def post(self, request, *args, **kwargs):
feature = None
aoi = request.POST.get('aoi')
geometry = request.POST.get('geometry')
geojson = json.loads(geometry)
properties = geojson.get('properties')
aoi = AOI.objects.get(id=aoi)
job = getattr(aoi, 'job')
project = getattr(job, 'project')
template = properties.get('template') if properties else None
# TODO: handle exceptions
if template:
template = FeatureType.objects.get(id=template)
attrs = dict(aoi=aoi,
job=job,
project=project,
analyst=request.user,
template=template)
geometry = geojson.get('geometry')
attrs['the_geom'] = GEOSGeometry(json.dumps(geometry))
try:
response = Feature(**attrs)
response.full_clean()
response.save()
except ValidationError as e:
return HttpResponse(content=json.dumps(dict(errors=e.messages)),
mimetype="application/json",
status=400)
return HttpResponse([response], mimetype="application/json")
def add_feature(data, user):
feature = Feature()
feature.name = data[NAME]
feature.group = data[GROUP]
feature.updated_by = user
feature.save()
return feature
def post(self, request, *args, **kwargs):
feature = None
aoi = request.POST.get('aoi')
geometry = request.POST.get('geometry')
geojson = json.loads(geometry)
properties = geojson.get('properties')
aoi = AOI.objects.get(id=aoi)
job = getattr(aoi, 'job')
project = getattr(job, 'project')
template = properties.get('template') if properties else None
#TODO: handle exceptions
if template:
template = FeatureType.objects.get(id=template)
attrs = dict(aoi=aoi,
job=job,
project=project,
analyst=request.user,
template=template)
geometry = geojson.get('geometry')
attrs['the_geom'] = GEOSGeometry(json.dumps(geometry))
try:
response = Feature(**attrs)
response.full_clean()
response.save()
except ValidationError as e:
return HttpResponse(content=json.dumps(dict(errors=e.messages)), mimetype="application/json", status=400)
return HttpResponse([response], mimetype="application/json")
def vector_catalog_save_layer(tenant, layer, vector_layer, features):
connection.close()
connection.set_schema(tenant)
features = VECTOR_LAYERS[vector_layer]['geometries_by_id'](features)
with transaction.atomic():
union = GEOSGeometry('POINT EMPTY')
keys = None
for g, props in features:
if not keys:
keys = props.keys()
union = union.union(g)
g.transform(3857)
s = hashlib.sha1()
s.update(GeometryCollection(g).ewkb)
props['shaid'] = s.hexdigest()
f = Feature(layer=layer,
geometry=GeometryCollection(g),
properties=props)
f.save()
envelope = union.envelope.coords[0]
layer.bounds = envelope[2] + envelope[0]
layer.status = 0
layer.field_names = list(set(layer.field_names).union(set(keys)))
layer.schema['properties'] = {n: "str" for n in layer.field_names}
layer.save()
def post(self, request, *args, **kwargs):
feature = None
tpi = request.META.get('HTTP_TEMP_POINT_ID', "none")
aoi = request.POST.get('aoi')
geometry = request.POST.get('geometry')
geojson = json.loads(geometry)
properties = geojson.get('properties')
aoi = AOI.objects.get(id=aoi)
job = getattr(aoi, 'job')
project = getattr(job, 'project')
template = properties.get('template') if properties else None
# TODO: handle exceptions
if template:
template = FeatureType.objects.get(id=template)
attrs = dict(aoi=aoi,
job=job,
project=project,
analyst=request.user,
template=template)
geometry = geojson.get('geometry')
geom_obj = GEOSGeometry(json.dumps(geometry))
attrs['the_geom'] = geom_obj
county_list = Counties.objects.filter(
poly__contains=geom_obj.centroid.wkt)
county = None
if len(county_list):
county = str(county_list[0].name)
try:
feature = Feature(**attrs)
feature.full_clean()
if not feature.properties:
feature.properties = {}
