Author: bugman
Date: Tue Oct 13 20:00:34 2009
New Revision: 9763
URL: http://svn.gna.org/viewcvs/relax?rev=9763&view=rev
Log:
The BMRB SoftwareCitation tag category is now being created.
This points back to the relevant Citation saveframe.
Modified:
branches/bmrb/bmrblib/experimental_details/software.py
branches/bmrb/data/exp_info.py
branches/bmrb/generic_fns/bmrb.py
branches/bmrb/generic_fns/exp_info.py
branches/bmrb/prompt/bmrb.py
Modified: branches/bmrb/bmrblib/experimental_details/software.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/experimental_details/software.py?rev=9763&r1=9762&r2=9763&view=diff
==============================================================================
--- branches/bmrb/bmrblib/experimental_details/software.py (original)
+++ branches/bmrb/bmrblib/experimental_details/software.py Tue Oct 13
20:00:34 2009
@@ -53,7 +53,7 @@
self.add_tag_categories()
- def add(self, name, version=None, vendor_name=None, vendor_address=None,
vendor_eaddress=None, task=None):
+ def add(self, name, version=None, vendor_name=None, vendor_address=None,
vendor_eaddress=None, task=None, cite_ids=None):
"""Add the software info to the data nodes.
@param name: The name of the software program.
@@ -68,6 +68,8 @@
@type vendor_eaddress: None or str
@keyword task: The task of the software.
@type task: str
+ @keyword cite_ids: The citation ID numbers.
+ @type cite_ids: None or list of int
"""
# Check.
@@ -81,6 +83,7 @@
self.vendor_address = translate(vendor_address)
self.vendor_eaddress = translate(vendor_eaddress)
self.task = translate(task)
+ self.cite_ids = translate(cite_ids)
# Increment the ID number.
self.software_num = self.software_num + 1
@@ -94,6 +97,7 @@
# Create the tag categories.
self.Software.create()
+ self.Software_citation.create()
self.Vendor.create()
self.Task.create()
@@ -116,7 +120,7 @@
"""Base class for the Software tag category."""
def create(self):
- """Create the ChemShiftAnisotropy tag category."""
+ """Create the Software tag category."""
# The save frame category.
self.sf.frame.tagtables.append(self.create_tag_table([['SfCategory',
'cat_name']], free=True))
@@ -153,6 +157,43 @@
class SoftwareCitation(TagCategory):
"""Base class for the SoftwareCitation tag category."""
+
+
+ def create(self):
+ """Create the Software tag category."""
+
+ # Keys and objects.
+ info = [
+ ['CitationID', 'cite_ids'],
+ ['SoftwareID', 'software_id_num']
+ ]
+
+ # Get the TabTable.
+ table = self.create_tag_table(info)
+
+ # Add the tagtable to the save frame.
+ self.sf.frame.tagtables.append(table)
+
+
+ def tag_setup(self, tag_category_label=None, sep=None):
+ """Replacement method for setting up the tag names.
+
+ @keyword tag_category_label: The tag name prefix specific for the
tag category.
+ @type tag_category_label: None or str
+ @keyword sep: The string separating the tag name
prefix and suffix.
+ @type sep: str
+ """
+
+ # Category label.
+ if not tag_category_label:
+ tag_category_label='Software_citation'
+
+ # Execute the base class tag_setup() method.
+ TagCategory.tag_setup(self, tag_category_label=tag_category_label,
sep=sep)
+
+ # Tag names for the relaxation data.
+ self.tag_names['CitationID'] = 'Citation_ID'
+ self.tag_names['SoftwareID'] = 'Software_ID'
class Task(TagCategory):
Modified: branches/bmrb/data/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/data/exp_info.py?rev=9763&r1=9762&r2=9763&view=diff
==============================================================================
--- branches/bmrb/data/exp_info.py (original)
+++ branches/bmrb/data/exp_info.py Tue Oct 13 20:00:34 2009
@@ -121,7 +121,7 @@
return len(self.citations)
- def software_setup(self, name, version=None, url=None, vendor_name=None,
cite=None, tasks=None):
+ def software_setup(self, name, version=None, url=None, vendor_name=None,
cite_ids=None, tasks=None):
"""Set up the software information.
