Merge pull request #33 from galaxyproject/shed_diff

Implement shed_diff.

docs/commands.rst

@@ -16,6 +16,7 @@ documentation describes these commands.
 .. include:: commands/lint.rst
 .. include:: commands/project_init.rst
 .. include:: commands/serve.rst
+.. include:: commands/shed_diff.rst
 .. include:: commands/shed_upload.rst
 .. include:: commands/syntax.rst
 .. include:: commands/test.rst

docs/commands/shed_diff.rst

@@ -0,0 +1,47 @@
+
+``shed_diff`` command
+===============================
+
+This section is auto-generated from the help text for the planemo command
+``shed_diff``. This help message can be generated with ``planemo shed_diff
+--help``.
+
+**Usage**::
+
+    planemo shed_diff [OPTIONS] PROJECT
+
+**Help**
+
+Produce diff between local repository and Tool Shed contents.
+
+By default, this will produce a diff between this repository and what
+would be uploaded to the Tool Shed with the `shed_upload` command - but
+this command can be made to compare other combinations of repositories.
+Here are some examples::
+
+    % # diff for this repository and the main Tool Shed
+    % planemo shed_diff
+    % # diff for this repository and the test Tool Shed
+    % planemo shed_diff --shed_target testtoolshed
+    % # diff for the test Tool Shed and main Tool Shed
+    % planemo shed_diff --shed_target_source testtoolshed
+    % # diff for two an explicitly specified repositories (ignores
+    % # current project's shed YAML file.)
+    % planemo shed_diff --owner peterjc --name blast_rbh
+        --shed_target_source testtoolshed
+
+**Options**::
+
+
+      --owner TEXT               Tool Shed repository owner (username).
+      --name TEXT                Tool Shed repository name (defaults to the
+                                 inferred tool directory name).
+      --shed_target TEXT         Tool Shed to target (this can be 'toolshed',
+                                 'testtoolshed', 'local' (alias for
+                                 http://localhost:9009/) or an arbitraryurl).
+      --shed_target_source TEXT  Source Tool Shed to diff against (will ignore
+                                 local project info specified). To compare the
+                                 main Tool Shed against the test, set this to
+                                 testtoolshed.
+      --help                     Show this message and exit.
+    

docs/commands/shed_upload.rst

@@ -18,15 +18,18 @@ Upload a tool directory as a tarball to a tool shed.
 
 
       --message TEXT        Commit message for tool shed upload.
-      --owner TEXT          Tool shed repository owner (username).
-      --name TEXT           Repository name (default to tool directory name).
-      --shed_target TEXT    Tool shed to target (toolshed/testtoolshed/local/url).
-      --shed_key TEXT       API key for shed access (required unless e-mail/pass
-                            specified).
-      --shed_email TEXT     E-mail for shed auth (required unless shed_key is
-                            specified).
-      --shed_password TEXT  Password for shed auth (required unless shed_key is
+      --owner TEXT          Tool Shed repository owner (username).
+      --name TEXT           Tool Shed repository name (defaults to the inferred
+                            tool directory name).
+      --shed_target TEXT    Tool Shed to target (this can be 'toolshed',
+                            'testtoolshed', 'local' (alias for
+                            http://localhost:9009/) or an arbitraryurl).
+      --shed_key TEXT       API key for Tool Shed access (required unless
+                            e-mail/pass specified).
+      --shed_email TEXT     E-mail for Tool Shed auth (required unless shed_key is
                             specified).
+      --shed_password TEXT  Password for Tool Shed auth (required unless shed_key
+                            is specified).
       --tar_only            Produce tar file for upload but do not publish to a
                             tool shed.
       --tar PATH            Specify a pre-existing tar file instead of

planemo/commands/cmd_project_init.py

@@ -6,13 +6,12 @@
 
 from planemo.cli import pass_context
 from planemo import options
-from planemo.io import warn, shell
-from galaxy.tools.deps.commands import which
+from planemo.io import warn, untar_to
 
