Author: bugman
Date: Wed Oct 14 15:27:54 2009
New Revision: 9769
URL: http://svn.gna.org/viewcvs/relax?rev=9769&view=rev
Log:
The BMRB file now uses the citation ID numbers properly.
Modified:
branches/bmrb/generic_fns/bmrb.py
branches/bmrb/generic_fns/exp_info.py
branches/bmrb/prompt/bmrb.py
Modified: branches/bmrb/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/bmrb.py?rev=9769&r1=9768&r2=9769&view=diff
==============================================================================
--- branches/bmrb/generic_fns/bmrb.py (original)
+++ branches/bmrb/generic_fns/bmrb.py Wed Oct 14 15:27:54 2009
@@ -103,11 +103,11 @@
mkdir_nofail(directory, verbosity=0)
# Add the relax citations.
- cite1 = cdp.exp_info.add_citation(authors=exp_info.RELAX_CITE1_AUTHORS,
doi=exp_info.RELAX_CITE1_DOI, pubmed_id=exp_info.RELAX_CITE1_PUBMED_ID,
full_citation=exp_info.RELAX_CITE1_FULL_CITATION,
title=exp_info.RELAX_CITE1_TITLE, status=exp_info.RELAX_CITE1_STATUS,
type=exp_info.RELAX_CITE1_TYPE,
journal_abbrev=exp_info.RELAX_CITE1_JOURNAL_ABBREV,
journal_full=exp_info.RELAX_CITE1_JOURNAL_FULL,
volume=exp_info.RELAX_CITE1_VOLUME, issue=exp_info.RELAX_CITE1_ISSUE,
page_first=exp_info.RELAX_CITE1_PAGE_FIRST,
page_last=exp_info.RELAX_CITE1_PAGE_LAST, year=exp_info.RELAX_CITE1_YEAR)
- cite2 = cdp.exp_info.add_citation(authors=exp_info.RELAX_CITE2_AUTHORS,
doi=exp_info.RELAX_CITE2_DOI, pubmed_id=exp_info.RELAX_CITE2_PUBMED_ID,
full_citation=exp_info.RELAX_CITE2_FULL_CITATION,
title=exp_info.RELAX_CITE2_TITLE, status=exp_info.RELAX_CITE2_STATUS,
type=exp_info.RELAX_CITE2_TYPE,
journal_abbrev=exp_info.RELAX_CITE2_JOURNAL_ABBREV,
journal_full=exp_info.RELAX_CITE2_JOURNAL_FULL,
volume=exp_info.RELAX_CITE2_VOLUME, issue=exp_info.RELAX_CITE2_ISSUE,
page_first=exp_info.RELAX_CITE2_PAGE_FIRST,
page_last=exp_info.RELAX_CITE2_PAGE_LAST, year=exp_info.RELAX_CITE2_YEAR)
+ cdp.exp_info.add_citation(cite_id='relax_ref1',
authors=exp_info.RELAX_CITE1_AUTHORS, doi=exp_info.RELAX_CITE1_DOI,
pubmed_id=exp_info.RELAX_CITE1_PUBMED_ID,
full_citation=exp_info.RELAX_CITE1_FULL_CITATION,
title=exp_info.RELAX_CITE1_TITLE, status=exp_info.RELAX_CITE1_STATUS,
type=exp_info.RELAX_CITE1_TYPE,
journal_abbrev=exp_info.RELAX_CITE1_JOURNAL_ABBREV,
journal_full=exp_info.RELAX_CITE1_JOURNAL_FULL,
volume=exp_info.RELAX_CITE1_VOLUME, issue=exp_info.RELAX_CITE1_ISSUE,
page_first=exp_info.RELAX_CITE1_PAGE_FIRST,
page_last=exp_info.RELAX_CITE1_PAGE_LAST, year=exp_info.RELAX_CITE1_YEAR)
+ cdp.exp_info.add_citation(cite_id='relax_ref2',
authors=exp_info.RELAX_CITE2_AUTHORS, doi=exp_info.RELAX_CITE2_DOI,
pubmed_id=exp_info.RELAX_CITE2_PUBMED_ID,
full_citation=exp_info.RELAX_CITE2_FULL_CITATION,
title=exp_info.RELAX_CITE2_TITLE, status=exp_info.RELAX_CITE2_STATUS,
type=exp_info.RELAX_CITE2_TYPE,
journal_abbrev=exp_info.RELAX_CITE2_JOURNAL_ABBREV,
journal_full=exp_info.RELAX_CITE2_JOURNAL_FULL,
volume=exp_info.RELAX_CITE2_VOLUME, issue=exp_info.RELAX_CITE2_ISSUE,
page_first=exp_info.RELAX_CITE2_PAGE_FIRST,
page_last=exp_info.RELAX_CITE2_PAGE_LAST, year=exp_info.RELAX_CITE2_YEAR)