if county:
feature.properties['county'] = county
feature.save()
except ValidationError as e:
response = HttpResponse(content=json.dumps(
dict(errors=e.messages)),
mimetype="application/json",
status=400)
response['Temp-Point-Id'] = tpi
return response
# This feels a bit ugly but it does get the GeoJSON into the response
feature_json = serializers.serialize('json', [
feature,
])
feature_list = json.loads(feature_json)
feature_list[0]['geojson'] = feature.geoJSON(True)
response = HttpResponse(json.dumps(feature_list),
mimetype="application/json")
response['Temp-Point-Id'] = tpi
return response
def save(self, json_str):
json_obj = json.loads(json_str)
feature_name = json_obj['feature']['feature_name']
feature_desc = json_obj['feature']['feature_description']
feature_save = Feature().fill(feature_name, feature_desc, '', '')
feature_save.save()
# scenarios = json_obj['feature']['scenarios']
# for sce in scenarios:
# self.CommonSaver.save_new_scenario(feature_save, sce)
return feature_save
def post(self, request, *args, **kwargs):
feature = None
tpi = request.META.get('HTTP_TEMP_POINT_ID', "none")
aoi = request.POST.get('aoi')
geometry = request.POST.get('geometry')
geojson = json.loads(geometry)
properties = geojson.get('properties')
aoi = AOI.objects.get(id=aoi)
job = getattr(aoi, 'job')
project = getattr(job, 'project')
template = properties.get('template') if properties else None
# TODO: handle exceptions
if template:
template = FeatureType.objects.get(id=template)
attrs = dict(aoi=aoi,
job=job,
project=project,
analyst=request.user,
template=template)
geometry = geojson.get('geometry')
geom_obj = GEOSGeometry(json.dumps(geometry))
attrs['the_geom'] = geom_obj
county_list = Counties.objects.filter(poly__contains=geom_obj.centroid.wkt)
county = None
if len(county_list):
county = str(county_list[0].name)
try:
feature = Feature(**attrs)
feature.full_clean()
if not feature.properties:
feature.properties = {}
if county:
feature.properties['county'] = county
feature.save()
except ValidationError as e:
response = HttpResponse(content=json.dumps(dict(errors=e.messages)), mimetype="application/json", status=400)
response['Temp-Point-Id'] = tpi
return response
# This feels a bit ugly but it does get the GeoJSON into the response
feature_json = serializers.serialize('json', [feature,])
feature_list = json.loads(feature_json)
feature_list[0]['geojson'] = feature.geoJSON(True)
response = HttpResponse(json.dumps(feature_list), mimetype="application/json")
response['Temp-Point-Id'] = tpi
return response
def test06_geometryfield(self):
"Testing GeometryField."
f1 = Feature(name='Point', geom=Point(1, 1))
f2 = Feature(name='LineString', geom=LineString((0, 0), (1, 1), (5, 5)))
f3 = Feature(name='Polygon', geom=Polygon(LinearRing((0, 0), (0, 5), (5, 5), (5, 0), (0, 0))))
f4 = Feature(name='GeometryCollection',
geom=GeometryCollection(Point(2, 2), LineString((0, 0), (2, 2)),
Polygon(LinearRing((0, 0), (0, 5), (5, 5), (5, 0), (0, 0)))))
f1.save()
f2.save()
f3.save()
f4.save()
f_1 = Feature.objects.get(name='Point')
self.assertEqual(True, isinstance(f_1.geom, Point))
self.assertEqual((1.0, 1.0), f_1.geom.tuple)
f_2 = Feature.objects.get(name='LineString')
self.assertEqual(True, isinstance(f_2.geom, LineString))
self.assertEqual(((0.0, 0.0), (1.0, 1.0), (5.0, 5.0)), f_2.geom.tuple)
f_3 = Feature.objects.get(name='Polygon')
self.assertEqual(True, isinstance(f_3.geom, Polygon))
f_4 = Feature.objects.get(name='GeometryCollection')
self.assertEqual(True, isinstance(f_4.geom, GeometryCollection))
self.assertEqual(f_3.geom, f_4.geom[2])
def test06_geometryfield(self):
"Testing GeometryField."
