adding pull command for shub, and testing get_files command

Author: vsoch

singularity/analysis/classify.py

@@ -22,6 +22,8 @@
 from singularity.package import package as make_package
 from singularity.utils import (
     get_installdir,
+    remove_uri,
+    read_file,
     update_dict,
     update_dict_sum
 )
@@ -175,6 +177,33 @@ def get_tags(container=None,image_package=None,sudopw=None,search_folders=None,d
 ###################################################################################
 
 
+def get_files(container,S=None):
+    '''get_files will return a list of files inside a container, sorted by name
+    :param container: the container to use, either shub:// or docker:// or actual
+    '''
+    files = None
+    tmpdir = tempfile.mkdtemp()
+    tmpfile = "%s/files.txt" %tmpdir
+    container_name = remove_uri(container)
+    command = 'ls -LR >> %s 2>/dev/null' %(tmpfile)
+    if S==None:
+        S = Singularity(sudo=None)
+    result = S.execute(container,command)
+    if os.path.exists(tmpfile):
+        os.system("sed -i '/^$/d' %s" %(tmpfile))
+        os.system('sort %s -or %s' %(tmpfile,tmpfile))
+        files = read_file(tmpfile)
+        rootfs=None
+        if len(files) > 0:
+            files = [x for x in files if x.startswith('.')]
+            files = [x.split(container_name)[1:] for x in files]
+            files = [x for x in files if len(x) > 0]
+            files = [x[0] for x in files]    
+    shutil.rmtree(tmpdir)
+    return files
+
+        
+
 def file_counts(container=None,patterns=None,image_package=None,sudopw=None,diff=None):
     '''file counts will return a list of files that match one or more regular expressions.
     if no patterns is defined, a default of readme is used. All patterns and files are made

singularity/build/converter.py

@@ -218,7 +218,7 @@ def get_mapping():
     workdir_command = {"section": "%post","fun": parse_workdir, "json": False }  
     entry_command = {"section": "%runscript", "fun": parse_entry, "json": True }
 
-    return {"ADD": add_command,
+    return {"ADD":add_command,
             "COPY":copy_command,
             "CMD":cmd_command,
             "ENTRYPOINT":entry_command,
@@ -228,7 +228,7 @@ def get_mapping():
             "WORKDIR":workdir_command,
             "MAINTAINER":comment_command,
             "VOLUME":comment_command,
-            "PORT":port_command,
+            "EXPOSE":port_command,
             "LABEL":label_command}
 
 

singularity/cli.py

@@ -27,7 +27,8 @@
 
 class Singularity:
 
-    def __init__(self,sudo=True,sudopw=None,debug=False):
+
+    def __init__(self,sudo=False,sudopw=None,debug=False):
        '''upon init, store user password to not ask for it again'''
 
        self.sudopw = sudopw
@@ -117,7 +118,7 @@ def execute(self,image_path,command,writable=False,contain=False):
         if self.debug == True:
             cmd = ["singularity",'--debug',"exec"]
         else:
-            cmd = ["singularity","exec"]
+            cmd = ["singularity",'--quiet',"exec"]
 
         cmd = self.add_flags(cmd,writable=writable,contain=contain)
 
@@ -194,6 +195,21 @@ def importcmd(self,image_path,input_source,import_type=None,command=None):
         return None
 
 
+    def pull(self,image_path):
+        '''pull will pull a singularity hub image
+        :param image_path: full path to image
+        ''' 
+        if not image_path.startswit('shub://'):
+            bot.logger.error("pull is only valid for the shub://uri, %s is invalid.",image_name)
+            sys.exit(1)           
+
+        if self.debug == True:
+            cmd = ['singularity','--debug','pull',image_path]
+        else:
+            cmd = ['singularity','pull',image_path]
+        return self.run_command(cmd)
+
+
 
     def run(self,image_path,command,writable=False,contain=False):
         '''run will run a command inside the container, probably not intended for within python
@@ -213,6 +229,7 @@ def run(self,image_path,command,writable=False,contain=False):
         # Run the command
         return self.run_command(cmd,sudo=sudo)
 
+
     def start(self,image_path,writable=False,contain=False):
         '''start will start a container
         '''
@@ -276,7 +293,7 @@ def get_image(image,return_existed=False,sudopw=None,size=None,debug=False):
             cli = Singularity(debug=debug) # This command will ask the user for sudo
 
         tmpdir = tempfile.mkdtemp()
-        image_name = "%s.img" %image.replace("docker://","") 
+        image_name = "%s.img" %image.replace("docker://","").replace("/","-")
         bot.logger.info("Found docker image %s, creating and importing...",image_name)
         image_path = "%s/%s" %(tmpdir,image_name)
         cli.create(image_path,size=size)

singularity/utils.py

@@ -304,6 +304,12 @@ def format_container_name(name,special_characters=None):
     return ''.join(e.lower() for e in name if e.isalnum() or e in special_characters)
 
 
+def remove_uri(container):
+    '''remove_uri will remove docker:// or shub:// from the uri
+    '''
+    return container.replace('docker://','').replace('shub://','')
+
+
 def download_repo(repo_url,destination,commit=None):
     '''download_repo
     :param repo_url: the url of the repo to clone from

singularity/version.py

@@ -1,4 +1,4 @@
-__version__ = "1.0.10"
+__version__ = "1.1.0"
 AUTHOR = 'Vanessa Sochat'
 AUTHOR_EMAIL = '[email protected]'
 NAME = 'singularity'