def test_refresh(self):
"User refreshes the current, non-default template"
w = self.window
with temp_directory_with_files(TESTDATA / 'test.inselect_template') as tempdir,\
patch.object(QSettings, 'setValue') as mock_setvalue:
path = tempdir / 'test.inselect_template'
retval = str(path), w.view_metadata.popup_button.FILE_FILTER
# Load the test template in tempdir
with patch.object(QFileDialog, 'getOpenFileName', return_value=retval) as mock_gofn:
w.view_metadata.popup_button.choose()
self.assertEqual(1, mock_gofn.call_count)
self.assertEqual('Test user template',
user_template_choice().current.name)
self.assertEqual('Test user template',
self.window.view_metadata.popup_button.text())
# Write a new template to the file and refresh
template = """Name: An updated test template
Fields:
- Name: catalogNumber
"""
with path.open('w') as outfile:
outfile.write(template)
# Refresh loaded template
with patch.object(QSettings, 'value', return_value=str(path)) as mock_value:
w.view_metadata.popup_button.refresh()
self.assertEqual(1, mock_value.call_count)
self.assertEqual("An updated test template",
user_template_choice().current.name)
self.assertEqual('An updated test template',
self.window.view_metadata.popup_button.text())
def test_open_save_existing_modified(self, mock_question):
"User chooses to save the existing modified document"
w = self.window
# Create a temporary inselect document so that it can be modified
with temp_directory_with_files(TESTDATA / 'test_segment.inselect',
TESTDATA /
'test_segment.png') as tempdir:
# Oopen the temp doc and modify it
self._load_and_modify(tempdir / 'test_segment.inselect')
# Open another doc - user says not to save
w.open_file(TESTDATA / 'test_subsegment.inselect')
self.assertTrue(mock_question.called)
expected = "Save the document before closing?"
self.assertTrue(expected in mock_question.call_args[0])
self.assertEqual(1, w.model.rowCount())
self.assertEqual('Inselect [test_subsegment]', w.windowTitle())
# Original document should have changed - it should contain no boxes
w.open_file(tempdir / 'test_segment.inselect')
self.assertEqual(0, w.model.rowCount())
self.assertEqual('Inselect [test_segment]', w.windowTitle())
def test_cancel_save_crops(self):
"User cancels save crops"
with temp_directory_with_files(TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png') as tempdir:
doc = InselectDocument.load(tempdir / 'shapes.inselect')
# Create crops dir with some data
doc.crops_dir.mkdir()
with doc.crops_dir.joinpath('a_file').open('w') as outfile:
outfile.write('Some data\n')
class CancelExport(Exception):
pass
def progress(msg):
"A progress function that cancels the export"
raise CancelExport()
self.assertRaises(CancelExport,
DocumentExport(self.TEMPLATE).save_crops,
doc,
progress=progress)
# Nothing should have changed within tempdir
self.assertEqual(
['shapes.inselect', 'shapes.png', doc.crops_dir.name],
sorted(p.name for p in tempdir.iterdir()))
self.assertEqual(['a_file'],
[p.name for p in doc.crops_dir.iterdir()])
def test_export_do_not_overwite_existing_csv(self, mock_information,
mock_question):
"User does not want to overwrite existing CSV file"
w = self.window
# Load document and write the CSV file
with temp_directory_with_files(TESTDATA / 'test_segment.inselect',
TESTDATA /
'test_segment.png') as tempdir:
# Create a CSV file to force the GUI to prompt for over-write
(tempdir / 'test_segment.csv').open('w')
# Load document and export CSV file
w.open_document(tempdir / 'test_segment.inselect')
w.export_csv()
# File should not have been altered
self.assertEqual('', (tempdir / 'test_segment.csv').open().read())
# User should not have been told about the export
self.assertFalse(mock_information.called)
# User should have been prompted to overwrite the existing file
self.assertTrue(mock_question.called)
question = 'Overwrite the existing CSV file?'