f1 = Feature(name='Point', geom=Point(1, 1))
f2 = Feature(name='LineString',
geom=LineString((0, 0), (1, 1), (5, 5)))
f3 = Feature(name='Polygon',
geom=Polygon(
LinearRing((0, 0), (0, 5), (5, 5), (5, 0), (0, 0))))
f4 = Feature(name='GeometryCollection',
geom=GeometryCollection(
Point(2, 2), LineString((0, 0), (2, 2)),
Polygon(
LinearRing((0, 0), (0, 5), (5, 5), (5, 0),
(0, 0)))))
f1.save()
f2.save()
f3.save()
f4.save()
f_1 = Feature.objects.get(name='Point')
self.assertEqual(True, isinstance(f_1.geom, Point))
self.assertEqual((1.0, 1.0), f_1.geom.tuple)
f_2 = Feature.objects.get(name='LineString')
self.assertEqual(True, isinstance(f_2.geom, LineString))
self.assertEqual(((0.0, 0.0), (1.0, 1.0), (5.0, 5.0)), f_2.geom.tuple)
f_3 = Feature.objects.get(name='Polygon')
self.assertEqual(True, isinstance(f_3.geom, Polygon))
f_4 = Feature.objects.get(name='GeometryCollection')
self.assertEqual(True, isinstance(f_4.geom, GeometryCollection))
self.assertEqual(f_3.geom, f_4.geom[2])
def post(self, request, *args, **kwargs):
feature = None
aoi = request.POST.get('aoi')
geometry = request.POST.get('geometry')
geojson = json.loads(geometry)
properties = geojson.get('properties')
aoi = AOI.objects.get(id=aoi)
job = getattr(aoi, 'job')
project = getattr(job, 'project')
template = properties.get('template') if properties else None
# TODO: handle exceptions
if template:
template = FeatureType.objects.get(id=template)
attrs = dict(aoi=aoi,
job=job,
project=project,
analyst=request.user,
template=template)
geometry = geojson.get('geometry')
attrs['the_geom'] = GEOSGeometry(json.dumps(geometry))
try:
feature = Feature(**attrs)
feature.full_clean()
feature.save()
except ValidationError as e:
return HttpResponse(content=json.dumps(dict(errors=e.messages)),
mimetype="application/json",
status=400)
# This feels a bit ugly but it does get the GeoJSON into the response
feature_json = serializers.serialize('json', [
feature,
])
feature_list = json.loads(feature_json)
feature_list[0]['geojson'] = feature.geoJSON(True)
return HttpResponse(json.dumps(feature_list),
mimetype="application/json")
def post(self, request, *args, **kwargs):
feature = None
aoi = request.POST.get('aoi')
geometry = request.POST.get('geometry')
geojson = json.loads(geometry)
properties = geojson.get('properties')
aoi = AOI.objects.get(id=aoi)
job = getattr(aoi, 'job')
project = getattr(job, 'project')
template = properties.get('template') if properties else None
# TODO: handle exceptions
if template:
template = FeatureType.objects.get(id=template)
attrs = dict(aoi=aoi,
job=job,
project=project,
analyst=request.user,
template=template)
geometry = geojson.get('geometry')
attrs['the_geom'] = GEOSGeometry(json.dumps(geometry))
try:
feature = Feature(**attrs)
feature.full_clean()
feature.save()
except ValidationError as e:
return HttpResponse(content=json.dumps(dict(errors=e.messages)), mimetype="application/json", status=400)
# This feels a bit ugly but it does get the GeoJSON into the response
feature_json = serializers.serialize('json', [feature,])
feature_list = json.loads(feature_json)
feature_list[0]['geojson'] = feature.geoJSON(True)
return HttpResponse(json.dumps(feature_list), mimetype="application/json")
def importexc(request):
if request.method == "GET":
form = ImportExcForm()
return render_to_response("importexc.html",
{'form' : form})
elif request.method == "POST":
form = ImportExcForm(request.POST,
request.FILES)
if form.is_valid():
excfile = request.FILES['import_exc']
character_encoding = request.POST['character_encoding']
excel_file = xlrd.open_workbook(file_contents=excfile.read())
filename=excel_file.sheet_names()
filename = filename[0]
dirpath = tempfile.mkdtemp()
sh = excel_file.sheet_by_index(0)
w = shapefile.Writer(shapefile.POINT)
w.field('Station','I')
w.field('Longitude', 'F')
w.field('Latitude', 'F')
w.field('Gravel_pc', 'F')
w.field('Sand_pc', 'F')
w.field('Mud_pc', 'F')
for rownum in range(sh.nrows):
if rownum == 0:
continue
else:
x_coord = sh.cell_value(rowx=rownum, colx=1)
y_coord = sh.cell_value(rowx=rownum, colx=2)
w.point(x_coord, y_coord)
w.record(Station=sh.cell_value(rowx=rownum, colx=0),Latitude=sh.cell_value(rowx=rownum, colx=2),
Longitude=sh.cell_value(rowx=rownum, colx=1),Gravel_pc=sh.cell_value(rowx=rownum, colx=3),
