def test_basic_table_no_content(self):
t = Table(('Key', 'Value'))
self.assertEqual(t.nrows, 0)
self.assertEqual(
t.html(), "<table>\n"
"<tr><th>Key</th><th>Value</th></tr>\n"
"</table>")
def test_basic_table(self):
t = Table(('Key', 'Value'))
idx = t.add_row(Key="Employee name", Value="John Doe")
self.assertEqual(idx, 0)
self.assertEqual(t.nrows, 1)
self.assertEqual(
t.html(), "<table>\n"
"<tr><th>Key</th><th>Value</th></tr>\n"
"<tr><td>Employee name</td><td>John Doe</td></tr>\n"
"</table>")
def test_table_with_column_aliases(self):
t = Table(('name', 'date', 'result'),
name="Experiment",
date="Date run",
result="Final result")
idx = t.add_row(name="Test setup", date="10/10/2017", result="Ok")
self.assertEqual(idx, 0)
self.assertEqual(t.nrows, 1)
self.assertEqual(
t.html(), "<table>\n"
"<tr><th>Experiment</th><th>Date run</th><th>Final result</th></tr>\n"
"<tr><td>Test setup</td><td>10/10/2017</td><td>Ok</td></tr>\n"
"</table>")
def test_table_append_columns(self):
t = Table(('Key', 'Person1'))
t.add_row(Key="Name", Person1="John Doe")
t.add_row(Key="D.O.B", Person1="12/06/1982")
self.assertEqual(
t.html(), "<table>\n"
"<tr><th>Key</th><th>Person1</th></tr>\n"
"<tr><td>Name</td><td>John Doe</td></tr>\n"
"<tr><td>D.O.B</td><td>12/06/1982</td></tr>\n"
"</table>")
t.append_columns("Person2", "Person3")
self.assertEqual(
t.html(), "<table>\n"
"<tr><th>Key</th><th>Person1</th><th>Person2</th><th>Person3</th></tr>\n"
"<tr><td>Name</td><td>John Doe</td><td> </td><td> </td></tr>\n"
"<tr><td>D.O.B</td><td>12/06/1982</td><td> </td><td> </td></tr>\n"
"</table>")
def test_table_no_header(self):
t = Table(('Key', 'Value'))
t.add_row(Key="Employee name", Value="John Doe")
self.assertEqual(
t.html(), "<table>\n"
"<tr><th>Key</th><th>Value</th></tr>\n"
"<tr><td>Employee name</td><td>John Doe</td></tr>\n"
"</table>")
t.no_header()
self.assertEqual(
t.html(), "<table>\n"
"<tr><td>Employee name</td><td>John Doe</td></tr>\n"
"</table>")
def test_table_append_columns_fails_with_multiple_names(self):
t = Table(('Key','Person1'))
t.add_row(Key="Name",Person1="John Doe")
t.add_row(Key="D.O.B",Person1="12/06/1982")
self.assertRaises(KeyError,
t.append_columns,
"Person1")
def test_table_render_with_css_id(self):
t = Table(('Key', 'Value'))
t.add_row(Key="Employee name", Value="John Doe")
self.assertEqual(
t.html(), "<table>\n"
"<tr><th>Key</th><th>Value</th></tr>\n"
"<tr><td>Employee name</td><td>John Doe</td></tr>\n"
"</table>")
self.assertEqual(
t.html(css_id="employee-tbl"), "<table id='employee-tbl'>\n"
"<tr><th>Key</th><th>Value</th></tr>\n"
"<tr><td>Employee name</td><td>John Doe</td></tr>\n"
"</table>")
def test_table_multiple_rows(self):
t = Table(('Key', 'Value'))
idx = t.add_row(Key="Name", Value="John Doe")
self.assertEqual(idx, 0)
self.assertEqual(t.nrows, 1)
idx = t.add_row(Key="D.O.B", Value="12/06/1982")
self.assertEqual(idx, 1)
self.assertEqual(t.nrows, 2)
idx = t.add_row(Key="Mobile", Value="+44 1726254")
self.assertEqual(idx, 2)
self.assertEqual(t.nrows, 3)
self.assertEqual(
t.html(), "<table>\n"
"<tr><th>Key</th><th>Value</th></tr>\n"
"<tr><td>Name</td><td>John Doe</td></tr>\n"
"<tr><td>D.O.B</td><td>12/06/1982</td></tr>\n"
"<tr><td>Mobile</td><td>+44 1726254</td></tr>\n"
"</table>")
def test_table_add_css_classes_to_column(self):
t = Table(('Key', 'Value'))
t.add_row(Key="Employee name", Value="John Doe")
t.add_row(Key="D.O.B", Value="12/06/1982")
self.assertEqual(
t.html(), "<table>\n"
