def fesomMeshQueryXY(dbcon, fesominfo, geoWKT):
"""Return fesom mesh grid as [lon, lat, depth]"""
pnt=[]
pnt_id=[]
for entry in fesomMeshQuery(dbcon, fesominfo, geoWKT):
tmp=shpextract(entry)
xy = np.array([[tmp.x, tmp.y]])
pnt_id.append(entry._row[1])
tmp_id = np.array(entry._row[1])
# tri_temp =
if len(pnt)==0:
pnt=xy
# pnt_id2= tmp_id
else:
pnt = np.concatenate((pnt,xy))
# pnt_id2 = np.concatenate((pnt_id2,tmp_id))
# pnt_id2.extend(tmp_id)
return pnt, pnt_id
def queryMonthlyArgo(dbcon, geoWKT, tstart, tend):
"""Query the database for lists of monthly Argo profiles within a certain polygon and time span"""
out = {}
for entry in argoQuery(dbcon,
geoWKT=geoWKT,
tspan=[tstart, tend],
tsort=True):
epoch = (entry.tlocation.year, entry.tlocation.month)
pnt = shpextract(entry)
tmpdict = {
"uri": entry.uri,
"iprof": entry.iprof,
"lonlat": (pnt.x, pnt.y)
}
if not epoch in out:
out[epoch] = [tmpdict]
else:
out[epoch].append(tmpdict)
return out
def fesomMeshQueryWKB(dbcon, fesominfo, geoWKT):
"""Query the database positions of OBP points"""
return [(shpextract(x)) for x in fesomMeshQueryXY(dbcon, fesominfo, geoWKT)]
def awipiesWKB(dbcon, tspan, geoWKT=False):
"""Query the database positions of OBP points"""
return [(shpextract(x)) for x in awipiesQuery(dbcon,tspan)]
def exportQuery(qryresult,
outputfile,
layer=None,
driver="SQLITE",
packFiles=False,
striproot=None):
"""Export a query without a geometry column, and possibly pack corresponding files"""
if "geom" in qryresult.keys():
useGeoPandas = True
else:
useGeoPandas = False
if useGeoPandas and driver not in ["GPKG"]:
raise RunTimeError("no geometry found in the specified query")
if useGeoPandas:
df = gpd.GeoDataFrame()
df["geometry"] = None
else:
df = pd.DataFrame()
#initialize columns
for ky in (ky for ky in qryresult.keys() if ky not in ["geom", "id"]):
df[ky] = None
if packFiles:
#open a tgz archive
farchive = os.path.splitext(outputfile)[0] + "_files.tgz"
farchivetmp = os.path.splitext(outputfile)[0] + "_files.tar"
if striproot:
mmap = MirrorMap(striproot, farchive + ":/")
#open/reopen archive
if os.path.exists(farchive):
#unzip to a temporary file
farchivetmp = os.path.splitext(outputfile)[0] + "_files.tar"
with gzip.open(farchive, 'rb') as gzid:
with open(farchivetmp, 'wb') as fid:
shutil.copyfileobj(gzid, fid)
tarar = tarfile.open(farchivetmp, mode='a')
else:
tarar = tarfile.open(farchive, mode='w:gz')
else:
tarar = None
#add new rows
for entry in qryresult:
entrymod = {}
for ky, val in entry.items():
if useGeoPandas and ky == "geom":
val = shpextract(entry)
ky = "geometry"
elif ky == "id":
val = None
elif ky == "data":
#convert to json
val = json.dumps(val)
elif ky == "uri" and packFiles:
#modify the uri and add file in the archive
if not striproot:
#try stripping of everything before and including 'geoslurp' from the path
striproot = re.search("^.*/geoslurp/", val).group(0)
mmap = MirrorMap(striproot, farchive + ":/")
uriorig = val
val = mmap.apply(val)
#create a new tarfile member if needed
try:
basef = mmap.strip(uriorig)
tinfo = tarar.getmember(basef)
except KeyError:
#create a new member
tarar.add(name=uriorig, arcname=basef)
if val:
entrymod[ky] = val
df = df.append(entrymod, ignore_index=True)
if packFiles:
tarar.close()
if os.path.exists(farchivetmp):
#rezip the tar archive and clean up
with gzip.open(farchive, 'wb') as gzid:
with open(farchivetmp, 'rb') as fid:
shutil.copyfileobj(fid, gzid)
os.remove(farchivetmp)
#export to file
if useGeoPandas:
df.to_file(outputfile, layer=layer, driver=driver)
else:
if driver == "SQLITE":
writeToSQLite(outputfile, df, layer)
else:
raise InputError("Don't know how to interpret output driver" %
driver)