# Add the relax software package.
- cdp.exp_info.software_setup(name=exp_info.RELAX_NAME,
version=version_full(), vendor_name=exp_info.RELAX_AUTHORS,
url=exp_info.RELAX_URL, cite_ids=[cite1, cite2], tasks=exp_info.RELAX_TASKS)
+ cdp.exp_info.software_setup(name=exp_info.RELAX_NAME,
version=version_full(), vendor_name=exp_info.RELAX_AUTHORS,
url=exp_info.RELAX_URL, cite_ids=['relax_ref1', 'relax_ref2'],
tasks=exp_info.RELAX_TASKS)
# Execute the specific BMRB writing code.
write_function(file_path, version=version)
Modified: branches/bmrb/generic_fns/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/exp_info.py?rev=9769&r1=9768&r2=9769&view=diff
==============================================================================
--- branches/bmrb/generic_fns/exp_info.py (original)
+++ branches/bmrb/generic_fns/exp_info.py Wed Oct 14 15:27:54 2009
@@ -121,8 +121,13 @@
# Loop over the software.
if hasattr(cdp, 'exp_info') and hasattr(cdp.exp_info, 'software'):
for software in cdp.exp_info.software:
+ # Get the citation ID numbers.
+ cite_id_nums = []
+ for cite in software.cite_ids:
+ cite_id_nums.append(cdp.exp_info.get_cite_id_num(cite))
+
# The program info.
- star.software.add(name=software.name, version=software.version,
vendor_name=software.vendor_name, vendor_eaddress=software.url,
task=software.tasks, cite_ids=software.cite_ids)
+ star.software.add(name=software.name, version=software.version,
vendor_name=software.vendor_name, vendor_eaddress=software.url,
task=software.tasks, cite_ids=cite_id_nums)
# relax cannot be the only program used!
else:
@@ -217,19 +222,19 @@
# relax.
if name == 'relax':
# Add the citations.
- cite1 = cdp.exp_info.add_citation(authors=RELAX_CITE1_AUTHORS,
doi=RELAX_CITE1_DOI, pubmed_id=RELAX_CITE1_PUBMED_ID,
full_citation=RELAX_CITE1_FULL_CITATION, title=RELAX_CITE1_TITLE,
status=RELAX_CITE1_STATUS, type=RELAX_CITE1_TYPE,
journal_abbrev=RELAX_CITE1_JOURNAL_ABBREV,
journal_full=RELAX_CITE1_JOURNAL_FULL, volume=RELAX_CITE1_VOLUME,
issue=RELAX_CITE1_ISSUE, page_first=RELAX_CITE1_PAGE_FIRST,
page_last=RELAX_CITE1_PAGE_LAST, year=RELAX_CITE1_YEAR)
- cite2 = cdp.exp_info.add_citation(authors=RELAX_CITE2_AUTHORS,
doi=RELAX_CITE2_DOI, pubmed_id=RELAX_CITE2_PUBMED_ID,
full_citation=RELAX_CITE2_FULL_CITATION, title=RELAX_CITE2_TITLE,
status=RELAX_CITE2_STATUS, type=RELAX_CITE2_TYPE,
journal_abbrev=RELAX_CITE2_JOURNAL_ABBREV,
journal_full=RELAX_CITE2_JOURNAL_FULL, volume=RELAX_CITE2_VOLUME,
issue=RELAX_CITE2_ISSUE, page_first=RELAX_CITE2_PAGE_FIRST,
page_last=RELAX_CITE2_PAGE_LAST, year=RELAX_CITE2_YEAR)
+ cdp.exp_info.add_citation(cite_id='relax_ref1',
authors=RELAX_CITE1_AUTHORS, doi=RELAX_CITE1_DOI,
pubmed_id=RELAX_CITE1_PUBMED_ID, full_citation=RELAX_CITE1_FULL_CITATION,
title=RELAX_CITE1_TITLE, status=RELAX_CITE1_STATUS, type=RELAX_CITE1_TYPE,
journal_abbrev=RELAX_CITE1_JOURNAL_ABBREV,
journal_full=RELAX_CITE1_JOURNAL_FULL, volume=RELAX_CITE1_VOLUME,
issue=RELAX_CITE1_ISSUE, page_first=RELAX_CITE1_PAGE_FIRST,
page_last=RELAX_CITE1_PAGE_LAST, year=RELAX_CITE1_YEAR)
+ cdp.exp_info.add_citation(cite_id='relax_ref2',
authors=RELAX_CITE2_AUTHORS, doi=RELAX_CITE2_DOI,
pubmed_id=RELAX_CITE2_PUBMED_ID, full_citation=RELAX_CITE2_FULL_CITATION,
title=RELAX_CITE2_TITLE, status=RELAX_CITE2_STATUS, type=RELAX_CITE2_TYPE,
journal_abbrev=RELAX_CITE2_JOURNAL_ABBREV,
journal_full=RELAX_CITE2_JOURNAL_FULL, volume=RELAX_CITE2_VOLUME,
issue=RELAX_CITE2_ISSUE, page_first=RELAX_CITE2_PAGE_FIRST,
page_last=RELAX_CITE2_PAGE_LAST, year=RELAX_CITE2_YEAR)
