Merge pull request #57 from vsoch/add/client

Add/client

Author: vsoch

MANIFEST.in

@@ -1,5 +1,6 @@
 include README.md
 include LICENSE
+recursive-include singularity/hub *
 recursive-include singularity/templates *
 recursive-include singularity/static *
 recursive-include singularity/build *

examples/reproducibility/assess_replication.py

@@ -0,0 +1,60 @@
+from glob import glob
+
+from singularity.reproduce import (
+    assess_replication, 
+    assess_differences
+)
+
+image_files=glob('*.img')
+
+# ASSESS REPLICATION #######################################
+# returns booleans for if the hashes for levels are the same
+
+assess_replication(image_files[0],image_files[1])
+
+{'BASE': False,
+ 'ENVIRONMENT': False,
+ 'IDENTICAL': False,
+ 'LABELS': True,
+ 'RECIPE': False,
+ 'REPLICATE': False,
+ 'RUNSCRIPT': False}
+
+assess_replication(image_files[0],image_files[0])
+
+{'BASE': True,
+ 'ENVIRONMENT': True,
+ 'IDENTICAL': True,
+ 'LABELS': True,
+ 'RECIPE': True,
+ 'REPLICATE': True,
+ 'RUNSCRIPT': True}
+
+# ASSESS DIFFERENCES #######################################
+# returns dictionary with 
+
+report = assess_differences(image_files[0],image_files[1])
+
+report.keys()
+# dict_keys(['different', 'missing', 'same'])
+
+# These files are equivalent between the images
+print(len(report['same']))
+5663
+
+# These files are present in both, but different
+print(report['different'])
+['./etc/hosts', 
+ './.exec', 
+ './environment', 
+ './etc/mtab', 
+ './etc/resolv.conf', 
+ './.run', 
+ './.shell', 
+ './singularity']
+
+# These files are found in the first image, but not the second
+print(report['missing'])
+['./var/lib/apt/lists/.wh.archive.ubuntu.com_ubuntu_dists_xenial-updates_main_i18n_Translation-en', 
+ './bin/gunzip']
+

examples/reproducibility/generate_image_hash.py

@@ -0,0 +1,54 @@
+from glob import glob
+
+from singularity.reproduce import (
+    get_image_hash,
+    get_levels,
+    get_content_hashes,
+    get_image_file_hash    
+)
+
+image_files = glob("*.img")
+image_path = image_files[0]
+
+########################################################
+# Get Image Hash (Single Container --> Single Value)
+########################################################
+
+# This function will return a hash specific to a level of 
+# reproducibility, meaning a subset  of files within the 
+# image. You can see the levels for selection:
+
+levels = get_levels()
+
+levels.keys()
+# dict_keys(['IDENTICAL', 'BASE', 'REPLICATE', 'RECIPE', 'RUNSCRIPT', 'ENVIRONMENT', 'LABELS'])
+
+# or specify a different version:
+
+levels = get_levels(version=2.3)
+
+# We can, then generate an image hash, and by default the level "REPLICATION" will be used:
+
+get_image_hash(image_path)
+#'bf8e242931e25ae9496015868ab2e8cc8d156ffd'
+
+# But we can also specify a level that we want:
+get_image_hash(image_path,level="IDENTICAL")
+#'3f4dcf64b58d314ac9ef0c02f641cd2109a07d64'
+
+########################################################
+# Get Image Content Digest (One Container --> Multiple)
+########################################################
+
+
+# We might want to get a dictionary of content hashes for all files
+# of one container at one level!
+digest = get_content_hashes(image_path)
+digest['./usr/bin/pinky']
+# 'ee2b438c278011bdac1a3a927e2d37519a8ed9c7'
+
+# We can also get a hash of the entire image file, this is done on the
+# binary file and not contents inside.
+
+file_hash = get_image_file_hash(image_path)
+# e'13775a83962ae60744d691eb7f7fd1e96599e656'

examples/run_singularity/singularity_client.py

@@ -4,37 +4,43 @@
 
 from singularity.cli import Singularity
 
-# The default will ask for your sudo password, and then not ask again to
-# run commands. It is not stored anywhere, however you should not save / pickle
-# the object as it will expose your password. 
+# Create a client
 S = Singularity()
 
 # Get general help:
 S.help()
 
 # These are the defaults, which can be specified
-S = Singularity(sudo=True,verbose=False)
-
-# Let's define a path to an image
-# wget http://www.vbmis.com/bmi/project/singularity/package_image/ubuntu:latest-2016-04-06.img
-image_path = 'ubuntu:latest-2016-04-06.img'
-
-# Run singularity --exec
-S.execute(image_path=image_path,command='ls')
-# $'docker2singularity.sh\nget_docker_container_id.sh\nget_docker_meta.py\nmakeBases.py\nsingularity\nubuntu:latest-2016-04-06.img\n'
-# These are the defaults, which can be specified
+S = Singularity(sudo=False,sudopw=None,debug=False)
+
+# Create an image
+image = S.create('myimage.img')
+
+# Import into it
+S.importcmd(image,'docker://ubuntu:latest')
+
+# Execute command to container
+result = S.execute(image,command='cat /singularity')
+print(result)
+'''
+#!/bin/sh
+
+if test -x /bin/bash; then
+    exec /bin/bash "$@"
+elif test -x /bin/sh; then
+    exec /bin/sh "$@"
+else
+    echo "ERROR: No valid shell within container"
+    exit 255
+fi
+'''
 
 # For any function you can get the docs:
 S.help(command="exec")
 
-# or return as string
-help = S.help(command="exec",stdout=False)
-
-# export an image, default export_type="tar" , pipe=False , output_file = None will produce file in tmp
-tmptar = S.export(image_path=image_path)
-
-# create an empty image
-S.create(image_path='test.img')
+# export an image as a byte array
+byte_array = S.export(image,pipe=True)
 
-# import a docker image
-S.importcmd(image_path,input_source='docker://ubuntu:latest')
+# Get an in memory tar
+from singularity.reproduce import get_memory_tar
+tar = get_memory_tar(image)