"<tr><th>Key</th><th>Value</th></tr>\n"
"<tr><td>Employee name</td><td>John Doe</td></tr>\n"
"<tr><td>D.O.B</td><td>12/06/1982</td></tr>\n"
"</table>")
t.add_css_classes("key-column", column="Key")
self.assertEqual(
t.html(), "<table>\n"
"<tr><th class='key-column'>Key</th><th>Value</th></tr>\n"
"<tr><td class='key-column'>Employee name</td><td>John Doe</td></tr>\n"
"<tr><td class='key-column'>D.O.B</td><td>12/06/1982</td></tr>\n"
"</table>")
t.add_css_classes("summary", "sunny", column="Key")
self.assertEqual(
t.html(), "<table>\n"
"<tr><th class='key-column summary sunny'>Key</th><th>Value</th></tr>\n"
"<tr><td class='key-column summary sunny'>Employee name</td><td>John Doe</td></tr>\n"
"<tr><td class='key-column summary sunny'>D.O.B</td><td>12/06/1982</td></tr>\n"
"</table>")
self.assertRaises(KeyError,
t.add_css_classes,
"blah",
column="doesntexist")
def test_table_add_css_classes(self):
t = Table(('Key', 'Value'))
t.add_row(Key="Employee name", Value="John Doe")
self.assertEqual(
t.html(), "<table>\n"
"<tr><th>Key</th><th>Value</th></tr>\n"
"<tr><td>Employee name</td><td>John Doe</td></tr>\n"
"</table>")
t.add_css_classes("employee-data")
self.assertEqual(
t.html(), "<table class='employee-data'>\n"
"<tr><th>Key</th><th>Value</th></tr>\n"
"<tr><td>Employee name</td><td>John Doe</td></tr>\n"
"</table>")
t.add_css_classes("summary", "sunny")
self.assertEqual(
t.html(), "<table class='employee-data summary sunny'>\n"
"<tr><th>Key</th><th>Value</th></tr>\n"
"<tr><td>Employee name</td><td>John Doe</td></tr>\n"
"</table>")
def test_table_set_value(self):
t = Table(('Key', 'Value'))
t.add_row(Key="Name", Value="John Doe")
t.add_row(Key="D.O.B", Value="12/06/1982")
t.add_row(Key="Mobile", Value="+44 1726254")
self.assertEqual(
t.html(), "<table>\n"
"<tr><th>Key</th><th>Value</th></tr>\n"
"<tr><td>Name</td><td>John Doe</td></tr>\n"
"<tr><td>D.O.B</td><td>12/06/1982</td></tr>\n"
"<tr><td>Mobile</td><td>+44 1726254</td></tr>\n"
"</table>")
t.append_columns("Value2")
t.set_value(0, "Value2", "Jane Doe")
t.set_value(1, "Value2", "19/04/1979")
t.set_value(2, "Value2", "+44 1745262")
self.assertEqual(
t.html(), "<table>\n"
"<tr><th>Key</th><th>Value</th><th>Value2</th></tr>\n"
"<tr><td>Name</td><td>John Doe</td><td>Jane Doe</td></tr>\n"
"<tr><td>D.O.B</td><td>12/06/1982</td><td>19/04/1979</td></tr>\n"
"<tr><td>Mobile</td><td>+44 1726254</td><td>+44 1745262</td></tr>\n"
"</table>")
toc_list = List()
toc.add(toc_list)
# Files
files_info = report.add_section("Stats files")
stats_files = "Statistics: %s" % Link(
"[TSV]", os.path.relpath(stats_file, os.path.dirname(out_file)))
if xlsx_file is not None:
stats_files += " | %s" % Link(
"[XLSX]", os.path.relpath(xlsx_file, os.path.dirname(out_file)))
files_info.add(stats_files)
toc_list.add_item(Link(files_info.title, files_info))
# General info
general_info = report.add_section("General info", name="general_info")
tbl = Table(columns=('name', 'value'))
tbl.no_header()
data_items = (('Total #reads', 'total_reads'), ('Total assigned #reads',
'total_assigned_reads'),
('Total #barcodes', 'total_barcodes'), ('Assigned #barcodes',
'assigned_barcodes'))
for item in data_items:
name, key = item
tbl.add_row(name=name, value=data[key])
general_info.add(tbl)
# Reads at each stage
cols = ['Nreads', 'Nreads_filtered', 'Nreads_trimmed']
if contaminant_filtered:
cols.append('Nreads_contaminant_filtered')
plot_filen = os.path.join(out_dir, "reads_per_stage.png")