Implement run/test/workflow_edit/autoupdate from non default tool sheds

planemo/autoupdate.py

@@ -19,20 +19,21 @@
 
 import requests
 import yaml
-from bioblend import toolshed
 from bioblend.toolshed import ToolShedInstance
 from galaxy.tool_util.deps import conda_util
 from galaxy.tool_util.version import parse_version
 
 import planemo.conda
+from planemo.galaxy.workflows import (
+    get_tool_ids_for_workflow,
+    get_toolshed_url_for_tool_id,
+    MAIN_TOOLSHED_URL,
+)
 from planemo.io import (
     error,
     info,
 )
-from planemo.workflow_lint import (
-    find_repos_from_tool_id,
-    MAIN_TOOLSHED_URL,
-)
+from planemo.workflow_lint import find_repos_from_tool_id
 
 if TYPE_CHECKING:
     from planemo.cli import PlanemoCliContext
@@ -294,7 +295,7 @@ def get_newest_tool_id(tool_ids: List[str]) -> str:
 
 
 def outdated_tools(  # noqa: C901
-    ctx: "PlanemoCliContext", wf_dict: Dict[str, Any], ts: ToolShedInstance, tools_to_skip: List[str]
+    ctx: "PlanemoCliContext", wf_dict: Dict[str, Any], tools_to_skip: List[str]
 ) -> Dict[str, Dict[str, str]]:
     """
     tools_to_skip should be a list of base tool ids.
@@ -305,8 +306,12 @@ def base_tool_id(tool_id: str) -> str:
 
     def check_tool_step(tool_id: str) -> Dict[str, Dict[str, str]]:
         """
-        Return a dict with current and newest tool version, in case they don't match
+        Return a dict with current and newest tool version, in case they don't match.
         """
+        tool_shed_url = get_toolshed_url_for_tool_id(tool_id)
+        if not tool_shed_url:
+            return {}
+        ts = ToolShedInstance(tool_shed_url)
         warning_msg, repos = find_repos_from_tool_id(tool_id, ts)
         if warning_msg != "":
             ctx.log(warning_msg)
@@ -328,20 +333,12 @@ def check_tool_step(tool_id: str) -> Dict[str, Dict[str, str]]:
             return {}
 
     def outdated_tools_rec(wf_dict: Dict[str, Any]) -> None:
-        steps = wf_dict["steps"].values() if isinstance(wf_dict["steps"], dict) else wf_dict["steps"]
-        for step in steps:
-            if step.get("type", "tool") == "tool" and not step.get("run", {}).get("class") == "GalaxyWorkflow":
-                tool_id = step["tool_id"]
-                base_id = base_tool_id(tool_id)
-                if base_id not in checked_tools:
-                    outdated_tool_dict.update(check_tool_step(tool_id))
-                    checked_tools.append(base_id)
-            elif step.get("type") == "subworkflow":  # GA SWF
-                outdated_tools_rec(step["subworkflow"])
-            elif step.get("run", {}).get("class") == "GalaxyWorkflow":  # gxformat2 SWF
-                outdated_tools_rec(step["run"])
-            else:
-                continue
+        tool_ids = get_tool_ids_for_workflow(wf_dict)
+        for tool_id in tool_ids:
+            base_id = base_tool_id(tool_id)
+            if base_id not in checked_tools:
+                outdated_tool_dict.update(check_tool_step(tool_id))
+                checked_tools.append(base_id)
 
     outdated_tool_dict: Dict[str, Dict[str, str]] = {}
     # Initialize the list of tools already checked with a copy of tools_to_skip
@@ -359,8 +356,7 @@ def get_tools_to_update(
     with open(workflow.path) as f:
         wf_dict = yaml.load(f, Loader=yaml.SafeLoader)
 
