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Posted to commits@sdap.apache.org by sk...@apache.org on 2022/05/24 21:17:34 UTC
[incubator-sdap-nexus] branch SDAP-387 created (now a951945)
This is an automated email from the ASF dual-hosted git repository.
skperez pushed a change to branch SDAP-387
in repository https://gitbox.apache.org/repos/asf/incubator-sdap-nexus.git
at a951945 Remove todos, add newline to end of file
This branch includes the following new commits:
new 86d8e84 NetCDF matchup output
new 54e0532 Updated netCDF builder code to look at new param names
new 0309e6c Integrated Vardis feedback
new a951945 Remove todos, add newline to end of file
The 4 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "add" were already present in the repository and have only
been added to this reference.
[incubator-sdap-nexus] 03/04: Integrated Vardis feedback
Posted by sk...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
skperez pushed a commit to branch SDAP-387
in repository https://gitbox.apache.org/repos/asf/incubator-sdap-nexus.git
commit 0309e6cd48c8411732da1ad876b5a68dc051145b
Author: skorper <st...@gmail.com>
AuthorDate: Mon May 16 17:56:23 2022 -0700
Integrated Vardis feedback
---
.../webservice/algorithms/doms/BaseDomsHandler.py | 38 +++++++++++-----------
1 file changed, 19 insertions(+), 19 deletions(-)
diff --git a/analysis/webservice/algorithms/doms/BaseDomsHandler.py b/analysis/webservice/algorithms/doms/BaseDomsHandler.py
index 3aafa9b..0423d30 100644
--- a/analysis/webservice/algorithms/doms/BaseDomsHandler.py
+++ b/analysis/webservice/algorithms/doms/BaseDomsHandler.py
@@ -259,11 +259,11 @@ class DomsNetCDFFormatter:
@staticmethod
def create(executionId, results, params, details):
- t = tempfile.mkstemp(prefix="doms_", suffix=".nc")
+ t = tempfile.mkstemp(prefix="cdms_", suffix=".nc")
tempFileName = t[1]
dataset = Dataset(tempFileName, "w", format="NETCDF4")
- dataset.DOMS_matchID = executionId
+ dataset.CDMS_matchID = executionId
DomsNetCDFFormatter.__addNetCDFConstants(dataset)
dataset.date_modified = datetime.utcnow().replace(tzinfo=UTC).strftime(ISO_8601)
@@ -271,9 +271,9 @@ class DomsNetCDFFormatter:
dataset.time_coverage_start = params["startTime"].strftime(ISO_8601)
dataset.time_coverage_end = params["endTime"].strftime(ISO_8601)
dataset.time_coverage_resolution = "point"
- dataset.DOMS_match_up = params["matchup"]
- dataset.DOMS_num_matchup_matched = details["numInSituMatched"]
- dataset.DOMS_num_primary_matched = details["numGriddedMatched"]
+ dataset.CDMS_secondary = params["matchup"]
+ dataset.CDMS_num_matchup_matched = details["numInSituMatched"]
+ dataset.CDMS_num_primary_matched = details["numGriddedMatched"]
bbox = geo.BoundingBox(asString=params["bbox"])
dataset.geospatial_lat_max = bbox.north
@@ -287,22 +287,22 @@ class DomsNetCDFFormatter:
dataset.geospatial_vertical_units = "m"
dataset.geospatial_vertical_positive = "down"
- dataset.DOMS_TimeWindow = params["timeTolerance"] / 60 / 60
- dataset.DOMS_TimeWindow_Units = "hours"
- dataset.DOMS_SearchRadius = float(params["radiusTolerance"])
- dataset.DOMS_SearchRadius_Units = "m"
+ dataset.CDMS_TimeWindow = params["timeTolerance"] / 60 / 60
+ dataset.CDMS_TimeWindow_Units = "hours"
+ dataset.CDMS_SearchRadius = float(params["radiusTolerance"])
+ dataset.CDMS_SearchRadius_Units = "m"
dataset.URI_Matchup = "https://doms.jpl.nasa.gov/domsresults?id=" + executionId + "&output=NETCDF"
- dataset.DOMS_ParameterPrimary = params["parameter"] if "parameter" in params else ""
- dataset.DOMS_platforms = params["platforms"]
- dataset.DOMS_primary = params["primary"]
- dataset.DOMS_time_to_complete = details["timeToComplete"]
- dataset.DOMS_time_to_complete_units = "seconds"
+ dataset.CDMS_ParameterPrimary = params["parameter"] if "parameter" in params else ""
+ dataset.CDMS_platforms = params["platforms"]
+ dataset.CDMS_primary = params["primary"]
+ dataset.CDMS_time_to_complete = details["timeToComplete"]
+ dataset.CDMS_time_to_complete_units = "seconds"
insituDatasets = params["matchup"]
insituLinks = set()
for insitu in insituDatasets:
insituLinks.add(config.METADATA_LINKS[insitu])
- dataset.DOMS_DatasetMetadata = ', '.join(insituLinks)
+ dataset.CDMS_DatasetMetadata = ', '.join(insituLinks)
platforms = set()
for primaryValue in results:
@@ -339,15 +339,15 @@ class DomsNetCDFFormatter:
@staticmethod
def __addNetCDFConstants(dataset):
dataset.product_version = "1.0"
- dataset.Conventions = "CF-1.6, ACDD-1.3"
- dataset.title = "DOMS satellite-insitu machup output file"
- dataset.history = "Processing_Version = V1.0, Software_Name = DOMS, Software_Version = 1.03"
+ dataset.Conventions = "CF-1.8, ACDD-1.3"
+ dataset.title = "CDMS satellite-insitu machup output file"
+ dataset.history = "Processing_Version = V1.0, Software_Name = CDMS, Software_Version = 1.03"
