From 4680ff80b0370f889d53da06c8a66e1520c8e81e Mon Sep 17 00:00:00 2001
From: Pablo Reyes <pablo.reyes@sri.com>
Date: Mon, 10 Jun 2019 14:18:23 -0700
Subject: [PATCH 01/14] Fixing the check of bucket name.

---
 resen/resencmd.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/resen/resencmd.py b/resen/resencmd.py
index 2f9b42f..d726fa7 100644
--- a/resen/resencmd.py
+++ b/resen/resencmd.py
@@ -47,6 +47,13 @@ def do_create_bucket(self,args):
             print("Syntax Error. Usage: create_bucket bucket_name")
             return
 
+        # check if creating bucket with name bucket_name is possible:
+        print("Creating bucket with name: %s" % bucket_name)
+        status = self.program.create_bucket(bucket_name)
+        if not status:
+            print("Failed to create bucket!")
+            return
+
         # First, ask user about the bucket they want to create
         # resen-core version?
         valid_versions = sorted([x['version'] for x in self.program.bucket_manager.valid_cores])
@@ -93,13 +100,6 @@ def do_create_bucket(self,args):
         msg = '>>> Start bucket and jupyterlab? (y/n): '
         start = self.get_valid_input(msg,valid_inputs) == 'y'
 
-        # Now that we have the bucket creation recipe, let's actually create it.
-        print("Creating bucket with name: %s" % bucket_name)
-        status = self.program.create_bucket(bucket_name)
-        if not status:
-            print("Failed to create bucket!")
-            return
-
         success = True
         print("...adding core...")
         status = self.program.add_image(bucket_name,docker_image)

From 2c15359506ab2ce00d603f34852a7fa934515e0c Mon Sep 17 00:00:00 2001
From: Leslie Lamarche <leslie.lamarche@sri.com>
Date: Mon, 10 Jun 2019 16:28:05 -0700
Subject: [PATCH 02/14] Added input validating functions to resencmd.py.

---
 resen/resencmd.py | 84 ++++++++++++++++++++++++++++++-----------------
 1 file changed, 53 insertions(+), 31 deletions(-)

diff --git a/resen/resencmd.py b/resen/resencmd.py
index d726fa7..ff3dcab 100644
--- a/resen/resencmd.py
+++ b/resen/resencmd.py
@@ -35,24 +35,11 @@ def __init__(self,resen):
     def do_create_bucket(self,args):
         """Usage:
 create_bucket bucket_name : Create a new bucket with name bucket_name. Must start with a letter, <=20 characters, and no spaces."""
-        inputs,num_inputs = self.parse_args(args)
-        if num_inputs != 1:
-            print("Syntax Error")
-            return
 
-        bucket_name = inputs[0]
-        # check if bucket_name has spaces in it and is greater than 20 characters
-        # also bucket name must start with a letter
-        if ' ' in bucket_name or len(bucket_name) > 20 or not bucket_name[0].isalpha():
-            print("Syntax Error. Usage: create_bucket bucket_name")
-            return
-
-        # check if creating bucket with name bucket_name is possible:
-        print("Creating bucket with name: %s" % bucket_name)
-        status = self.program.create_bucket(bucket_name)
-        if not status:
-            print("Failed to create bucket!")
-            return
+        # First, ask user for bucket name
+        print('Please enter a name for your bucket.  Valid names must be less than 20 characters and start with an aphabetic character')
+        msg = '>>> Enter bucket name: '
+        bucket_name = self.get_valid_name(msg)
 
         # First, ask user about the bucket they want to create
         # resen-core version?
@@ -66,23 +53,29 @@ def do_create_bucket(self,args):
         local_port = self.get_port()
         container_port = local_port
 
-        # Ask user about storage locations to mount
+        # Mounting persistent storage
+        print('Local directories can be mounted to either /home/jovyan/work/ or /home/jovyan/mount/ in a bucket.  You will have rw privileges to everything mounted in work, but can specified permissions as either r or rw for directories in mount.  Code and data created in a bucket can ONLY be accessed outside the bucket or after the bucket has been deleted if it is saved in a mounted local directory.')
         mounts = list()
-        valid_inputs = ['y','n']
+
         msg = '>>> Mount storage to /home/jovyan/work? (y/n): '
-        answer = self.get_valid_input(msg,valid_inputs)
-        if answer == 'y':
-            msg = '>>> Enter local path: '
-            local_path = self.get_valid_path(msg)
-            container_path = '/home/jovyan/work'
-            permissions = 'rw'
-            mounts.append([local_path,container_path,permissions])
+        while True:
+            answer = self.get_yn(msg)
+            if answer == 'n':
+                break
+            else:
+                msg = '>>> Enter local path: '
+                local_path = self.get_valid_path(msg)
+                # container_path = '/home/jovyan/work'
+                msg = '>>> Enter bucket path: '
+                container_path = self.get_valid_path(msg,base='/home/jovyan/work')
+                permissions = 'rw'
+                mounts.append([local_path,container_path,permissions])
+                msg = '>>> Mount additional storage to /home/jovyan/work? (y/n): '
 
