Merge pull request #62 from EarthCubeInGeo/develop

[MNT]: 2020.1.0 release

HISTORY.rst

@@ -0,0 +1,22 @@
+
+.. :changelog:
+
+2020.1.0 (2020-06-24)
++++++++++++++++++++++
+
+- Add new available resen-core: 2020.1.0
+- bug fixed when importing a bucket: now tar files of mounted paths are removed after a successful import.
+- fixed bug causing enabling sudo access for user jovyan failed
+
+2019.1.1 (2019-12-10)
++++++++++++++++++++++
+
+- Raise exceptions added when local storage not found
+- Add detection of resen running on a windows system
+- if docker toolbox, change path to be the docker VM path instead of the host machine path
+- find a port that is available
+
+2019.1.0 (2019-11-24)
++++++++++++++++++++++
+
+- Initial release.

README.rst

@@ -18,7 +18,7 @@ Resen requires both python 3 and docker to be installed.
 
 1. Install `Python 3 <https://www.python.org/>`_
 2. Install `docker <https://docs.docker.com/install/>`_
-3. Install Resen with pip ``pip install git+https://github.com/EarthCubeInGeo/resen.git@v2019.1.1``
+3. Install Resen with pip ``pip install git+https://github.com/EarthCubeInGeo/resen.git@v2020.1.0``
 
 Please refer to the `installation documentation <https://resen.readthedocs.io/en/latest/installation/index.html>`_ for more detailed instructions.
 

docs/index.rst

@@ -9,3 +9,7 @@ Contents
    installation/index
    usage
 
+Changelog
+---------
+
+.. include:: ../HISTORY.rst

docs/installation/installation.general.rst

@@ -33,4 +33,4 @@ Resen
 
 Install Resen from a python 3 environment using ``pip``::
 
-    pip install git+https://github.com/EarthCubeInGeo/resen.git@v2019.1.1
+    pip install git+https://github.com/EarthCubeInGeo/resen.git@v2020.1.0

docs/usage.rst

@@ -12,7 +12,7 @@ This will open the resen tool::
        |   / _|\__ \ _|| .` |
        |_|_\___|___/___|_|\_|
 
-    Resen 2019.1.0 -- Reproducible Software Environment
+    Resen 2020.1.0 -- Reproducible Software Environment
 
     [resen] >>>
 
@@ -54,8 +54,8 @@ Setup a New Bucket
    Next, the user is asked to specify the version of resen-core to use::
 
      Please choose a version of resen-core.
-     Available versions: 2019.1.0
-     >>> Select a version: 2019.1.0
+     Available versions: 2019.1.0, 2020.1.0
+     >>> Select a version: 2020.1.0
 
    Optionally, one may then specify a local directory to mount into the bucket at ``/home/jovyan/mount``::
 
@@ -88,7 +88,7 @@ Setup a New Bucket
      amber
      =====
    
-     Resen-core Version:  2019.1.0
+     Resen-core Version:  2020.1.0
      Status:  running
      Jupyter Token:  e7a11fc1ea42a445807b4e24146b9908e1abff82bacbf6f2
      Jupyter Port:  9002
@@ -110,7 +110,7 @@ Work with a Bucket
 
     [resen] >>> list
     Bucket Name         Docker Image             Status
-    amber               2019.1.0                 running
+    amber               2020.1.0                 running
 
    If a bucket is running, it will consume system resources accordingly.
 
@@ -122,7 +122,7 @@ Work with a Bucket
 
     [resen] >>> list
     Bucket Name         Docker Image             Status
-    amber               2019.1.0                 exited
+    amber               2020.1.0                 exited
 
    The bucket will still exist and can be restarted at any time, even after quitting and restarting resen.
 
@@ -134,7 +134,7 @@ Work with a Bucket
 
     [resen] >>> status
     Bucket Name         Docker Image             Status
-    amber               2019.1.0                 running
+    amber               2020.1.0                 running
 
 4. Export bucket ``amber``::
 
@@ -208,6 +208,11 @@ Work with a Bucket
     ...starting jupyterlab...
     Jupyter lab can be accessed in a browser at: http://localhost:9003/?token=70532767bab0ddc4febe2790efaaf974961e961e78e6025a
 
+Sudo-enabled buckets
+--------------------
+
+When starting a bucket with resen, `sudo` is enabled for the jovyan user to allow special installation and configuration
+where root security privileges are needed. The password for running `sudo` commands with user jovyan is: `ganimede`.
 
