simplify travis build

.travis.yml

@@ -1,28 +1,38 @@
-language: python
-python:
-  - "3.5"
-install:
-  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-  - bash Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
+sudo: required
 
-  - conda config --add channels conda-forge
-  - conda config --add channels bioconda
-  - conda config --set always_yes yes --set changeps1 no
-  - conda config --set show_channel_urls True
+dist: bionic
 
-  - ENV_NAME='testing'
-  - conda create --quiet -n $ENV_NAME python=$TRAVIS_PYTHON_VERSION
-  - source activate $ENV_NAME
-  - conda install --quiet --file requirements.txt
-  - conda list
-  - conda info -a
+language: python
+  - "3.6"
+install:
+  - sudo apt-get install python3-h5py
+  - sudo apt-get install hdf5-helpers hdf5-tools
+  - sudo apt-get install libhdf5-dev
+  - dpkg -L libhdf5-dev
+  - sudo apt-get install python3-requests
+  - sudo apt-cache search netcdf
+  - sudo apt-get install libnetcdf-dev
+  - sudo apt-get install netcdf-bin
+  - sudo apt-get install python3-jinja2
+  - sudo apt-get install python3-six
+  - sudo apt-get install python3-pip
+  - sudo pip3 install setuptools --upgrade
+  - sudo pip3 install pyparsing
+  - sudo pip3 install rdflib
+  - export HDF5_DIR=/usr/include/hdf5
+  - export USE_SETUPCFG=0
+  - export HDF5_INCDIR=/usr/include
+  - export HDF5_LIBDIR=/usr/lib/x86_64-linux-gnu
+  - sudo pip3 install netCDF4
   - wget https://github.com/marqh/terra/archive/master.zip
   - unzip master.zip
   - cd terra-master
-  - python setup.py --quiet install
+  - sudo python3 setup.py --quiet install
   - cd ..
-  - python setup.py --quiet install
+  - sudo python3 setup.py --quiet install
+  - python3 -c 'import bald; print(bald); print(bald.__version__)'
+  - which python3
+  - python3 -c "import numpy; print('numpy: ' + numpy.__version__); import netCDF4; print('netCDF4: ' + netCDF4.__version__); print('###')"
 
 script:
-  python -m unittest discover -s bald.tests -v
+  python3 -m unittest discover -s bald.tests -v

lib/bald/__init__.py

@@ -254,16 +254,21 @@ def __getitem__(self, item):
         if not self.is_http_uri(item):
             raise ValueError('{} is not a HTTP URI.'.format(item))
         if item not in self.cache:
+            # null response, as a fall back
+            self.cache[item] = requests.models.Response()
             # now = time.time()
             try:
                 # print('trying: {}'.format(item))
 
                 headers = {'Accept': 'application/rdf+xml'}
                 self.cache[item] = requests.get(item, headers=headers, timeout=11)
             except Exception:
-                # print('retrying: {}'.format(item))
-                headers = {'Accept': 'text/html'}
-                self.cache[item] = requests.get(item, headers=headers, timeout=11)
+                try:
+                    # print('retrying: {}'.format(item))
+                    headers = {'Accept': 'text/html'}
+                    self.cache[item] = requests.get(item, headers=headers, timeout=11)
+                except Exception:
+                    pass
 
         # print('in {} seconds'.format(time.time() - then))
         return self.cache[item]
@@ -577,7 +582,7 @@ def rdfgraph(self):
         """
         graph = rdflib.Graph()
         graph.bind('bald', 'http://binary-array-ld.net/latest/')
-        graph.bind('ns1', self.baseuri + '/')
+        graph.bind('this', self.baseuri + '/')
         for prefix_name in self.prefixes():
 