         # query for more mounts
+        msg = '>>> Mount storage to /home/jovyan/mount? (y/n): '
         while True:
-            valid_inputs = ['y','n']
-            msg = '>>> Mount additional storage to /home/jovyan/mount? (y/n): '
-            answer = self.get_valid_input(msg,valid_inputs)
+            answer = self.get_yn(msg)
             if answer == 'n':
                 break
             else:
@@ -94,11 +87,11 @@ def do_create_bucket(self,args):
                 msg = '>>> Enter permissions (r/rw): '
                 permissions = self.get_valid_input(msg,valid_inputs)
                 mounts.append([local_path,container_path,permissions])
+                msg = '>>> Mount additional storage to /home/jovyan/mount? (y/n): '
 
         # should we start jupyterlab when done creating bucket?
-        valid_inputs = ['y','n']
         msg = '>>> Start bucket and jupyterlab? (y/n): '
-        start = self.get_valid_input(msg,valid_inputs) == 'y'
+        start = self.get_yn(msg) == 'y'
 
         success = True
         print("...adding core...")
@@ -319,6 +312,35 @@ def parse_args(self,args):
         num_inputs = len(inputs)
         return inputs,num_inputs
 
+    def get_yn(self,msg):
+        valid_inputs = ['y', 'n']
+        while True:
+            answer = input(msg)
+            if answer in valid_inputs:
+                return answer
+            else:
+                print("Invalid input. Valid input are {} or {}.".format(valid_inputs[0],valid_inputs[1]))
+
+    def get_valid_name(self,msg):
+        while True:
+            name = input(msg)
+
+            # check if bucket_name has spaces in it and is greater than 20 characters
+            # also bucket name must start with a letter
+            if ' ' in name:
+                print("Bucket names may not contain spaces.")
+            elif len(name) > 20:
+                print("Bucket names must be less than 20 characters.")
+            elif not name[0].isalpha():
+                print("Bucket names must start with alphabetic characters.")
+            else:
+                # check if bucket with that name already exists
+                status = self.program.create_bucket(name)
+                if not status:
+                    print("Cannot use the same name as an existing bucket!")
+                else:
+                    return name
+
     def get_valid_input(self,msg,valid_inputs):
         if len(valid_inputs) == 1:
             valid_msg = valid_inputs[0]

From b62d14d0446f942f3209184820fad41947222540 Mon Sep 17 00:00:00 2001
From: Leslie Lamarche <leslie.lamarche@sri.com>
Date: Tue, 11 Jun 2019 08:29:16 -0700
Subject: [PATCH 03/14] Cleaned up input validation funcitons and added local
 path checking.

---
 resen/resencmd.py | 135 +++++++++++++++++++++++-----------------------
 1 file changed, 68 insertions(+), 67 deletions(-)

diff --git a/resen/resencmd.py b/resen/resencmd.py
index ff3dcab..2dfa9a7 100644
--- a/resen/resencmd.py
+++ b/resen/resencmd.py
@@ -17,6 +17,7 @@
 import resen
 import socket
 import pathlib
+import os
 
 version = resen.__version__
 
@@ -34,19 +35,18 @@ def __init__(self,resen):
     # if 
     def do_create_bucket(self,args):
         """Usage:
-create_bucket bucket_name : Create a new bucket with name bucket_name. Must start with a letter, <=20 characters, and no spaces."""
+create_bucket : Create a new bucket by responding to the prompts provided."""
 
         # First, ask user for bucket name
-        print('Please enter a name for your bucket.  Valid names must be less than 20 characters and start with an aphabetic character')
-        msg = '>>> Enter bucket name: '
-        bucket_name = self.get_valid_name(msg)
+        print('Please enter a name for your bucket.')
+        # msg = '>>> Enter bucket name: '
+        bucket_name = self.get_valid_name('>>> Enter bucket name: ')
 
         # First, ask user about the bucket they want to create
         # resen-core version?
         valid_versions = sorted([x['version'] for x in self.program.bucket_manager.valid_cores])
-        print('Please choose a version of resen-core. Available versions: %s' % ", ".join(valid_versions))
-        msg = '>>> Select a version: '
-        docker_image = self.get_valid_input(msg,valid_versions)
+        print('Please choose a version of resen-core.')
+        docker_image = self.get_valid_version('>>> Select a version: ',valid_versions)
 
 
         # Figure out a port to use
@@ -57,37 +57,23 @@ def do_create_bucket(self,args):
         print('Local directories can be mounted to either /home/jovyan/work/ or /home/jovyan/mount/ in a bucket.  You will have rw privileges to everything mounted in work, but can specified permissions as either r or rw for directories in mount.  Code and data created in a bucket can ONLY be accessed outside the bucket or after the bucket has been deleted if it is saved in a mounted local directory.')
         mounts = list()
 