 Remove a Bucket
 ---------------

resen/DockerHelper.py

@@ -104,12 +104,12 @@ def stop_container(self,bucket):
         return container.status
 
 
-    def execute_command(self,bucket,command,user='jovyan',detach=True):
+    def execute_command(self,bucket,command,user='jovyan',detach=True,tty=False):
         '''
         Execute a command in a container.  Returns the exit code and output
         '''
         container = self.docker.containers.get(bucket['container'])
-        result = container.exec_run(command,user=user,detach=detach)
+        result = container.exec_run(command,user=user,detach=detach,tty=tty)
         return result.exit_code, result.output
 
 

resen/Resen.py

@@ -461,7 +461,7 @@ def stop_bucket(self,bucket_name):
         return
 
 
-    def execute_command(self,bucket_name,command,user='jovyan',detach=True):
+    def execute_command(self,bucket_name,command,user='jovyan',detach=True,tty=False):
         '''
         Execute a command in the bucket.  Returns the exit code and output form the command, if applicable (if not detached?).
         '''
@@ -474,7 +474,7 @@ def execute_command(self,bucket_name,command,user='jovyan',detach=True):
             raise RuntimeError('Bucket %s is not running!' % (bucket['name']))
 
         # execute command
-        result = self.dockerhelper.execute_command(bucket,command,user=user,detach=detach)
+        result = self.dockerhelper.execute_command(bucket,command,user=user,detach=detach,tty=tty)
         code, output = result
         if (detach and code is not None) or (not detach and code!=0):
             raise RuntimeError('Failed to execute command %s' % (command))
@@ -487,7 +487,7 @@ def set_sudo(self, bucket_name, password='ganimede'):
         Add jovyan user to sudoers
         '''
         cmd = "bash -cl 'echo \"jovyan:{}\" | chpasswd && usermod -aG sudo jovyan && sed --in-place \"s/^#\s*\(%sudo\s\+ALL=(ALL:ALL)\s\+ALL\)/\\1/\" /etc/sudoers'".format(password)
-        self.execute_command(bucket_name, cmd, user='root')
+        self.execute_command(bucket_name,cmd,user='root',detach=False,tty=True)
 
         return
 
@@ -726,6 +726,8 @@ def import_bucket(self,bucket_name,filename,extract_dir=None,img_repo=None,img_t
             with tarfile.open(str(extract_dir.joinpath(mount[0]))) as tar:
                 tar.extractall(path=str(extract_dir))
                 local = extract_dir.joinpath(tar.getnames()[0])
+            # remove mount tar file
+            os.remove(str(extract_dir.joinpath(mount[0])))
             # add mount to bucket with original container path
             self.add_storage(bucket_name,str(local),mount[1],permissions=mount[2])
 
@@ -835,7 +837,13 @@ def __get_valid_cores(self):
         #       and if that fails, fallback to hardcoded list
         return [{"version":"2019.1.0","repo":"resen-core","org":"earthcubeingeo",
                  "image_id":'sha256:5300c6652851f35d2fabf866491143f471a7e121998fba27a8dff6b3c064af35',
-                 "repodigest":'sha256:a8ff4a65aa6fee6b63f52290c661501f6de5bf4c1f05202ac8823583eaad4296'},]
+                 "repodigest":'sha256:a8ff4a65aa6fee6b63f52290c661501f6de5bf4c1f05202ac8823583eaad4296'},
+                {"version":"2020.1.0","repo":"resen-core","org":"earthcubeingeo",
+                 "image_id":'sha256:b1f1c9013924c95f678a0aa7403e343cc2ee103f438b1a237193f091170ba077',
+                 "repodigest":'sha256:7bf4e28cf06e40b0e12cb0474232d6d3b520ec1a8c2d361d83fc0cb97083989c'},
+               ]
+
+
 
 
     def _get_config_dir(self):

resen/__init__.py

@@ -1,3 +1,3 @@
-__version__ = '2019.1.1'
+__version__ = '2020.1.0'
 
 from .Resen import Resen

resen/resencmd.py

@@ -260,7 +260,7 @@ def do_import(self,args):
         resen_home_dir = self.program.resen_home_dir
         default_import = os.path.join(resen_home_dir,bucket_name)
         print("The default directory to extract the bucket metadata and mounts to is {}.".format(default_import))
-        rsp = self.get_yn(">>> Would you like to specify and alternate directory? (y/n): ")
+        rsp = self.get_yn(">>> Would you like to specify an alternate directory? (y/n): ")
         if rsp=='y':
             while True:
                 extract_dir = input('>>> Enter path to directory: ')

setup.py

@@ -23,7 +23,7 @@
     # Versions should comply with PEP440.  For a discussion on single-sourcing
     # the version across setup.py and the project code, see
     # https://packaging.python.org/en/latest/single_source_version.html
-    version='2019.1.1',    #TODO: parse this from resen/__init__.py
+    version='2020.1.0',    #TODO: parse this from resen/__init__.py
 
     description='A python package for watching, copying, and transporting files around.',
     long_description=long_description,