Merge pull request #34 from macarthur-lab/fix_pip_install_calls

replace pip.main(..) with os.system('pip install ..') calls

create_snapshot.py

@@ -1,13 +1,10 @@
-import pip
+import os
+os.system("pip install elasticsearch")  # this used to be `import pip; pip.main(['install', 'elasticsearch']);`, but pip.main is deprecated as of pip v10
 
 from utils.elasticsearch_client import ElasticsearchClient
-
-pip.main(['install', 'elasticsearch'])
-
 import argparse
 import elasticsearch
 import logging
-import os
 from pprint import pprint
 import time
 

entire_vds_pipeline.py

@@ -1,8 +1,10 @@
 #!/usr/bin/env python
 
-import pip
-for dependency in ['six==1.10.0', 'elasticsearch==5.4.0', 'requests==2.13.0']:
-    pip.main(['install', dependency])
+#for dependency in ['six==1.10.0', 'elasticsearch', 'requests']:
+#    pip.main(['install', dependency])
+# make sure elasticsearch is installed
+#import os
+#os.system("pip install elasticsearch")  # this used to be `import pip; pip.main(['install', 'elasticsearch']);`, but pip.main is deprecated as of pip v10
 
 import argparse
 import json

list_repositories.py

@@ -1,6 +1,5 @@
-import pip
-
-pip.main(['install', 'elasticsearch'])
+import os
+os.system("pip install elasticsearch")  # this used to be `import pip; pip.main(['install', 'elasticsearch']);`, but pip.main is deprecated as of pip v10
 
 import argparse
 import elasticsearch

print_elasticsearch_stats.py

@@ -1,7 +1,7 @@
-import argparse
-import pip
-pip.main(['install', 'elasticsearch'])
+import os
+os.system("pip install elasticsearch")  # this used to be `import pip; pip.main(['install', 'elasticsearch']);`, but pip.main is deprecated as of pip v10
 
+import argparse
 from utils.elasticsearch_client import ElasticsearchClient
 
 p = argparse.ArgumentParser()

print_snapshot_status.py

@@ -1,6 +1,5 @@
-import pip
-
-pip.main(['install', 'elasticsearch'])
+import os
+os.system("pip install elasticsearch")  # this used to be `import pip; pip.main(['install', 'elasticsearch']);`, but pip.main is deprecated as of pip v10
 
 import argparse
 import elasticsearch

register_snapshot_repository.py

@@ -1,6 +1,5 @@
-import pip
-
-pip.main(['install', 'elasticsearch'])
+import os
+os.system("pip install elasticsearch")  # this used to be `import pip; pip.main(['install', 'elasticsearch']);`, but pip.main is deprecated as of pip v10
 
 import argparse
 import elasticsearch

restore_snapshot.py

@@ -1,6 +1,5 @@
-import pip
-
-pip.main(['install', 'elasticsearch'])
+import os
+os.system("pip install elasticsearch")  # this used to be `import pip; pip.main(['install', 'elasticsearch']);`, but pip.main is deprecated as of pip v10
 
 import argparse
 import elasticsearch

utils/elasticsearch_client.py

@@ -1,3 +1,7 @@
+# make sure elasticsearch is installed
+import os
+os.system("pip install elasticsearch")  # this used to be `import pip; pip.main(['install', 'elasticsearch']);`, but pip.main is deprecated as of pip v10
+
 import logging
 
 from utils.elasticsearch_utils import DEFAULT_GENOTYPE_FIELDS_TO_EXPORT, \
@@ -6,11 +10,6 @@
     ELASTICSEARCH_CREATE, ELASTICSEARCH_UPDATE, ELASTICSEARCH_UPSERT
 
 handlers = set(logging.root.handlers)
-
-# make sure elasticsearch is installed
-import pip
-pip.main(['install', 'elasticsearch'])
-
 logging.root.handlers = list(handlers)
 
 import elasticsearch

utils/elasticsearch_utils.py

@@ -1,11 +1,10 @@
+# make sure elasticsearch is installed
+import os
+os.system("pip install elasticsearch")  # this used to be `import pip; pip.main(['install', 'elasticsearch']);`, but pip.main is deprecated as of pip v10
+
 import logging
 
 handlers = set(logging.root.handlers)
-
-# make sure elasticsearch is installed
-import pip
-pip.main(['install', 'elasticsearch'])
-
 logging.root.handlers = list(handlers)
 
 import collections