 SOURCE_HOST = "https://codeload.github.com"
 DOWNLOAD_URL = "%s/galaxyproject/planemo/tar.gz/master" % SOURCE_HOST
 UNTAR_FILTER = "--strip-components=3 --wildcards --no-anchored '%s/**'"
-UNTAR_CMD = "tar -C %s -zxvf - " + UNTAR_FILTER
+UNTAR_ARGS = "-C %s -zxvf - " + UNTAR_FILTER
 
 
 @click.command("project_init")
@@ -32,10 +31,5 @@ def cli(ctx, path, template=None, **kwds):
     if template is None:
         return
 
-    if which("wget"):
-        download_cmd = "wget -O - %s"
-    else:
-        download_cmd = "curl %s"
-    download_cmd = download_cmd % DOWNLOAD_URL
-    untar_cmd = UNTAR_CMD % (path, template)
-    shell("%s | %s" % (download_cmd, untar_cmd))
+    untar_args = UNTAR_ARGS % (path, template)
+    untar_to(DOWNLOAD_URL, path, untar_args)

planemo/commands/cmd_shed_diff.py

@@ -0,0 +1,90 @@
+"""
+"""
+import os
+import shutil
+import tempfile
+
+import click
+
+from planemo.cli import pass_context
+from planemo.io import shell
+from planemo import options
+from planemo import shed
+
+
+@click.command("shed_diff")
+@options.optional_project_arg(exists=True)
+@options.shed_owner_option()
+@options.shed_name_option()
+@options.shed_target_option()
+@click.option(
+    '--shed_target_source',
+    help="Source Tool Shed to diff against (will ignore local project info"
+         " specified). To compare the main Tool Shed against the test, set"
+         " this to testtoolshed.",
+    default=None,
+)
+@pass_context
+def cli(ctx, path, **kwds):
+    """Produce diff between local repository and Tool Shed contents.
+
+    By default, this will produce a diff between this repository and what
+    would be uploaded to the Tool Shed with the `shed_upload` command - but
+    this command can be made to compare other combinations of repositories.
+    Here are some examples::
+
+        % # diff for this repository and the main Tool Shed
+        % planemo shed_diff
+        % # diff for this repository and the test Tool Shed
+        % planemo shed_diff --shed_target testtoolshed
+        % # diff for the test Tool Shed and main Tool Shed
+        % planemo shed_diff --shed_target_source testtoolshed
+        % # diff for two an explicitly specified repositories (ignores
+        % # current project's shed YAML file.)
+        % planemo shed_diff --owner peterjc --name blast_rbh
+            --shed_target_source testtoolshed
+    """
+    working = tempfile.mkdtemp(prefix="tool_shed_diff_")
+    try:
+        diff_in(ctx, working, path, **kwds)
+    finally:
+        shutil.rmtree(working)
+
+
+def diff_in(ctx, working, path, **kwds):
+    shed_target_source = kwds.get("shed_target_source", None)
+
+    label_a = "_%s_" % (shed_target_source if shed_target_source else "local")
+    label_b = "_%s_" % kwds.get("shed_target", "B")
+
+    mine = os.path.join(working, label_a)
+    other = os.path.join(working, label_b)
+
+    tsi = shed.tool_shed_client(ctx, read_only=True, **kwds)
+    shed.download_tarball(
+        ctx,
+        tsi,
+        path,
+        destination=other,
+        clean=True,
+        **kwds
+    )
+
+    if shed_target_source:
+        new_kwds = kwds.copy()
+        new_kwds["shed_target"] = shed_target_source
+        tsi = shed.tool_shed_client(ctx, read_only=True, **new_kwds)
+        shed.download_tarball(
+            ctx,
+            tsi,
+            path,
+            destination=mine,
+            clean=True,
+            **new_kwds
+        )
+    else:
+        tar_path = shed.build_tarball(path)
+        cmd_template = 'mkdir "%s"; tar -xzf "%s" -C "%s"; rm -rf %s'
+        shell(cmd_template % (mine, tar_path, mine, tar_path))
+
+    shell('cd "%s"; diff -r %s %s' % (working, label_a, label_b))