             #strip the double underscore suffix

lib/bald/tests/integration/CDL/array_geo.cdl

@@ -8,6 +8,7 @@ variables:
   		prefix_list:rdf__ = "http://www.w3.org/1999/02/22-rdf-syntax-ns#" ;
 		prefix_list:rdfs__ = "http://www.w3.org/2000/01/rdf-schema#" ;
 		prefix_list:cf__ = "http://def.scitools.org.uk/CFTerms/" ;
+		prefix_list:nc__ = "http://def.scitools.org.uk/NetCDF/" ;
 		prefix_list:geo__ = "http://www.opengis.net/ont/geosparql#" ;
 		prefix_list:nc__ = "http://def.scitools.org.uk/NetCDF/" ;
 

lib/bald/tests/integration/CDL/array_multitypes.cdl

@@ -8,6 +8,7 @@ variables:
   		prefix_list:rdf__ = "http://www.w3.org/1999/02/22-rdf-syntax-ns#" ;
 		prefix_list:rdfs__ = "http://www.w3.org/2000/01/rdf-schema#" ;
 		prefix_list:cf__ = "http://def.scitools.org.uk/CFTerms/" ;
+		prefix_list:nc__ = "http://def.scitools.org.uk/NetCDF/" ;
 		prefix_list:geo__ = "http://www.opengis.net/ont/geosparql#" ;
 		prefix_list:nc__ = "http://def.scitools.org.uk/NetCDF/" ;
 

lib/bald/tests/integration/TTL/GEMS_CO2_Apr2006.ttl

@@ -2,32 +2,32 @@
 @prefix NetCDF: <http://def.scitools.org.uk/NetCDF/> .
 @prefix bald: <http://binary-array-ld.net/latest/> .
 @prefix cf_sname: <http://vocab.nerc.ac.uk/standard_name/> .
-@prefix ns1: <file://CDL/GEMS_CO2_Apr2006.cdl/> .
 @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix this: <file://CDL/GEMS_CO2_Apr2006.cdl/> .
 @prefix xml: <http://www.w3.org/XML/1998/namespace> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 
 <file://CDL/GEMS_CO2_Apr2006.cdl> a bald:Container ;
-    bald:contains ns1:co2,
-        ns1:co2_latitude_ref,
-        ns1:co2_levelist_ref,
-        ns1:co2_time_ref,
-        ns1:latitude,
-        ns1:levelist,
-        ns1:lnsp,
-        ns1:lnsp_latitude_ref,
-        ns1:lnsp_levelist_ref,
-        ns1:lnsp_time_ref,
-        ns1:longitude,
-        ns1:time ;
+    bald:contains this:co2,
+        this:co2_latitude_ref,
+        this:co2_levelist_ref,
+        this:co2_time_ref,
+        this:latitude,
+        this:levelist,
+        this:lnsp,
+        this:lnsp_latitude_ref,
+        this:lnsp_levelist_ref,
+        this:lnsp_time_ref,
+        this:longitude,
+        this:time ;
     NetCDF:Conventions "CF-1.0" .
 
-ns1:co2 a bald:Array ;
-    bald:references ns1:co2_latitude_ref,
-        ns1:co2_levelist_ref,
-        ns1:co2_time_ref,
-        ns1:longitude ;
+this:co2 a bald:Array ;
+    bald:references this:co2_latitude_ref,
+        this:co2_levelist_ref,
+        this:co2_time_ref,
+        this:longitude ;
     bald:shape "(1, 60, 181, 360)" ;
     CFTerms:missing_value "-32767" ;
     CFTerms:standard_name <http://vocab.nerc.ac.uk/standard_name/mass_fraction_of_carbon_dioxide_in_air/> ;
@@ -37,77 +37,77 @@ ns1:co2 a bald:Array ;
     NetCDF:scale_factor 0.000981685145029486 ;
     NetCDF:units "kg kg**-1" .
 
-ns1:lnsp a bald:Array ;
-    bald:references ns1:lnsp_latitude_ref,
-        ns1:lnsp_levelist_ref,
-        ns1:lnsp_time_ref,
-        ns1:longitude ;
+this:lnsp a bald:Array ;
+    bald:references this:lnsp_latitude_ref,
+        this:lnsp_levelist_ref,
+        this:lnsp_time_ref,
+        this:longitude ;
     bald:shape "(1, 60, 181, 360)" ;
     CFTerms:missing_value "-32767" ;
     NetCDF:FillValue "-32767" ;
     NetCDF:add_offset 11.2087164280841 ;
     NetCDF:long_name "Logarithm of surface pressure" ;
     NetCDF:scale_factor 1.03952457840347e-05 .
 