self.assertTrue(question in mock_question.call_args[0])
def test_load_images(self):
"Load document's images"
source = TESTDATA / 'shapes.inselect'
with temp_directory_with_files(TESTDATA / 'shapes.inselect') as tempdir:
doc_temp = tempdir / 'shapes.inselect'
with doc_temp.open('w') as outfile, source.open() as infile:
outfile.write(infile.read())
# Document load with neither scanned image file nor thumbnail
self.assertRaises(InselectError, InselectDocument.load, doc_temp)
# Document load with thumbnail but no scanned image file
thumbnail_temp = tempdir / 'shapes_thumbnail.jpg'
thumbnail_temp.touch() # File only needs to exist
doc = InselectDocument.load(doc_temp)
self.assertFalse(doc.scanned.available)
self.assertTrue(doc.thumbnail.available)
# Document load with both scanned and thumbnail files
scanned_temp = tempdir / 'shapes.png'
scanned_temp.touch() # File only needs to exist
actual = InselectDocument.load(doc_temp)
self.assertEqual(InselectDocument.load(source).items, actual.items)
self.assertTrue(actual.scanned.available)
self.assertTrue(actual.thumbnail.available)
# Document load with scanned image file but not thumbnail
os.unlink(str(thumbnail_temp))
actual = InselectDocument.load(doc_temp)
self.assertEqual(InselectDocument.load(source).items, actual.items)
self.assertTrue(actual.scanned.available)
self.assertFalse(actual.thumbnail.available)
def test_export_do_not_overwite_existing_csv(self, mock_information, mock_question):
"User does not want to overwrite existing CSV file"
w = self.window
# Load document and write the CSV file
with temp_directory_with_files(TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png') as tempdir:
# Create a CSV file to force the GUI to prompt for over-write
(tempdir / 'shapes.csv').touch()
# Load document and export CSV file
w.open_document(tempdir / 'shapes.inselect')
w.export_csv(user_template=DWC)
# File should not have been altered
with (tempdir / 'shapes.csv').open() as infile:
self.assertEqual('', infile.read())
# User should not have been told about the export
self.assertFalse(mock_information.called)
# User should have been prompted to overwrite the existing file
self.assertTrue(mock_question.called)
question = 'Overwrite the existing CSV file?'
self.assertTrue(question in mock_question.call_args[0])
def test_export_overwite_existing_csv(self, mock_information,
mock_question):
"User wants to overwrite existing CSV file"
w = self.window
# Load document and write the CSV file
with temp_directory_with_files(TESTDATA / 'test_segment.inselect',
TESTDATA /
'test_segment.png') as tempdir:
# Create a CSV file to force the GUI to prompt for over-write
(tempdir / 'test_segment.csv').open('w')
# Load document and export CSV file
w.open_document(tempdir / 'test_segment.inselect')
w.export_csv()
self._test_csv()
# User should have been told about the export
self.assertTrue(mock_information.called)
expected = u"Data for 5 boxes written to {0}"
expected = expected.format(tempdir / 'test_segment.csv')
self.assertTrue(expected in mock_information.call_args[0])
# User should have been prompted to overwrite the existing file
self.assertTrue(mock_question.called)
question = 'Overwrite the existing CSV file?'
self.assertTrue(question in mock_question.call_args[0])
def test_export_overwite_existing_csv(self, mock_information, mock_question):
"User wants to overwrite existing CSV file"
w = self.window
# Load document and write the CSV file
with temp_directory_with_files(TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png') as tempdir:
# Create a CSV file to force the GUI to prompt for over-write
(tempdir / 'shapes.csv').touch()
# Load document and export CSV file
w.open_document(path=tempdir / 'shapes.inselect')
w.export_csv(user_template=DWC)
self._test_csv()
# User should have been told about the export
self.assertTrue(mock_information.called)
expected = "Data for 5 boxes written to {0}"
expected = expected.format(tempdir / 'shapes.csv')
self.assertTrue(expected in mock_information.call_args[0])
# User should have been prompted to overwrite the existing file
self.assertTrue(mock_question.called)
question = 'Overwrite the existing CSV file?'
self.assertTrue(question in mock_question.call_args[0])
def test_save_crops(self):
"Save crops"
with temp_directory_with_files(TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png') as tempdir:
main([str(tempdir)])
crops = tempdir / 'shapes_crops'
self.assertEqual(5, len(list(crops.glob('*jpg'))))
def test_copy_to_new_document(self, mock_new_document):
"User copies boxes to a new document"
