Author: bugman
Date: Wed Oct 14 14:52:55 2009
New Revision: 9766
URL: http://svn.gna.org/viewcvs/relax?rev=9766&view=rev
Log:
Citation ID strings are now handled by the bmrb.citation() user function.
Modified:
branches/bmrb/data/exp_info.py
branches/bmrb/generic_fns/exp_info.py
branches/bmrb/prompt/bmrb.py
Modified: branches/bmrb/data/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/data/exp_info.py?rev=9766&r1=9765&r2=9766&view=diff
==============================================================================
--- branches/bmrb/data/exp_info.py (original)
+++ branches/bmrb/data/exp_info.py Wed Oct 14 14:52:55 2009
@@ -43,9 +43,11 @@
self.blacklist = ["citations", "software"]
- def add_citation(self, authors=None, doi=None, pubmed_id=None,
full_citation=None, title=None, status=None, type=None, journal_abbrev=None,
journal_full=None, volume=None, issue=None, page_first=None, page_last=None,
year=None):
+ def add_citation(self, cite_id=None, authors=None, doi=None,
pubmed_id=None, full_citation=None, title=None, status=None, type=None,
journal_abbrev=None, journal_full=None, volume=None, issue=None,
page_first=None, page_last=None, year=None):
"""Store a citation.
+ @keyword cite_id: The citation ID string.
+ @type cite_id: str
@keyword authors: The list of authors. Each author
element is a list of four elements: the first name, last name, first initial,
and middle initials.
@type authors: list of lists of str
@keyword doi: The DOI number, e.g. "10.1000/182".
@@ -99,6 +101,7 @@
cite.element_desc = "Literature citation"
# Set the attributes.
+ cite.cite_id = cite_id
cite.authors = authors
cite.doi = doi
cite.pubmed_id = pubmed_id
Modified: branches/bmrb/generic_fns/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/exp_info.py?rev=9766&r1=9765&r2=9766&view=diff
==============================================================================
--- branches/bmrb/generic_fns/exp_info.py (original)
+++ branches/bmrb/generic_fns/exp_info.py Wed Oct 14 14:52:55 2009
@@ -129,9 +129,11 @@
raise RelaxError("relax cannot be the only program used in the
analysis - spectral analysis programs, etc. must also have been used. Please
use the relevant BMRB user functions to specify these.")
-def citation(authors=None, doi=None, pubmed_id=None, full_citation=None,
title=None, status=None, type=None, journal_abbrev=None, journal_full=None,
volume=None, issue=None, page_first=None, page_last=None, year=None):
+def citation(cite_id=None, authors=None, doi=None, pubmed_id=None,
full_citation=None, title=None, status=None, type=None, journal_abbrev=None,
journal_full=None, volume=None, issue=None, page_first=None, page_last=None,
year=None):
"""Store a citation.
+ @keyword cite_id: The citation ID string.
+ @type cite_id: str
@keyword authors: The list of authors. Each author element is
a list of four elements: the first name, last name, first initial, and middle
initials.
@type authors: list of lists of str
@keyword doi: The DOI number, e.g. "10.1000/182".
@@ -167,7 +169,7 @@
cdp.exp_info = ExpInfo()
# Place the data in the container.
- return cdp.exp_info.add_citation(authors=authors, doi=doi,
pubmed_id=pubmed_id, full_citation=full_citation, title=title, status=status,
type=type, journal_abbrev=journal_abbrev, journal_full=journal_full,
volume=volume, issue=issue, page_first=page_first, page_last=page_last,
year=year)
+ cdp.exp_info.add_citation(cite_id=cite_id, authors=authors, doi=doi,
pubmed_id=pubmed_id, full_citation=full_citation, title=title, status=status,
type=type, journal_abbrev=journal_abbrev, journal_full=journal_full,
volume=volume, issue=issue, page_first=page_first, page_last=page_last,
year=year)
def software(name=None, version=None, url=None, vendor_name=None,
cite_ids=None, tasks=None):
Modified: branches/bmrb/prompt/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/bmrb.py?rev=9766&r1=9765&r2=9766&view=diff
==============================================================================
--- branches/bmrb/prompt/bmrb.py (original)
+++ branches/bmrb/prompt/bmrb.py Wed Oct 14 14:52:55 2009
@@ -37,11 +37,13 @@
class BMRB(User_fn_class):
"""Class for interfacing with the BMRB (http://www.bmrb.wisc.edu/)."""
- def citation(self, authors=None, doi=None, pubmed_id=None,
full_citation=None, title=None, status='published', type='journal',
journal_abbrev=None, journal_full=None, volume=None, issue=None,
page_first=None, page_last=None, year=None):
+ def citation(self, cite_id=None, authors=None, doi=None, pubmed_id=None,
full_citation=None, title=None, status='published', type='journal',
journal_abbrev=None, journal_full=None, volume=None, issue=None,
page_first=None, page_last=None, year=None):
"""Specify a citation to be added the BMRB data file.
Keyword Arguments
~~~~~~~~~~~~~~~~~
+
+ cite_id: The citation ID string.
authors: The list of authors. Each author element is a list of
four elements: the first
name, last name, first initial, and middle initials.
@@ -125,7 +127,8 @@
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "bmrb.citation("
- text = text + "authors=" + repr(authors)
+ text = text + "cite_id=" + repr(cite_id)
+ text = text + ", authors=" + repr(authors)
text = text + ", doi=" + repr(doi)
text = text + ", pubmed_id=" + repr(pubmed_id)
text = text + ", full_citation=" + repr(full_citation)
@@ -142,6 +145,7 @@
print(text)
# The argument checks.
+ check.is_str(cite_id, 'citation ID string')
check.is_str_list(authors, 'authors', list_of_lists=True)
check.is_str(doi, 'DOI number', can_be_none=True)
check.is_str(pubmed_id, 'Pubmed ID number', can_be_none=True)
@@ -158,7 +162,7 @@
check.is_int(year, 'publication year')
# Execute the functional code.
- return exp_info.citation(authors=authors, doi=doi,
pubmed_id=pubmed_id, full_citation=full_citation, title=title, status=status,
type=type, journal_abbrev=journal_abbrev, journal_full=journal_full,
volume=volume, issue=issue, page_first=page_first, page_last=page_last,
year=year)
+ exp_info.citation(cite_id=cite_id, authors=authors, doi=doi,
pubmed_id=pubmed_id, full_citation=full_citation, title=title, status=status,
type=type, journal_abbrev=journal_abbrev, journal_full=journal_full,
volume=volume, issue=issue, page_first=page_first, page_last=page_last,
year=year)
def display(self, version='3.1'):
r9766 - in /branches/bmrb: data/exp_info.py generic_fns/exp_info.py prompt/bmrb.py