-    ts = toolshed.ToolShedInstance(url=MAIN_TOOLSHED_URL)
-    return outdated_tools(ctx, wf_dict, ts, tools_to_skip)
+    return outdated_tools(ctx, wf_dict, tools_to_skip)
 
 
 def autoupdate_wf(ctx: "PlanemoCliContext", config: "LocalGalaxyConfig", wf: "Runnable") -> Dict[str, Any]:

planemo/galaxy/config.py

@@ -35,7 +35,10 @@
 from planemo.config import OptionSource
 from planemo.deps import ensure_dependency_resolvers_conf_configured
 from planemo.docker import docker_host_args
-from planemo.galaxy.workflows import remote_runnable_to_workflow_id
+from planemo.galaxy.workflows import (
+    get_toolshed_url_for_tool_id,
+    remote_runnable_to_workflow_id,
+)
 from planemo.io import (
     communicate,
     kill_pid_file,
@@ -48,6 +51,7 @@
     write_file,
 )
 from planemo.mulled import build_involucro_context
+from planemo.runnable import RunnableType
 from planemo.shed import tool_shed_url
 from .api import (
     DEFAULT_ADMIN_API_KEY,
@@ -60,6 +64,7 @@
     find_tool_ids,
     import_workflow,
     install_shed_repos,
+    MAIN_TOOLSHED_URL,
 )
 
 if TYPE_CHECKING:
@@ -258,7 +263,7 @@ def config_join(*args):
         shed_tool_path = kwds.get("shed_tool_path") or config_join("shed_tools")
         _ensure_directory(shed_tool_path)
 
-        sheds_config_path = _configure_sheds_config_file(ctx, config_directory, **kwds)
+        sheds_config_path = _configure_sheds_config_file(ctx, config_directory, runnables, **kwds)
         port = _get_port(kwds)
         properties = _shared_galaxy_properties(config_directory, kwds, for_tests=for_tests)
         _handle_container_resolution(ctx, kwds, properties)
@@ -389,7 +394,7 @@ def config_join(*args):
         shed_tool_path = kwds.get("shed_tool_path") or config_join("shed_tools")
         _ensure_directory(shed_tool_path)
 
-        sheds_config_path = _configure_sheds_config_file(ctx, config_directory, **kwds)
+        sheds_config_path = _configure_sheds_config_file(ctx, config_directory, runnables, **kwds)
 
         database_location = config_join("galaxy.sqlite")
         master_api_key = _get_master_api_key(kwds)
@@ -568,19 +573,27 @@ def _all_tool_paths(
     all_tool_paths = {r.path for r in runnables if r.has_tools and not r.data_manager_conf_path}
     extra_tools = _expand_paths(galaxy_root, extra_tools=extra_tools)
     all_tool_paths.update(extra_tools)
-    for runnable in runnables:
-        if runnable.type.name == "galaxy_workflow":
-            tool_ids = find_tool_ids(runnable.path)
-            for tool_id in tool_ids:
-                tool_paths = DISTRO_TOOLS_ID_TO_PATH.get(tool_id)
-                if tool_paths:
-                    if isinstance(tool_paths, str):
-                        tool_paths = [tool_paths]
-                    all_tool_paths.update(tool_paths)
+    for tool_id in get_tool_ids_for_runnables(runnables):
+        tool_paths = DISTRO_TOOLS_ID_TO_PATH.get(tool_id)
+        if tool_paths:
+            if isinstance(tool_paths, str):
+                tool_paths = [tool_paths]
+            all_tool_paths.update(tool_paths)
 
     return all_tool_paths
 
 
+def get_workflow_runnables(runnables: List["Runnable"]) -> List["Runnable"]:
+    return [r for r in runnables if r.type == RunnableType.galaxy_workflow and r.has_path]
+
+
+def get_tool_ids_for_runnables(runnables) -> List[str]:
+    tool_ids = []
+    for r in get_workflow_runnables(runnables):
+        tool_ids.extend(find_tool_ids(r.path))
+    return list(dict.fromkeys(tool_ids))
+
+
 def _shared_galaxy_properties(config_directory, kwds, for_tests):
     """Setup properties useful for local and Docker Galaxy instances.
 
