Author: bugman
Date: Thu Oct 29 15:45:47 2009
New Revision: 9850
URL: http://svn.gna.org/viewcvs/relax?rev=9850&view=rev
Log:
Changed how the built in citations are handled.
They are now all stored in the CITE dictionary.
Modified:
branches/bmrb/generic_fns/exp_info.py
Modified: branches/bmrb/generic_fns/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/exp_info.py?rev=9850&r1=9849&r2=9850&view=diff
==============================================================================
--- branches/bmrb/generic_fns/exp_info.py (original)
+++ branches/bmrb/generic_fns/exp_info.py Thu Oct 29 15:45:47 2009
@@ -30,72 +30,109 @@
from version import version_full
-# relax fixed info.
-RELAX_NAME = "relax"
-RELAX_AUTHORS = "The relax development team"
-RELAX_URL = "http://nmr-relax.com";
-RELAX_TASKS = ["data processing"]
-RELAX_CITE1_AUTHORS = [["Edward", "d'Auvergne", "E.", "J."], ["Paul",
"Gooley", "P.", "R."]]
-RELAX_CITE1_DOI = "10.1007/s10858-007-9214-2"
-RELAX_CITE1_PUBMED_ID = "18085410"
-RELAX_CITE1_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."
-RELAX_CITE1_TITLE = "Optimisation of NMR dynamic models I. Minimisation
algorithms and their performance within the model-free and Brownian
rotational diffusion spaces."
-RELAX_CITE1_STATUS = "published"
-RELAX_CITE1_TYPE = "journal"
-RELAX_CITE1_JOURNAL_ABBREV = "J. Biomol. NMR"
-RELAX_CITE1_JOURNAL_FULL = "Journal of Biomolecular NMR"
-RELAX_CITE1_VOLUME = 40
-RELAX_CITE1_ISSUE = 2
-RELAX_CITE1_PAGE_FIRST = 107
-RELAX_CITE1_PAGE_LAST = 119
-RELAX_CITE1_YEAR = 2008
-RELAX_CITE2_AUTHORS = [["Edward", "d'Auvergne", "E.", "J."], ["Paul",
"Gooley", "P.", "R."]]
-RELAX_CITE2_DOI = "10.1007/s10858-007-9213-3"
-RELAX_CITE2_PUBMED_ID = "18085411"
-RELAX_CITE2_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."
-RELAX_CITE2_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."
-RELAX_CITE2_STATUS = "published"
-RELAX_CITE2_TYPE = "journal"
-RELAX_CITE2_JOURNAL_ABBREV = "J. Biomol. NMR"
-RELAX_CITE2_JOURNAL_FULL = "Journal of Biomolecular NMR"
-RELAX_CITE2_VOLUME = 40
-RELAX_CITE2_ISSUE = 2
-RELAX_CITE2_PAGE_FIRST = 121
-RELAX_CITE2_PAGE_LAST = 133
-RELAX_CITE2_YEAR = 2008
-
-
-# NMRPipe fixed info.
-NMRPIPE_NAME = "NMRPipe"
-NMRPIPE_AUTHORS = "Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G.,
Pfeifer, J., and Bax, A"
-NMRPIPE_URL = "http://spin.niddk.nih.gov/NMRPipe/";
-NMRPIPE_TASKS = ["processing"]
-NMRPIPE_CITE_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]]
-NMRPIPE_CITE_DOI = "10.1007/BF00197809"
-NMRPIPE_CITE_PUBMED_ID = "8520220"
-NMRPIPE_CITE_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."
-NMRPIPE_CITE_TITLE = "NMRPipe: a multidimensional spectral processing system
based on UNIX pipes."
-NMRPIPE_CITE_STATUS = "published"
-NMRPIPE_CITE_TYPE = "journal"
-NMRPIPE_CITE_JOURNAL_ABBREV = "J. Biomol. NMR"
-NMRPIPE_CITE_JOURNAL_FULL = "Journal of Biomolecular NMR"
-NMRPIPE_CITE_VOLUME = 6
-NMRPIPE_CITE_PAGE_FIRST = 277
-NMRPIPE_CITE_PAGE_LAST = 293
-NMRPIPE_CITE_YEAR = 1995
-
-
-# Sparky fixed info.
-SPARKY_NAME = "Sparky"
-SPARKY_AUTHORS = "Goddard, T. D. and Kneller, D. G."
-SPARKY_REF = "Goddard, T. D. and Kneller, D. G., SPARKY 3, University of
California, San Francisco."