dataset.institution = "JPL, FSU, NCAR, Saildrone"
dataset.source = "doms.jpl.nasa.gov"
dataset.standard_name_vocabulary = "CF Standard Name Table v27", "BODC controlled vocabulary"
dataset.cdm_data_type = "Point/Profile, Swath/Grid"
dataset.processing_level = "4"
- dataset.project = "Distributed Oceanographic Matchup System (DOMS)"
+ dataset.project = "Cloud-Based Data Matchup Service (CDMS)"
dataset.keywords_vocabulary = "NASA Global Change Master Directory (GCMD) Science Keywords"
dataset.keywords = "SATELLITES, OCEAN PLATFORMS, SHIPS, BUOYS, MOORINGS, AUVS, ROV, NASA/JPL/PODAAC, " \
"FSU/COAPS, UCAR/NCAR, SALINITY, SEA SURFACE TEMPERATURE, SURFACE WINDS"
[incubator-sdap-nexus] 04/04: Remove todos, add newline to end of file
Posted by sk...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
skperez pushed a commit to branch SDAP-387
in repository https://gitbox.apache.org/repos/asf/incubator-sdap-nexus.git
commit a951945233f39fe0b6bfdca416479b45554ab31c
Author: skorper <st...@gmail.com>
AuthorDate: Tue May 24 14:17:25 2022 -0700
Remove todos, add newline to end of file
---
analysis/webservice/algorithms/doms/BaseDomsHandler.py | 4 +---
.../webservice/nexus_tornado/request/renderers/NexusNETCDFRenderer.py | 2 +-
2 files changed, 2 insertions(+), 4 deletions(-)
diff --git a/analysis/webservice/algorithms/doms/BaseDomsHandler.py b/analysis/webservice/algorithms/doms/BaseDomsHandler.py
index 0423d30..bb32146 100644
--- a/analysis/webservice/algorithms/doms/BaseDomsHandler.py
+++ b/analysis/webservice/algorithms/doms/BaseDomsHandler.py
@@ -390,7 +390,7 @@ class DomsNetCDFFormatter:
class DomsNetCDFValueWriter:
- def __init__(self, group, matchup_parameter): # TODO how do we want this matchup param to be used?
+ def __init__(self, group, matchup_parameter):
group.createDimension("dim", size=None)
self.group = group
@@ -457,8 +457,6 @@ class DomsNetCDFValueWriter:
self.__enrichDepth(depthVar, self.__calcMin(self.depth), max(self.depth))
depthVar[:] = self.depth
- print(self.data_map)
-
for variable_name, data in self.data_map.items():
# Create a variable for each data point
data_variable = self.group.createVariable(variable_name, 'f4', ('dim',), fill_value=-32767.0)
diff --git a/analysis/webservice/nexus_tornado/request/renderers/NexusNETCDFRenderer.py b/analysis/webservice/nexus_tornado/request/renderers/NexusNETCDFRenderer.py
index b2236f6..2476419 100644
--- a/analysis/webservice/nexus_tornado/request/renderers/NexusNETCDFRenderer.py
+++ b/analysis/webservice/nexus_tornado/request/renderers/NexusNETCDFRenderer.py
@@ -14,4 +14,4 @@ class NexusNETCDFRenderer(object):
tornado_handler.write(result.toNetCDF())
except:
traceback.print_exc(file=sys.stdout)
- raise NexusProcessingException(reason="Unable to convert results to NetCDF.")
\ No newline at end of file
+ raise NexusProcessingException(reason="Unable to convert results to NetCDF.")
[incubator-sdap-nexus] 02/04: Updated netCDF builder code to look at new param names
Posted by sk...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
skperez pushed a commit to branch SDAP-387
in repository https://gitbox.apache.org/repos/asf/incubator-sdap-nexus.git
commit 54e05328afdc4b7cee272df56b7f251eef17ca7d
Author: skorper <st...@gmail.com>
AuthorDate: Mon May 16 09:36:35 2022 -0700
Updated netCDF builder code to look at new param names
---
analysis/webservice/algorithms/doms/BaseDomsHandler.py | 16 ++++++++++------
1 file changed, 10 insertions(+), 6 deletions(-)
diff --git a/analysis/webservice/algorithms/doms/BaseDomsHandler.py b/analysis/webservice/algorithms/doms/BaseDomsHandler.py
index 8e6fba4..3aafa9b 100644
--- a/analysis/webservice/algorithms/doms/BaseDomsHandler.py
+++ b/analysis/webservice/algorithms/doms/BaseDomsHandler.py
@@ -408,12 +408,12 @@ class DomsNetCDFValueWriter:
Populate DomsNetCDFValueWriter fields from matchup results dict
"""
non_data_fields = [
- 'id', 'x', 'y',
+ 'id', 'lon', 'lat',
'source', 'device',
'platform', 'time', 'matches'
]
- self.lat.append(result_item.get('y', None))
- self.lon.append(result_item.get('x', None))
+ self.lat.append(result_item.get('lon', None))
+ self.lon.append(result_item.get('lat', None))
self.time.append(time.mktime(result_item.get('time').timetuple()))
# All other variables are assumed to be science variables.
@@ -462,8 +462,14 @@ class DomsNetCDFValueWriter:
for variable_name, data in self.data_map.items():
# Create a variable for each data point
data_variable = self.group.createVariable(variable_name, 'f4', ('dim',), fill_value=-32767.0)
- self.__enrichVariable(data_variable, min(data), max(data), has_depth=self.depth)
+ # Find min/max for data variables. It is possible for 'None' to
+ # be in this list, so filter those out when doing the calculation.
