def setup_example():
# generate OdmlTable object
xlstable = odml_xls_table.OdmlXlsTable()
# customize odmldtypes to use
xlstable.odtypes.add_synonym('string', 'pers')
dtypes = xlstable.odtypes
# generating odml document with template structure
# this could also be done in excel using odmltables
odml_doc = get_odml_doc(dtypes)
# enter animal specifications in template structure
# this would typically be done manually once per animal
enrich_animal_specifications(odml_doc)
# enter developmental data in template structure
# this would typically be done manually on a daily basis using odmltables
enrich_developmental_specifications(odml_doc)
# load odml structure into odmltable object
xlstable.load_from_odmldoc(odml_doc)
# adapt header of excel file to be written
xlstable.change_header(Path=1,
PropertyName=2,
Value=3,
DataUnit=4,
odmlDatatype=5,
PropertyDefinition=6)
xlstable.write2file('example3.xls')
xlstable.write2odml('example3.odml')
def createfile(settings):
odmldoc = setup_tutorodml()
table = odml_xls_table.OdmlXlsTable()
table.load_from_odmldoc(odmldoc)
table.changing_point = None
table.show_all_sections = False
table.show_all_properties = False
title_translator = {v: k for k, v in iteritems(table._header_titles)}
# mandatory_titles = [title_translator[m] for m in mandatory_headers]
# setting custom header columns
output_headers = [title_translator[str(
settings.get_object('LWselectedcolumns').item(index).text())]
for index in
list(range(settings.get_object('LWselectedcolumns').count()))]
table.change_header(
**dict(zip(output_headers, list(range(1, len(output_headers) + 1)))))
# table.mark_columns(
# *[h for i, h in enumerate(output_headers) if h in mandatory_titles])
# set all styles to plan black and white
styles = ['first_style', 'second_style', 'first_marked_style',
'second_marked_style', 'highlight_style']
for style in styles:
setattr(getattr(table, style), 'backcolor', 'white')
setattr(getattr(table, style), 'fontcolor', 'black')
table.highlight_defaults = True
# saving file
table.write2file(settings.get_object('outputfilename'))
def run_example():
# Generate OdmlXlsTable object
xlstable = odml_xls_table.OdmlXlsTable()
# Load data from xls
xlstable.load_from_xls_table('example1-2.xls')
# Save as odml file
xlstable.write2odml('example1-2.odml')
pass
def run_example():
# generating OdmlXlsTable object
xlstable = odml_xls_table.OdmlXlsTable()
# loading data from odml
xlstable.load_from_file(pre_enriched_file)
xlstable.write2file('automatically_enriched.xls')
# mimicing manual entry of data in the xls
manual_enrichment()
xlstable.load_from_xls_table('manually_enriched.xls')
xlstable.write2odml('example2-2.odml')
def run_example():
# generating OdmlXlsTable object
xlstable = odml_xls_table.OdmlXlsTable()
# loading data from xls file
xlstable.load_from_xls_table('example3.xls')
# filtering only for developmental age and body weight properties
xlstable.filter(PropertyName=['DevelopmentalAge', 'Weight'],
comparison_func=lambda x, y: (x in y))
# removing templates
xlstable.filter(invert=True,
Path='template',
comparison_func=lambda x, y: x.endswith(y))
xlstable.write2file('example3_Output.xls')
def manual_enrichment():
# mimic manual enrichment of xls
doc = automatic_enrichment()
surgery_props = doc['Animal']['Surgery'].properties
surgery_props['Surgeon'].values = 'Surgeon1'
surgery_props['Date'].values = datetime.datetime.today().date()
surgery_props['Weight'].values = 100.0
surgery_props['Quality'].values = 'good'
surgery_props['Anaesthetic'].values = 'urethane'
surgery_props['Painkiller'].values = ''
surgery_props['Link'].values = '../../surgery/protocols/protocol1.pdf'
xlstable = odml_xls_table.OdmlXlsTable()
xlstable.load_from_odmldoc(doc)
xlstable.write2file('manually_enriched.xls')
def setup_example():
# We are using the same csv table as used in the tutorial
filename = '../../doc/source/csv/example1-2.csv'
xlstable = odml_xls_table.OdmlXlsTable()
xlstable.load_from_csv_table(filename)
# turn off color of table cells
basic_style = XlsStyle(backcolor='white', fontcolor='black', fontstyle='')
xlstable.highlight_defaults = False
xlstable.highlight_style = basic_style
xlstable.header_style = basic_style
xlstable.first_style = basic_style
xlstable.second_style = basic_style
xlstable.first_marked_style = basic_style
xlstable.second_marked_style = basic_style
xlstable.document_info_style = basic_style
# saving as file to be comparable to tutorial
xlstable.write2file('example1-2.xls')