@param name: The name of the software program.
@@ -132,8 +132,8 @@
@type url: None or str
@keyword vendor_name: The name of the company or person behind the
program.
@type vendor_name: str
- @keyword cite: The literature citation.
- @type cite: None or str
+ @keyword cite_ids: The citation ID numbers.
+ @type cite_ids: None or str
@keyword tasks: The tasks performed by the program.
@type tasks: list of str
"""
@@ -163,7 +163,7 @@
software.url = url
software.version = version
software.vendor_name = vendor_name
- software.cite = cite
+ software.cite_ids = cite_ids
software.tasks = tasks
# Append the container.
Modified: branches/bmrb/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/bmrb.py?rev=9763&r1=9762&r2=9763&view=diff
==============================================================================
--- branches/bmrb/generic_fns/bmrb.py (original)
+++ branches/bmrb/generic_fns/bmrb.py Tue Oct 13 20:00:34 2009
@@ -29,9 +29,11 @@
# relax module imports.
from data import Relax_data_store; ds = Relax_data_store()
from data.exp_info import ExpInfo
+from generic_fns import exp_info
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
+from version import version_full
def display(version='3.1'):
@@ -100,5 +102,12 @@
# Create the directories.
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)
+
+ # 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)
+
# 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=9763&r1=9762&r2=9763&view=diff
==============================================================================
--- branches/bmrb/generic_fns/exp_info.py (original)
+++ branches/bmrb/generic_fns/exp_info.py Tue Oct 13 20:00:34 2009
@@ -87,10 +87,6 @@
@type star: NMR_STAR instance
"""
- # First add relax.
- 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)
-
# Loop over the citations.
if hasattr(cdp, 'exp_info') and hasattr(cdp.exp_info, 'citations'):
for citations in cdp.exp_info.citations:
@@ -104,14 +100,11 @@
@type star: NMR_STAR instance
"""
- # First add relax.
- star.software.add(name=RELAX_NAME, version=version_full(),
vendor_name=RELAX_AUTHORS, vendor_eaddress=RELAX_URL, task=RELAX_TASKS)
-
# Loop over the software.
if hasattr(cdp, 'exp_info') and hasattr(cdp.exp_info, 'software'):
for software in cdp.exp_info.software:
# The program info.
- star.software.add(name=software.name, version=software.version,
vendor_name=software.vendor_name, vendor_eaddress=software.url,
task=software.tasks)
+ 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)
# relax cannot be the only program used!
else:
@@ -156,10 +149,10 @@
cdp.exp_info = ExpInfo()
# Place the data in the container.
- 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)
-
-
-def software(name=None, version=None, url=None, vendor_name=None, cite=None,
tasks=None):
+ 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)
+
+
+def software(name=None, version=None, url=None, vendor_name=None,
cite_ids=None, tasks=None):
"""Select by name the software used in the analysis.
@param name: The name of the software program.
@@ -170,8 +163,8 @@
@type url: None or str
@keyword vendor_name: The name of the company or person behind the
program.
@type vendor_name: str
- @keyword cite: The literature citation.
- @type cite: None or str
+ @keyword cite_ids: The citation ID numbers.
+ @type cite:_ids None or str
@keyword tasks: The tasks performed by the program.
@type tasks: list of str
"""
@@ -181,7 +174,7 @@
cdp.exp_info = ExpInfo()
# Place the data in the container.
- cdp.exp_info.software_setup(name=name, version=version, url=url,
vendor_name=vendor_name, cite=cite, tasks=tasks)
+ cdp.exp_info.software_setup(name=name, version=version, url=url,
vendor_name=vendor_name, cite_ids=cite_ids, tasks=tasks)
def software_select(name, version=None):
@@ -208,7 +201,7 @@
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)