# open_file delegates to new_document, which runs an operation runs in a
# worker thread - I could not think of a way to test the complete
# operation in a single test.
# This test checks that new_document is called as expected.
w = self.window
w.open_file(path=TESTDATA / 'shapes.inselect')
# Take a copy of the metadata
expected_metadata = w.document.items
with temp_directory_with_files(TESTDATA / 'shapes.png') as tempdir:
image = tempdir / 'other_image.png'
(tempdir / 'shapes.png').rename(image)
retval = str(image), w.IMAGE_FILE_FILTER
with patch.object(QFileDialog, 'getOpenFileName', return_value=retval) as mock_gofn:
w.copy_to_new_document()
self.assertEqual(1, mock_gofn.call_count)
# New document should have been called with the path to the image
self.assertTrue(mock_new_document.called)
mock_new_document.assert_called_once_with(
image, default_metadata_items=expected_metadata
)
# Orignal document should have been closed
self.assertIsNone(self.window.document)
def test_cancel_save_crops(self):
"User cancels save crops"
with temp_directory_with_files(TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png') as tempdir:
doc = InselectDocument.load(tempdir / 'shapes.inselect')
# Create crops dir with some data
doc.crops_dir.mkdir()
with doc.crops_dir.joinpath('a_file').open('w') as outfile:
outfile.write('Some data\n')
class CancelExport(Exception):
pass
def progress(msg):
"A progress function that cancels the export"
raise CancelExport()
self.assertRaises(
CancelExport,
DocumentExport(self.TEMPLATE).save_crops, doc, progress=progress
)
# Nothing should have changed within tempdir
self.assertEqual(
['shapes.inselect', 'shapes.png', doc.crops_dir.name],
sorted(p.name for p in tempdir.iterdir()))
self.assertEqual(
['a_file'],
[p.name for p in doc.crops_dir.iterdir()]
)
def test_load_images(self):
"Load document's images"
source = TESTDATA / 'shapes.inselect'
with temp_directory_with_files(TESTDATA /
'shapes.inselect') as tempdir:
doc_temp = tempdir / 'shapes.inselect'
with doc_temp.open('w') as outfile, source.open() as infile:
outfile.write(infile.read())
# Document load with neither scanned image file nor thumbnail
self.assertRaises(InselectError, InselectDocument.load, doc_temp)
# Document load with thumbnail but no scanned image file
thumbnail_temp = tempdir / 'shapes_thumbnail.jpg'
thumbnail_temp.touch() # File only needs to exist
doc = InselectDocument.load(doc_temp)
self.assertFalse(doc.scanned.available)
self.assertTrue(doc.thumbnail.available)
# Document load with both scanned and thumbnail files
scanned_temp = tempdir / 'shapes.png'
scanned_temp.touch() # File only needs to exist
actual = InselectDocument.load(doc_temp)
self.assertEqual(InselectDocument.load(source).items, actual.items)
self.assertTrue(actual.scanned.available)
self.assertTrue(actual.thumbnail.available)
# Document load with scanned image file but not thumbnail
os.unlink(str(thumbnail_temp))
actual = InselectDocument.load(doc_temp)
self.assertEqual(InselectDocument.load(source).items, actual.items)
self.assertTrue(actual.scanned.available)
self.assertFalse(actual.thumbnail.available)
def test_read_barcodes_no_scanned_image(self, mock_warning):
"""The user is informed that barcodes cannot be read without the
scanned image
"""
with temp_directory_with_files(TESTDATA / 'barcodes.inselect') as tempdir:
# Create thumbnail file
shutil.copy(str(TESTDATA.joinpath('barcodes.jpg')),
str(tempdir.joinpath('barcodes_thumbnail.jpg')))
self.window.open_document(path=tempdir / 'barcodes.inselect')
self.window.run_plugin(2)
expected = ('Unable to read barcodes because the original '
'full-resolution image file does not exist.')
self.assertTrue(expected in mock_warning.call_args[0])
model = self.window.model
# Metadata should be unaltered
indexes = (model.index(row, 0) for row in range(3))
self.assertEqual(
[None, None, None],
[model.data(i, MetadataRole).get('catalogNumber') for i in indexes]
)
self.assertFalse(model.is_modified)
def test_export_csv(self):
"Export metadata to CSV"
with temp_directory_with_files(TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png') as tempdir:
# Create an empty CSV file
csv = tempdir / 'shapes.csv'
with csv.open('w'):
pass
main([str(tempdir), '--overwrite'])
csv = tempdir / 'shapes.csv'
self.assertTrue(csv.is_file())
# Check CSV contents
doc = InselectDocument.load(tempdir / 'shapes.inselect')
with csv.open('rb') as f:
res = unicodecsv.DictReader(f, encoding='utf-8')