# Add the software info.
- cdp.exp_info.software_setup(name=RELAX_NAME, version=version_full(),
vendor_name=RELAX_AUTHORS, url=RELAX_URL, cite_ids=[cite1, cite2],
tasks=RELAX_TASKS)
+ cdp.exp_info.software_setup(name=RELAX_NAME, version=version_full(),
vendor_name=RELAX_AUTHORS, url=RELAX_URL, cite_ids=['relax_ref1',
'relax_ref2'], tasks=RELAX_TASKS)
# NMRPipe.
if name == 'NMRPipe':
# Add the citations.
- cite_index = cdp.exp_info.add_citation(authors=NMRPIPE_CITE_AUTHORS,
doi=NMRPIPE_CITE_DOI, pubmed_id=NMRPIPE_CITE_PUBMED_ID,
full_citation=NMRPIPE_CITE_FULL_CITATION, title=NMRPIPE_CITE_TITLE,
status=NMRPIPE_CITE_STATUS, type=NMRPIPE_CITE_TYPE,
journal_abbrev=NMRPIPE_CITE_JOURNAL_ABBREV,
journal_full=NMRPIPE_CITE_JOURNAL_FULL, volume=NMRPIPE_CITE_VOLUME,
page_first=NMRPIPE_CITE_PAGE_FIRST, page_last=NMRPIPE_CITE_PAGE_LAST,
year=NMRPIPE_CITE_YEAR)
+ cdp.exp_info.add_citation(cite_id='nmrpipe_ref',
authors=NMRPIPE_CITE_AUTHORS, doi=NMRPIPE_CITE_DOI,
pubmed_id=NMRPIPE_CITE_PUBMED_ID, full_citation=NMRPIPE_CITE_FULL_CITATION,
title=NMRPIPE_CITE_TITLE, status=NMRPIPE_CITE_STATUS, type=NMRPIPE_CITE_TYPE,
journal_abbrev=NMRPIPE_CITE_JOURNAL_ABBREV,
journal_full=NMRPIPE_CITE_JOURNAL_FULL, volume=NMRPIPE_CITE_VOLUME,
page_first=NMRPIPE_CITE_PAGE_FIRST, page_last=NMRPIPE_CITE_PAGE_LAST,
year=NMRPIPE_CITE_YEAR)
# Add the software info.
- cdp.exp_info.software_setup(name=NMRPIPE_NAME, version=version,
vendor_name=NMRPIPE_AUTHORS, url=NMRPIPE_URL, cite_ids=[cite_index],
tasks=NMRPIPE_TASKS)
+ cdp.exp_info.software_setup(name=NMRPIPE_NAME, version=version,
vendor_name=NMRPIPE_AUTHORS, url=NMRPIPE_URL, cite_ids=['nmrpipe_ref'],
tasks=NMRPIPE_TASKS)
# Sparky.
elif name == 'Sparky':
@@ -238,7 +243,7 @@
raise RelaxError("The Sparky version number has not been
supplied.")
# Add the citations.
- cite_index = cdp.exp_info.add_citation(authors=SPARKY_CITE_AUTHORS,
full_citation=SPARKY_CITE_FULL_CITATION, status=SPARKY_CITE_STATUS,
type=SPARKY_CITE_TYPE)
+ cite_index = cdp.exp_info.add_citation(cite_id='sparky_ref',
authors=SPARKY_CITE_AUTHORS, full_citation=SPARKY_CITE_FULL_CITATION,
status=SPARKY_CITE_STATUS, type=SPARKY_CITE_TYPE)
# Add the software info.
- cdp.exp_info.software_setup(name=SPARKY_NAME, version=version,
vendor_name=SPARKY_AUTHORS, url=SPARKY_URL, cite_ids=[cite_index],
tasks=SPARKY_TASKS)
+ cdp.exp_info.software_setup(name=SPARKY_NAME, version=version,
vendor_name=SPARKY_AUTHORS, url=SPARKY_URL, cite_ids=['sparky_ref'],
tasks=SPARKY_TASKS)
Modified: branches/bmrb/prompt/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/bmrb.py?rev=9769&r1=9768&r2=9769&view=diff
==============================================================================
--- branches/bmrb/prompt/bmrb.py (original)
+++ branches/bmrb/prompt/bmrb.py Wed Oct 14 15:27:54 2009
@@ -278,7 +278,7 @@
check.is_str(version, 'version', can_be_none=True)
check.is_str(url, 'url', can_be_none=True)
check.is_str(vendor_name, 'vendor_name', can_be_none=True)
- check.is_int_list(cite_ids, 'citation ID numbers', can_be_none=True)
+ check.is_str_list(cite_ids, 'citation ID numbers', can_be_none=True)
check.is_str_list(tasks, 'tasks', can_be_none=True)
# Execute the functional code.
r9769 - in /branches/bmrb: generic_fns/bmrb.py generic_fns/exp_info.py prompt/bmrb.py