# Add the software info.
- cdp.exp_info.software_setup(name=RELAX_NAME, version=version_full(),
vendor_name=RELAX_AUTHORS, url=RELAX_URL, cite=[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=[cite1, cite2],
tasks=RELAX_TASKS)
# NMRPipe.
if name == 'NMRPipe':
@@ -216,7 +209,7 @@
#cite_index = cdp.exp_info.add_citation(authors=[["The relax
development team", None, None, None]])
cite_index = 1
- cdp.exp_info.software_setup(name=NMRPIPE_NAME, version=version,
vendor_name=NMRPIPE_AUTHORS, url=NMRPIPE_URL, cite=cite_index,
tasks=NMRPIPE_TASKS)
+ cdp.exp_info.software_setup(name=NMRPIPE_NAME, version=version,
vendor_name=NMRPIPE_AUTHORS, url=NMRPIPE_URL, cite_ids=[cite_index],
tasks=NMRPIPE_TASKS)
# Sparky.
elif name == 'Sparky':
@@ -229,4 +222,4 @@
cite_index = 1
# Add the data.
- cdp.exp_info.software_setup(name=SPARKY_NAME, version=version,
vendor_name=SPARKY_AUTHORS, url=SPARKY_URL, cite=cite_index,
tasks=SPARKY_TASKS)
+ cdp.exp_info.software_setup(name=SPARKY_NAME, version=version,
vendor_name=SPARKY_AUTHORS, url=SPARKY_URL, cite_ids=[cite_index],
tasks=SPARKY_TASKS)
Modified: branches/bmrb/prompt/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/bmrb.py?rev=9763&r1=9762&r2=9763&view=diff
==============================================================================
--- branches/bmrb/prompt/bmrb.py (original)
+++ branches/bmrb/prompt/bmrb.py Tue Oct 13 20:00:34 2009
@@ -158,7 +158,7 @@
check.is_int(year, 'publication year')
# Execute the functional code.
- 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)
+ 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)
def display(self, version='3.1'):
@@ -208,7 +208,7 @@
bmrb.read(file=file, directory=dir, version=version)
- def software(self, name=None, version=None, url=None, vendor_name=None,
cite=None, tasks=None):
+ def software(self, name=None, version=None, url=None, vendor_name=None,
cite_ids=None, tasks=None):
"""Specify the software used in the analysis.
Keyword Arguments
@@ -222,7 +222,7 @@
vendor_name: The name of the company or person behind the program.
- cite: The literature citation for the software.
+ cite_ids: A list of the citation ID numbers.
tasks: A list of all the tasks performed by the software.
@@ -251,10 +251,11 @@
For BMRB deposition, to say that Sparky was used in the analysis,
type:
+ relax> cite_id = bmrb.citation(authors=[['Tom', 'Goddard', 'T.',
'D.'], ['D', 'Kneller',
+ 'D.', 'G.']], title=""Goddard, T. D. and Kneller, D. G.,
SPARKY 3, University of
+ California, San Francisco."
relax> bmrb.software('Sparky', version='3.110',
url="http://www.cgl.ucsf.edu/home/sparky/";,
- vendor_name="Goddard, T. D.", cite="Goddard, T.
D. and Kneller, D. G.,
- SPARKY 3, University of California, San
Francisco.",
- tasks=["spectral analysis"])
+ vendor_name="Goddard, T. D.", cite_ids=[cite_id],
tasks=["spectral analysis"])
"""
# Function intro text.
@@ -264,7 +265,7 @@
text = text + ", version=" + repr(version)
text = text + ", url=" + repr(url)
text = text + ", vendor_name=" + repr(vendor_name)
- text = text + ", cite=" + repr(cite)
+ text = text + ", cite_ids=" + repr(cite_ids)
text = text + ", tasks=" + repr(tasks) + ")"
print(text)
@@ -273,11 +274,11 @@
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_str(cite, 'cite', can_be_none=True)
+ check.is_int_list(cite_ids, 'citation ID numbers', can_be_none=True)
check.is_str_list(tasks, 'tasks', can_be_none=True)
# Execute the functional code.
- exp_info.software(name=name, version=version, url=url,
vendor_name=vendor_name, cite=cite, tasks=tasks)
+ exp_info.software(name=name, version=version, url=url,
vendor_name=vendor_name, cite_ids=cite_ids, tasks=tasks)
def software_select(self, name=None, version=None):
r9763 - in /branches/bmrb: bmrblib/experimental_details/ data/ generic_fns/ prompt/