for index, item, row in zip(count(), doc.items, res):
expected = item['fields']
expected.update({
'ItemNumber': str(1+index),
'Cropped_image_name': '{0:04}.jpg'.format(1+index)
})
actual = {
k: v for k, v in row.items()
if v and k not in BOUNDING_BOX_FIELD_NAMES
}
self.assertEqual(expected, actual)
def test_csv_export(self):
"CSV data are exported as expected"
with temp_directory_with_files(TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png') as tempdir:
doc = InselectDocument.load(tempdir / 'shapes.inselect')
csv_path = DocumentExport(self.TEMPLATE).export_csv(doc)
self.assertEqual(csv_path, tempdir / 'shapes.csv')
# Check CSV contents
with csv_path.open('rb') as f:
reader = unicodecsv.reader(f, encoding='utf8')
headers = [
'Cropped_image_name', 'ItemNumber',
'NormalisedLeft', 'NormalisedTop', 'NormalisedRight',
'NormalisedBottom', 'ThumbnailLeft', 'ThumbnailTop',
'ThumbnailRight', 'ThumbnailBottom', 'OriginalLeft',
'OriginalTop', 'OriginalRight', 'OriginalBottom',
'catalogNumber', 'Department', 'scientificName',
'scientificName-value'
]
self.assertEqual(headers, next(reader))
# Check only the metadata columns and 'original' coordinates
# columns, ignoring thumbnail (which doesn't exist)
# and normalised (which are floating point) coordinates
metadata_cols = itemgetter(0, 1, 10, 11, 12, 13, 14, 15, 16, 17)
self.assertEqual(
('01_1.png', '1',
'0', '0', '189', '189',
'1', 'Entomology', 'A', '1'),
metadata_cols(next(reader))
)
self.assertEqual(
('02_2.png', '2',
'271', '0', '459', '189',
'2', 'Entomology', 'B', '2'),
metadata_cols(next(reader))
)
self.assertEqual(
('03_10.png', '3',
'194', '196', '257', '232',
'3', 'Entomology', 'インセクト', '10'),
metadata_cols(next(reader))
)
self.assertEqual(
('04_3.png', '4',
'0', '248', '189', '437',
'4', 'Entomology', 'Elsinoë', '3'),
metadata_cols(next(reader))
)
self.assertEqual(
('05_4.png', '5',
'271', '248', '459', '437',
'5', 'Entomology', 'D', '4'),
metadata_cols(next(reader))
)
self.assertIsNone(next(reader, None))
def test_reveal_path_windows(self, mock_subprocess):
"User reveals a path"
with temp_directory_with_files() as tempdir:
path = tempdir / 'xyz'
path.touch()
reveal_path(path)
expected = "explorer.exe /select,{0}".format(path.resolve())
mock_subprocess.assert_called_once_with(expected)
def test_reveal_path_windows(self, mock_subprocess):
"User reveals a path"
with temp_directory_with_files() as tempdir:
path = tempdir / 'xyz'
path.touch()
reveal_path(path)
expected = "explorer.exe /select,{0}".format(path.resolve())
mock_subprocess.assert_called_once_with(expected)
def test_new_from_thumbnail(self):
"Can't create a document from a thumbnail image"
with temp_directory_with_files(TESTDATA / 'test_segment.png') as tempdir:
doc = InselectDocument.new_from_scan(tempdir / 'test_segment.png')
doc.ensure_thumbnail(width=2048)
doc = None
self.assertRaises(InselectError, InselectDocument.new_from_scan,
tempdir / 'test_segment_thumbnail.png')
def test_ensure_thumbnail(self):
"Thumbnail is created"
source_doc = TESTDATA / 'test_segment.inselect'
source_img = TESTDATA / 'test_segment.png'
with temp_directory_with_files(source_doc, source_img) as tempdir:
# Document load with no scanned image file
doc = InselectDocument.load(tempdir / 'test_segment.inselect')
self.assertTrue(doc.thumbnail is None)
doc.ensure_thumbnail(width=2048)
self.assertEqual(2048, doc.thumbnail.array.shape[1])
def test_ensure_thumbnail_silly_size(self):
"Can't create thumbnail with a silly size"
source_doc = TESTDATA / 'test_segment.inselect'
source_img = TESTDATA / 'test_segment.png'
with temp_directory_with_files(source_doc, source_img) as tempdir:
doc = InselectDocument.load(tempdir / 'test_segment.inselect')
self.assertRaises(InselectError, doc.ensure_thumbnail, -1)
self.assertRaises(InselectError, doc.ensure_thumbnail, 50)
self.assertRaises(InselectError, doc.ensure_thumbnail, 20000)
def test_new_from_thumbnail(self):
"Can't create a document from a thumbnail image"
with temp_directory_with_files(TESTDATA / 'shapes.png') as tempdir:
doc = InselectDocument.new_from_scan(tempdir / 'shapes.png',
thumbnail_width_pixels=2048)
thumbnail = tempdir / 'shapes_thumbnail.jpg'
self.assertTrue(thumbnail.is_file())
self.assertTrue(doc.thumbnail.available)
self.assertEqual(2048, doc.thumbnail.array.shape[1])
self.assertRaises(InselectError, InselectDocument.new_from_scan,
thumbnail)
def test_new_from_scan(self):
"New document is created and saved"