+ min_data = min(val for val in data if val is not None)
+ max_data = max(val for val in data if val is not None)
+ self.__enrichVariable(data_variable, min_data, max_data, has_depth=self.depth)
data_variable[:] = data
+ data_variable.long_name = variable_name
+ data_variable.standard_name = variable_name
#
# Lists may include 'None" values, to calc min these must be filtered out
@@ -479,8 +485,6 @@ class DomsNetCDFValueWriter:
if not has_depth:
coordinates = ['lat', 'lon', 'time']
- var.long_name = var
- var.standard_name = var
var.units = 'UNKNOWN' # TODO populate this field once this metadata is in place
var.valid_min = var_min
var.valid_max = var_max
[incubator-sdap-nexus] 01/04: NetCDF matchup output
Posted by sk...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
skperez pushed a commit to branch SDAP-387
in repository https://gitbox.apache.org/repos/asf/incubator-sdap-nexus.git
commit 86d8e84fc548138d2eb490a3182a69301be27c6d
Author: skorper <st...@gmail.com>
AuthorDate: Fri Apr 29 09:00:42 2022 -0700
NetCDF matchup output
---
.../tests/algorithms/test_base_doms_handler.py | 2359 +++++++++++++++++++-
.../webservice/algorithms/doms/BaseDomsHandler.py | 222 +-
.../request/renderers/NexusNETCDFRenderer.py | 2 +-
3 files changed, 2421 insertions(+), 162 deletions(-)
diff --git a/analysis/tests/algorithms/test_base_doms_handler.py b/analysis/tests/algorithms/test_base_doms_handler.py
index dbb579f..87e6847 100644
--- a/analysis/tests/algorithms/test_base_doms_handler.py
+++ b/analysis/tests/algorithms/test_base_doms_handler.py
@@ -1,15 +1,14 @@
import datetime
import uuid
import csv
-from webservice.algorithms.doms.BaseDomsHandler import DomsCSVFormatter
+import pytest
+from netCDF4 import Dataset
+import io
+from webservice.algorithms.doms.BaseDomsHandler import DomsCSVFormatter, DomsNetCDFFormatter
-def test_csv():
- """
- Test that CSV is constructed properly given result, params, and
- details.
- """
- test_execution_id = str(uuid.uuid4())
+@pytest.fixture()
+def test_input():
results = [
{
"id": "9c08c026-eff7-30a7-ab1e-413a64f507ff[[0 0 3]]",
@@ -81,6 +80,18 @@ def test_csv():
'timeToComplete': 26
}
+ yield results, params, details
+
+
+def test_csv(test_input):
+ """
+ Test that CSV is constructed properly given result, params, and
+ details.
+ """
+ test_execution_id = str(uuid.uuid4())
+
+ results, params, details = test_input
+
csv_formatter = DomsCSVFormatter()
csv_result = csv_formatter.create(
executionId=test_execution_id,
@@ -111,3 +122,2337 @@ def test_csv():
if 'id' == row[0]:
header = row
+
+
+def test_netcdf(test_input):
+ """
+ Test that the /domsresults endpoint results in a properly
+ structured NetCDF file.
+ """
+ test_execution_id = str(uuid.uuid4())
+
+ results, params, details = test_input
+
+ nc_formatter = DomsNetCDFFormatter()
+ nc_result = nc_formatter.create(
+ executionId=test_execution_id,
+ results=results,
+ params=params,
+ details=details
+ )
+
+ ds = Dataset('test', memory=nc_result)
+
+ # with open('small_matchup.nc', 'wb') as f:
+ # f.write(nc_result)
+
+ assert 'PrimaryData' in ds.groups
+ assert 'SecondaryData' in ds.groups
+
+ assert 'sst_anomaly' in ds.groups['PrimaryData'].variables
+ assert 'analysis_error' in ds.groups['PrimaryData'].variables
+ assert 'analysed_sst' in ds.groups['PrimaryData'].variables
+
+ assert 'sea_water_temperature' in ds.groups['SecondaryData'].variables
+
+def test_netcdf_big(test_input): # TODO remove this. jUst for testing.
