def to_csv(self, target_path, target_proj4=None, **kw):
try:
t = concatenate_tables(
_get_instance_for_csv(
x,
source_proj4 or LONGITUDE_LATITUDE_PROJ4,
target_proj4,
) for source_proj4, x in self.groupby('geometry_proj4'))
except ValueError:
t = self
excluded_column_names = []
unique_geometry_layers = t['geometry_layer'].unique()
unique_geometry_proj4s = t['geometry_proj4'].unique()
if len(unique_geometry_layers) == 1:
excluded_column_names.append('geometry_layer')
if len(unique_geometry_proj4s) == 1:
excluded_column_names.append('geometry_proj4')
geometry_proj4 = unique_geometry_proj4s[0]
if geometry_proj4 != LONGITUDE_LATITUDE_PROJ4:
open(replace_file_extension(target_path, '.proj4'),
'wt').write(geometry_proj4)
if len(t) == 0:
excluded_column_names.extend(
['geometry_layer', 'geometry_proj4', 'geometry_object'])
t['wkt'] = ''
t = t.drop(columns=excluded_column_names)
with TemporaryStorage() as storage:
temporary_path = join(storage.folder, 'geotable.csv')
super(GeoTable, t).to_csv(temporary_path, **kw)
if has_archive_extension(target_path):
compress(storage.folder, target_path)
else:
move_path(target_path, temporary_path)
def to_gdal(self,
target_path,
target_proj4=None,
driver_name='ESRI Shapefile'):
gdal_driver = gdal.GetDriverByName(driver_name)
if not gdal_driver:
raise GeoTableError('gdal driver missing (%s)' % driver_name)
try:
geometry_columns = _get_geometry_columns(self)
except GeoTableError as e:
table = self
else:
table = self.drop(columns=geometry_columns)
as_archive = has_archive_extension(target_path)
as_kmz = target_path.endswith('.kmz')
with TemporaryStorage() as storage:
if as_archive:
gdal_dataset_path = storage.folder
elif as_kmz:
gdal_dataset_path = join(storage.folder,
get_file_stem(target_path) + '.kml')
else:
gdal_dataset_path = target_path
gdal_dataset = gdal_driver.Create(gdal_dataset_path, 0, 0)
for layer_name, layer_t in table.groupby('geometry_layer'):
_prepare_gdal_layer(layer_t, gdal_dataset, target_proj4,
layer_name)
gdal_dataset.FlushCache()
if as_archive:
compress(storage.folder, target_path)
elif as_kmz:
compress_zip(storage.folder, target_path)
def test_resolve_source_folder_link(self, sandbox, target_folder):
source_folder = sandbox.source_folder_link_path
target_path = source_folder + self.extension
compress(source_folder, target_path, [
sandbox.external_folder])
target_folder = uncompress(target_path, target_folder)
assert_archive_contents(target_folder, sandbox)
def run():
target_folder = mkdtemp()
journal_names = sorted(set(
request.form.get('journal_names', '').splitlines()))
text_terms = sorted(set(
request.form.get('text_terms', '').splitlines()))
mesh_terms = sorted(set(
request.form.get('mesh_terms', '').splitlines()))
custom_expression = request.form.get('custom_expression', '')
try:
from_date = parse_date(request.form.get('from_date'))
to_date = parse_date(request.form.get('to_date'))
except (TypeError, ValueError):
from_date, to_date = None, None
date_interval_in_years = int(
request.form.get('date_interval_in_years'))
result_properties = run_script(
target_folder, journal_names, text_terms, mesh_terms,
custom_expression, from_date, to_date, date_interval_in_years)
timestamp = datetime.datetime.now().strftime('%Y%m%d-%M%H')
archive_nickname = '%s-%s' % (
timestamp, security.make_random_string(16))
archive_path = join(results_folder, archive_nickname + '.zip')
disk.compress(target_folder, archive_path)
source_image_path = join(target_folder, result_properties['image_name'])
target_image_path = join(results_folder, archive_nickname + '.png')
shutil.copy(source_image_path, target_image_path)
return render_template(
'response.html',
archive_name=basename(archive_path),
image_name=basename(target_image_path),
result_properties=result_properties)
def test_include_external_link(self, sandbox, target_folder):
source_folder = sandbox.source_folder
target_path = source_folder + self.extension
with raises(IOError):
compress(source_folder, target_path)
target_folder = uncompress(target_path, target_folder)
assert_archive_contents(target_folder, sandbox)
target_path = compress(source_folder, target_path,
[sandbox.external_folder])
target_folder = uncompress(target_path, target_folder)
assert_archive_contents(target_folder, sandbox)