-ns1:co2_latitude_ref a bald:Reference,
+this:co2_latitude_ref a bald:Reference,
         bald:Subject ;
-    bald:array ns1:latitude ;
+    bald:array this:latitude ;
     bald:childBroadcast "(1, 1, 181, 1)" .
 
-ns1:co2_levelist_ref a bald:Reference,
+this:co2_levelist_ref a bald:Reference,
         bald:Subject ;
-    bald:array ns1:levelist ;
+    bald:array this:levelist ;
     bald:childBroadcast "(1, 60, 1, 1)" .
 
-ns1:co2_time_ref a bald:Reference,
+this:co2_time_ref a bald:Reference,
         bald:Subject ;
-    bald:array ns1:time ;
+    bald:array this:time ;
     bald:childBroadcast "(1, 1, 1, 1)" .
 
-ns1:lnsp_latitude_ref a bald:Reference,
+this:lnsp_latitude_ref a bald:Reference,
         bald:Subject ;
-    bald:array ns1:latitude ;
+    bald:array this:latitude ;
     bald:childBroadcast "(1, 1, 181, 1)" .
 
-ns1:lnsp_levelist_ref a bald:Reference,
+this:lnsp_levelist_ref a bald:Reference,
         bald:Subject ;
-    bald:array ns1:levelist ;
+    bald:array this:levelist ;
     bald:childBroadcast "(1, 60, 1, 1)" .
 
-ns1:lnsp_time_ref a bald:Reference,
+this:lnsp_time_ref a bald:Reference,
         bald:Subject ;
-    bald:array ns1:time ;
+    bald:array this:time ;
     bald:childBroadcast "(1, 1, 1, 1)" .
 
-ns1:latitude a bald:Array,
+this:latitude a bald:Array,
         bald:Reference ;
-    bald:array ns1:latitude ;
+    bald:array this:latitude ;
     bald:first_value 90.0 ;
     bald:last_value -90.0 ;
     bald:shape "(181,)" ;
     CFTerms:standard_name <http://vocab.nerc.ac.uk/standard_name/latitude/> ;
     NetCDF:units "degrees_north" .
 
-ns1:levelist a bald:Array,
+this:levelist a bald:Array,
         bald:Reference ;
-    bald:array ns1:levelist ;
+    bald:array this:levelist ;
     bald:first_value 1 ;
     bald:last_value 60 ;
     bald:shape "(60,)" ;
     NetCDF:long_name "model_level_number" .
 
-ns1:longitude a bald:Array,
+this:longitude a bald:Array,
         bald:Reference ;
-    bald:array ns1:longitude ;
+    bald:array this:longitude ;
     bald:first_value 0.0 ;
     bald:last_value 359.0 ;
     bald:shape "(360,)" ;
     CFTerms:standard_name <http://vocab.nerc.ac.uk/standard_name/longitude/> ;
     NetCDF:units "degrees_east" .
 
-ns1:time a bald:Array,
+this:time a bald:Array,
         bald:Reference ;
-    bald:array ns1:time ;
+    bald:array this:time ;
     bald:first_value "2006-04-01T00:00:00"^^xsd:dateTime ;
     bald:shape "(1,)" ;
     CFTerms:standard_name <http://vocab.nerc.ac.uk/standard_name/time/> ;

lib/bald/tests/integration/TTL/ProcessChain0300.ttl

@@ -4,27 +4,27 @@
 @prefix StatPP: <https://codes.nws.noaa.gov/StatisticalPostProcessing> .
 @prefix bald: <http://binary-array-ld.net/latest/> .
 @prefix cf_sname: <http://vocab.nerc.ac.uk/standard_name/> .
-@prefix ns1: <file://CDL/ProcessChain0300.cdl/> .
 @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix this: <file://CDL/ProcessChain0300.cdl/> .
 @prefix xml: <http://www.w3.org/XML/1998/namespace> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 
 <file://CDL/ProcessChain0300.cdl> a bald:Container ;
-    ns1:process_chain "gfsmos_process_chain" ;
-    bald:contains ns1:gfsmos_process_chain,
-        ns1:step1,
-        ns1:step2 ;
+    this:process_chain "gfsmos_process_chain" ;
+    bald:contains this:gfsmos_process_chain,
+        this:step1,
+        this:step2 ;
     bald:isPrefixedBy "prefix_list" .
 