+ test_execution_id = str(uuid.uuid4())
+
+ results, params, details = test_input
+
+ results = big_results
+
+ nc_formatter = DomsNetCDFFormatter()
+ nc_result = nc_formatter.create(
+ executionId=test_execution_id,
+ results=results,
+ params=params,
+ details=details
+ )
+
+ ds = Dataset('test', memory=nc_result)
+
+
+
+big_results = [
+ {
+ 'id': '163a81c4-bbf1-3ba4-85c9-e1ce645dcb9a[[0, 2, 17]]',
+ 'lon': -123.125,
+ 'lat': 15.625,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 24, 9, 0),
+ 'sea_surface_foundation_temperature': 27.90301513671875,
+ 'matches': [{
+ 'id': 'Buoys_20171003(7172)',
+ 'lon': -123.119,
+ 'lat': 15.629,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 10, 3, 10, 0),
+ 'sea_water_temperature': 27.9
+ }]
+ }, {
+ 'id': 'd75bd15c-967e-33a4-8485-d3b466f1709d[[0, 23, 13]]',
+ 'lon': -139.125,
+ 'lat': 20.875,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 28, 9, 0),
+ 'sea_surface_foundation_temperature': 25.00201416015625,
+ 'matches': [{
+ 'id': 'argo_spurs_20171006(1250)',
+ 'lon': -139.129,
+ 'lat': 20.867,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting subsurface profiling float',
+ 'time': datetime.datetime(2017, 10, 5, 23, 19, 47),
+ 'sea_water_salinity': 34.97,
+ 'sea_water_salinity_depth': 4.47223342927,
+ 'sea_water_temperature': 24.78,
+ 'sea_water_temperature_depth': 4.47223342927
+ }]
+ }, {
+ 'id': '7deab803-ca0e-3887-a4f7-09081c35d9fa[[0, 23, 4]]',
+ 'lon': -148.875,
+ 'lat': 13.375,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 26, 9, 0),
+ 'sea_surface_foundation_temperature': 28.147003173828125,
+ 'matches': [{
+ 'id': 'Buoys_20170918(1164)',
+ 'lon': -148.875,
+ 'lat': 13.376,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 9, 18, 7, 0),
+ 'sea_water_temperature': 27.9
+ }]
+ }, {
+ 'id': 'e5f90fe2-0de1-323e-9bed-a26011d52cbf[[0, 4, 14]]',
+ 'lon': -146.375,
+ 'lat': 23.625,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 29, 9, 0),
+ 'sea_surface_foundation_temperature': 25.4849853515625,
+ 'matches': [{
+ 'id': 'Buoys_20170903(742)',
+ 'lon': -146.378,
+ 'lat': 23.617,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 9, 3, 6, 0),
+ 'sea_water_temperature': 25.6
+ }]
+ }, {
+ 'id': 'ba867010-507b-3c62-8893-140ae07da30b[[0, 18, 24]]',
+ 'lon': -143.875,
+ 'lat': 12.125,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 27, 9, 0),
+ 'sea_surface_foundation_temperature': 28.625,
+ 'matches': [{
+ 'id': 'Buoys_20170829(1970)',
+ 'lon': -143.879,
+ 'lat': 12.126,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 8, 29, 6, 0),
+ 'sea_water_temperature': 28.8
+ }]
+ }, {
+ 'id': 'eccb9006-463b-3554-aa25-0de14224e0c4[[0, 23, 4]]',
+ 'lon': -148.875,
+ 'lat': 13.375,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 25, 9, 0),
+ 'sea_surface_foundation_temperature': 28.1669921875,
+ 'matches': [{
+ 'id': 'Buoys_20170918(1164)',
+ 'lon': -148.875,
+ 'lat': 13.376,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 9, 18, 7, 0),
+ 'sea_water_temperature': 27.9
+ }]
+ }, {
+ 'id': '7deab803-ca0e-3887-a4f7-09081c35d9fa[[0, 13, 12]]',
+ 'lon': -146.875,
+ 'lat': 10.875,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 26, 9, 0),
+ 'sea_surface_foundation_temperature': 28.441009521484375,
+ 'matches': [{
+ 'id': 'Buoys_20171003(1210)',
+ 'lon': -146.874,
+ 'lat': 10.871,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 10, 3, 7, 0),
+ 'sea_water_temperature': 28.6
+ }]
+ }, {
+ 'id': 'f790a842-600a-3225-810d-1ac2c47d2945[[0, 8, 25]]',
+ 'lon': -151.125,
+ 'lat': 17.125,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 24, 9, 0),
+ 'sea_surface_foundation_temperature': 27.3330078125,
+ 'matches': [{
+ 'id': 'Buoys_20171022(485)',
+ 'lon': -151.13,
+ 'lat': 17.127,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 10, 22, 6, 50),
+ 'sea_water_temperature': 26.4
+ }]
+ }, {
+ 'id': 'c9cb10ab-ebae-3c8b-a498-d7aef5cf53ed[[0, 2, 23]]',
+ 'lon': -144.125,
+ 'lat': 15.625,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 29, 9, 0),
+ 'sea_surface_foundation_temperature': 27.798004150390625,
+ 'matches': [{
+ 'id': 'Buoys_20171005(7542)',
+ 'lon': -144.13,
+ 'lat': 15.632,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 10, 5, 16, 0),
+ 'sea_water_temperature': 27.7
+ }]
+ }, {
+ 'id': '1bfa3b4a-a310-3661-b1d9-2648c0d61a9a[[0, 5, 8]]',
+ 'lon': -147.875,
+ 'lat': 16.375,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 26, 9, 0),
+ 'sea_surface_foundation_temperature': 27.47100830078125,
+ 'matches': [{
+ 'id': 'Buoys_20171025(7730)',
+ 'lon': -147.881,
+ 'lat': 16.375,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 10, 25, 17, 0),
+ 'sea_water_temperature': 27.1
+ }]
+ }, {
+ 'id': '47693152-084f-3a92-b74c-3cef41a2cc36[[0, 14, 7]]',
+ 'lon': -140.625,
+ 'lat': 11.125,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 26, 9, 0),