@@ -1201,12 +1214,36 @@ def _search_tool_path_for(path, target, extra_paths=None):
     return None
 
 
-def _configure_sheds_config_file(ctx, config_directory, **kwds):
-    if "shed_target" not in kwds:
-        kwds = kwds.copy()
-        kwds["shed_target"] = "toolshed"
-    shed_target_url = tool_shed_url(ctx, **kwds)
-    contents = _sub(TOOL_SHEDS_CONF, {"shed_target_url": shed_target_url})
+def get_tool_sheds_conf_for_runnables(runnables: Optional[List["Runnable"]]) -> Optional[str]:
+    if runnables:
+        tool_ids = get_tool_ids_for_runnables(runnables)
+        return get_shed_tools_conf_string_for_tool_ids(tool_ids)
+    return None
+
+
+def get_shed_tools_conf_string_for_tool_ids(tool_ids: List[str]) -> str:
+    tool_shed_urls = set(get_toolshed_url_for_tool_id(tool_id) for tool_id in tool_ids if tool_id)
+    # always add main toolshed
+    tool_shed_urls.add(MAIN_TOOLSHED_URL)
+    cleaned_tool_shed_urls = set(_ for _ in tool_shed_urls if _ is not None)
+    TOOL_SHEDS_CONF_TEMPLATE = Template("""<tool_sheds>${tool_shed_lines}</tool_sheds>""")
+    tool_sheds: List[str] = []
+    # sort tool_shed_urls from shortest to longest, as https://github.com/galaxyproject/galaxy/blob/c7cb47a1b18ccd5b39075a705bbd2f34572755fe/lib/galaxy/util/tool_shed/tool_shed_registry.py#L106-L118
+    # has a bug where a toolshed that is an exact substring of another registered toolshed would wrongly be selected.
+    for shed_url in sorted(cleaned_tool_shed_urls, key=lambda url: len(url)):
+        tool_sheds.append(f'<tool_shed name="{shed_url.split("://")[-1]}" url="{shed_url}" />')
+    return TOOL_SHEDS_CONF_TEMPLATE.substitute(tool_shed_lines="".join(tool_sheds))
+
+
+def _configure_sheds_config_file(ctx, config_directory, runnables, **kwds):
+    # Find tool sheds to add to config
+    contents = get_tool_sheds_conf_for_runnables(runnables)
+    if not contents:
+        if "shed_target" not in kwds:
+            kwds = kwds.copy()
+            kwds["shed_target"] = "toolshed"
+        shed_target_url = tool_shed_url(ctx, **kwds)
+        contents = _sub(TOOL_SHEDS_CONF, {"shed_target_url": shed_target_url})
     tool_sheds_conf = os.path.join(config_directory, "tool_sheds_conf.xml")
     write_file(tool_sheds_conf, contents)
     return tool_sheds_conf

planemo/galaxy/workflows.py

@@ -3,14 +3,17 @@
 import json
 import os
 from collections import namedtuple
+from functools import lru_cache
 from typing import (
     Any,
     Callable,
     Dict,
     List,
+    Optional,
 )
 from urllib.parse import urlparse
 
+import requests
 import yaml
 from ephemeris import (
     generate_tool_list_from_ga_workflow_files,
@@ -35,6 +38,35 @@
 FAILED_REPOSITORIES_MESSAGE = "Failed to install one or more repositories."
 GALAXY_WORKFLOWS_PREFIX = "gxid://workflows/"
 GALAXY_WORKFLOW_INSTANCE_PREFIX = "gxid://workflow-instance/"
+MAIN_TOOLSHED_URL = "https://toolshed.g2.bx.psu.edu"
+
+
+@lru_cache(maxsize=None)
+def guess_tool_shed_url(tool_shed_fqdn: str) -> Optional[str]:
+    if tool_shed_fqdn in MAIN_TOOLSHED_URL:
+        return MAIN_TOOLSHED_URL
+    else:
+        # guess if tool shed is served over https or http
+        https_tool_shed_url = f"https://{tool_shed_fqdn}"
+        r = requests.get(https_tool_shed_url)
+        if r.status_code == 200:
+            return https_tool_shed_url
+        else:
+            http_tool_shed_url = f"http://{tool_shed_fqdn}"
+            r = requests.get(http_tool_shed_url)
+            if r.status_code == 200:
+                return http_tool_shed_url
+            else:
+                warn(f"Could not connect to {tool_shed_fqdn}")
+    return None
+
+
+def get_toolshed_url_for_tool_id(tool_id: str) -> Optional[str]:
+    components = tool_id.split("/repos")
+    if len(components) > 1:
+        tool_shed_fqdn = components[0]
+        return guess_tool_shed_url(tool_shed_fqdn=tool_shed_fqdn)
+    return None
 