-SPARKY_URL = "http://www.cgl.ucsf.edu/home/sparky/";
-SPARKY_TASKS = ["spectral analysis"]
-SPARKY_CITE_AUTHORS = [["Tom", "Goddard", "T.", "D."], ["Donald", "Kneller",
"D.", "G."]]
-SPARKY_CITE_FULL_CITATION = "Goddard, T. D. and Kneller, D. G., SPARKY 3,
University of California, San Francisco."
-SPARKY_CITE_TITLE = "Sparky."
-SPARKY_CITE_STATUS = "unpublished"
-SPARKY_CITE_TYPE = "internet"
+# Storage container.
+class Cite_store:
+ """Citation storage container."""
+
+ def __init__(self):
+ """Initialise all variables."""
+
+ self.name = None
+ self.authors = None
+ self.url = None
+ self.tasks = None
+ self.cite_authors = None
+ self.cite_doi = None
+ self.cite_pubmed_id = None
+ self.cite_full_citation = None
+ self.cite_title = None
+ self.cite_status = None
+ self.cite_type = None
+ self.cite_journal_abbrev = None
+ self.cite_journal_full = None
+ self.cite_volume = None
+ self.cite_issue = None
+ self.cite_page_first = None
+ self.cite_page_last = None
+ self.cite_year = None
+
+
+# Citation data structure.
+CITE = {}
+
+# relax citations.
+CITE['relax 1'] = Cite_store()
+CITE['relax 1'].name = "relax"
+CITE['relax 1'].authors = "The relax development team"
+CITE['relax 1'].url = "http://nmr-relax.com";
+CITE['relax 1'].tasks = ["data processing"]
+CITE['relax 1'].cite_authors = [["Edward", "d'Auvergne", "E.", "J."],
["Paul", "Gooley", "P.", "R."]]
+CITE['relax 1'].cite_doi = "10.1007/s10858-007-9214-2"
+CITE['relax 1'].cite_pubmed_id = "18085410"
+CITE['relax 1'].cite_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'].cite_title = "Optimisation of NMR dynamic models I.
Minimisation algorithms and their performance within the model-free and
Brownian rotational diffusion spaces."
+CITE['relax 1'].cite_status = "published"
+CITE['relax 1'].cite_type = "journal"
+CITE['relax 1'].cite_journal_abbrev = "J. Biomol. NMR"
+CITE['relax 1'].cite_journal_full = "Journal of Biomolecular NMR"
+CITE['relax 1'].cite_volume = 40
+CITE['relax 1'].cite_issue = 2
+CITE['relax 1'].cite_page_first = 107
+CITE['relax 1'].cite_page_last = 119
+CITE['relax 1'].cite_year = 2008
+
+CITE['relax 2'] = Cite_store()
+CITE['relax 1'].name = "relax"
+CITE['relax 1'].authors = "The relax development team"
+CITE['relax 1'].url = "http://nmr-relax.com";
+CITE['relax 1'].tasks = ["data processing"]
+CITE['relax 2'].cite_authors = [["Edward", "d'Auvergne", "E.", "J."],
["Paul", "Gooley", "P.", "R."]]
+CITE['relax 2'].cite_doi = "10.1007/s10858-007-9213-3"
+CITE['relax 2'].cite_pubmed_id = "18085411"
+CITE['relax 2'].cite_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'].cite_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'].cite_status = "published"
+CITE['relax 2'].cite_type = "journal"
+CITE['relax 2'].cite_journal_abbrev = "J. Biomol. NMR"
+CITE['relax 2'].cite_journal_full = "Journal of Biomolecular NMR"
+CITE['relax 2'].cite_volume = 40
+CITE['relax 2'].cite_issue = 2
+CITE['relax 2'].cite_page_first = 121
+CITE['relax 2'].cite_page_last = 133
+CITE['relax 2'].cite_year = 2008
+
+# NMRPipe citation.
+CITE['NMRPipe'] = Cite_store()
+CITE['NMRPipe'].name = "NMRPipe"
+CITE['NMRPipe'].authors = "Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu,
G., Pfeifer, J., and Bax, A"
+CITE['NMRPipe'].url = "http://spin.niddk.nih.gov/NMRPipe/";
+CITE['NMRPipe'].tasks = ["processing"]
+CITE['NMRPipe'].cite_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'].cite_doi = "10.1007/BF00197809"
+CITE['NMRPipe'].cite_pubmed_id = "8520220"
+CITE['NMRPipe'].cite_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'].cite_title = "NMRPipe: a multidimensional spectral
processing system based on UNIX pipes."