+ 'sea_surface_foundation_temperature': 28.592987060546875,
+ 'matches': [{
+ 'id': 'Buoys_20171015(1659)',
+ 'lon': -140.626,
+ 'lat': 11.127,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 10, 15, 3, 0),
+ 'sea_water_temperature': 28.3
+ }]
+ }, {
+ 'id': 'c63f3a16-42ac-3185-b8d2-25e26bf9401c[[0, 23, 13]]',
+ 'lon': -139.125,
+ 'lat': 20.875,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 25, 9, 0),
+ 'sea_surface_foundation_temperature': 25.2760009765625,
+ 'matches': [{
+ 'id': 'argo_spurs_20171006(1250)',
+ 'lon': -139.129,
+ 'lat': 20.867,
+ 'source': 'spurs2',
+ 'device': 'CTD',
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+ 'matches': [{
+ 'id': 'Buoys_20170920(7966)',
+ 'lon': -148.131,
+ 'lat': 20.124,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 9, 20, 12, 0),
+ 'sea_water_temperature': 26.3
+ }]
+ }, {
+ 'id': 'eccb9006-463b-3554-aa25-0de14224e0c4[[0, 16, 19]]',
+ 'lon': -145.125,
+ 'lat': 11.625,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 25, 9, 0),
+ 'sea_surface_foundation_temperature': 28.891998291015625,
+ 'matches': [{
+ 'id': 'Buoys_20171009(942)',
+ 'lon': -145.129,
+ 'lat': 11.629,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 10, 9, 6, 0),
+ 'sea_water_temperature': 28.4
+ }]
+ }, {
+ 'id': 'c63f3a16-42ac-3185-b8d2-25e26bf9401c[[0, 22, 21]]',
+ 'lon': -137.125,
+ 'lat': 20.625,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 25, 9, 0),
+ 'sea_surface_foundation_temperature': 25.13299560546875,
+ 'matches': [{
+ 'id': 'Buoys_20170908(558)',
+ 'lon': -137.13,
+ 'lat': 20.632,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 9, 8, 10, 50),
+ 'sea_water_temperature': 25.0
+ }]
+ }, {
+ 'id': '575795cc-14e5-3ee3-a53d-89edf8f5d018[[0, 13, 16]]',
+ 'lon': -138.375,
+ 'lat': 10.875,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 27, 9, 0),
+ 'sea_surface_foundation_temperature': 28.272003173828125,
+ 'matches': [{
+ 'id': 'Buoys_20170930(1889)',
+ 'lon': -138.367,
+ 'lat': 10.872,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 9, 30, 15, 0),
+ 'sea_water_temperature': 28.1
+ }]
+ }, {
+ 'id': 'eccb9006-463b-3554-aa25-0de14224e0c4[[0, 13, 8]]',
+ 'lon': -147.875,
+ 'lat': 10.875,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 25, 9, 0),
+ 'sea_surface_foundation_temperature': 28.447998046875,
+ 'matches': [{
+ 'id': 'Buoys_20171013(1175)',
+ 'lon': -147.87,
+ 'lat': 10.879,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 10, 13, 5, 0),
+ 'sea_water_temperature': 28.4
+ }]
+ }, {
+ 'id': '8532e3e5-3fdd-304f-a9d7-1382d9658b36[[0, 15, 16]]',
+ 'lon': -145.875,
+ 'lat': 11.375,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 29, 9, 0),
+ 'sea_surface_foundation_temperature': 28.597015380859375,
+ 'matches': [{
+ 'id': 'Buoys_20171010(715)',
+ 'lon': -145.868,
+ 'lat': 11.378,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 10, 10, 16, 0),
+ 'sea_water_temperature': 28.2
+ }]
+ }, {
+ 'id': '35263cc2-f801-3954-b769-38f150ae09bf[[0, 22, 21]]',
+ 'lon': -137.125,
+ 'lat': 20.625,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 27, 9, 0),
+ 'sea_surface_foundation_temperature': 24.865997314453125,
+ 'matches': [{
+ 'id': 'Buoys_20170908(558)',
+ 'lon': -137.13,
+ 'lat': 20.632,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 9, 8, 10, 50),
+ 'sea_water_temperature': 25.0
+ }]
+ }, {
+ 'id': 'd14b58a0-ed21-3ed9-a95e-2915ffc93676[[0, 8, 25]]',
+ 'lon': -151.125,
+ 'lat': 17.125,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 28, 9, 0),
+ 'sea_surface_foundation_temperature': 27.37298583984375,
+ 'matches': [{
+ 'id': 'Buoys_20171022(485)',
+ 'lon': -151.13,
+ 'lat': 17.127,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 10, 22, 6, 50),
+ 'sea_water_temperature': 26.4
+ }]
+ }, {
+ 'id': 'c9cb10ab-ebae-3c8b-a498-d7aef5cf53ed[[0, 5, 8]]',
+ 'lon': -147.875,
+ 'lat': 16.375,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 29, 9, 0),
+ 'sea_surface_foundation_temperature': 27.2869873046875,
+ 'matches': [{
+ 'id': 'Buoys_20171025(7730)',
+ 'lon': -147.881,
+ 'lat': 16.375,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 10, 25, 17, 0),
+ 'sea_water_temperature': 27.1
+ }]
+ }, {
+ 'id': '8532e3e5-3fdd-304f-a9d7-1382d9658b36[[0, 23, 4]]',
+ 'lon': -148.875,
+ 'lat': 13.375,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 29, 9, 0),
+ 'sea_surface_foundation_temperature': 28.196990966796875,
+ 'matches': [{
+ 'id': 'Buoys_20170918(1164)',
+ 'lon': -148.875,
+ 'lat': 13.376,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 9, 18, 7, 0),
+ 'sea_water_temperature': 27.9
+ }]
+ }, {
+ 'id': '17905d2a-ccdd-3d7b-91a7-388c0cc6ef58[[0, 2, 17]]',
+ 'lon': -123.125,
+ 'lat': 15.625,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 27, 9, 0),
+ 'sea_surface_foundation_temperature': 27.8389892578125,
+ 'matches': [{