-ns1:gfsmos_process_chain a bald:Subject ;
-    ns1:OM_Process ( ns1:step1 ns1:step2 ) .
+this:gfsmos_process_chain a bald:Subject ;
+    this:OM_Process ( this:step1 this:step2 ) .
 
-ns1:step1 a bald:Subject ;
-    ns1:LE_ProcessStep <https://codes.nws.noaa.gov/NumericalWeatherPrediction/Models/GFS13> ;
-    ns1:LE_Source <https://codes.nws.noaa.gov/DataAssimilation/Methods/GDAS13> .
+this:step1 a bald:Subject ;
+    this:LE_ProcessStep <https://codes.nws.noaa.gov/NumericalWeatherPrediction/Models/GFS13> ;
+    this:LE_Source <https://codes.nws.noaa.gov/DataAssimilation/Methods/GDAS13> .
 
-ns1:step2 a bald:Subject ;
-    ns1:LE_ProcessStep <https://codes.nws.noaa.gov/StatisticalPostProcessing/Methods/GFSMOS05> ;
-    ns1:LE_Source <https://codes.nws.noaa.gov/NumericalWeatherPrediction/Models/GFS13> .
+this:step2 a bald:Subject ;
+    this:LE_ProcessStep <https://codes.nws.noaa.gov/StatisticalPostProcessing/Methods/GFSMOS05> ;
+    this:LE_Source <https://codes.nws.noaa.gov/NumericalWeatherPrediction/Models/GFS13> .
 

lib/bald/tests/integration/TTL/array_reference.ttl

@@ -1,21 +1,21 @@
 @prefix bald: <http://binary-array-ld.net/latest/> .
-@prefix ns1: <file://CDL/array_reference.cdl/> .
 @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix this: <file://CDL/array_reference.cdl/> .
 @prefix xml: <http://www.w3.org/XML/1998/namespace> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 
 <file://CDL/array_reference.cdl> a bald:Container ;
-    bald:contains ns1:child_variable,
-        ns1:parent_variable ;
+    bald:contains this:child_variable,
+        this:parent_variable ;
     bald:isPrefixedBy "prefix_list" .
 
-ns1:parent_variable a bald:Array ;
-    bald:references ns1:child_variable ;
+this:parent_variable a bald:Array ;
+    bald:references this:child_variable ;
     bald:shape "(11, 17)" .
 
-ns1:child_variable a bald:Array,
+this:child_variable a bald:Array,
         bald:Reference ;
-    bald:array ns1:child_variable ;
+    bald:array this:child_variable ;
     bald:shape "(11, 17)" .
 

lib/bald/tests/integration/TTL/array_reference_withbase.ttl

@@ -1,21 +1,21 @@
 @prefix bald: <http://binary-array-ld.net/latest/> .
-@prefix ns1: <http://example.org/base/> .
 @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix this: <http://example.org/base/> .
 @prefix xml: <http://www.w3.org/XML/1998/namespace> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 
 <http://example.org/base> a bald:Container ;
-    bald:contains ns1:child_variable,
-        ns1:parent_variable ;
+    bald:contains this:child_variable,
+        this:parent_variable ;
     bald:isPrefixedBy "prefix_list" .
 
-ns1:parent_variable a bald:Array ;
-    bald:references ns1:child_variable ;
+this:parent_variable a bald:Array ;
+    bald:references this:child_variable ;
     bald:shape "(11, 17)" .
 
-ns1:child_variable a bald:Array,
+this:child_variable a bald:Array,
         bald:Reference ;
-    bald:array ns1:child_variable ;
+    bald:array this:child_variable ;
     bald:shape "(11, 17)" .