#!/usr/bin/env python
# coding: utf-8

# In[1]:


import pandas as pd


# In[2]:


import os
import boto3
import botocore
import paramiko


# In[3]:


mergedMatricesDir='/nrnb/users/btsui/Data/all_seq/rnaseq_merged/'
inFnameS=pd.Series(os.listdir(mergedMatricesDir))


# In[4]:


include_m1=(inFnameS.str.contains('gene_symbol')&(~inFnameS.str.contains('.gz')))
include_m2=inFnameS.isin(['merged_kallisto_run_info.pickle'])
transferFnames=inFnameS[include_m1|include_m2]


# In[5]:


key = paramiko.RSAKey.from_private_key_file('/cellar/users/btsui/.ssh/jupyter_hub.pem')
client = paramiko.SSHClient()
client.set_missing_host_key_policy(paramiko.AutoAddPolicy())


# 
# * [Launch the T3 micro instance on AWS with k8s.ebs_20g.efs_automount (ami-04052dc36ee4ac5c1)](https://us-west-2.console.aws.amazon.com/ec2/v2/home?region=us-west-2#Instances:sort=launchTime)
# * Modify the instance_ip to the AWS for data uploading instance

# In[6]:


instance_ip='ec2-34-215-138-8.us-west-2.compute.amazonaws.com'
mountEfs='sudo mount -t efs fs-e1636448:/ efs'

#try:
# Here 'ubuntu' is user name and 'instance_ip' is public IP of EC2
client.connect(hostname=instance_ip, username="ec2-user", pkey=key)
# Execute a command(cmd) after connecting/ssh to an instance
cmd='mkdir ~/efs'
stdin, stdout, stderr = client.exec_command(cmd)
cmd='sudo mount -t nfs4 -o nfsvers=4.1,rsize=1048576,wsize=1048576,hard,timeo=600,retrans=2 fs-e1636448.efs.us-west-2.amazonaws.com:/ ~/efs'
stdin, stdout, stderr = client.exec_command(cmd)


# In[7]:


print(stdout.read(),stderr.read())


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remoteDir='~/efs/all_seq/rnaseq_merged/'


# In[9]:


cmd='mkdir '+remoteDir
stdin, stdout, stderr = client.exec_command(cmd)
print (stdout.read())
print (stderr.read())


# In[10]:


addHostVerificationCmd="ssh -o StrictHostKeyChecking=no -i $HOME/.ssh/jupyter_hub.pem ec2-user@{instance_ip}  ls".format(instance_ip=instance_ip)
os.system(addHostVerificationCmd)


# In[11]:


myRsyncDirFormat='rsync  -Pvu -e "ssh -i $HOME/.ssh/jupyter_hub.pem" {localFDir} ec2-user@{instance_ip}:{remoteDir}'


# In[ ]:


for localFname in transferFnames.values:
    localFDir= (mergedMatricesDir+localFname)
    rsyncCmd=myRsyncDirFormat.format(localFDir=localFDir,instance_ip=instance_ip,remoteDir=remoteDir+'.')
    print (rsyncCmd)
    
    print (os.system(rsyncCmd))


# In[13]:


#!rsync  -Pvu -e "ssh -i $HOME/.ssh/jupyter_hub.pem" /nrnb/users/btsui/Data/all_seq/rnaseq_merged/Canis_familiaris.gene_symbol.tpm.index.txt ec2-user@ec2-52-13-69-172.us-west-2.compute.amazonaws.com:~/efs/all_seq/rnaseq_merged/.


# In[21]:


#!rsync  -Pvu -e "ssh -i $HOME/.ssh/jupyter_hub.pem" /nrnb/users/btsui/Data/all_seq/rnaseq_merged/Canis_familiaris.gene_symbol.tpm.index.txt \
#ec2-user@ec2-52-24-55-248.us-west-2.compute.amazonaws.com:~/.


# In[18]:


#!ls $HOME/.ssh/


# In[105]:


import seaborn


# In[2]:


#!cp ./upload_AWS.ipynb ./../../Update_SRA_meta_data/.


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