Author: bugman
Date: Wed Feb 24 01:27:24 2010
New Revision: 10885
URL: http://svn.gna.org/viewcvs/relax?rev=10885&view=rev
Log:
All references are now taken from the Info_box.bib dictionary
The CITE structure has therefore been deleted.
Modified:
branches/bmrb/generic_fns/bmrb.py
branches/bmrb/generic_fns/exp_info.py
Modified: branches/bmrb/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/bmrb.py?rev=10885&r1=10884&r2=10885&view=diff
==============================================================================
--- branches/bmrb/generic_fns/bmrb.py (original)
+++ branches/bmrb/generic_fns/bmrb.py Wed Feb 24 01:27:24 2010
@@ -30,6 +30,7 @@
from data import Relax_data_store; ds = Relax_data_store()
from data.exp_info import ExpInfo
from generic_fns import exp_info
+from info import Info_box
from relax_errors import RelaxError, RelaxFileError,
RelaxFileOverwriteError, RelaxNoPipeError
from relax_io import get_file_path, mkdir_nofail
from specific_fns.setup import get_specific_fn
@@ -102,9 +103,16 @@
# Create the directories.
mkdir_nofail(directory, verbosity=0)
+ # Get the info box.
+ info = Info_box()
+
# Add the relax citations.
- for id, key in zip(['relax_ref1', 'relax_ref2'], ['relax 1', 'relax 2']):
- cdp.exp_info.add_citation(cite_id=id,
authors=exp_info.CITE[key].authors, doi=exp_info.CITE[key].doi,
pubmed_id=exp_info.CITE[key].pubmed_id,
full_citation=exp_info.CITE[key].full_citation,
title=exp_info.CITE[key].title, status=exp_info.CITE[key].status,
type=exp_info.CITE[key].type,
journal_abbrev=exp_info.CITE[key].journal_abbrev,
journal_full=exp_info.CITE[key].journal_full,
volume=exp_info.CITE[key].volume, issue=exp_info.CITE[key].issue,
page_first=exp_info.CITE[key].page_first,
page_last=exp_info.CITE[key].page_last, year=exp_info.CITE[key].year)
+ for id, key in zip(['relax_ref1', 'relax_ref2'], ['dAuvergneGooley08a',
'dAuvergneGooley08b']):
+ # Alias the bib entry.
+ bib = info.bib[key]
+
+ # Add.
+ cdp.exp_info.add_citation(cite_id=id, authors=bib.author2,
doi=bib.doi, pubmed_id=bib.pubmed_id, full_citation=bib.cite_short(doi=False,
url=False), title=bib.title, status=bib.status, type=bib.type,
journal_abbrev=bib.journal, journal_full=bib.journal_full, volume=bib.volume,
issue=bib.number, page_first=bib.page_first, page_last=bib.page_last,
year=bib.year)
# Add the relax software package.
cdp.exp_info.software_setup(name=exp_info.SOFTWARE['relax'].name,
version=version_full(), vendor_name=exp_info.SOFTWARE['relax'].authors,
url=exp_info.SOFTWARE['relax'].url, cite_ids=['relax_ref1', 'relax_ref2'],
tasks=exp_info.SOFTWARE['relax'].tasks)
Modified: branches/bmrb/generic_fns/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/exp_info.py?rev=10885&r1=10884&r2=10885&view=diff
==============================================================================
--- branches/bmrb/generic_fns/exp_info.py (original)
+++ branches/bmrb/generic_fns/exp_info.py Wed Feb 24 01:27:24 2010
@@ -22,9 +22,6 @@
# Module docstring.
"""Module containing functions for specifying the experimental details."""
-
-# Python module imports.
-from string import split
# relax module imports.
from info import Info_box
@@ -34,29 +31,6 @@
from version import version_full
-# Storage containers.
-class Cite_store:
- """Citation storage container."""
-
- def __init__(self):
- """Initialise all variables."""
-
- self.authors = None
- self.doi = None
- self.pubmed_id = None
- self.full_citation = None
- self.title = None
- self.status = None
- self.type = None
- self.journal_abbrev = None
- self.journal_full = None
- self.volume = None
- self.issue = None
- self.page_first = None
- self.page_last = None
- self.year = None
-
-
class Software_store:
"""Software storage container."""
@@ -69,8 +43,7 @@
self.tasks = None
-# Citation and software data structures.
-CITE = {}
+# Software data structure.
SOFTWARE = {}
# relax software.
@@ -80,60 +53,12 @@
SOFTWARE['relax'].url = "http://nmr-relax.com";
SOFTWARE['relax'].tasks = ["data processing"]
-# relax citation 1.
