Implement shed_init command.

Currently just creates .shed.yml files from command-line arguments. Arguably the tool author could just open this file and start editing but at least --help provides some sort guidance of what fields are available and validates categories for instance. The real reason to add this however is as a stepping stone toward #118.

Author: jmchilton

planemo/commands/cmd_shed_init.py

@@ -0,0 +1,47 @@
+import click
+import sys
+
+from planemo.cli import pass_context
+
+from planemo import options
+from planemo import shed
+
+
+@click.command("shed_init")
+@options.optional_project_arg()
+# TODO:
+# @click.option(
+#    "--from_workflow",
+#    type=click.Path(exists=True, file_okay=True, resolve_path=True),
+#    help=('Attempt to generate repository dependencies from specified '
+#          'workflow.')
+# )
+@click.option(
+    "--description",
+    help='Specify repository description for .shed.yml.'
+)
+@click.option(
+    "--long_description",
+    help='Specify repository long_description for .shed.yml.'
+)
+@click.option(
+    "--remote_repository_url",
+    help='Specify repository remote_repository_url for .shed.yml.'
+)
+@click.option(
+    "--homepage_url",
+    help='Specify repository homepage_url for .shed.yml.'
+)
+@click.option(
+    "--category",
+    multiple=True,
+    help='Specify repository category for .shed.yml (may specify multiple).',
+    type=click.Choice(shed.CURRENT_CATEGORIES)
+)
+@options.shed_owner_option()
+@options.shed_name_option()
+@options.force_option()
+@pass_context
+def cli(ctx, path, **kwds):
+    exit_code = shed.shed_init(ctx, path, **kwds)
+    sys.exit(exit_code)

planemo/commands/cmd_tool_init.py

@@ -1,6 +1,10 @@
 import os
+import sys
+
 import click
+
 from planemo.cli import pass_context
+from planemo import options
 from planemo import io
 from planemo import tool_builder
 
@@ -18,12 +22,7 @@
     prompt=True,
     help="Short identifier for new tool (no whitespace)",
 )
-@click.option(
-    "-f",
-    "--force",
-    is_flag=True,
-    help="Overwrite existing tool if present.",
-)
+@options.force_option(what="tool")
 @click.option(
     "-t",
     "--tool",
@@ -190,9 +189,8 @@ def cli(ctx, **kwds):
     output = kwds.get("tool")
     if not output:
         output = "%s.xml" % kwds.get("id")
-    if not kwds["force"] and os.path.exists(output):
-        io.error("%s already exists, exiting." % output)
-        return 1
+    if not io.can_write_to_path(output, **kwds):
+        sys.exit(1)
     tool_description = tool_builder.build(**kwds)
     open(output, "w").write(tool_description.contents)
     io.info("Tool written to %s" % output)

planemo/io.py

@@ -18,6 +18,13 @@ def info(message, *args):
     _echo(click.style(message, bold=True, fg='green'))
 
 
+def can_write_to_path(path, **kwds):
+    if not kwds["force"] and os.path.exists(path):
+        error("%s already exists, exiting." % path)
+        return False
+    return True
+
+
 def error(message, *args):
     if args:
         message = message % args

planemo/options.py

@@ -4,6 +4,15 @@
 from galaxy.tools.deps import docker_util
 
 
+def force_option(what="files"):
+    return click.option(
+        "-f",
+        "--force",
+        is_flag=True,
+        help="Overwrite existing %s if present." % what,
+    )
+
+
 def test_data_option():
     return click.option(
         "--test_data",

planemo/shed.py

@@ -16,8 +16,11 @@
 except ImportError:
     toolshed = None
 
-from planemo.io import error
-from planemo.io import untar_to
+from planemo.io import (
+    error,
+    untar_to,
+    can_write_to_path,
+)
 
 SHED_CONFIG_NAME = '.shed.yml'
 NO_REPOSITORIES_MESSAGE = ("Could not find any .shed.yml files or a --name to "
@@ -57,6 +60,54 @@
 REPO_TYPE_TOOL_DEP = "tool_dependency_definition"
 REPO_TYPE_SUITE = "repository_suite_definition"
 
+# Generate with python scripts/categories.py
+CURRENT_CATEGORIES = [
+    "Assembly",
+    "ChIP-seq",
+    "Combinatorial Selections",
+    "Computational chemistry",
+    "Convert Formats",
+    "Data Managers",
+    "Data Source",
+    "Fasta Manipulation",
+    "Fastq Manipulation",
+    "Genome-Wide Association Study",
+    "Genomic Interval Operations",
+    "Graphics",
+    "Imaging",
+    "Metabolomics",
+    "Metagenomics",
+    "Micro-array Analysis",
+    "Next Gen Mappers",
+    "Ontology Manipulation",
+    "Phylogenetics",
+    "Proteomics",
+    "RNA",
+    "SAM",
+    "Sequence Analysis",
+    "Statistics",
+    "Systems Biology",
+    "Text Manipulation",
+    "Tool Dependency Packages",
+    "Tool Generators",
+    "Transcriptomics",
+    "Variant Analysis",
+    "Visualization",
+    "Web Services",
+]
+
+
+def shed_init(ctx, path, **kwds):
+    if not os.path.exists(path):
+        os.makedirs(path)
+    shed_config_path = os.path.join(path, SHED_CONFIG_NAME)
+    if not can_write_to_path(shed_config_path, **kwds):
+        # .shed.yml exists and no --force sent.
+        return 1
+
+    _create_shed_config(ctx, shed_config_path, **kwds)
+    return 0
+
 
 def shed_repo_config(path):
     shed_yaml_path = os.path.join(path, SHED_CONFIG_NAME)
@@ -290,6 +341,34 @@ def realize_effective_repositories(path, **kwds):
         shutil.rmtree(temp_directory)
 
