From 0813eafae11218ee5b4c6a75bb9b39eb62bf6cfd Mon Sep 17 00:00:00 2001
From: bw2 <weisburd@broadinstitute.org>
Date: Mon, 2 Apr 2018 15:07:18 -0400
Subject: [PATCH] switch from pip.main to os.system('pip install ..') since
 pip.main is getting deprecated in pip v10

---
 create_snapshot.py              | 7 ++-----
 entire_vds_pipeline.py          | 8 +++++---
 list_repositories.py            | 5 ++---
 print_elasticsearch_stats.py    | 6 +++---
 print_snapshot_status.py        | 5 ++---
 register_snapshot_repository.py | 5 ++---
 restore_snapshot.py             | 5 ++---
 utils/elasticsearch_client.py   | 9 ++++-----
 utils/elasticsearch_utils.py    | 9 ++++-----
 9 files changed, 26 insertions(+), 33 deletions(-)

diff --git a/create_snapshot.py b/create_snapshot.py
index cace091f2..5c4466ddd 100755
--- a/create_snapshot.py
+++ b/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
 
diff --git a/entire_vds_pipeline.py b/entire_vds_pipeline.py
index 61ad5ba1e..894c6923e 100644
--- a/entire_vds_pipeline.py
+++ b/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
diff --git a/list_repositories.py b/list_repositories.py
index 50a218b38..6f6afb868 100644
--- a/list_repositories.py
+++ b/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
diff --git a/print_elasticsearch_stats.py b/print_elasticsearch_stats.py
index 5dab4bbe8..1d62cdc54 100644
--- a/print_elasticsearch_stats.py
+++ b/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()
diff --git a/print_snapshot_status.py b/print_snapshot_status.py
index 9ff1ac1f0..fd941ab95 100644
--- a/print_snapshot_status.py
+++ b/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
diff --git a/register_snapshot_repository.py b/register_snapshot_repository.py
index 19d2d2533..05f6a9f64 100644
--- a/register_snapshot_repository.py
+++ b/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
diff --git a/restore_snapshot.py b/restore_snapshot.py
index 91483d850..88d9ddf7f 100644
--- a/restore_snapshot.py
+++ b/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
diff --git a/utils/elasticsearch_client.py b/utils/elasticsearch_client.py
index 7a0b1dd22..98a56e2a6 100644
--- a/utils/elasticsearch_client.py
+++ b/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
diff --git a/utils/elasticsearch_utils.py b/utils/elasticsearch_utils.py
index 26b7717c2..8ff4b38b6 100644
--- a/utils/elasticsearch_utils.py
+++ b/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