Add function to create volumes for mounting on login

.gitignore

@@ -5,6 +5,7 @@ tmp
 .images
 images/test-install/requirements.txt
 biobox_verify
+.biobox_tmp
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

biobox_cli/assets/login_parameters.yml

@@ -1,2 +1,17 @@
 ---
-short_read_assembler: "params"
+short_read_assembler:
+  - /bbx/output:
+  - /bbx/input:
+    - type: path
+      src: genome_paired_reads.fq.gz
+      dst: reads.fq.gz
+    - type: literal
+      dst: biobox.yaml
+      src: |
+        version: 0.9.0
+        arguments:
+        - fastq:
+          - value: /bbx/input/reads.fq.gz
+            type: paired
+            id: 0
+

biobox_cli/command/login.py

@@ -14,12 +14,17 @@
 """
 
 import yaml
+import os.path
+import shutil
 
 import biobox_cli.util.misc   as util
 import biobox_cli.util.assets as asset
 import biobox_cli.util.error  as error
 import biobox_cli.container   as docker
 
+TEMPORARY_DIRECTORY = '.biobox_tmp'
+
+
 def get_login_parameters(biobox_type):
     """
     Determines if the biobox type is currently supported for login. Returns
@@ -33,18 +38,22 @@ def get_login_parameters(biobox_type):
 
 
 def create_login_file(dir_, params):
-    from os.path import join
-    from shutil  import copyfile
-
     is_literal = params['type'] == 'literal'
-    dst = join(dir_, params['dst'])
+    dst = os.path.join(dir_, params['dst'])
 
     if is_literal:
         with open(dst, 'w') as f:
             f.write(params['src'])
     else:
         src = asset.get_data_file_path(params['src'])
-        copyfile(src, dst)
+        shutil.copyfile(src, dst)
+
+
+def create_login_volume((dir_name, files)):
+    src = util.mkdir_p(os.path.join(TEMPORARY_DIRECTORY, dir_name.strip("/")))
+    for f in files:
+        create_login_file(src, f)
+    return docker.mount_string(src, dir_name, False)
 
 
 def run(argv):
@@ -55,14 +64,14 @@ def run(argv):
     tty         = not "--no-tty" in opts["<args>"]
     remove      = not "--no-rm"  in opts["<args>"]
 
+    docker.exit_if_no_image_available(image)
+
     params = get_login_parameters(biobox_type)
     if params is None:
         error.err_exit("unknown_command",
                 {"command_type" : "biobox type", "command" : biobox_type})
-
-    docker.exit_if_no_image_available(image)
-
-    ctnr = docker.create_tty(image, tty)
+    volumes = map(create_login_volume, params)
+    ctnr = docker.create_tty(image, tty, volumes)
     docker.login(ctnr)
 
     if remove:

biobox_cli/container.py

@@ -38,6 +38,9 @@ def mount_string(host_dir, container_dir, read_only = True):
 def output_directory_mount_string(directory):
     return mount_string(directory, "/bbx/output", False)
 
+def input_directory_mount_string(directory):
+    return mount_string(directory, "/bbx/input", True)
+
 def biobox_file_mount_string(directory):
     return mount_string(directory, "/bbx/input")
 

biobox_cli/util/misc.py

@@ -1,4 +1,5 @@
 import sys
+import os.path
 import biobox_cli.util.error  as error
 
 def select_module(module, name):
@@ -20,3 +21,14 @@ def parse_docopt(doc, argv, is_main_module):
                   argv          = argv,
                   version       = __version__,
                   options_first = is_main_module)
+
+# http://stackoverflow.com/a/600612
+def mkdir_p(path):
+    import os, errno
+    try:
+        os.makedirs(path)
+    except OSError as exc: # Python >2.5
+        if exc.errno == errno.EEXIST and os.path.isdir(path):
+            pass
+        else: raise
+    return os.path.abspath(path)

features/login.feature

@@ -18,3 +18,4 @@ Feature: Allow a user to ssh into an image to test internally
       input:
       biobox.yaml reads.fq.gz
       """
+    And the directory ".biobox_tmp" should not exist

test/helper.py

@@ -1,4 +1,5 @@
-import os
+import os, os.path
+import nose.tools           as nose
 import biobox_cli.container as ctn
 
 def project_root():
@@ -10,3 +11,12 @@ def is_ci_server():
 def remove_container(container):
     if not is_ci_server():
         ctn.remove(container)
+
+def assert_file_not_empty(file_):
+    file_size = os.stat(file_).st_size
+    nose.assert_not_equal(file_size, 0,
+            "File should not be empty but is: {}".format(file_))
+
+def assert_file_contents_equal(file_, contents):
+    with open(file_, 'r') as f:
+        nose.assert_equal(f.read(), contents)

test/test_login.py

@@ -3,24 +3,42 @@
 import helper                   as hlpr
 import tempfile                 as tmp
 
-from os.path import join
-from os      import stat
+import os.path
+import shutil
 
 def test_get_login_parameters_with_unknown_type():
     nose.assert_equal(None, login.get_login_parameters('unknown'))
 
+
+TMP_DIR       = tmp.mkdtemp()
+TMP_FILE_NAME = 'tmp_file'
+TMP_PATH      = os.path.join(TMP_DIR, TMP_FILE_NAME)
+
+def rm_tmp_file():
+    if os.path.exists(TMP_PATH):
+        os.remove(TMP_PATH)
+
+def rm_tmp_login_dir():
+    shutil.rmtree(login.TEMPORARY_DIRECTORY)
+
+@nose.with_setup(teardown = rm_tmp_file)
 def test_create_login_file_literal():
-    file_name = 'file_name'
-    value = {'type': 'literal', 'src': 'literal_string', 'dst': file_name}
-    directory = tmp.mkdtemp()
-    login.create_login_file(directory, value)
-    with open(join(directory, file_name)) as f:
-        nose.assert_equal('literal_string', f.read())
+    value = {'type': 'literal', 'src': 'literal_string', 'dst': TMP_FILE_NAME}
+    login.create_login_file(TMP_DIR, value)
+    hlpr.assert_file_contents_equal(TMP_PATH, 'literal_string')
 
+@nose.with_setup(teardown = rm_tmp_file)
 def test_create_login_file_path():
-    file_name = 'file_name'
-    value = {'type': 'path', 'src': 'genome_paired_reads.fq.gz', 'dst': file_name}
-    directory = tmp.mkdtemp()
-    login.create_login_file(directory, value)
-    file_size = stat(join(directory, file_name)).st_size
-    nose.assert_not_equal(file_size, 0)
+    value = {'type': 'path', 'src': 'genome_paired_reads.fq.gz', 'dst': TMP_FILE_NAME}
+    login.create_login_file(TMP_DIR, value)
+    hlpr.assert_file_not_empty(TMP_PATH)
+
+@nose.with_setup(teardown = rm_tmp_login_dir)
+def test_create_login_volume():
+    dst_dir = '/bbx/input'
+    value     = [dst_dir, [{'type': 'literal', 'src': 'literal_string', 'dst': TMP_FILE_NAME}]]
+    volume = login.create_login_volume(value)
+    dir_path = os.path.join(login.TEMPORARY_DIRECTORY, dst_dir.strip("/"))
+    hlpr.assert_file_not_empty(os.path.join(dir_path, TMP_FILE_NAME))
+    hlpr.assert_file_contents_equal(os.path.join(dir_path, TMP_FILE_NAME), 'literal_string')
+    nose.assert_in(':'.join([dir_path, dst_dir, 'rw']), volume)