with temp_directory_with_files(TESTDATA / 'shapes.png') as tempdir:
doc = InselectDocument.new_from_scan(tempdir / 'shapes.png')
self.assertTrue(doc.document_path.is_file())
self.assertEqual(tempdir / 'shapes.png', doc.scanned.path)
# Saved on time should be within last 2 seconds
now = datetime.now(pytz.timezone("UTC"))
created_on = doc.properties['Created on']
self.assertLessEqual((now - created_on).seconds, 2)
def test_new_from_scan(self):
"New document is created and saved"
with temp_directory_with_files(TESTDATA / 'test_segment.png') as tempdir:
doc = InselectDocument.new_from_scan(tempdir / 'test_segment.png')
self.assertTrue(doc.document_path.is_file())
self.assertEqual(tempdir / 'test_segment.png', doc.scanned.path)
# Saved on time should be within last 2 seconds
now = datetime.now(pytz.timezone("UTC"))
created_on = doc.properties['Created on']
self.assertLessEqual((now - created_on).seconds, 2)
def test_new_from_thumbnail(self):
"Can't create a document from a thumbnail image"
with temp_directory_with_files(TESTDATA / 'test_segment.png') as tempdir:
doc = InselectDocument.new_from_scan(
tempdir / 'test_segment.png',
thumbnail_width_pixels=2048
)
thumbnail = tempdir / 'test_segment_thumbnail.jpg'
self.assertTrue(thumbnail.is_file())
self.assertEqual(2048, doc.thumbnail.array.shape[1])
self.assertRaises(InselectError, InselectDocument.new_from_scan,
thumbnail)
def test_thumbnail_silly_size(self):
"Can't create thumbnail with a silly size"
with temp_directory_with_files(TESTDATA / 'shapes.png') as tempdir:
self.assertRaisesRegex(InselectError, "width should be between",
InselectDocument.new_from_scan,
tempdir / 'shapes.png', -1)
self.assertRaisesRegex(InselectError, "width should be between",
InselectDocument.new_from_scan,
tempdir / 'shapes.png', 50)
self.assertRaisesRegex(InselectError, "width should be between",
InselectDocument.new_from_scan,
tempdir / 'shapes.png', 20000)
def test_reveal_path_os_x(self, mock_subprocess):
"User reveals a path"
with temp_directory_with_files() as tempdir:
path = tempdir / 'xyz'
path.touch()
reveal_path(path)
expected = [
'/usr/bin/osascript', '-e',
'tell application "Finder" to reveal POSIX file "{0}"'.format(
str(path.resolve()))
]
mock_subprocess.assert_any_call(expected)
def test_save_crops_with_existing(self):
"Attempt to save crops over an existing directory"
with temp_directory_with_files(TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png') as tempdir:
# Create crops dir
crops = tempdir / 'shapes_crops'
crops.mkdir()
main([str(tempdir)])
# nose hooks up stdout to a file-like object
stdout = sys.stdout.getvalue()
self.assertIn('exists - skipping', stdout)
def test_shapes(self):
"Segment an existing document"
with temp_directory_with_files(TESTDATA / 'shapes.png') as tempdir:
# Create a new document
ingest_image(tempdir / 'shapes.png', tempdir)
main([str(tempdir)])
doc_path = tempdir / 'shapes.inselect'
self.assertTrue(doc_path.is_file())
doc = InselectDocument.load(doc_path)
self.assertEqual(5, len(doc.items))
def test_segment(self):
"Segment an existing document"
with temp_directory_with_files(TESTDATA / 'test_segment.png') as tempdir:
# Create a new document
ingest_image(tempdir / 'test_segment.png', tempdir)
main([unicode(tempdir)])
doc_path = tempdir / 'test_segment.inselect'
self.assertTrue(doc_path.is_file())
doc = InselectDocument.load(doc_path)
self.assertEqual(5, len(doc.items))
def test_new_document(self, mock_new_document):
"""Open an image file for which no inselect document exists
"""
# open_file delegates to new_document, which runs an operation runs in a
# worker thread - I could not think of a way to test the complete
# operation in a single test.
# This test checks that new_document is called as expected.
with temp_directory_with_files(TESTDATA /
'test_segment.png') as tempdir:
self.window.open_file(tempdir / 'test_segment.png')
self.assertTrue(mock_new_document.called)
self.assertEqual(tempdir / 'test_segment.png',
mock_new_document.call_args[0][0])
def test_open_readonly_doc(self, mock_warning):
"User is warned when opening a read-only inselect document"
with temp_directory_with_files(TESTDATA / 'test_segment.inselect',
TESTDATA / 'test_segment.png',
) as tempdir:
make_readonly(tempdir / 'test_segment.inselect')
self.window.open_file(tempdir / 'test_segment.inselect')
self.assertTrue(mock_warning.called)
expected = (u'The file [test_segment.inselect] is read-only.\n\n'
u'You will not be able to save any changes that you '
'make.')