-        msg = '>>> Mount storage to /home/jovyan/work? (y/n): '
-        while True:
-            answer = self.get_yn(msg)
-            if answer == 'n':
-                break
-            else:
-                msg = '>>> Enter local path: '
-                local_path = self.get_valid_path(msg)
-                # container_path = '/home/jovyan/work'
-                msg = '>>> Enter bucket path: '
-                container_path = self.get_valid_path(msg,base='/home/jovyan/work')
-                permissions = 'rw'
-                mounts.append([local_path,container_path,permissions])
-                msg = '>>> Mount additional storage to /home/jovyan/work? (y/n): '
-
-        # query for more mounts
-        msg = '>>> Mount storage to /home/jovyan/mount? (y/n): '
-        while True:
-            answer = self.get_yn(msg)
-            if answer == 'n':
-                break
-            else:
-                msg = '>>> Enter local path: '
-                local_path = self.get_valid_path(msg)
-                msg = '>>> Enter bucket path: '
-                container_path = self.get_valid_path(msg,base='/home/jovyan/mount')
-                valid_inputs = ['r','rw']
-                msg = '>>> Enter permissions (r/rw): '
-                permissions = self.get_valid_input(msg,valid_inputs)
-                mounts.append([local_path,container_path,permissions])
-                msg = '>>> Mount additional storage to /home/jovyan/mount? (y/n): '
+        # query for mounts to work
+        answer = self.get_yn('>>> Mount storage to /home/jovyan/work? (y/n): ')
+        while answer == 'y':
+            local_path = self.get_valid_local_path('>>> Enter local path: ')
+            container_path = self.get_valid_container_path('>>> Enter bucket path: ','/home/jovyan/work')
+            permissions = 'rw'
+            mounts.append([local_path,container_path,permissions])
+            answer = self.get_yn('>>> Mount additional storage to /home/jovyan/work? (y/n): ')
+
+        # query for mounts to mount
+        answer = self.get_yn('>>> Mount storage to /home/jovyan/mount? (y/n): ')
+        while answer == 'y':
+            local_path = self.get_valid_local_path('>>> Enter local path: ')
+            container_path = self.get_valid_container_path('>>> Enter bucket path: ','/home/jovyan/mount')
+            permissions = self.get_permissions('>>> Enter permissions (r/rw): ')
+            mounts.append([local_path,container_path,permissions])
+            answer = self.get_yn('>>> Mount additional storage to /home/jovyan/mount? (y/n): ')
 
         # should we start jupyterlab when done creating bucket?
         msg = '>>> Start bucket and jupyterlab? (y/n): '
@@ -312,6 +298,8 @@ def parse_args(self,args):
         num_inputs = len(inputs)
         return inputs,num_inputs
 
+    # The following functions are highly specialized
+
     def get_yn(self,msg):
         valid_inputs = ['y', 'n']
         while True:
@@ -322,6 +310,7 @@ def get_yn(self,msg):
                 print("Invalid input. Valid input are {} or {}.".format(valid_inputs[0],valid_inputs[1]))
 
     def get_valid_name(self,msg):
+        print('Valid names may not contain spaces and must start with a letter and be less than 20 characters long.')
         while True:
             name = input(msg)
 
@@ -332,43 +321,25 @@ def get_valid_name(self,msg):
             elif len(name) > 20:
                 print("Bucket names must be less than 20 characters.")
             elif not name[0].isalpha():
-                print("Bucket names must start with alphabetic characters.")
+                print("Bucket names must start with an alphabetic character.")
             else:
                 # check if bucket with that name already exists
+                # Is the only reason create_bucket fails if the name is already take?  May need a more rigerous check
                 status = self.program.create_bucket(name)
-                if not status:
-                    print("Cannot use the same name as an existing bucket!")
-                else:
+                if status:
                     return name
+                else:
+                    print("Cannot use the same name as an existing bucket!")
 
-    def get_valid_input(self,msg,valid_inputs):
-        if len(valid_inputs) == 1:
-            valid_msg = valid_inputs[0]
-        elif len(valid_inputs) == 2:
-            valid_msg = " or ".join(valid_inputs)
-        else:
-            valid_msg = ", ".join(valid_inputs[:-1])
-            valid_msg += ", or %s" % valid_inputs[-1]
+    def get_valid_version(self,msg,valid_versions):
+        print('Available versions: {}'.format(", ".join(valid_versions)))
         while True:
-            answer = input(msg)
-            if not valid_inputs:
-                return answer
-            if answer in valid_inputs:
-                return answer
+            version = input(msg)
+            if version in valid_versions:
+                return version
             else:
-                print("Invalid input. Valid inputs are: %s" % valid_msg)
+                print("Invalid version. Available versions: {}".format(", ".join(valid_versions)))
 
-    def get_valid_path(self,msg,base=None):
-        while True:
-            answer = input(msg)
-            path = pathlib.PurePosixPath(answer)
-            if not base is None:
-                if base in [str(x) for x in list(path.parents)]:
-                    return str(path)
-                else:
-                    print("Invalid path. Must start with: %s" % base)
-                    continue
-            return str(path)
 
     def get_port(self):
         # this is not atomic, so it is possible that another process might snatch up the port
@@ -382,6 +353,36 @@ def get_port(self):
             else:
                 port += 1
 
