Author: bugman
Date: Thu Oct 29 11:23:53 2009
New Revision: 9838
URL: http://svn.gna.org/viewcvs/relax?rev=9838&view=rev
Log:
Added support for the method saveframe.
Added:
branches/bmrb/bmrblib/experimental_details/method.py
- copied, changed from r9831,
branches/bmrb/bmrblib/experimental_details/software.py
Modified:
branches/bmrb/bmrblib/experimental_details/__init__.py
Modified: branches/bmrb/bmrblib/experimental_details/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/experimental_details/__init__.py?rev=9838&r1=9837&r2=9838&view=diff
==============================================================================
--- branches/bmrb/bmrblib/experimental_details/__init__.py (original)
+++ branches/bmrb/bmrblib/experimental_details/__init__.py Thu Oct 29
11:23:53 2009
@@ -27,4 +27,6 @@
http://www.bmrb.wisc.edu/dictionary/3.1html/SuperGroupPage.html.
"""
-__all__ = []
+__all__ = ['method',
+ 'software'
+]
Copied: branches/bmrb/bmrblib/experimental_details/method.py (from r9831,
branches/bmrb/bmrblib/experimental_details/software.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/experimental_details/method.py?p2=branches/bmrb/bmrblib/experimental_details/method.py&p1=branches/bmrb/bmrblib/experimental_details/software.py&r1=9831&r2=9838&rev=9838&view=diff
==============================================================================
--- branches/bmrb/bmrblib/experimental_details/software.py (original)
+++ branches/bmrb/bmrblib/experimental_details/method.py Thu Oct 29 11:23:53
2009
@@ -21,9 +21,9 @@
###############################################################################
# Module docstring.
-"""The software saveframe category.
-
-For example, see
http://www.bmrb.wisc.edu/dictionary/3.1html_frame/frame_SaveFramePage.html#software
+"""The method saveframe category.
+
+For example, see
http://www.bmrb.wisc.edu/dictionary/3.1html_frame/frame_SaveFramePage.html#method
"""
# relax module imports.
@@ -33,8 +33,8 @@
from bmrblib.misc import translate
-class SoftwareSaveframe(BaseSaveframe):
- """The software saveframe class."""
+class MethodSaveframe(BaseSaveframe):
+ """The method saveframe class."""
def __init__(self, datanodes):
"""Initialise the class, placing the pystarlib data nodes into the
namespace.
@@ -46,131 +46,116 @@
# Place the data nodes into the namespace.
self.datanodes = datanodes
- # The number of software programs used.
- self.software_num = 0
+ # The number of methods used.
+ self.method_num = 0
# Add the specific tag category objects.
self.add_tag_categories()
- 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.
+ def add(self, name=None, details=None, cite_ids=None, file_name=None,
file_text=None, param_file_name=None, param_file_text=None):
+ """Add the method info to the data nodes.
+
+ @keyword name: The unique name describing this method.
@type name: str
- @keyword version: The software version.
- @type version: None or str
- @keyword vendor_name: The vendor or developers of the software.
- @type vendor_name: None or str
- @keyword vendor_address: The vendor address.
- @type vendor_address: None or str
- @keyword vendor_eaddress: The vendor electronic address.
- @type vendor_eaddress: None or str
- @keyword task: The task of the software.
- @type task: str
+ @keyword details: Text description providing additional
information about the reported method.
+ @type details: None or str
@keyword cite_ids: The citation ID numbers.
@type cite_ids: None or list of int
- @return: The software ID number.
- @rtype: int
- """
+ @keyword file_name: The name of the file containing the
source code or protocol for the reported method.
+ @type file_name: str
+ @keyword file_text: The method provided as an ASCII text
document that is included in the NMR-STAR file.
+ @type file_text: str
+ @keyword param_file_name: The name of the file that contains
parameters required to execute the method.
+ @type param_file_name: None or str
+ @keyword param_file_text: The text of the parameter file.
+ @type param_file_text: None or str
+ """
+
+ # Check that nothing is missing.
+ no_missing(name, 'method name')
# Check.
- if not isinstance(task, list):
- raise NameError, "The task argument '%s' is invalid." % task
+ if not isinstance(cite_ids, list):
+ raise NameError, "The cite_ids argument '%s' should be a list."
% cite_ids
# Place the args into the namespace.
- self.program_name = name
- self.program_version = version
- self.vendor_name = translate(vendor_name)
- 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
- self.software_id_num = [str(translate(self.software_num))]
+ self.method_num = self.method_num + 1
+ self.method_id_num = [str(translate(self.method_num))]
# The category name.
- self.cat_name = ['Software']
+ self.cat_name = ['Method']
# Initialise the save frame.
- self.frame = SaveFrame(title=self.program_name)
+ self.frame = SaveFrame(title='method')
# Create the tag categories.
- self.Software.create()
- self.Software_citation.create()
- self.Vendor.create()
- self.Task.create()
+ self.Method.create()
+ self.Method_citation.create()
+ self.Method_file.create()
+ self.Method_parameter_file.create()
# Add the saveframe to the data nodes.
self.datanodes.append(self.frame)
- # Return the software ID number.
- return self.software_num
-
def add_tag_categories(self):
"""Create the tag categories."""
# The tag category objects.
- self.Software = Software(self)
- self.Software_citation = SoftwareCitation(self)
- self.Task = Task(self)
- self.Vendor = Vendor(self)
-
-
-
-class Software(TagCategory):
- """Base class for the Software tag category."""