self.assertTrue(expected in mock_warning.call_args[0])
def test_path_is_thumbnail_file(self):
with temp_directory_with_files() as tempdir:
thumbnail = tempdir / 'xx_thumbnail.jpg'
thumbnail.open('w') # File only needs to exist
# Thumbnail file exists but there is no corresponding .inselect doc
self.assertFalse(InselectDocument.path_is_thumbnail_file(thumbnail))
doc = tempdir / 'xx.inselect'
doc.open('w') # File only needs to exist
# Thumbnail file and corresponding .inselect file both exist
self.assertTrue(InselectDocument.path_is_thumbnail_file(thumbnail))
def test_thumbnail_read_only(self):
"Can't write thumbnail to a read-only directory"
# This case is doing more than simply testing filesystem behavour
# because it tests the failure code in InselectDocument
with temp_directory_with_files(TESTDATA / 'shapes.png') as tempdir:
mode = make_readonly(tempdir)
self.assertRaises(InselectError,
InselectDocument.new_from_scan,
tempdir / 'shapes.png',
thumbnail_width_pixels=2048)
# Restor the original mode
tempdir.chmod(mode)
def test_reveal_path_os_x(self, mock_subprocess):
"User reveals a path"
with temp_directory_with_files() as tempdir:
path = tempdir / 'xyz'
path.touch()
reveal_path(path)
expected = [
'/usr/bin/osascript',
'-e',
'tell application "Finder" to reveal POSIX file "{0}"'.format(
str(path.resolve())
)
]
mock_subprocess.assert_any_call(expected)
def test_path_is_thumbnail_file(self):
with temp_directory_with_files() as tempdir:
thumbnail = tempdir / 'xx_thumbnail.jpg'
thumbnail.touch() # File only needs to exist
# Thumbnail file exists but there is no corresponding .inselect doc
self.assertFalse(
InselectDocument.path_is_thumbnail_file(thumbnail))
doc = tempdir / 'xx.inselect'
doc.touch() # File only needs to exist
# Thumbnail file and corresponding .inselect file both exist
self.assertTrue(InselectDocument.path_is_thumbnail_file(thumbnail))
def test_save(self):
"Document save writes items"
source = TESTDATA / 'test_segment.inselect'
temp = tempfile.mkdtemp()
with temp_directory_with_files(TESTDATA / 'test_segment.inselect',
TESTDATA / 'test_segment.png') as tempdir:
items = [ {'fields': {}, 'rect': Rect(0.1, 0.2, 0.5, 0.5) }, ]
doc_temp = tempdir / 'test_segment.inselect'
d = InselectDocument.load(doc_temp)
d.set_items(items)
d.save()
self.assertEqual(items, InselectDocument.load(doc_temp).items)
def test_thumbnail_read_only(self):
"Can't write thumbnail to a read-only directory"
# This case is doing more than simply testing filesystem behavour
# because it tests the failure code in InselectDocument
with temp_directory_with_files(TESTDATA / 'test_segment.png') as tempdir:
mode = make_readonly(tempdir)
self.assertRaises(
InselectError, InselectDocument.new_from_scan,
tempdir / 'test_segment.png', thumbnail_width_pixels=2048
)
# Restor the original mode
tempdir.chmod(mode)
def test_new_document(self, mock_new_document):
"""Open an image file for which no inselect document exists
"""
# open_file delegates to new_document, which runs an operation runs in a
# worker thread - I could not think of a way to test the complete
# operation in a single test.
# This test checks that new_document is called as expected.
with temp_directory_with_files() as tempdir:
# Check that open_file accepts images with a file extension that is
# not all lower case.
shutil.copy(str(TESTDATA / 'shapes.png'),
str(tempdir / 'shapes.Png'))
self.window.open_file(path=tempdir / 'shapes.Png')
mock_new_document.assert_called_once_with(tempdir / 'shapes.Png')
def test_open_readonly_doc(self, mock_warning):
"User is warned when opening a read-only inselect document"
with temp_directory_with_files(
TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png',
) as tempdir:
make_readonly(tempdir / 'shapes.inselect')
self.window.open_file(path=tempdir / 'shapes.inselect')
self.assertTrue(mock_warning.called)
expected = ('The file [shapes.inselect] is read-only.\n\n'
'You will not be able to save any changes that you '
'make.')
self.assertTrue(expected in mock_warning.call_args[0])
def test_new_document(self, mock_new_document):
"""Open an image file for which no inselect document exists
"""
# open_file delegates to new_document, which runs an operation runs in a
# worker thread - I could not think of a way to test the complete
# operation in a single test.
# This test checks that new_document is called as expected.
with temp_directory_with_files() as tempdir:
# Check that open_file accepts images with a file extension that is
# not all lower case.
shutil.copy(str(TESTDATA / 'test_segment.png'),
str(tempdir / 'test_segment.Png'))
self.window.open_file(tempdir / 'test_segment.Png')
mock_new_document.assert_called_once_with(tempdir / 'test_segment.Png')
def test_open_non_ascii(self):
"Open an inselect document with non-ascii characters in the filename"
with temp_directory_with_files() as tempdir:
stem = 'åland'
path = tempdir.joinpath('{0}.inselect'.format(stem))
shutil.copy(str(TESTDATA.joinpath('shapes.inselect')), str(path))
shutil.copy(str(TESTDATA.joinpath('shapes.png')),
str(tempdir.joinpath('{0}.png'.format(stem))))
doc = InselectDocument.load(path)
# Properties are as expected
self.assertEqual(doc.document_path, path)
def test_ensure_thumbnail_read_only(self):
"Can't write thumbnail to a read-only directory"
# This case is doing more than simply testing filesystem behavour
# because it tests the failure code in InselectDocument
source_doc = TESTDATA / 'test_segment.inselect'
source_img = TESTDATA / 'test_segment.png'
with temp_directory_with_files(source_doc, source_img) as tempdir:
doc = InselectDocument.load(tempdir / 'test_segment.inselect')
mode = make_readonly(tempdir)
self.assertRaises(InselectError, doc.ensure_thumbnail)
# Restor the original mode
tempdir.chmod(mode)
def test_thumbnail_silly_size(self):
"Can't create thumbnail with a silly size"
with temp_directory_with_files(TESTDATA / 'test_segment.png') as tempdir:
self.assertRaisesRegexp(
InselectError, "width should be between",
InselectDocument.new_from_scan, tempdir / 'test_segment.png', -1
)
self.assertRaisesRegexp(
InselectError, "width should be between",
InselectDocument.new_from_scan, tempdir / 'test_segment.png', 50
)
self.assertRaisesRegexp(
InselectError, "width should be between",
InselectDocument.new_from_scan, tempdir / 'test_segment.png',
20000
)
def test_open_non_ascii(self):
"Open an inselect document with non-ascii characters in the filename"
with temp_directory_with_files() as tempdir:
stem = 'åland'
path = tempdir.joinpath('{0}.inselect'.format(stem))
shutil.copy(str(TESTDATA.joinpath('shapes.inselect')), str(path))
shutil.copy(
str(TESTDATA.joinpath('shapes.png')),
str(tempdir.joinpath('{0}.png'.format(stem)))
)
doc = InselectDocument.load(path)
# Properties are as expected
self.assertEqual(doc.document_path, path)
def test_open_thumbnail_of_doc(self):
"""Open the thumbnail image file of an existing inselect document - the
inselect document should be opened
"""
with temp_directory_with_files(TESTDATA / 'test_segment.inselect',
TESTDATA / 'test_segment.png',
) as tempdir:
thumbnail = tempdir / 'test_segment_thumbnail.jpg'
# The test document contains no thumbnail file - create one now
shutil.copy(str(tempdir / 'test_segment.png'), str(thumbnail))
self.window.open_file(thumbnail)
self.assertEqual(5, self.window.model.rowCount())
self.assertFalse(self.window.model.is_modified)
self.assertWindowTitleOpenDocument()
def test_save_crops(self):
"Cropped specimen images are written correctly"
with temp_directory_with_files(TESTDATA / 'test_segment.inselect',
TESTDATA / 'test_segment.png') as tempdir:
doc = InselectDocument.load(tempdir / 'test_segment.inselect')
crops_dir = doc.save_crops()
self.assertTrue(crops_dir.is_dir())
self.assertEqual(crops_dir, doc.crops_dir)
self.assertEqual(5, len(list(crops_dir.glob('*.png'))))
# Check the contents of each file
boxes = doc.scanned.from_normalised([i['rect'] for i in doc.items])
for box, path in izip(boxes, sorted(crops_dir.glob('*.png'))):
x0, y0, x1, y1 = box.coordinates
self.assertTrue(np.all(doc.scanned.array[y0:y1, x0:x1] ==
cv2.imread(str(path))))
def test_modified_cleared(self):
"Alter document and clear"
with temp_directory_with_files(TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png') as tempdir:
m = Model()
m.from_document(InselectDocument.load(tempdir / 'shapes.inselect'))
# Alter data
mock_modified_changed = self._new_mock_modified_changed(m)
m.setData(m.index(0, 0), -90, RotationRole)
mock_modified_changed.assert_called_once_with()
self.assertTrue(m.is_modified)
# Clear
m.clear()
self.assertEqual(2, mock_modified_changed.call_count)
self.assertFalse(m.is_modified)
def test_export_no_existing_csv(self, mock_information):
"User exported CSV"
w = self.window
# Load document and write the CSV file
with temp_directory_with_files(TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png') as tempdir:
# Load document and export CSV file
w.open_document(path=tempdir / 'shapes.inselect')
w.export_csv(user_template=DWC)
self._test_csv()
# User should have been told about the export
self.assertTrue(mock_information.called)
expected = "Data for 5 boxes written to {0}"
expected = expected.format(tempdir / 'shapes.csv')
self.assertTrue(expected in mock_information.call_args[0])
def test_export_csv_with_template(self):
"Export metadata to CSV using a metadata template"
with temp_directory_with_files(TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png') as tempdir:
main([str(tempdir),
'--template={0}'.format(TESTDATA / 'test.inselect_template')])
# nose hooks up stdout to a file-like object
stdout = sys.stdout.getvalue()
self.assertIn('because there are validation problems', stdout)
self.assertIn('Box [1] [0001] lacks mandatory field [Taxonomy]', stdout)
self.assertIn('Box [1] [0001] lacks mandatory field [Location]', stdout)
self.assertIn(
'Could not parse value of [catalogNumber] [1] for box [1] [0001]',
stdout
)
csv = tempdir / 'shapes.csv'
self.assertFalse(csv.is_file())
def test_export_no_existing_csv(self, mock_information):
"User exported CSV"
w = self.window
# Load document and write the CSV file
with temp_directory_with_files(TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png') as tempdir:
# Load document and export CSV file
w.open_document(path=tempdir / 'shapes.inselect')
w.export_csv(user_template=DWC)
self._test_csv()
# User should have been told about the export
self.assertTrue(mock_information.called)
expected = "Data for 5 boxes written to {0}"
expected = expected.format(tempdir / 'shapes.csv')
self.assertTrue(expected in mock_information.call_args[0])
def test_modified_cleared(self):
"Alter document and clear"
with temp_directory_with_files(TESTDATA / 'test_segment.inselect',
TESTDATA / 'test_segment.png') as tempdir:
m = Model()
m.from_document(InselectDocument.load(tempdir / 'test_segment.inselect'))
# Alter data
mock_modified_changed = self._new_mock_modified_changed(m)
m.setData(m.index(0, 0), -90, RotationRole)
mock_modified_changed.assert_called_once_with()
self.assertTrue(m.is_modified)
# Clear
m.clear()
self.assertEqual(2, mock_modified_changed.call_count)
self.assertFalse(m.is_modified)
def test_save_crops_no_scanned_image(self, mock_warning):
"The user is informed that there is no scanned image"
with temp_directory_with_files(TESTDATA / 'shapes.inselect') as tempdir:
# Create thumbnail file
img = cv2.imread(str(TESTDATA.joinpath('shapes.png')))
cv2.imwrite(str(tempdir.joinpath('shapes_thumbnail.jpg')), img)
self.window.open_document(path=tempdir / 'shapes.inselect')
crops_dir = tempdir / 'shapes_crops'
self.assertFalse(crops_dir.is_dir())
self.window.save_crops(user_template=DWC)
expected = ('Unable to save crops because the original '
'full-resolution image file does not exist.')
self.assertTrue(expected in mock_warning.call_args[0])
# Crops should not have been written
self.assertFalse(crops_dir.is_dir())
def test_save_crops_overwrite(self, mock_warning, mock_information):
"The user is prompted to overwrite existing crops"
with temp_directory_with_files(TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png') as tempdir:
self.window.open_document(path=tempdir / 'shapes.inselect')
crops_dir = tempdir / 'shapes_crops'
crops_dir.mkdir()
self.assertTrue(crops_dir.is_dir())
# Answer with 'no'
with patch.object(QMessageBox, 'question',
return_value=QMessageBox.No) as mock_question:
self.window.save_crops(user_template=DWC)
expected = 'Overwrite the existing object images?'
self.assertTrue(expected in mock_question.call_args[0])
# Crops dir still contains no files
self.assertTrue(crops_dir.is_dir())
self.assertEqual(0, len(list(crops_dir.iterdir())))
# Confirmation of saving crops was not shown
self.assertFalse(mock_information.called)
# Answer with 'no'
with patch.object(QMessageBox, 'question',
return_value=QMessageBox.Yes) as mock_question:
self.run_async_operation(
partial(self.window.save_crops, user_template=DWC)
)
expected = 'Overwrite the existing object images?'
self.assertTrue(expected in mock_question.call_args[0])
# Five crops written
self.assertTrue(crops_dir.is_dir())
self.assertEqual(5, len(list(crops_dir.iterdir())))
# Confirmation of saving crops was shown
self.assertTrue(mock_information.called)
# User should not have been warned about missing scanned image
self.assertFalse(mock_warning.called)
def test_read_barcodes(self):
"Read barcodes"
with temp_directory_with_files(TESTDATA / 'barcodes.inselect',
TESTDATA / 'barcodes.jpg') as tempdir:
doc_path = tempdir.joinpath('barcodes.inselect')
# Doc should not have any catalog numbers
doc = InselectDocument.load(doc_path)
self.assertFalse(
any(v.get('fields', {}).get('catalogNumber') for v in doc.items)
)
main([str(tempdir), 'libdmtx'])
# Doc should not have expected catalog numbers
doc = InselectDocument.load(doc_path)
self.assertEqual(
['1681107', '1681110', '1681112'],
sorted(v['fields']['catalogNumber'] for v in doc.items)
)
def test_save(self):
"Save document"
with temp_directory_with_files(TESTDATA / 'test_segment.inselect',
TESTDATA / 'test_segment.png') as tempdir:
items = [{
'fields': {'type': u'インセクト'},
'rect': Rect(0.1, 0.2, 0.5, 0.5),
}]
doc_temp = tempdir / 'test_segment.inselect'
d = InselectDocument.load(doc_temp)
d.set_items(items)
d.save()
self.assertEqual(items, InselectDocument.load(doc_temp).items)
# Saved on time should be within last 2 seconds
now = datetime.now(pytz.timezone("UTC"))
saved_on = d.properties['Saved on']
self.assertLessEqual((now - saved_on).seconds, 2)