+ 'id': 'Buoys_20171003(7172)',
+ 'lon': -123.119,
+ 'lat': 15.629,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 10, 3, 10, 0),
+ 'sea_water_temperature': 27.9
+ }]
+ }, {
+ 'id': 'be519f66-de2e-3ffe-a929-be8033717020[[0, 23, 4]]',
+ 'lon': -148.875,
+ 'lat': 13.375,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 24, 9, 0),
+ 'sea_surface_foundation_temperature': 28.1669921875,
+ 'matches': [{
+ 'id': 'Buoys_20170918(1164)',
+ 'lon': -148.875,
+ 'lat': 13.376,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 9, 18, 7, 0),
+ 'sea_water_temperature': 27.9
+ }]
+ }, {
+ 'id': 'dfee49fc-11d5-3bf3-b515-50e698a80f55[[0, 4, 14]]',
+ 'lon': -146.375,
+ 'lat': 23.625,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 27, 9, 0),
+ 'sea_surface_foundation_temperature': 25.6090087890625,
+ 'matches': [{
+ 'id': 'Buoys_20170903(742)',
+ 'lon': -146.378,
+ 'lat': 23.617,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 9, 3, 6, 0),
+ 'sea_water_temperature': 25.6
+ }]
+ }, {
+ 'id': 'e812f91f-4796-3109-90a7-e20834b2a4e9[[0, 20, 7]]',
+ 'lon': -148.125,
+ 'lat': 20.125,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 25, 9, 0),
+ 'sea_surface_foundation_temperature': 26.364013671875,
+ 'matches': [{
+ 'id': 'Buoys_20170920(7966)',
+ 'lon': -148.131,
+ 'lat': 20.124,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 9, 20, 12, 0),
+ 'sea_water_temperature': 26.3
+ }]
+ }, {
+ 'id': 'e5f90fe2-0de1-323e-9bed-a26011d52cbf[[0, 3, 25]]',
+ 'lon': -143.625,
+ 'lat': 23.375,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 29, 9, 0),
+ 'sea_surface_foundation_temperature': 25.22198486328125,
+ 'matches': [{
+ 'id': 'Buoys_20171029(225)',
+ 'lon': -143.62,
+ 'lat': 23.372,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 10, 29, 3, 0),
+ 'sea_water_temperature': 24.0
+ }]
+ }, {
+ 'id': 'fc6f3c08-cefc-36a8-8b2e-9212fe2b4afe[[0, 10, 4]]',
+ 'lon': -148.875,
+ 'lat': 10.125,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 28, 9, 0),
+ 'sea_surface_foundation_temperature': 28.670013427734375,
+ 'matches': [{
+ 'id': 'Buoys_20171028(1182)',
+ 'lon': -148.874,
+ 'lat': 10.13,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 10, 28, 4, 0),
+ 'sea_water_temperature': 28.5
+ }]
+ }, {
+ 'id': 'ac22e67b-95f5-3c51-ae05-1396b838276c[[0, 14, 7]]',
+ 'lon': -140.625,
+ 'lat': 11.125,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 28, 9, 0),
+ 'sea_surface_foundation_temperature': 28.699005126953125,
+ 'matches': [{
+ 'id': 'Buoys_20171015(1659)',
+ 'lon': -140.626,
+ 'lat': 11.127,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 10, 15, 3, 0),
+ 'sea_water_temperature': 28.3
+ }]
+ }, {
+ 'id': '83c72b56-824b-3dcd-be76-9bb25927c6ce[[0, 4, 14]]',
+ 'lon': -146.375,
+ 'lat': 23.625,
+ 'source': 'MUR25-JPL-L4-GLOB-v04.2',
+ 'device': 'radiometers',
+ 'platform': 'orbiting satellite',
+ 'time': datetime.datetime(2017, 9, 26, 9, 0),
+ 'sea_surface_foundation_temperature': 25.64300537109375,
+ 'matches': [{
+ 'id': 'Buoys_20170903(742)',
+ 'lon': -146.378,
+ 'lat': 23.617,
+ 'source': 'spurs2',
+ 'device': 'CTD',
+ 'platform': 'drifting surface float',
+ 'time': datetime.datetime(2017, 9, 3, 6, 0),
+ 'sea_water_temperature': 25.6
+ }]
+ }
+]
diff --git a/analysis/webservice/algorithms/doms/BaseDomsHandler.py b/analysis/webservice/algorithms/doms/BaseDomsHandler.py
index b5834f9..8e6fba4 100644
--- a/analysis/webservice/algorithms/doms/BaseDomsHandler.py
+++ b/analysis/webservice/algorithms/doms/BaseDomsHandler.py
@@ -21,6 +21,7 @@ from datetime import datetime
import time
import itertools
import importlib_metadata
+from collections import defaultdict
from decimal import Decimal
import numpy as np
@@ -310,8 +311,8 @@ class DomsNetCDFFormatter:
platforms.add(match['platform'])
dataset.platform = ', '.join(platforms)
- satellite_group_name = "SatelliteData"
- insitu_group_name = "InsituData"
+ satellite_group_name = 'PrimaryData'
+ insitu_group_name = "SecondaryData"
#Create Satellite group, variables, and attributes
satelliteGroup = dataset.createGroup(satellite_group_name)
@@ -389,54 +390,58 @@ class DomsNetCDFFormatter:
class DomsNetCDFValueWriter:
- def __init__(self, group, matchup_parameter):
+ def __init__(self, group, matchup_parameter): # TODO how do we want this matchup param to be used?
group.createDimension("dim", size=None)
self.group = group
self.lat = []
self.lon = []
self.time = []
- self.sea_water_salinity = []
- self.wind_speed = []
- self.wind_u = []
- self.wind_v = []
- self.wind_direction = []
- self.sea_water_temperature = []
self.depth = []
- self.satellite_group_name = "SatelliteData"
- self.insitu_group_name = "InsituData"
-
- #
- # Only include the depth variable related to the match-up parameter. If the match-up parameter is
- # not sss or sst then do not include any depth data, just fill values.
