"
+ % (dep.properties['name'], row[pub], row[pub].count(' and '), authors_string, authors_string.count(',')))
+ else:
+ logger.debug("Author string changed in %s: '%s' -> '%s'"
+ % (dep.properties['name'], row[pub], authors_string))
+ row[pub] = authors_string
+ if 'published' not in dep.properties:
+ dep.properties['published'] = {}
+ if pub in dep.properties['published']:
+ if dep.properties['published'][pub] == row[pub]:
+ rmpub.write("%s: %s: Published-%s: %s" % (taskname, dep.properties['name'], pub, row[pub]))
+ logger.info("%s/%s: Publication-%s = %s can be removed" % (taskname, dep.properties['name'], pub, row[pub]))
+ else:
+ logger.info("%s conflicting fields Publication-%s in tasks file with value '%s' and in UDD with value '%s'" % (dep.properties['name'], pub, dep.properties['published'][pub], row[pub]))
+ dep.properties['published'][pub] = row[pub]
class Tasks:
@@ -1528,7 +1528,7 @@ class TaskDependencies:
logger.info("Edam topics found for package %s: %s" % (dep.properties['name'], str(row['edam_topics'])))
# Publications
- dep.SetPublications(self.task, row)
+ setPublications(dep, self.task, row)
pkgs_in_pool.append(dep.properties['name'])
# DEBUG
@@ -1580,7 +1580,7 @@ class TaskDependencies:
(_name, _url) = email.utils.parseaddr(row['maintainer'])
dep.properties['maintainer'] = {'name': _name, 'email': _url}
- dep.SetPublications(self.task, row)
+ setPublications(dep, self.task, row)
if row['changed_by']:
try:
changed = row['changed_by']
@@ -1659,7 +1659,7 @@ class TaskDependencies:
vcs[prop] = row['vcs-' + prop]
if int(row['wnpp']) > 0:
dep.properties['wnpp'] = row['wnpp']
- dep.SetPublications(self.task, row)
+ setPublications(dep, self.task, row)
dep.properties['desc']['en']['short'] = row['description_en']
dep.properties['desc']['en']['long'] = PrepareMarkdownInput(row['long_description_en'])
if row['maintainer']:
diff --git a/webtools/blendstasktools_udd.py b/webtools/blendstasktools_udd.py
index 81dd9cd..ef39ea9 100644
--- a/webtools/blendstasktools_udd.py
+++ b/webtools/blendstasktools_udd.py
@@ -711,60 +711,60 @@ class DependantPackage:
return ret
- def SetPublications(self, taskname, row):
- for pub in ("year", "title", "authors", "doi", "pubmed", "url",
- "journal", "volume", "number", "pages", "eprint"):
- if row[pub]:
- if pub == "pages":
- row[pub] = re.sub("--", "-", row[pub])
- if (pub == "authors" and row[pub].count(" and ") or row[pub].count(" AND ")):
- # assume "authors" string is a regular BibTeX "and" separated list of authors
- row[pub] = re.sub("AND", "and", row[pub].strip())
- authors_list = row[pub].split(" and ")
- # normalize several BibTeX styles to "First Last, First Last and First Last":
- # 1. "First Last and First Last and First Last"
- # 2. "Last, First and Last, First and Last, First"
- # 3. "First Last, First Last and First Last"
- authors_string = ""
- while (authors_list):
- author = authors_list.pop(0)
- if (author.count(",") > 1):
- # 3. "First Last, First Last and First Last"
- # authors string is already in desired format, keep it
- authors_string = row[pub].strip()
- break
- elif (row[pub].count(",") == row[pub].count(" and ") + 1):
- # 2. "Last, First and Last, First and Last, First"
- # reverse last and first name
- (last, first) = author.split(", ")
- full_author = first + " " + last
- else:
- # 1. "First Last and First Last and First Last"
- full_author = author
- if (len(authors_list) > 1):
- authors_string += full_author + ", "
- elif (len(authors_list) > 0):
- authors_string += full_author + " and "
- else:
- authors_string += full_author
- if row[pub] != authors_string:
- # emergency brake if algorithm fails to detect non-names like '1000 Genome Project Data Processing Subgroup'
- if authors_string.count(',') > row[pub].count(' and '):
- logger.warning("Refuse to change Author string in %s: '%s'(%i) -> '%s'(%i)"