+CITE['NMRPipe'].cite_status = "published"
+CITE['NMRPipe'].cite_type = "journal"
+CITE['NMRPipe'].cite_journal_abbrev = "J. Biomol. NMR"
+CITE['NMRPipe'].cite_journal_full = "Journal of Biomolecular NMR"
+CITE['NMRPipe'].cite_volume = 6
+CITE['NMRPipe'].cite_page_first = 277
+CITE['NMRPipe'].cite_page_last = 293
+CITE['NMRPipe'].cite_year = 1995
+
+# Sparky citation.
+CITE['Sparky'] = Cite_store()
+CITE['Sparky'].name = "Sparky"
+CITE['Sparky'].authors = "Goddard, T. D. and Kneller, D. G."
+CITE['Sparky'].ref = "Goddard, T. D. and Kneller, D. G., SPARKY 3,
University of California, San Francisco."
+CITE['Sparky'].url = "http://www.cgl.ucsf.edu/home/sparky/";
+CITE['Sparky'].tasks = ["spectral analysis"]
+CITE['Sparky'].cite_authors = [["Tom", "Goddard", "T.", "D."], ["Donald",
"Kneller", "D.", "G."]]
+CITE['Sparky'].cite_full_citation = "Goddard, T. D. and Kneller, D. G.,
SPARKY 3, University of California, San Francisco."
+CITE['Sparky'].cite_title = "Sparky."
+CITE['Sparky'].cite_status = "unpublished"
+CITE['Sparky'].cite_type = "internet"
@@ -298,22 +335,24 @@
if not hasattr(cdp, 'exp_info'):
cdp.exp_info = ExpInfo()
+ # Init.
+ cite_ids = []
+ keys = []
+ versions = []
+
# relax.
if name == 'relax':
- # Add the citations.
- 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=['relax_ref1',
'relax_ref2'], tasks=RELAX_TASKS)
+ # The info.
+ cite_ids.append(['relax_ref1', 'relax_ref2'])
+ keys.append(['Relax 1', 'Relax 2'])
+ versions.append(version_full())
# NMRPipe.
if name == 'NMRPipe':
- # Add the citations.
- 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=['nmrpipe_ref'],
tasks=NMRPIPE_TASKS)
+ # The info.
+ cite_ids.append(['nmrpipe_ref'])
+ keys.append(['NMRPipe'])
+ versions.append(version)
# Sparky.
elif name == 'Sparky':
@@ -321,11 +360,19 @@
if not version:
raise RelaxError("The Sparky version number has not been
supplied.")
- # Add the citations.
- cite_index = cdp.exp_info.add_citation(cite_id='sparky_ref',
authors=SPARKY_CITE_AUTHORS, full_citation=SPARKY_CITE_FULL_CITATION,
title=SPARKY_CITE_TITLE, status=SPARKY_CITE_STATUS, type=SPARKY_CITE_TYPE)
+ # The info.
+ cite_ids.append(['sparky_ref'])
+ keys.append(['Sparky'])
+ versions.append(version)
+
+ # Loop over the citations.
+ for i in range(len(cite_ids)):
+ for j in range(len(cite_ids[i])):
+ # Add the citations.
+ cdp.exp_info.add_citation(cite_id=cite_ids[i][j],
authors=CITE[keys[i][j]].cite_authors, doi=CITE[keys[i][j]].cite_doi,
pubmed_id=CITE[keys[i][j]].cite_pubmed_id,
full_citation=CITE[keys[i][j]].cite_full_citation,
title=CITE[keys[i][j]].cite_title, status=CITE[keys[i][j]].cite_status,
type=CITE[keys[i][j]].cite_type,
journal_abbrev=CITE[keys[i][j]].cite_journal_abbrev,
journal_full=CITE[keys[i][j]].cite_journal_full,
volume=CITE[keys[i][j]].cite_volume,
page_first=CITE[keys[i][j]].cite_page_first,
page_last=CITE[keys[i][j]].cite_page_last, year=CITE[keys[i][j]].cite_year)
# Add the software info.
- cdp.exp_info.software_setup(name=SPARKY_NAME, version=version,
vendor_name=SPARKY_AUTHORS, url=SPARKY_URL, cite_ids=['sparky_ref'],
tasks=SPARKY_TASKS)
+ cdp.exp_info.software_setup(name=CITE[keys[i][0]].name,
version=versions, vendor_name=CITE[keys[i][0]].authors,
url=CITE[keys[i][0]].url, cite_ids=cite_ids, tasks=CITE[keys[i][0]].tasks)
def thiol_state(state=None):
r9850 - /branches/bmrb/generic_fns/exp_info.py