+    def get_valid_local_path(self,msg):
+        while True:
+            path = input(msg)
+            path = pathlib.PurePosixPath(path)
+            if os.path.isdir(path):
+                return str(path)
+            else:
+                print('Cannot find local path entered.')
+
+    def get_valid_container_path(self,msg,base):
+        while True:
+            path = input(msg)
+            path = pathlib.PurePosixPath(path)
+            if base in [str(x) for x in list(path.parents)]:
+                return str(path)
+            else:
+                print("Invalid path. Must start with: {}".format(base))
+
+    def get_permissions(self,msg):
+        valid_inputs = ['r', 'rw']
+        while True:
+            answer = input(msg)
+            if answer in valid_inputs:
+                return answer
+            else:
+                print("Invalid input. Valid input are {} or {}.".format(valid_inputs[0],valid_inputs[1]))
+
+
+
+
 
 def main():
 

From 6b07e2d74a12710dc403caa70cb7959b6e6c6829 Mon Sep 17 00:00:00 2001
From: Leslie Lamarche <leslie.lamarche@sri.com>
Date: Tue, 11 Jun 2019 09:43:27 -0700
Subject: [PATCH 04/14] Modified do_start_jupyter so it starts a bucket if it
 is not already running.

---
 resen/resencmd.py | 43 ++++++++++++++++++++++++++++---------------
 1 file changed, 28 insertions(+), 15 deletions(-)

diff --git a/resen/resencmd.py b/resen/resencmd.py
index 2dfa9a7..8e89dc1 100644
--- a/resen/resencmd.py
+++ b/resen/resencmd.py
@@ -39,7 +39,6 @@ def do_create_bucket(self,args):
 
         # First, ask user for bucket name
         print('Please enter a name for your bucket.')
-        # msg = '>>> Enter bucket name: '
         bucket_name = self.get_valid_name('>>> Enter bucket name: ')
 
         # First, ask user about the bucket they want to create
@@ -169,29 +168,43 @@ def do_status(self,args):
 
     def do_start_jupyter(self,args):
         """Usage:
->>> start_jupyter bucket_name local_port bucket_port\t: Start a jupyter notebook server on port bucket_port available at local_port.
->>> start_jupyter bucket_name local_port bucket_port --lab\t: Start a jupyter lab server on port bucket_port available at local_port.
+>>> start_jupyter bucket_name
         """
         inputs,num_inputs = self.parse_args(args)
-        lab = False
-        if num_inputs == 3:
+
+        if num_inputs == 1:
             pass
-        elif num_inputs == 4:
-            if inputs[3][0] == '-':
-                if inputs[3] == '--lab':
-                    lab = True
-                else:
-                    print("Syntax Error. See 'help start_jupyter'.")
-                    return
         else:
             print("Syntax Error. See 'help start_jupyter'.")
             return
 
+
+        # get bucket name from input
         bucket_name = inputs[0]
-        local_port = int(inputs[1])
-        bucket_port = int(inputs[2])
+        lab = True
+
+        # get bucket infomrmation (ports and status)
+        # This stuff may be better suited to exist in some kind of "status query" inside of Resen.py
+        ind = self.program.bucket_manager.bucket_names.index(bucket_name)
+        bucket = self.program.bucket_manager.buckets[ind]
+        # This automatically selects the first port in the list of ports
+        # TODO: Manage multiple ports assigned to one bucket
+        ports = bucket['docker']['port'][0]
+        running_status = bucket['docker']['status']
+
+
+        # if bucket is not running, first start bucket
+        if running_status != 'running':
+            status = self.program.start_bucket(bucket_name)
+
+        # check if jupyter server running
+
+        # then start jupyter 
+        status = self.program.start_jupyter(bucket_name,ports[0],ports[1],lab=lab)
+
+
+
 
-        status = self.program.start_jupyter(bucket_name,local_port,bucket_port,lab=lab)
 
 #     def do_add_storage(self,args):
 #         """Usage:

From 2447412969e154ad839edbd45bb60ef6830ad638 Mon Sep 17 00:00:00 2001
From: Ashton Reimer <ashtonsethreimer@gmail.com>
Date: Wed, 12 Jun 2019 16:47:35 -0700
Subject: [PATCH 05/14] changed mount /home/jovyan/work back to being standard
 location for workspace, updated mount message

---
 resen/resencmd.py | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/resen/resencmd.py b/resen/resencmd.py
index 8e89dc1..a0b7e28 100644
--- a/resen/resencmd.py
+++ b/resen/resencmd.py
@@ -3,7 +3,7 @@
 #
 #  Title: resen
 #
-#  Author: asreimer
+#  Author: resen developer team
 #  Description: The resen tool for working with resen-core locally
 #               which allows for listing available core docker
 #               images, creating resen buckets, starting buckets,
@@ -53,17 +53,23 @@ def do_create_bucket(self,args):
         container_port = local_port
 
