def export_families(filename_prefix, families, file_format, include_project_column=False, include_case_review_columns=False):
"""Export Families table.
Args:
filename_prefix (string): Filename wihtout
families (list): List of Django Family objects to include in the table
file_format (string): "xls" or "tsv"
include_project_column (bool): whether to add a column with the project name
include_case_review_columns (bool): whether to include Case Review-related columns
Returns:
Django HttpResponse object with the table data as an attachment.
"""
header = []
if include_project_column:
header.extend(['project'])
header.extend([
'family_id',
'display_name',
'created_date',
'description',
'analysis_status',
'analysis_summary',
'analysis_notes',
])
if include_case_review_columns:
header.extend([
'internal_case_review_summary',
'internal_case_review_notes',
])
rows = []
analysis_status_lookup = dict(Family.ANALYSIS_STATUS_CHOICES)
for f in families:
row = []
if include_project_column:
row.extend([f.project.name or f.project.project_id])
row.extend([
f.family_id,
f.display_name,
f.created_date,
f.description,
analysis_status_lookup.get(f.analysis_status, f.analysis_status),
_convert_html_to_plain_text(f.analysis_summary, remove_line_breaks=(file_format == 'tsv')),
_convert_html_to_plain_text(f.analysis_notes, remove_line_breaks=(file_format == 'tsv')),
])
if include_case_review_columns:
row.extend([
_convert_html_to_plain_text(f.internal_case_review_summary, remove_line_breaks=(file_format == 'tsv')),
_convert_html_to_plain_text(f.internal_case_review_notes, remove_line_breaks=(file_format == 'tsv')),
])
rows.append(row)
return export_table(filename_prefix, header, rows, file_format)
def export_individuals(filename_prefix,
individuals,
file_format,
include_project_column=False,
include_display_name=False,
include_dates=False,
include_case_review_columns=False,
include_phenotips_columns=False):
"""Export Individuals table.
Args:
filename_prefix (string): Filename without the file extension.
individuals (list): List of Django Individual objects to include in the table
file_format (string): "xls" or "tsv"
include_project_column (bool):
include_display_name (bool):
include_dates (bool):
include_case_review_columns (bool):
include_phenotips_columns (bool):
Returns:
Django HttpResponse object with the table data as an attachment.
"""
header = []
if include_project_column:
header.extend(['project'])
header.extend([
'family_id',
'individual_id',
'paternal_id',
'maternal_id',
'sex',
'affected_status',
'notes',
])
if include_display_name:
header.extend(['display_name'])
if include_dates:
header.extend(['created_date'])
if include_case_review_columns:
header.extend([
'case_review_status',
'case_review_status_last_modified_date',
'case_review_status_last_modified_by',
'case_review_discussion',
])
if include_phenotips_columns:
phenotips_columns_header = [
'phenotips_features_present', 'phenotips_features_absent',
'paternal_ancestry', 'maternal_ancestry', 'age_of_onset'
]
header.extend(phenotips_columns_header)
rows = []
for i in individuals:
row = []
if include_project_column:
row.extend([i.family.project.name or i.family.project.project_id])
row.extend([
i.family.family_id,
i.individual_id,
i.paternal_id,
i.maternal_id,
_SEX_TO_EXPORT_VALUE.get(i.sex),
_AFFECTED_TO_EXPORT_VALUE.get(i.affected),
_convert_html_to_plain_text(i.notes),
])
if include_display_name:
row.extend([i.display_name])
if include_dates:
row.extend([i.created_date])
if include_case_review_columns:
row.extend([
Individual.CASE_REVIEW_STATUS_LOOKUP.get(
i.case_review_status, ''),
i.case_review_status_last_modified_date,
_user_to_string(i.case_review_status_last_modified_by),
i.case_review_discussion,
])
if include_phenotips_columns:
if i.phenotips_data:
phenotips_json = json.loads(i.phenotips_data)
phenotips_fields = _parse_phenotips_data(phenotips_json)
row.extend(
[phenotips_fields[h] for h in phenotips_columns_header])
else:
row.extend(['' for h in phenotips_columns_header])
rows.append(row)
return export_table(filename_prefix, header, rows, file_format)
def export_families(
filename_prefix,
families,
file_format,
include_project_name=False,
include_internal_case_review_summary=False,
include_internal_case_review_notes=False,
):
"""Export Families table.
Args:
filename_prefix (string): Filename wihtout
families (list): List of Django Family objects to include in the table
file_format (string): "xls" or "tsv"
Returns:
Django HttpResponse object with the table data as an attachment.