- % (self.properties['name'], row[pub], row[pub].count(' and '), authors_string, authors_string.count(',')))
- else:
- logger.debug("Author string changed in %s: '%s' -> '%s'"
- % (self.properties['name'], row[pub], authors_string))
- row[pub] = authors_string
- if 'published' not in self.properties:
- self.properties['published'] = {}
- if pub in self.properties['published']:
- if self.properties['published'][pub] == row[pub]:
- rmpub.write("%s: %s: Published-%s: %s" % (taskname, self.properties['name'], pub, row[pub]))
- logger.info("%s/%s: Publication-%s = %s can be removed" % (taskname, self.properties['name'], pub, row[pub]))
+def setPublications(dep, taskname, row):
+ for pub in ("year", "title", "authors", "doi", "pubmed", "url",
+ "journal", "volume", "number", "pages", "eprint"):
+ if row[pub]:
+ if pub == "pages":
+ row[pub] = re.sub("--", "-", row[pub])
+ if (pub == "authors" and row[pub].count(" and ") or row[pub].count(" AND ")):
+ # assume "authors" string is a regular BibTeX "and" separated list of authors
+ row[pub] = re.sub("AND", "and", row[pub].strip())
+ authors_list = row[pub].split(" and ")
+ # normalize several BibTeX styles to "First Last, First Last and First Last":
+ # 1. "First Last and First Last and First Last"
+ # 2. "Last, First and Last, First and Last, First"
+ # 3. "First Last, First Last and First Last"
+ authors_string = ""
+ while (authors_list):
+ author = authors_list.pop(0)
+ if (author.count(",") > 1):
+ # 3. "First Last, First Last and First Last"
+ # authors string is already in desired format, keep it
+ authors_string = row[pub].strip()
+ break
+ elif (row[pub].count(",") == row[pub].count(" and ") + 1):
+ # 2. "Last, First and Last, First and Last, First"
+ # reverse last and first name
+ (last, first) = author.split(", ")
+ full_author = first + " " + last
else:
- logger.info("%s conflicting fields Publication-%s in tasks file with value '%s' and in UDD with value '%s'" % (self.properties['name'], pub, self.properties['published'][pub], row[pub]))
- self.properties['published'][pub] = row[pub]
+ # 1. "First Last and First Last and First Last"
+ full_author = author
+ if (len(authors_list) > 1):
+ authors_string += full_author + ", "
+ elif (len(authors_list) > 0):
+ authors_string += full_author + " and "
+ else:
+ authors_string += full_author
+ if row[pub] != authors_string:
+ # emergency brake if algorithm fails to detect non-names like '1000 Genome Project Data Processing Subgroup'
+ if authors_string.count(',') > row[pub].count(' and '):
+ logger.warning("Refuse to change Author string in %s: '%s'(%i) -> '%s'(%i)"
+ % (dep.properties['name'], row[pub], row[pub].count(' and '), authors_string, authors_string.count(',')))
+ else:
+ logger.debug("Author string changed in %s: '%s' -> '%s'"
+ % (dep.properties['name'], row[pub], authors_string))
+ row[pub] = authors_string
+ if 'published' not in dep.properties:
+ dep.properties['published'] = {}
+ if pub in dep.properties['published']:
+ if dep.properties['published'][pub] == row[pub]:
+ rmpub.write("%s: %s: Published-%s: %s" % (taskname, dep.properties['name'], pub, row[pub]))
+ logger.info("%s/%s: Publication-%s = %s can be removed" % (taskname, dep.properties['name'], pub, row[pub]))
+ else:
+ logger.info("%s conflicting fields Publication-%s in tasks file with value '%s' and in UDD with value '%s'" % (dep.properties['name'], pub, dep.properties['published'][pub], row[pub]))
+ dep.properties['published'][pub] = row[pub]
class Tasks:
@@ -1167,7 +1167,7 @@ class TaskDependencies:
dep.properties['remark'] = {'short': shortDesc, 'long': longDesc}
# Publications
- dep.SetPublications(self.task, row)
+ setPublications(dep, self.task, row)
self._AppendDependency2List(dep)
--
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