 
+def _create_shed_config(ctx, path, **kwds):
+    name = kwds.get("name", None) or path_to_repo_name(os.path.dirname(path))
+    owner = kwds.get("owner", None)
+    if owner is None:
+        owner = ctx.global_config.get("shed_username", None)
+    description = kwds.get("description", None) or name
+    long_description = kwds.get("long_description", None)
+    remote_repository_url = kwds.get("remote_repository_url", None)
+    homepage_url = kwds.get("homepage_url", None)
+    categories = kwds.get("category", [])
+    config = dict(
+        name=name,
+        owner=owner,
+        description=description,
+        long_description=long_description,
+        remote_repository_url=remote_repository_url,
+        homepage_url=homepage_url,
+        categories=categories,
+    )
+    # Remove empty entries...
+    for k in list(config.keys()):
+        if config[k] is None:
+            del config[k]
+
+    with open(path, "w") as f:
+        yaml.dump(config, f)
+
+
 def _find_raw_repositories(path, **kwds):
     name = kwds.get("name", None)
     recursive = kwds.get("recursive", False)

planemo/shed_lint.py

@@ -8,6 +8,7 @@
     REPO_TYPE_UNRESTRICTED,
     REPO_TYPE_TOOL_DEP,
     REPO_TYPE_SUITE,
+    CURRENT_CATEGORIES,
 )
 from planemo.tool_lint import (
     build_lint_args,
@@ -111,6 +112,7 @@ def _lint_if_present(key, func, *args):
     _lint_if_present("owner", _validate_repo_owner)
     _lint_if_present("name", _validate_repo_name)
     _lint_if_present("type", _validate_repo_type, effective_name)
+    _lint_if_present("categories", _validate_categories)
 
 
 def _validate_repo_type(repo_type, name):
@@ -152,3 +154,18 @@ def _validate_repo_owner(owner):
     if not(VALID_PUBLICNAME_RE.match(owner)):
         msg = "Owner must contain only lower-case letters, numbers and '-'"
     return msg
+
+
+def _validate_categories(categories):
+    msg = None
+    if len(categories) == 0:
+        msg = "Repository should specify one or more categories."
+    else:
+        for category in categories:
+            unknown_categories = []
+            if category not in CURRENT_CATEGORIES:
+                unknown_categories.append(category)
+            if unknown_categories:
+                msg = "Categories [%s] unknown." % unknown_categories
+
+    return msg

scripts/categories.py

@@ -0,0 +1,11 @@
+from __future__ import print_function
+import requests
+
+
+categories = requests.get("https://testtoolshed.g2.bx.psu.edu/api/categories").json()
+print("CURRENT_CATEGORIES = [")
+for c in map(lambda c: c["name"], categories):
+     if c["
+     print('    "%s",' % c)
+print("]")
+ 

tests/data/repos/single_tool/.shed.yml

@@ -5,4 +5,4 @@ type: "unrestricted"
 remote_repository_url: "https://github.com/galaxyproject/planemo/tree/master/tests/data/repos/single_tool"
 homepage_url: "http://planemo.readthedocs.org/en/latest/"
 categories:
-  - "Text Utils"
+  - "Text Manipulation"

tests/shed_app_test_utils.py

@@ -21,7 +21,7 @@ def mock_model(directory):
     return InMemoryShedDataModel(
         directory
     ).add_category(
-        "c1", "Text Utils"
+        "c1", "Text Manipulation"
     ).add_category(
         "c2", "Sequence Analysis"
     ).add_repository(

tests/test_shed_init.py

@@ -0,0 +1,52 @@
+import os
+
+import yaml
+
+from .test_utils import CliShedTestCase
+
+
+class ShedInitTestCase(CliShedTestCase):
+
+    def test_minimal(self):
+        with self._isolate() as f:
+            name = os.path.basename(os.path.abspath(f))
+            self._check_exit_code(["shed_init", "--owner", "iuc"])
+            shed_config_path = os.path.join(f, ".shed.yml")
+            assert os.path.exists(shed_config_path)
+            shed_config = yaml.load(open(shed_config_path, "r"))
+            assert shed_config["name"] == name
+            assert shed_config["owner"] == "iuc"
+            assert shed_config["description"] == name
+            assert len(shed_config["categories"]) == 0
+
+    def test_more_options(self):
+        with self._isolate() as f:
+            repo_url = "https://github.com/galaxyproject/tools-devteam"
+            init_command = [
+                "shed_init",
+                "--owner", "devteam",
+                "--name", "samtools-filter",
+                "--description", "A samtools repo",
+                "--long_description", "A longer description.",
+                "--remote_repository_url",
+                repo_url,
+                "--homepage_url", "https://example.com/",
+                "--category", "SAM",
+                "--category", "Sequence Analysis",
+                "--category", "Statistics",
+            ]
+            self._check_exit_code(init_command)
+            shed_config_path = os.path.join(f, ".shed.yml")
+            assert os.path.exists(shed_config_path)
+            shed_config = yaml.load(open(shed_config_path, "r"))
+            assert shed_config["name"] == "samtools-filter"
+            assert shed_config["owner"] == "devteam"
+            assert shed_config["description"] == "A samtools repo"
+            assert shed_config["long_description"] == "A longer description."
+            assert shed_config["remote_repository_url"] == repo_url
+            assert shed_config["homepage_url"] == "https://example.com/"
+
+            categories = shed_config["categories"]
+            assert len(categories) == 3
+            assert "SAM" in categories
+            assert "Statistics" in categories