def test_include_external_link(self, sandbox, target_folder):
source_folder = sandbox.source_folder
target_path = source_folder + self.extension
with raises(IOError):
compress(source_folder, target_path)
target_folder = uncompress(target_path, target_folder)
assert_archive_contents(target_folder, sandbox)
target_path = compress(source_folder, target_path, [
sandbox.external_folder])
target_folder = uncompress(target_path, target_folder)
assert_archive_contents(target_folder, sandbox)
def run():
target_folder = mkdtemp()
journal_names = load_terms(request.form.get('journal_names', ''))
author_names = load_terms(request.form.get('author_names', ''))
text_terms = load_terms(request.form.get('text_terms', ''))
mesh_terms = load_terms(request.form.get('mesh_terms', ''))
custom_expression = request.form.get('custom_expression', '')
try:
from_date = parse_date(request.form.get('from_date'))
to_date = parse_date(request.form.get('to_date'))
except (TypeError, ValueError):
from_date, to_date = None, None
if request.form.get('date_interval_in_years') is not None:
date_interval_in_years = int(
request.form.get('date_interval_in_years'))
else:
date_interval_in_years = None
result_properties = run_script(
target_folder, journal_names, text_terms, mesh_terms,
custom_expression, author_names, from_date,
to_date, date_interval_in_years)
timestamp = datetime.datetime.now().strftime('%Y%m%d-%M%H')
archive_nickname = '%s-%s' % (timestamp, make_random_string(16))
archive_path = join(results_folder, archive_nickname + '.zip')
compress(target_folder, archive_path)
if 'image_name' in result_properties:
source_image_path = join(
target_folder, result_properties['image_name'])
target_image_path = join(results_folder, archive_nickname + '.png')
shutil.copy(source_image_path, target_image_path)
return render_template(
'response.html',
archive_name=basename(archive_path),
image_name=basename(target_image_path),
result_properties=result_properties)
else:
return render_template(
'author_response.html',
archive_name=basename(archive_path),
name_count_packs=zip(
result_properties['author_names'],
result_properties['article_counts']))
def post(self):
try:
server_token = expect_variable('server_token')
except KeyError as e:
self.set_status(401)
return self.write({})
server_url = expect_variable('server_url', 'https://crosscompute.com')
notebook_id = expect_variable('notebook_id', '')
notebook_path = self.get_argument('notebook_path')
try:
tool_definition = IPythonNotebookTool.prepare_tool_definition(
notebook_path, with_debugging=False)
except CrossComputeError as e:
self.set_status(400)
return self.write({'text': str(e)})
archive_path = compress(tool_definition['configuration_folder'])
response = requests.post(
server_url + '/tools.json',
headers={
'Authorization': 'Bearer ' + server_token,
},
data={
'notebook_id': notebook_id,
'notebook_path': notebook_path,
'environment_level': expect_variable('environment_level', 0),
'processor_level': expect_variable('processor_level', 0),
'memory_level': expect_variable('memory_level', 0),
} if notebook_id else {},
files={
'tool_folder': open(archive_path, 'rb'),
})
status_code = response.status_code
if status_code != 200:
self.set_status(status_code)
return self.write({})
try:
d = response.json()
tool_url = d['tool_url']
except Exception:
self.set_status(503)
return self.write({})
self.write({'tool_url': server_url + tool_url})
def test_resolve_source_folder_link(self, sandbox, target_folder):
source_folder = sandbox.source_folder_link_path
target_path = source_folder + self.extension
compress(source_folder, target_path, [sandbox.external_folder])
target_folder = uncompress(target_path, target_folder)
assert_archive_contents(target_folder, sandbox)
def test_resolve_source_folder_link(self, sandbox, tmpdir):
source_folder = sandbox.source_folder_link_path
target_path = compress(source_folder, source_folder + self.extension)
target_folder = uncompress(target_path, str(tmpdir))
assert_contents(target_folder, sandbox)
def test_include_external_link(self, sandbox, tmpdir):
source_folder = sandbox.source_folder
target_path = compress(source_folder, source_folder + self.extension)
target_folder = uncompress(target_path, str(tmpdir))
assert_contents(target_folder, sandbox)