-CITE['relax 1'] = Cite_store()
-CITE['relax 1'].authors = [["Edward", "d'Auvergne", "E.", "J."], ["Paul",
"Gooley", "P.", "R."]]
-CITE['relax 1'].doi = "10.1007/s10858-007-9214-2"
-CITE['relax 1'].pubmed_id = "18085410"
-CITE['relax 1'].full_citation = "d'Auvergne, E. J. and Gooley, P. R. (2008).
Optimisation of NMR dynamic models I. Minimisation algorithms and their
performance within the model-free and Brownian rotational diffusion spaces.
J. Biomol. NMR, 40(2), 107-119."
-CITE['relax 1'].title = "Optimisation of NMR dynamic models I. Minimisation
algorithms and their performance within the model-free and Brownian
rotational diffusion spaces."
-CITE['relax 1'].status = "published"
-CITE['relax 1'].type = "journal"
-CITE['relax 1'].journal_abbrev = "J. Biomol. NMR"
-CITE['relax 1'].journal_full = "Journal of Biomolecular NMR"
-CITE['relax 1'].volume = 40
-CITE['relax 1'].issue = 2
-CITE['relax 1'].page_first = 107
-CITE['relax 1'].page_last = 119
-CITE['relax 1'].year = 2008
-
-# relax citation 2.
-CITE['relax 2'] = Cite_store()
-CITE['relax 2'].authors = [["Edward", "d'Auvergne", "E.", "J."], ["Paul",
"Gooley", "P.", "R."]]
-CITE['relax 2'].doi = "10.1007/s10858-007-9213-3"
-CITE['relax 2'].pubmed_id = "18085411"
-CITE['relax 2'].full_citation = "d'Auvergne, E. J. and Gooley, P. R. (2008).
Optimisation of NMR dynamic models II. A new methodology for the dual
optimisation of the model-free parameters and the Brownian rotational
diffusion tensor. J. Biomol. NMR, 40(2), 121-133."
-CITE['relax 2'].title = "Optimisation of NMR dynamic models II. A new
methodology for the dual optimisation of the model-free parameters and the
Brownian rotational diffusion tensor."
-CITE['relax 2'].status = "published"
-CITE['relax 2'].type = "journal"
-CITE['relax 2'].journal_abbrev = "J. Biomol. NMR"
-CITE['relax 2'].journal_full = "Journal of Biomolecular NMR"
-CITE['relax 2'].volume = 40
-CITE['relax 2'].issue = 2
-CITE['relax 2'].page_first = 121
-CITE['relax 2'].page_last = 133
-CITE['relax 2'].year = 2008
-
# NMRPipe software and citation.
SOFTWARE['NMRPipe'] = Software_store()
SOFTWARE['NMRPipe'].name = "NMRPipe"
SOFTWARE['NMRPipe'].authors = "Delaglio, F., Grzesiek, S., Vuister, G. W.,
Zhu, G., Pfeifer, J., and Bax, A"
SOFTWARE['NMRPipe'].url = "http://spin.niddk.nih.gov/NMRPipe/";
SOFTWARE['NMRPipe'].tasks = ["processing"]
-CITE['NMRPipe'] = Cite_store()
-CITE['NMRPipe'].authors = [["Frank", "Delaglio", "F.", None], ["Stephan",
"Grzesiek", "S.", None], ["Geerten", "Vuister", "G.", "W."], ["Guang", "Zhu",
"G.", None], ["John", "Pfeifer", "J.", None], ["Ad", "Bax", "A.", None]]
-CITE['NMRPipe'].doi = "10.1007/BF00197809"
-CITE['NMRPipe'].pubmed_id = "8520220"
-CITE['NMRPipe'].full_citation = "Delaglio, F., Grzesiek, S., Vuister, G. W.,
Zhu, G., Pfeifer, J., and Bax, A. (1995). NMRPipe: a multidimensional
spectral processing system based on UNIX pipes. J. Biomol. NMR. 6, 277-293."
-CITE['NMRPipe'].title = "NMRPipe: a multidimensional spectral processing
system based on UNIX pipes."
-CITE['NMRPipe'].status = "published"
-CITE['NMRPipe'].type = "journal"
-CITE['NMRPipe'].journal_abbrev = "J. Biomol. NMR"
-CITE['NMRPipe'].journal_full = "Journal of Biomolecular NMR"
-CITE['NMRPipe'].volume = 6
-CITE['NMRPipe'].page_first = 277
-CITE['NMRPipe'].page_last = 293
-CITE['NMRPipe'].year = 1995
# Sparky software and citation.
SOFTWARE['Sparky'] = Software_store()
@@ -142,12 +67,6 @@
SOFTWARE['Sparky'].ref = "Goddard, T. D. and Kneller, D. G., SPARKY 3,
University of California, San Francisco."