         # Mounting persistent storage
-        print('Local directories can be mounted to either /home/jovyan/work/ or /home/jovyan/mount/ in a bucket.  You will have rw privileges to everything mounted in work, but can specified permissions as either r or rw for directories in mount.  Code and data created in a bucket can ONLY be accessed outside the bucket or after the bucket has been deleted if it is saved in a mounted local directory.')
+        msg =  'Local directories can be mounted to either /home/jovyan/work or '
+        msg += '/home/jovyan/mount/ in a bucket. The /home/jovyan/work location is '
+        msg += 'a workspace and /home/jovyan/mount/ is intended for mounting in data. '
+        msg += 'You will have rw privileges to everything mounted in work, but can '
+        msg += 'specified permissions as either r or rw for directories in mount. Code '
+        msg += 'and data created in a bucket can ONLY be accessed outside the bucket or '
+        msg += 'after the bucket has been deleted if it is saved in a mounted local directory.'
+        print(msg)
         mounts = list()
 
-        # query for mounts to work
+        # query for mount to work
         answer = self.get_yn('>>> Mount storage to /home/jovyan/work? (y/n): ')
-        while answer == 'y':
+        if answer == 'y':
             local_path = self.get_valid_local_path('>>> Enter local path: ')
-            container_path = self.get_valid_container_path('>>> Enter bucket path: ','/home/jovyan/work')
+            container_path = '/home/jovyan/work'
             permissions = 'rw'
             mounts.append([local_path,container_path,permissions])
-            answer = self.get_yn('>>> Mount additional storage to /home/jovyan/work? (y/n): ')
 
         # query for mounts to mount
         answer = self.get_yn('>>> Mount storage to /home/jovyan/mount? (y/n): ')

From a3424ee2ef422e1c87db83a316fe70f9ec10d80a Mon Sep 17 00:00:00 2001
From: Ashton Reimer <ashtonsethreimer@gmail.com>
Date: Thu, 13 Jun 2019 03:27:27 -0700
Subject: [PATCH 06/14] Hardcoded in lab, notebook no longer an option.

---
 resen/Resen.py    | 15 +++++----------
 resen/resencmd.py |  5 ++---
 2 files changed, 7 insertions(+), 13 deletions(-)

diff --git a/resen/Resen.py b/resen/Resen.py
index e183ae1..57cecdd 100644
--- a/resen/Resen.py
+++ b/resen/Resen.py
@@ -76,8 +76,8 @@ def start_bucket(self,bucket_name):
     def stop_bucket(self,bucket_name):
         return self.bucket_manager.stop_bucket(bucket_name)
 
-    def start_jupyter(self,bucket_name,local,container,lab=True):
-        return self.bucket_manager.start_jupyter(bucket_name,local,container,lab=lab)
+    def start_jupyter(self,bucket_name,local,container):
+        return self.bucket_manager.start_jupyter(bucket_name,local,container)
 
     def _get_config_dir(self):
         appname = 'resen'
@@ -535,20 +535,15 @@ def execute_command(self,bucket_name,command,detach=True):
             print('ERROR: Bucket %s is not running!' % (bucket['bucket']['name']))
             return False
 
-    def start_jupyter(self,bucket_name,local_port,container_port,lab=True):
+    def start_jupyter(self,bucket_name,local_port,container_port):
         if not bucket_name in self.bucket_names:
             print("ERROR: Bucket with name: %s does not exist!" % bucket_name)
             return False
-
-        if lab:
-            style = 'lab'
-        else:
-            style = 'notebook'
         
         token = '%048x' % random.randrange(16**48)
 
-        command = "bash -cl 'source activate py36 && jupyter %s --no-browser --ip 0.0.0.0 --port %s --NotebookApp.token=%s --KernelSpecManager.ensure_native_kernel=False'"
-        command = command % (style, container_port, token)
+        command = "bash -cl 'source activate py36 && jupyter lab --no-browser --ip 0.0.0.0 --port %s --NotebookApp.token=%s --KernelSpecManager.ensure_native_kernel=False'"
+        command = command % (container_port, token)
 
         status = self.execute_command(bucket_name,command,detach=True)
         if status == False:
diff --git a/resen/resencmd.py b/resen/resencmd.py
index a0b7e28..e1859c1 100644
--- a/resen/resencmd.py
+++ b/resen/resencmd.py
@@ -108,7 +108,7 @@ def do_create_bucket(self,args):
                     return
                 # start jupyterlab
                 print("...starting jupyterlab...")
-                status = self.program.start_jupyter(bucket_name,local_port,container_port,lab=True)
+                status = self.program.start_jupyter(bucket_name,local_port,container_port)
         else:
             print("Failed to create bucket!")
             status = self.program.remove_bucket(bucket_name)
@@ -187,7 +187,6 @@ def do_start_jupyter(self,args):
 
         # get bucket name from input
         bucket_name = inputs[0]
-        lab = True
 
         # get bucket infomrmation (ports and status)
         # This stuff may be better suited to exist in some kind of "status query" inside of Resen.py
@@ -206,7 +205,7 @@ def do_start_jupyter(self,args):
         # check if jupyter server running
 
         # then start jupyter 
-        status = self.program.start_jupyter(bucket_name,ports[0],ports[1],lab=lab)
+        status = self.program.start_jupyter(bucket_name,ports[0],ports[1])
 
 
 