- #
- if matchup_parameter == "sss":
- self.matchup_depth = "sea_water_salinity_depth"
- elif matchup_parameter == "sst":
- self.matchup_depth = "sea_water_temperature_depth"
- else:
- self.matchup_depth = "NO_DEPTH"
-
- def addData(self, value):
- self.lat.append(value.get("y", None))
- self.lon.append(value.get("x", None))
- self.time.append(time.mktime(value.get("time").timetuple()))
- self.sea_water_salinity.append(value.get("sea_water_salinity", None))
- self.wind_speed.append(value.get("wind_speed", None))
- self.wind_u.append(value.get("wind_u", None))
- self.wind_v.append(value.get("wind_v", None))
- self.wind_direction.append(value.get("wind_direction", None))
- self.sea_water_temperature.append(value.get("sea_water_temperature", None))
- self.depth.append(value.get(self.matchup_depth, None))
+ self.primary_group_name = "PrimaryData"
+ self.secondary_group_name = "SecondaryData"
+ self.data_map = defaultdict(list)
+
+ def addData(self, result_item):
+ """
+ Populate DomsNetCDFValueWriter fields from matchup results dict
+ """
+ non_data_fields = [
+ 'id', 'x', 'y',
+ 'source', 'device',
+ 'platform', 'time', 'matches'
+ ]
+ self.lat.append(result_item.get('y', None))
+ self.lon.append(result_item.get('x', None))
+ self.time.append(time.mktime(result_item.get('time').timetuple()))
+
+ # All other variables are assumed to be science variables.
+ # Add DataPoints accordingly.
+ for key, value in result_item.items():
+ if 'depth' in key:
+ self.depth.append(result_item.get(key))
+ continue
+ if key not in non_data_fields:
+ if len(self.data_map[key]) != len(self.lat) - 1:
+ # If the counts mismatch, fill this variable with
+ # None so the data matches the size
+ size_diff = len(self.lat) - len(self.data_map[key]) - 1
+ self.data_map[key].extend([None] * size_diff)
+ self.data_map[key].append(value)
+
+ # Check if there are any variables that were not appended to.
+ # Append None, meaning that value is empty.
+ for var_name in set(self.data_map.keys()) - set(result_item.keys()):
+ self.data_map[var_name].append(None)
def writeGroup(self):
#
# Create variables, enrich with attributes, and add data
#
- lonVar = self.group.createVariable("lon", "f4", ("dim",), fill_value=-32767.0)
- latVar = self.group.createVariable("lat", "f4", ("dim",), fill_value=-32767.0)
- timeVar = self.group.createVariable("time", "f4", ("dim",), fill_value=-32767.0)
+ lonVar = self.group.createVariable('lon', 'f4', ('dim',), fill_value=-32767.0)
+ latVar = self.group.createVariable('lat', 'f4', ('dim',), fill_value=-32767.0)
+ timeVar = self.group.createVariable('time', 'f4', ('dim',), fill_value=-32767.0)
self.__enrichLon(lonVar, min(self.lon), max(self.lon))
self.__enrichLat(latVar, min(self.lat), max(self.lat))
@@ -446,54 +451,19 @@ class DomsNetCDFValueWriter:
lonVar[:] = self.lon
timeVar[:] = self.time
- if self.sea_water_salinity.count(None) != len(self.sea_water_salinity):
- if self.group.name == self.satellite_group_name:
- sssVar = self.group.createVariable("SeaSurfaceSalinity", "f4", ("dim",), fill_value=-32767.0)
- self.__enrichSSSMeasurements(sssVar, min(self.sea_water_salinity), max(self.sea_water_salinity))
- else: # group.name == self.insitu_group_name
- sssVar = self.group.createVariable("SeaWaterSalinity", "f4", ("dim",), fill_value=-32767.0)
- self.__enrichSWSMeasurements(sssVar, min(self.sea_water_salinity), max(self.sea_water_salinity))
- sssVar[:] = self.sea_water_salinity
-
- if self.wind_speed.count(None) != len(self.wind_speed):
- windSpeedVar = self.group.createVariable("WindSpeed", "f4", ("dim",), fill_value=-32767.0)
- self.__enrichWindSpeed(windSpeedVar, self.__calcMin(self.wind_speed), max(self.wind_speed))
- windSpeedVar[:] = self.wind_speed
-
- if self.wind_u.count(None) != len(self.wind_u):
- windUVar = self.group.createVariable("WindU", "f4", ("dim",), fill_value=-32767.0)
- windUVar[:] = self.wind_u
- self.__enrichWindU(windUVar, self.__calcMin(self.wind_u), max(self.wind_u))
-
- if self.wind_v.count(None) != len(self.wind_v):
- windVVar = self.group.createVariable("WindV", "f4", ("dim",), fill_value=-32767.0)
- windVVar[:] = self.wind_v
- self.__enrichWindV(windVVar, self.__calcMin(self.wind_v), max(self.wind_v))
-
- if self.wind_direction.count(None) != len(self.wind_direction):
- windDirVar = self.group.createVariable("WindDirection", "f4", ("dim",), fill_value=-32767.0)
- windDirVar[:] = self.wind_direction
- self.__enrichWindDir(windDirVar)
-
- if self.sea_water_temperature.count(None) != len(self.sea_water_temperature):
- if self.group.name == self.satellite_group_name:
- tempVar = self.group.createVariable("SeaSurfaceTemp", "f4", ("dim",), fill_value=-32767.0)
- self.__enrichSurfaceTemp(tempVar, self.__calcMin(self.sea_water_temperature), max(self.sea_water_temperature))
- else:
- tempVar = self.group.createVariable("SeaWaterTemp", "f4", ("dim",), fill_value=-32767.0)