planemo/commands/cmd_shed_download.py

@@ -0,0 +1,35 @@
+"""
+"""
+import click
+
+from planemo.cli import pass_context
+from planemo import options
+from planemo import shed
+
+target_path = click.Path(
+    file_okay=True,
+    writable=True,
+    resolve_path=True,
+)
+
+
+@click.command("shed_download")
+@options.optional_project_arg(exists=True)
+@click.option(
+    '--destination',
+    default="shed_download.tar.gz",
+    type=target_path,
+    help="Destination of tarball to download - if this doesn't end in 'gz' it "
+         "will be treated as a directory to extract tool contents into"
+         "(defaults to shed_download.tar.gz)."
+)
+@options.shed_owner_option()
+@options.shed_name_option()
+@options.shed_target_option()
+@pass_context
+def cli(ctx, path, **kwds):
+    """Download a tool repository as a tarball from the tool shed and extract
+    to the specified directory.
+    """
+    tsi = shed.tool_shed_client(ctx, read_only=True, **kwds)
+    shed.download_tarball(ctx, tsi, path, **kwds)

planemo/commands/cmd_shed_upload.py

@@ -26,30 +26,23 @@
     '--message',
     help="Commit message for tool shed upload."
 )
-@click.option(
-    '--owner',
-    help="Tool shed repository owner (username)."
-)
-@click.option(
-    '--name',
-    help="Repository name (default to tool directory name)."
-)
-@click.option(
-    '--shed_target',
-    help="Tool shed to target (toolshed/testtoolshed/local/url).",
-    default="toolshed",
-)
+@options.shed_owner_option()
+@options.shed_name_option()
+@options.shed_target_option()
 @click.option(
     '--shed_key',
-    help="API key for shed access (required unless e-mail/pass specified)."
+    help="API key for Tool Shed access (required unless e-mail/pass "
+         "specified)."
 )
 @click.option(
     '--shed_email',
-    help="E-mail for shed auth (required unless shed_key is specified)."
+    help="E-mail for Tool Shed auth (required unless shed_key is "
+         "specified)."
 )
 @click.option(
     '--shed_password',
-    help="Password for shed auth (required unless shed_key is specified)."
+    help="Password for Tool Shed auth (required unless shed_key is "
+         "specified)."
 )
 @click.option(
     '--tar_only',
@@ -64,7 +57,7 @@
     default=None,
 )
 @pass_context
-def cli(ctx, path, template=None, **kwds):
+def cli(ctx, path, **kwds):
     """Upload a tool directory as a tarball to a tool shed.
     """
     tar_path = kwds.get("tar", None)

planemo/io.py

@@ -1,5 +1,8 @@
+import os
+
 import click
 from galaxy.tools.deps import commands
+from galaxy.tools.deps.commands import which
 
 
 def shell(cmds, **kwds):
@@ -23,3 +26,19 @@ def warn(message, *args):
     if args:
         message = message % args
     click.echo(click.style(message, fg='red'), err=True)
+
+
+def untar_to(url, path, tar_args):
+    if which("wget"):
+        download_cmd = "wget -q --recursive -O - '%s'"
+    else:
+        download_cmd = "curl '%s'"
+    download_cmd = download_cmd % url
+    if tar_args:
+        if not os.path.exists(path):
+            os.makedirs(path)
+
+        untar_cmd = "tar %s" % tar_args
+        shell("%s | %s" % (download_cmd, untar_cmd))
+    else:
+        shell("%s > '%s'" % (download_cmd, path))

planemo/options.py

@@ -164,3 +164,28 @@ def docker_host_option():
         help="Docker host to target when executing docker commands " +
              "(defaults to localhost)."
     )
+
+
+def shed_owner_option():
+    return click.option(
+        '--owner',
+        help="Tool Shed repository owner (username)."
+    )
+
+
+def shed_name_option():
+    return click.option(
+        '--name',
+        help="Tool Shed repository name (defaults to the inferred "
+             "tool directory name)."
+    )
+
+
+def shed_target_option():
+    return click.option(
+        '--shed_target',
+        help="Tool Shed to target (this can be 'toolshed', 'testtoolshed', "
+             "'local' (alias for http://localhost:9009/) or an arbitrary"
+             "url).",
+        default="toolshed",
+    )