From 96d9823a3942567132afb635c5ee7b145e8ccf1a Mon Sep 17 00:00:00 2001
From: Ashton Reimer <ashtonsethreimer@gmail.com>
Date: Thu, 13 Jun 2019 03:28:21 -0700
Subject: [PATCH 07/14] removed start/stop_bucket commands from cmdline

---
 resen/resencmd.py | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/resen/resencmd.py b/resen/resencmd.py
index e1859c1..c4ff3f9 100644
--- a/resen/resencmd.py
+++ b/resen/resencmd.py
@@ -113,27 +113,27 @@ def do_create_bucket(self,args):
             print("Failed to create bucket!")
             status = self.program.remove_bucket(bucket_name)
 
-    def do_start_bucket(self,args):
-        """Usage:
-start_bucket bucket_name : Start bucket named bucket_name."""
-        inputs,num_inputs = self.parse_args(args)
-        if num_inputs != 1:
-            print("Syntax Error. Usage: start_bucket bucket_name")
-            return
+#     def do_start_bucket(self,args):
+#         """Usage:
+# start_bucket bucket_name : Start bucket named bucket_name."""
+#         inputs,num_inputs = self.parse_args(args)
+#         if num_inputs != 1:
+#             print("Syntax Error. Usage: start_bucket bucket_name")
+#             return
 
-        bucket_name = inputs[0]
-        status = self.program.start_bucket(bucket_name)
+#         bucket_name = inputs[0]
+#         status = self.program.start_bucket(bucket_name)
 
-    def do_stop_bucket(self,args):
-        """Usage:
-stop_bucket bucket_name : Stop bucket named bucket_name."""
-        inputs,num_inputs = self.parse_args(args)
-        if num_inputs != 1:
-            print("Syntax Error. Usage: stop_bucket bucket_name")
-            return
+#     def do_stop_bucket(self,args):
+#         """Usage:
+# stop_bucket bucket_name : Stop bucket named bucket_name."""
+#         inputs,num_inputs = self.parse_args(args)
+#         if num_inputs != 1:
+#             print("Syntax Error. Usage: stop_bucket bucket_name")
+#             return
 
-        bucket_name = inputs[0]
-        status = self.program.stop_bucket(bucket_name)
+#         bucket_name = inputs[0]
+#         status = self.program.stop_bucket(bucket_name)
 
     def do_remove_bucket(self,args):
         """Usage:

From 0401731636fc7df7778797ad5bba26af5bcaa8bb Mon Sep 17 00:00:00 2001
From: Ashton Reimer <ashtonsethreimer@gmail.com>
Date: Thu, 13 Jun 2019 04:45:25 -0700
Subject: [PATCH 08/14] Implemented stop_jupyter, fixed start_jupyter.

---
 resen/Resen.py    | 85 +++++++++++++++++++++++++++++++++++++++--------
 resen/resencmd.py | 10 ++++++
 2 files changed, 81 insertions(+), 14 deletions(-)

diff --git a/resen/Resen.py b/resen/Resen.py
index 57cecdd..7feee31 100644
--- a/resen/Resen.py
+++ b/resen/Resen.py
@@ -79,6 +79,9 @@ def stop_bucket(self,bucket_name):
     def start_jupyter(self,bucket_name,local,container):
         return self.bucket_manager.start_jupyter(bucket_name,local,container)
 
+    def stop_jupyter(self,bucket_name):
+        return self.bucket_manager.stop_jupyter(bucket_name)
+
     def _get_config_dir(self):
         appname = 'resen'
 
@@ -187,6 +190,9 @@ def create_bucket(self,bucket_name):
         params['docker']['port'] = list()
         params['docker']['storage'] = list()
         params['docker']['status'] = None
+        params['docker']['jupyter'] = dict()
+        params['docker']['jupyter']['token'] = None
+        params['docker']['jupyter']['port'] = None
 
         # now add the new bucket to the self.buckets config and then update the config file
         self.buckets.append(params)
@@ -539,9 +545,20 @@ def start_jupyter(self,bucket_name,local_port,container_port):
         if not bucket_name in self.bucket_names:
             print("ERROR: Bucket with name: %s does not exist!" % bucket_name)
             return False
-        
-        token = '%048x' % random.randrange(16**48)
 
+        ind = self.bucket_names.index(bucket_name)
+        bucket = self.buckets[ind]
+        pid = self.get_jupyter_pid(bucket['docker']['container'])
+
+        if not pid is None:
+            port = bucket['docker']['jupyter']['port']
+            token = bucket['docker']['jupyter']['token']
+            url = 'http://localhost:%s/?token=%s' % (port,token)
+            print("Jupyter lab is already running and can be accessed in a browser at: %s" % (url))
+            return True
+
+
+        token = '%048x' % random.randrange(16**48)
         command = "bash -cl 'source activate py36 && jupyter lab --no-browser --ip 0.0.0.0 --port %s --NotebookApp.token=%s --KernelSpecManager.ensure_native_kernel=False'"
         command = command % (container_port, token)
 