SOFTWARE['Sparky'].url = "http://www.cgl.ucsf.edu/home/sparky/";
SOFTWARE['Sparky'].tasks = ["spectral analysis"]
-CITE['Sparky'] = Cite_store()
-CITE['Sparky'].authors = [["Tom", "Goddard", "T.", "D."], ["Donald",
"Kneller", "D.", "G."]]
-CITE['Sparky'].full_citation = "Goddard, T. D. and Kneller, D. G., SPARKY 3,
University of California, San Francisco."
-CITE['Sparky'].title = "Sparky."
-CITE['Sparky'].status = "unpublished"
-CITE['Sparky'].type = "internet"
@@ -331,7 +250,7 @@
bib = info.bib[key]
# Add the citation.
- cdp.exp_info.add_citation(cite_id=id, authors=bib.author2,
doi=bib.doi, pubmed_id=bib.pubmed_id, full_citation=bib.cite_short(),
title=bib.title, status=bib.status, type=bib.type,
journal_abbrev=bib.journal, journal_full=bib.journal_full, volume=bib.volume,
page_first=split(bib.pages, '-')[0], page_last=split(bib.pages, '-')[1],
year=bib.year)
+ cdp.exp_info.add_citation(cite_id=id, authors=bib.author2,
doi=bib.doi, pubmed_id=bib.pubmed_id, full_citation=bib.cite_short(doi=False,
url=False), title=bib.title, status=bib.status, type=bib.type,
journal_abbrev=bib.journal, journal_full=bib.journal_full, volume=bib.volume,
page_first=bib.page_first, page_last=bib.page_last, year=bib.year)
# Place the data in the container.
cdp.exp_info.setup_script(file=file, dir=dir, text=text,
cite_ids=cite_id, analysis_type=analysis_type,
model_selection=model_selection, engine=engine, model_elim=model_elim,
universal_solution=universal_solution)
@@ -389,7 +308,7 @@
if name == 'relax':
# The info.
cite_ids.append(['relax_ref1', 'relax_ref2'])
- keys.append(['relax 1', 'relax 2'])
+ keys.append(['dAuvergneGooley08a', 'dAuvergneGooley08b'])
software_keys.append('relax')
versions.append(version_full())
@@ -397,7 +316,7 @@
if name == 'NMRPipe':
# The info.
cite_ids.append(['nmrpipe_ref'])
- keys.append(['NMRPipe'])
+ keys.append(['Delaglio95'])
software_keys.append('NMRPipe')
versions.append(version)
@@ -409,15 +328,21 @@
# The info.
cite_ids.append(['sparky_ref'])
- keys.append(['Sparky'])
+ keys.append(['GoddardKneller'])
software_keys.append('Sparky')
versions.append(version)
+
+ # Get the info box.
+ info = Info_box()
# Loop over the citations.
for i in range(len(cite_ids)):
for j in range(len(cite_ids[i])):
+ # Alias the bib entry.
+ bib = info.bib[keys[i][j]]
+
# Add the citations.
- cdp.exp_info.add_citation(cite_id=cite_ids[i][j],
authors=CITE[keys[i][j]].authors, doi=CITE[keys[i][j]].doi,
pubmed_id=CITE[keys[i][j]].pubmed_id,
full_citation=CITE[keys[i][j]].full_citation, title=CITE[keys[i][j]].title,
status=CITE[keys[i][j]].status, type=CITE[keys[i][j]].type,
journal_abbrev=CITE[keys[i][j]].journal_abbrev,
journal_full=CITE[keys[i][j]].journal_full, volume=CITE[keys[i][j]].volume,
page_first=CITE[keys[i][j]].page_first, page_last=CITE[keys[i][j]].page_last,
year=CITE[keys[i][j]].year)
+ cdp.exp_info.add_citation(cite_id=cite_ids[i][j],
authors=bib.author2, doi=bib.doi, pubmed_id=bib.pubmed_id,
full_citation=bib.cite_short(doi=False, url=False), title=bib.title,
status=bib.status, type=bib.type, journal_abbrev=bib.journal,
journal_full=bib.journal_full, volume=bib.volume, issue=bib.number,
page_first=bib.page_first, page_last=bib.page_last, year=bib.year)
# Add the software info.
cdp.exp_info.software_setup(name=SOFTWARE[software_keys[i]].name,
version=versions[i], vendor_name=SOFTWARE[software_keys[i]].authors,
url=SOFTWARE[software_keys[i]].url, cite_ids=cite_ids,
tasks=SOFTWARE[software_keys[i]].tasks)
r10885 - in /branches/bmrb/generic_fns: bmrb.py exp_info.py