Merge pull request #70 from roocs/apply_fixes_option

Apply fixes option

CHANGES.rst

@@ -1,6 +1,10 @@
 Changes
 *******
 
+Unreleased
+==========
+* ``apply_fixes`` option added for WPS processes and the ``Operator`` class.
+
 0.2.0 (2020-11-19)
 ==================
 

environment.yml

@@ -11,16 +11,15 @@ dependencies:
 - psutil
 # tests
 - pytest
-# daops
 - rtree>=0.9
 - cfunits
 - cftime>=1.2.1
 - udunits2>=2.2
 - xarray>=0.16
 - dask>=2.26
 - netcdf4>=1.4
-- daops>=0.3.0,<0.4
-- clisops>=0.4.0,<0.5
+#- daops>=0.3.0,<0.4
+# - clisops>=0.4.0,<0.5
 # workflow
 - networkx
 # provenance

requirements.txt

@@ -6,8 +6,8 @@ networkx
 xarray>=0.15
 dask[complete]
 netcdf4
-daops>=0.3.0
-clisops>=0.4.0
-roocs-utils>=0.1.5
+# daops>=0.3.0
+# clisops>=0.4.0
+# roocs-utils>=0.1.5
 prov>=2.0.0
 pydot

rook/operator.py

@@ -4,9 +4,10 @@
 
 
 class Operator(object):
-    def __init__(self, output_dir):
+    def __init__(self, output_dir, apply_fixes=True):
         self.config = {
             'output_dir': output_dir,
+            'apply_fixes': apply_fixes
             # 'chunk_rules': dconfig.chunk_rules,
             # 'filenamer': dconfig.filenamer,
         }

rook/processes/wps_average.py

@@ -25,6 +25,11 @@ def __init__(self):
                          default='0',
                          min_occurs=1,
                          max_occurs=1),
+            LiteralInput('apply_fixes', 'Apply Fixes', data_type='boolean',
+                         abstract='Apply fixes to datasets.',
+                         default='1',
+                         min_occurs=1,
+                         max_occurs=1),
         ]
         outputs = [
             ComplexOutput('output', 'METALINK v4 output',

rook/processes/wps_subset.py

@@ -41,6 +41,11 @@ def __init__(self):
                          default='0',
                          min_occurs=1,
                          max_occurs=1),
+            LiteralInput('apply_fixes', 'Apply Fixes', data_type='boolean',
+                         abstract='Apply fixes to datasets.',
+                         default='1',
+                         min_occurs=1,
+                         max_occurs=1),
         ]
         outputs = [
             ComplexOutput('output', 'METALINK v4 output',
@@ -86,6 +91,7 @@ def _handler(self, request, response):
 
         config_args = {
             'output_dir': self.workdir,
+            'apply_fixes': request.inputs['apply_fixes'][0].data
             # 'chunk_rules': dconfig.chunk_rules,
             # 'filenamer': dconfig.filenamer,
         }

setup.py

@@ -50,6 +50,9 @@
       packages=find_packages(),
       include_package_data=True,
       install_requires=[
+          "daops @ git+https://github.com/roocs/daops.git",
+          "clisops @ git+https://github.com/roocs/clisops.git",
+          "roocs-utils @ git+https://github.com/roocs/roocs-utils.git",
           reqs,
       ],
       extras_require={