@@ -549,23 +566,17 @@ def start_jupyter(self,bucket_name,local_port,container_port):
         if status == False:
             return False
         time.sleep(0.1)
+
         # now check that jupyter is running
         self.update_bucket_statuses()
-        ind = self.bucket_names.index(bucket_name)
-        bucket = self.buckets[ind]
-        result = self.dockerhelper.execute_command(bucket['docker']['container'],'ps -ef',detach=False)
-        output = result[1].decode('utf-8').split('\n')
+        pid = self.get_jupyter_pid(bucket['docker']['container'])
 
-        pid = None
-        for line in output:
-            if 'jupyter' in line and token in line:
-                parsed_line = [x for x in line.split(' ') if x != '']
-                pid = parsed_line[1]
-                break
-            
         if pid is not None:
+            self.buckets[ind]['docker']['jupyter']['token'] = token
+            self.buckets[ind]['docker']['jupyter']['port'] = local_port
+            self.save_config()
             url = 'http://localhost:%s/?token=%s' % (local_port,token)
-            print("Jupyter %s can be accessed in a browser at: %s" % (style, url))
+            print("Jupyter lab can be accessed in a browser at: %s" % (url))
             time.sleep(3)
             webbrowser.open(url)
             return True
@@ -573,6 +584,52 @@ def start_jupyter(self,bucket_name,local_port,container_port):
             print("ERROR: Failed to start jupyter server!")
             return False
 
+    def stop_jupyter(self,bucket_name):
+        if not bucket_name in self.bucket_names:
+            print("ERROR: Bucket with name: %s does not exist!" % bucket_name)
+            return False
+
+        ind = self.bucket_names.index(bucket_name)
+        bucket = self.buckets[ind]
+        pid = self.get_jupyter_pid(bucket['docker']['container'])
+
+        if pid is None:
+            return True
+
+        command = "kill -9 %s" % (pid)
+        status = self.execute_command(bucket_name,command,detach=True)
+        time.sleep(0.1)
+        self.update_bucket_statuses()
+
+        # now verify it is dead
+        pid = self.get_jupyter_pid(bucket['docker']['container'])
+        if not pid is None:
+            print("ERROR: Failed to stop jupyter lab.")
+            return False
+
+        self.buckets[ind]['docker']['jupyter']['token'] = None
+        self.buckets[ind]['docker']['jupyter']['port'] = None
+        self.save_config()
+
+        return True
+
+    def get_jupyter_pid(self,container):
+
+        result = self.dockerhelper.execute_command(container,'ps -ef',detach=False)
+        if result == False:
+            return None
+
+        output = result[1].decode('utf-8').split('\n')
+
+        pid = None
+        for line in output:
+            if ('jupyter-lab' in line or 'jupyter lab' in line) and '--no-browser --ip 0.0.0.0' in line:
+                parsed_line = [x for x in line.split(' ') if x != '']
+                pid = parsed_line[1]
+                break
+
+        return pid
+
     def update_bucket_statuses(self):
         for i,bucket in enumerate(self.buckets):
             container_id = bucket['docker']['container']
diff --git a/resen/resencmd.py b/resen/resencmd.py
index c4ff3f9..d869f28 100644
--- a/resen/resencmd.py
+++ b/resen/resencmd.py
@@ -208,7 +208,17 @@ def do_start_jupyter(self,args):
         status = self.program.start_jupyter(bucket_name,ports[0],ports[1])
 
 
+    def do_stop_jupyter(self,args):
+        """Usage:
+stop_jupyter bucket_name : Stop jupyter on bucket bucket_name."""
+        inputs,num_inputs = self.parse_args(args)
+        if num_inputs != 1:
+            print("Syntax Error. Usage: stop_bucket bucket_name")
+            return
 
+        bucket_name = inputs[0]
+        status = self.program.stop_jupyter(bucket_name)
+        status = self.program.stop_bucket(bucket_name)
 
 
 #     def do_add_storage(self,args):

From 7877605af2acbae59146e701445ea2ea893e9604 Mon Sep 17 00:00:00 2001
From: Ashton Reimer <ashtonsethreimer@gmail.com>
Date: Thu, 13 Jun 2019 05:33:27 -0700
Subject: [PATCH 09/14] Added check to make sure container is running before
 commanding it.

---
 resen/Resen.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/resen/Resen.py b/resen/Resen.py
index 7feee31..ba4b0a5 100644
--- a/resen/Resen.py
+++ b/resen/Resen.py
@@ -591,8 +591,10 @@ def stop_jupyter(self,bucket_name):
 
         ind = self.bucket_names.index(bucket_name)
         bucket = self.buckets[ind]
-        pid = self.get_jupyter_pid(bucket['docker']['container'])
+        if not bucket['docker']['status'] in ['running']:
+            return True
 
+        pid = self.get_jupyter_pid(bucket['docker']['container'])
         if pid is None:
             return True
 

From ba1d3bfa638afffa6c6521d45069fd469e9cfb34 Mon Sep 17 00:00:00 2001
From: Ashton Reimer <ashtonsethreimer@gmail.com>
Date: Thu, 13 Jun 2019 11:13:42 -0700
Subject: [PATCH 10/14] Fix start_jupyter crash if supplied with non-existent
 bucketname

