Merge pull request #74 from mhearne-usgs/containerfix

Fixed issues in container get*s functions, updated installer to use n…

.gitignore

@@ -4,6 +4,7 @@ build
 .DS_Store
 .ipynb_checkpoints/
 .cache
+.pytest_cache/
 .coverage
 .coverage.xml
 htmlcov

impactutils/io/container.py

@@ -158,6 +158,8 @@ def getDictionaries(self):
         Returns:
           (list) List of names of dictionaries stored in container.
         """
+        if GROUPS['dict'] not in self._hdfobj:
+            return []
         dictionaries = list(self._hdfobj[GROUPS['dict']].keys())
         dictionaries = [name.replace('__', '') for name in dictionaries]
         return dictionaries
@@ -219,6 +221,8 @@ def getLists(self):
         Returns:
             list: List of names of lists stored in container.
         """
+        if GROUPS['list'] not in self._hdfobj:
+            return []
         lists = list(self._hdfobj[GROUPS['list']].keys())
         lists = [name.replace('__', '') for name in lists]
         return lists
@@ -312,6 +316,8 @@ def getArrays(self):
         Returns:
             list: List of names of arrays stored in container.
         """
+        if GROUPS['array'] not in self._hdfobj:
+            return []
         arrays = list(self._hdfobj[GROUPS['array']].keys())
         arrays = [name.replace('__', '') for name in arrays]
         return arrays
@@ -386,6 +392,8 @@ def getStrings(self):
         Returns:
           (list) List of names of strings stored in container.
         """
+        if GROUPS['string'] not in self._hdfobj:
+            return []
         strings = list(self._hdfobj[GROUPS['string']].keys())
         strings = [name.replace('__', '') for name in strings]
         return strings
@@ -469,6 +477,8 @@ def getDataFrames(self):
         Returns:
             list: List of names of dictionaries stored in container.
         """
+        if GROUPS['dataframe'] not in self._hdfobj:
+            return []
         dataframes = list(self._hdfobj[GROUPS['dataframe']].keys())
         dataframes = [name.replace('__', '') for name in dataframes]
         return dataframes

install.sh

@@ -2,6 +2,13 @@
 
 VENV=impact
 
+unamestr=`uname`
+if [ "$unamestr" == 'Linux' ]; then
+    source ~/.bashrc
+elif [ "$unamestr" == 'FreeBSD' ] || [ "$unamestr" == 'Darwin' ]; then
+    source ~/.bash_profile
+fi
+
 # Is the reset flag set?
 reset=0
 while getopts r FLAG; do
@@ -15,12 +22,14 @@ done
 
 
 # Is conda installed?
-conda=$(which conda)
-if [ ! "$conda" ] ; then
+conda --version
+if [ $? -ne 0 ] ; then
     wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
         -O miniconda.sh;
     bash miniconda.sh -f -b -p $HOME/miniconda
-    export PATH="$HOME/miniconda/bin:$PATH"
+    # Need this to get conda into path
+    . $HOME/miniconda/etc/profile.d/conda.sh
+
 fi
 
 # Choose OS-specific environment file, which specifies
@@ -43,7 +52,7 @@ fi
 echo "Environment file: $env_file"
 
 # Turn off whatever other virtual environment user might be in
-source deactivate
+conda deactivate
 
 # Create a conda virtual environment
 echo "Creating the $VENV virtual environment:"
@@ -57,11 +66,11 @@ fi
 
 # Activate the new environment
 echo "Activating the $VENV virtual environment"
-source activate $VENV
+conda activate $VENV
 
 # This package
 echo "Installing impact-utils..."
 pip install -e .
 
 # Tell the user they have to activate this environment
-echo "Type 'source activate $VENV' to use this new virtual environment."
+echo "Type 'conda activate $VENV' to use this new virtual environment."

test/comcat/query_test.py

@@ -48,6 +48,7 @@ def test_cc():
                 'nc72592670': ['us200050nt', 'nn00531804']}
 
     for eventid, cmp_allids in eventids.items():
+        print(eventid)
         ccinfo = ComCatInfo(eventid)
         authid, allids = ccinfo.getAssociatedIds()
         authsource, othersources = ccinfo.getAssociatedSources()
@@ -60,6 +61,7 @@ def test_cc():
                     'at00o30yrz': 'ci37528064',
                     'us200050nt': 'nc72592670'}
     for eventid, cmp_authid in non_auth_ids.items():
+        print(eventid)
         ccinfo = ComCatInfo(eventid)
         authid, allids = ccinfo.getAssociatedIds()
         assert cmp_authid == authid
@@ -111,4 +113,4 @@ def test_cc():
 
 if __name__ == '__main__':
     test_cc()
-    test_geoserve()
+    geoserve()

test/io/container_test.py

@@ -21,6 +21,14 @@ def test_hdf_dictonaries():
     try:
         container = HDFContainer.create(testfile)
 
+        # before we put anything in here, let's make sure we get empty lists from
+        # all of the methods that are supposed to return lists of stuff.
+        assert container.getDictionaries() == []
+        assert container.getLists() == []
+        assert container.getArrays() == []
+        assert container.getStrings() == []
+        assert container.getDataFrames() == []
+
         # test simple dictionary
         print('Test simple dictionary...')
         indict1 = {'name': 'Fred', 'age': 34,