- self.__enrichWaterTemp(tempVar, self.__calcMin(self.sea_water_temperature), max(self.sea_water_temperature))
- tempVar[:] = self.sea_water_temperature
-
- if self.group.name == self.insitu_group_name:
- depthVar = self.group.createVariable("Depth", "f4", ("dim",), fill_value=-32767.0)
-
- if self.depth.count(None) != len(self.depth):
- self.__enrichDepth(depthVar, self.__calcMin(self.depth), max(self.depth))
- depthVar[:] = self.depth
- else:
- # If depth has no data, set all values to 0
- tempDepth = [0 for x in range(len(self.depth))]
- depthVar[:] = tempDepth
+ # Add depth variable, if present
+ if self.depth:
+ depthVar = self.group.createVariable('depth', 'f4', ('dim',), fill_value=-32767.0)
+ self.__enrichDepth(depthVar, self.__calcMin(self.depth), max(self.depth))
+ depthVar[:] = self.depth
+
+ print(self.data_map)
+
+ for variable_name, data in self.data_map.items():
+ # Create a variable for each data point
+ data_variable = self.group.createVariable(variable_name, 'f4', ('dim',), fill_value=-32767.0)
+ self.__enrichVariable(data_variable, min(data), max(data), has_depth=self.depth)
+ data_variable[:] = data
#
# Lists may include 'None" values, to calc min these must be filtered out
@@ -502,6 +472,19 @@ class DomsNetCDFValueWriter:
def __calcMin(var):
return min(x for x in var if x is not None)
+ @staticmethod
+ def __enrichVariable(var, var_min, var_max, has_depth):
+ coordinates = ['lat', 'lon', 'depth', 'time']
+
+ if not has_depth:
+ coordinates = ['lat', 'lon', 'time']
+
+ var.long_name = var
+ var.standard_name = var
+ var.units = 'UNKNOWN' # TODO populate this field once this metadata is in place
+ var.valid_min = var_min
+ var.valid_max = var_max
+ var.coordinates = ' '.join(coordinates)
#
# Add attributes to each variable
@@ -531,24 +514,6 @@ class DomsNetCDFValueWriter:
var.axis = "T"
var.units = "seconds since 1970-01-01 00:00:00 0:00"
- @staticmethod
- def __enrichSSSMeasurements(var, var_min, var_max):
- var.long_name = "Sea surface salinity"
- var.standard_name = "sea_surface_salinity"
- var.units = "1e-3"
- var.valid_min = var_min
- var.valid_max = var_max
- var.coordinates = "lon lat time"
-
- @staticmethod
- def __enrichSWSMeasurements(var, var_min, var_max):
- var.long_name = "Sea water salinity"
- var.standard_name = "sea_water_salinity"
- var.units = "1e-3"
- var.valid_min = var_min
- var.valid_max = var_max
- var.coordinates = "lon lat depth time"
-
@staticmethod
def __enrichDepth(var, var_min, var_max):
var.valid_min = var_min
@@ -559,54 +524,3 @@ class DomsNetCDFValueWriter:
var.axis = "Z"
var.positive = "Down"
- @staticmethod
- def __enrichWindSpeed(var, var_min, var_max):
- var.long_name = "Wind speed"
- var.standard_name = "wind_speed"
- var.units = "m s-1"
- var.valid_min = var_min
- var.valid_max = var_max
- var.coordinates = "lon lat depth time"
-
- @staticmethod
- def __enrichWindU(var, var_min, var_max):
- var.long_name = "Eastward wind"
- var.standard_name = "eastward_wind"
- var.units = "m s-1"
- var.valid_min = var_min
- var.valid_max = var_max
- var.coordinates = "lon lat depth time"
-
- @staticmethod
- def __enrichWindV(var, var_min, var_max):
- var.long_name = "Northward wind"
- var.standard_name = "northward_wind"
- var.units = "m s-1"
- var.valid_min = var_min
- var.valid_max = var_max
- var.coordinates = "lon lat depth time"
-
- @staticmethod
- def __enrichWaterTemp(var, var_min, var_max):
- var.long_name = "Sea water temperature"
- var.standard_name = "sea_water_temperature"
- var.units = "degree_C"
- var.valid_min = var_min
- var.valid_max = var_max
- var.coordinates = "lon lat depth time"
-
- @staticmethod
- def __enrichSurfaceTemp(var, var_min, var_max):
- var.long_name = "Sea surface temperature"
- var.standard_name = "sea_surface_temperature"
- var.units = "degree_C"
- var.valid_min = var_min
- var.valid_max = var_max
- var.coordinates = "lon lat time"
-
- @staticmethod
- def __enrichWindDir(var):
- var.long_name = "Wind from direction"
- var.standard_name = "wind_from_direction"
- var.units = "degree"
- var.coordinates = "lon lat depth time"
diff --git a/analysis/webservice/nexus_tornado/request/renderers/NexusNETCDFRenderer.py b/analysis/webservice/nexus_tornado/request/renderers/NexusNETCDFRenderer.py
index 9d6ca92..b2236f6 100644
--- a/analysis/webservice/nexus_tornado/request/renderers/NexusNETCDFRenderer.py
+++ b/analysis/webservice/nexus_tornado/request/renderers/NexusNETCDFRenderer.py
@@ -11,7 +11,7 @@ class NexusNETCDFRenderer(object):
tornado_handler.set_header("Content-Type", "application/x-netcdf")
tornado_handler.set_header("Content-Disposition", "filename=\"%s\"" % self._request.get_argument('filename', "download.nc"))
try:
- self.write(result.toNetCDF())
+ tornado_handler.write(result.toNetCDF())
except:
traceback.print_exc(file=sys.stdout)
raise NexusProcessingException(reason="Unable to convert results to NetCDF.")
\ No newline at end of file