---
 resen/resencmd.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/resen/resencmd.py b/resen/resencmd.py
index d869f28..7305382 100644
--- a/resen/resencmd.py
+++ b/resen/resencmd.py
@@ -188,6 +188,10 @@ def do_start_jupyter(self,args):
         # get bucket name from input
         bucket_name = inputs[0]
 
+        if not bucket_name in self.program.bucket_manager.bucket_names:
+            print("ERROR: Bucket with name: %s does not exist!" % bucket_name)
+            return False
+
         # get bucket infomrmation (ports and status)
         # This stuff may be better suited to exist in some kind of "status query" inside of Resen.py
         ind = self.program.bucket_manager.bucket_names.index(bucket_name)

From 280b8409110a57edeb4b3b413f4f4e08b9440408 Mon Sep 17 00:00:00 2001
From: Ashton Reimer <ashtonsethreimer@gmail.com>
Date: Thu, 13 Jun 2019 11:16:52 -0700
Subject: [PATCH 11/14] this should fix os.path.isdir problem with
 PurePosixPath pathlib

---
 resen/resencmd.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/resen/resencmd.py b/resen/resencmd.py
index 7305382..91e3999 100644
--- a/resen/resencmd.py
+++ b/resen/resencmd.py
@@ -389,7 +389,7 @@ def get_valid_local_path(self,msg):
         while True:
             path = input(msg)
             path = pathlib.PurePosixPath(path)
-            if os.path.isdir(path):
+            if os.path.isdir(str(path)):
                 return str(path)
             else:
                 print('Cannot find local path entered.')

From d89bec8cc88de3c994eeb550c786db5ee237189e Mon Sep 17 00:00:00 2001
From: Ashton Reimer <ashtonsethreimer@gmail.com>
Date: Thu, 13 Jun 2019 11:20:32 -0700
Subject: [PATCH 12/14] conforming docstring

---
 resen/resencmd.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/resen/resencmd.py b/resen/resencmd.py
index 91e3999..bbb0426 100644
--- a/resen/resencmd.py
+++ b/resen/resencmd.py
@@ -174,7 +174,7 @@ def do_status(self,args):
 
     def do_start_jupyter(self,args):
         """Usage:
->>> start_jupyter bucket_name
+>>> start_jupyter bucket_name : Start jupyter on bucket bucket_name
         """
         inputs,num_inputs = self.parse_args(args)
 

From 016a31c05216364792cb7d7edcaa7433067f67d1 Mon Sep 17 00:00:00 2001
From: Leslie Lamarche <leslie.lamarche@sri.com>
Date: Thu, 13 Jun 2019 13:19:12 -0700
Subject: [PATCH 13/14] Fixed the strange hanging bug.

---
 resen/Resen.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/resen/Resen.py b/resen/Resen.py
index ba4b0a5..6ce913f 100644
--- a/resen/Resen.py
+++ b/resen/Resen.py
@@ -529,7 +529,7 @@ def execute_command(self,bucket_name,command,detach=True):
 
         if bucket['docker']['status'] in ['running']:
             # then we can start the container and update status
-            result = self.dockerhelper.execute_command(bucket['docker']['container'],command)
+            result = self.dockerhelper.execute_command(bucket['docker']['container'],command,detach=detach)
             status, output = result
             if (detach and status is None) or (not detach and status==0):
                 return True
@@ -598,8 +598,9 @@ def stop_jupyter(self,bucket_name):
         if pid is None:
             return True
 
-        command = "kill -9 %s" % (pid)
-        status = self.execute_command(bucket_name,command,detach=True)
+        port = bucket['docker']['jupyter']['port']
+        command = "bash -cl 'source activate py36 && jupyter notebook stop %s'" % (port)
+        status = self.execute_command(bucket_name,command,detach=False)
         time.sleep(0.1)
         self.update_bucket_statuses()
 

From 4b376084fe1aba13d7f59370d8338047d5dada2e Mon Sep 17 00:00:00 2001
From: Ashton Reimer <ashtonsethreimer@gmail.com>
Date: Thu, 13 Jun 2019 17:42:35 -0700
Subject: [PATCH 14/14] Significantly improved the jupyter server shutdown.

---
 resen/Resen.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/resen/Resen.py b/resen/Resen.py
index 6ce913f..b21754e 100644
--- a/resen/Resen.py
+++ b/resen/Resen.py
@@ -599,9 +599,12 @@ def stop_jupyter(self,bucket_name):
             return True
 
         port = bucket['docker']['jupyter']['port']
-        command = "bash -cl 'source activate py36 && jupyter notebook stop %s'" % (port)
+        python_cmd = 'from notebook.notebookapp import shutdown_server, list_running_servers; '
+        python_cmd += 'svrs = [x for x in list_running_servers() if x[\\\"port\\\"] == %s]; ' % (port)
+        python_cmd += 'sts = True if len(svrs) == 0 else shutdown_server(svrs[0]); print(sts)'
+        command = "bash -cl '/home/jovyan/envs/py36/bin/python -c \"%s \"'" % (python_cmd)
         status = self.execute_command(bucket_name,command,detach=False)
-        time.sleep(0.1)
+
         self.update_bucket_statuses()
 
         # now verify it is dead