Sand_pc=sh.cell_value(rowx=rownum, colx=4),Mud_pc=sh.cell_value(rowx=rownum, colx=5))
w.save(os.path.join(dirpath,filename))
prj = open("%s.prj" % os.path.join(dirpath,filename), "w")
epsg = 'GEOGCS["WGS 84",DATUM["WGS_1984",SHEROID["WGS84",6378137,298.257223563]],PRIMEM["Greenwich",0],UNIT["degree",0.0174532925199433]]'
prj.write(epsg)
prj.close()
for item in os.listdir(dirpath):
if item.endswith(".shp"):
shapefileName = item
datasource = ogr.Open(os.path.join(dirpath, shapefileName))
layer = datasource.GetLayer(0)
layerDefinition = layer.GetLayerDefn()
srcSpatialRef = layer.GetSpatialRef()
geometryType = layer.GetLayerDefn().GetGeomType()
geometryName = utils.ogrTypeToGeometryName(geometryType)
shpfile = Shpfile(
filename=shapefileName,
srs_wkt=srcSpatialRef.ExportToWkt(),
geom_type=geometryName,
encoding=character_encoding
)
shpfile.save()
attributes = []
layerDef = layer.GetLayerDefn()
for i in range(layerDef.GetFieldCount()):
fieldDef = layerDef.GetFieldDefn(i)
attr = Attribute(
shpfile=shpfile,
name=fieldDef.GetName(),
type=fieldDef.GetType(),
width=fieldDef.GetWidth(),
)
attr.save()
attributes.append(attr)
for i in range(layer.GetFeatureCount()):
srcFeature = layer.GetFeature(i)
srcGeometry = srcFeature.GetGeometryRef()
geometry = GEOSGeometry(srcGeometry.ExportToWkt())
geometry = utils.wrapGEOSGeometry(geometry)
geometryField = utils.calcGeometryField(geometryName)
args = {}
args['shpfile'] = shpfile
args[geometryField] = geometry
feature = Feature(**args)
feature.save()
for attr in attributes:
success,result = utils.getOGRFeatureAttribute(
attr,
srcFeature,
character_encoding
)
if not success:
shutil.rmtree(dirpath)
shpfile.delete()
return result
attrValue = AttributeValue(
feature=feature,
attribute=attr,
value=result
)
attrValue.save()
shutil.rmtree(dirpath)
return HttpResponse("data imported!!")
def save_features(request, strain_id):
"""
seqid = line[0]
source = line[1]
type = line[2]
start = line[3]
end = line[4]
score = line[5]
strand = line[6] # "+", "-", or "."
phase = line[7]
attributes = line[8]
"""
theStrain = Strain.objects.get(pk = strain_id)
gffFile = request.FILES['gff_file']
gff = gffFile.read()
gff = gff.split('###')[0] # Throw away the sequence
gff = [x.split('\t') for x in gff.splitlines() if x[0] != '#'] # Throw away the header comments. Now we're left with just the meat of the file
contigMap = {}
for seqid, source, featureType, start, end, score, strand, phase, attributes in gff:
attributeParts = attributes.split(';')
attributeParts = [x.split('=') for x in attributeParts]
attributeParts = [(x[0], x[1].split(',')) for x in attributeParts]
attributeParts = [(x[0], [urllib.unquote(y) for y in x[1]]) for x in attributeParts]
attributeDict = {}
for key, value in attributeParts:
attributeDict[key] = value
if featureType == 'contig':
# We need to add this to the contigMap
try:
contigName = attributeDict['dbxref'][0].split(':')[-1]
except KeyError:
contigName = attributeDict['ID'][0]
contigMap[seqid] = contigName
elif featureType == 'chromosome':
contigMap[seqid] = seqid
else: # This is an actual feature line. It is assumed that we have already gone through all the contig lines
theContig = get_object_or_404(Contig, name=contigMap[seqid] ) # Get the Contig we're going to point to
feature = Feature()
feature.contig = theContig
try:
feature.feature_id = attributeDict['ID'][0]
except KeyError:
pass
else:
# This one has a name that might be found in the Reference table
if feature.feature_id.find(theStrain.name) != -1:
# Yup, it's one we need to link to the Reference table
referenceName = feature.feature_id.split("_")[0]
feature.reference = Reference.objects.get(feature_name = referenceName)
else: # just try and see if there is a reference with this unmodified feature_id
try:
feature.reference = Reference.objects.get(feature_name = feature.feature_id)
except ObjectDoesNotExist:
pass
if 'Parent' in attributeDict:
parent = get_object_or_404(Feature, feature_id = attributeDict['Parent'][0], contig = theContig)
feature.parent = parent
feature.feature_type = featureType
feature.start_coord = int(start)
feature.stop_coord = int(end)
feature.strand = strand
feature.createdDate = datetime.datetime.now()
feature.modifiedDate = datetime.datetime.now()
feature.save()
return HttpResponseRedirect('/strains/')