-
- def create(self):
- """Create the Software tag category."""
-
- # The save frame category.
+ self.Method = Method(self)
+ self.Method_citation = MethodCitation(self)
+ self.Method_file = MethodFile(self)
+ self.Method_parameter_file = MethodParam(self)
+
+
+
+class Method(TagCategory):
+ """Base class for the Method tag category."""
+
+ def create(self):
+ """Create the Method tag category."""
+
+ # The tags.
self.sf.frame.tagtables.append(self.create_tag_table([['SfCategory',
'cat_name']], free=True))
-
- # Software ID number.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['SoftwareID']],
tagvalues=[[str(self.sf.software_num)]]))
-
- # The program name.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['Name']], tagvalues=[[self.sf.program_name]]))
-
- # The program version.
- if self.sf.program_version:
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['Version']],
tagvalues=[[self.sf.program_version]]))
-
-
- 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
- """
-
- # Execute the base class tag_setup() method.
- TagCategory.tag_setup(self, tag_category_label='Software', sep=sep)
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['SfFramecode']],
tagvalues=[[str(self.sf.method_name)]]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['MethodID']],
tagvalues=[[str(self.sf.method_num)]]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['Details']], tagvalues=[[self.sf.details]]))
+
+
+ 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
+ """
+
+ # Execute the base class tag_setup() method.
+ TagCategory.tag_setup(self, tag_category_label='Method', sep=sep)
# Tag names for the relaxation data.
self.tag_names['SfCategory'] = 'Sf_category'
- self.tag_names['SoftwareID'] = 'ID'
- self.tag_names['Name'] = 'Name'
- self.tag_names['Version'] = 'Version'
-
-
-class SoftwareCitation(TagCategory):
- """Base class for the SoftwareCitation tag category."""
-
-
- def create(self):
- """Create the Software tag category."""
+ self.tag_names['SfFramecode'] = 'Sf_framecode'
+ self.tag_names['MethodID'] = 'ID'
+ self.tag_names['Details'] = 'Details'
+
+
+class MethodCitation(TagCategory):
+ """Base class for the MethodCitation tag category."""
+
+
+ def create(self):
+ """Create the Method tag category."""
# Keys and objects.
info = [
['CitationID', 'cite_ids'],
- ['SoftwareID', 'software_id_num']
+ ['MethodID', 'method_id_num']
]
# Get the TabTable.
@@ -191,26 +176,27 @@
# Category label.
if not tag_category_label:
- tag_category_label='Software_citation'
+ tag_category_label='Method_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):
- """Base class for the Task tag category."""
-
- def create(self):
- """Create the Task tag category."""
+ self.tag_names['MethodID'] = 'Method_ID'
+
+
+class MethodFile(TagCategory):
+ """Base class for the MethodFile tag category."""
+
+ def create(self):
+ """Create the MethodFile tag category."""
# Keys and objects.
info = [
- ['Task', 'task'],
- ['SoftwareID', 'software_id_num']
+ ['Name', 'file_name'],
+ ['Text', 'text'],
+ ['MethodID', 'method_id_num']
]
# Get the TabTable.
@@ -230,25 +216,26 @@
"""
# Execute the base class tag_setup() method.
- TagCategory.tag_setup(self, tag_category_label='Task', sep=sep)
-
- # Tag names for the relaxation data.
- self.tag_names['Task'] = 'Task'
- self.tag_names['SoftwareID'] = 'SoftwareID'
-
-
-class Vendor(TagCategory):
- """Base class for the Vendor tag category."""
-
- def create(self):
- """Create the Vendor tag category."""
+ TagCategory.tag_setup(self, tag_category_label='Method_file',
sep=sep)
+
+ # Tag names for the relaxation data.
+ self.tag_names['Name'] = 'Name'
+ self.tag_names['Text'] = 'Text'
+ self.tag_names['MethodID'] = 'Method_ID'
+
+
+class MethodParam(TagCategory):
+ """Base class for the MethodParam tag category."""
+
+ def create(self):
+ """Create the MethodParam tag category."""
# Keys and objects.
info = [
- ['Name', 'vendor_name'],
- ['Address', 'vendor_address'],
- ['ElectronicAddress', 'vendor_eaddress'],
- ['SoftwareID', 'software_id_num']
+ ['FileName', 'param_file_name'],
+ ['TextFormat', 'text_format'],
+ ['Text', 'param_file_text'],
+ ['MethodID', 'method_id_num']
]
# Get the TabTable.
@@ -268,10 +255,10 @@
"""
# Execute the base class tag_setup() method.
- TagCategory.tag_setup(self, tag_category_label='Vendor', sep=sep)
-
- # Tag names for the relaxation data.
- self.tag_names['Name'] = 'Name'
- self.tag_names['Address'] = 'Address'
- self.tag_names['ElectronicAddress'] = 'Electronic_address'
- self.tag_names['SoftwareID'] = 'SoftwareID'
+ TagCategory.tag_setup(self, tag_category_label='Method_param',
sep=sep)
+
+ # Tag names for the relaxation data.
+ self.tag_names['FileName'] = 'File_name'
+ self.tag_names['TextFormat'] = 'Text_format'
+ self.tag_names['Text'] = 'Text'
+ self.tag_names['MethodID'] = 'Method_ID'
r9838 - in /branches/bmrb/bmrblib/experimental_details: __init__.py method.py