"""
header = []
if include_project_name:
header.append('Project')
header.extend([
'Family ID',
'Display Name',
'Created Date',
'Description',
'Analysis Status',
'Analysis Summary',
'Analysis Notes',
])
if include_internal_case_review_summary:
header.append('Internal Case Review Summary')
if include_internal_case_review_notes:
header.append('Internal Case Review Notes')
rows = []
analysis_status_lookup = dict(Family.ANALYSIS_STATUS_CHOICES)
for family in families:
row = []
if include_project_name:
row.append(family.project.name or family.project.project_id)
row.extend([
family.family_id,
family.display_name,
family.created_date,
family.description,
analysis_status_lookup.get(family.analysis_status,
family.analysis_status),
_convert_html_to_plain_text(
family.analysis_summary,
remove_line_breaks=(file_format == 'tsv')),
_convert_html_to_plain_text(
family.analysis_notes,
remove_line_breaks=(file_format == 'tsv')),
])
if include_internal_case_review_summary:
row.append(
_convert_html_to_plain_text(
family.internal_case_review_summary,
remove_line_breaks=(file_format == 'tsv')), )
if include_internal_case_review_notes:
row.append(
_convert_html_to_plain_text(
family.internal_case_review_notes,
remove_line_breaks=(file_format == 'tsv')), )
rows.append(row)
return export_table(filename_prefix, header, rows, file_format)
def export_individuals(
filename_prefix,
individuals,
file_format,
include_project_name=False,
include_display_name=False,
include_created_date=False,
include_case_review_status=False,
include_case_review_last_modified_date=False,
include_case_review_last_modified_by=False,
include_case_review_discussion=False,
include_hpo_terms_present=False,
include_hpo_terms_absent=False,
include_paternal_ancestry=False,
include_maternal_ancestry=False,
include_age_of_onset=False,
):
"""Export Individuals table.
Args:
filename_prefix (string): Filename without the file extension.
individuals (list): List of Django Individual objects to include in the table
file_format (string): "xls" or "tsv"
Returns:
Django HttpResponse object with the table data as an attachment.
"""
header = []
if include_project_name:
header.append('Project')
header.extend([
'Family ID',
'Individual ID',
'Paternal ID',
'Maternal ID',
'Sex',
'Affected Status',
'Notes',
])
if include_display_name:
header.append('Display Name')
if include_created_date:
header.append('Created Date')
if include_case_review_status:
header.append('Case Review Status')
if include_case_review_last_modified_date:
header.append('Case Review Status Last Modified')
if include_case_review_last_modified_by:
header.append('Case Review Status Last Modified By')
if include_case_review_discussion:
header.append('Case Review Discussion')
if include_hpo_terms_present:
header.append('HPO Terms (present)')
if include_hpo_terms_absent:
header.append('HPO Terms (absent)')
if include_paternal_ancestry:
header.append('Paternal Ancestry')
if include_maternal_ancestry:
header.append('Maternal Ancestry')
if include_age_of_onset:
header.append('Age of Onset')
rows = []
for i in individuals:
row = []
if include_project_name:
row.extend([i.family.project.name or i.family.project.project_id])
row.extend([
i.family.family_id,
i.individual_id,
i.paternal_id,
i.maternal_id,
_SEX_TO_EXPORTED_VALUE.get(i.sex),
__AFFECTED_TO_EXPORTED_VALUE.get(i.affected),
_convert_html_to_plain_text(i.notes),
])
if include_display_name:
row.append(i.display_name)
if include_created_date:
row.append(i.created_date)
if include_case_review_status:
row.append(
Individual.CASE_REVIEW_STATUS_LOOKUP.get(
i.case_review_status, ''))
if include_case_review_last_modified_date:
row.append(i.case_review_status_last_modified_date)
if include_case_review_last_modified_by:
row.append(_user_to_string(i.case_review_status_last_modified_by))
if include_case_review_discussion:
row.append(i.case_review_discussion)
if (include_hpo_terms_present or \
include_hpo_terms_absent or \
include_paternal_ancestry or \
include_maternal_ancestry or \
include_age_of_onset):
if i.phenotips_data:
phenotips_json = json.loads(i.phenotips_data)
phenotips_fields = _parse_phenotips_data(phenotips_json)
else:
phenotips_fields = {}
if include_hpo_terms_present:
row.append(
phenotips_fields.get('phenotips_features_present', ''))
if include_hpo_terms_absent:
row.append(
phenotips_fields.get('phenotips_features_absent', ''))
if include_paternal_ancestry:
row.append(phenotips_fields.get('paternal_ancestry', ''))
if include_maternal_ancestry:
row.append(phenotips_fields.get('maternal_ancestry', ''))
if include_age_of_onset:
row.append(phenotips_fields.get('age_of_onset', ''))
rows.append(row)
return export_table(filename_prefix, header, rows, file_format)