 
 def load_shed_repos(runnable):
@@ -62,6 +94,12 @@ def load_shed_repos(runnable):
             if repository:
                 repository["tool_panel_section_label"] = "Tools from workflows"
                 tools.append(repository)
+    for repo in tools:
+        tool_shed = repo.get("tool_shed")
+        if tool_shed:
+            tool_shed_url = guess_tool_shed_url(tool_shed)
+            if tool_shed_url:
+                repo["tool_shed_url"] = tool_shed_url
     return tools
 
 
@@ -134,20 +172,25 @@ def _raw_dict(path, importer=None):
     return workflow
 
 
-def find_tool_ids(path):
-    tool_ids = set()
-    workflow = _raw_dict(path)
-
-    def register_tool_ids(tool_ids, workflow):
-        for step in workflow["steps"].values():
-            if step.get("subworkflow"):
-                register_tool_ids(tool_ids, step["subworkflow"])
-            elif step.get("tool_id"):
-                tool_ids.add(step["tool_id"])
+def get_tool_ids_for_workflow(wf_dict: Dict[str, Any], tool_ids: Optional[List[str]] = None) -> List[str]:
+    tool_ids = [] if tool_ids is None else tool_ids
+    steps = wf_dict["steps"].values() if isinstance(wf_dict["steps"], dict) else wf_dict["steps"]
+    for step in steps:
+        if step.get("type", "tool") == "tool" and not step.get("run", {}).get("class") == "GalaxyWorkflow":
+            tool_id = step["tool_id"]
+            tool_ids.append(tool_id)
+        elif step.get("type") == "subworkflow":  # GA SWF
+            get_tool_ids_for_workflow(step["subworkflow"], tool_ids=tool_ids)
+        elif step.get("run", {}).get("class") == "GalaxyWorkflow":  # gxformat2 SWF
+            get_tool_ids_for_workflow(step["run"], tool_ids=tool_ids)
+        else:
+            continue
+    return list(dict.fromkeys(tool_ids))
 
-    register_tool_ids(tool_ids, workflow)
 
-    return list(tool_ids)
+def find_tool_ids(path):
+    workflow = _raw_dict(path)
+    return get_tool_ids_for_workflow(workflow)
 
 
 WorkflowOutput = namedtuple("WorkflowOutput", ["order_index", "output_name", "label", "optional"])

planemo/workflow_lint.py

@@ -35,6 +35,7 @@
 )
 from planemo.galaxy.workflows import (
     input_labels,
+    MAIN_TOOLSHED_URL,
     output_labels,
     required_input_labels,
 )
@@ -51,8 +52,6 @@
 POTENTIAL_WORKFLOW_FILES = re.compile(r"^.*(\.yml|\.yaml|\.ga)$")
 DOCKSTORE_REGISTRY_CONF_VERSION = "1.2"
 
-MAIN_TOOLSHED_URL = "https://toolshed.g2.bx.psu.edu"
-
 
 class WorkflowLintContext(LintContext):
     # Setup training topic for linting - probably should pass this through
@@ -479,27 +478,44 @@ def find_repos_from_tool_id(tool_id: str, ts: ToolShedInstance) -> Tuple[str, Di
     """
     Return a string which indicates what failed and dict with all revisions for a given tool id
     """
-    if not tool_id.startswith(MAIN_TOOLSHED_URL[8:]):
+    if "/repos" not in tool_id:
         return ("", {})  # assume a built in tool
+    *_, owner, name, _tool_id, _version = tool_id.split("/")
+
     try:
-        repos = ts.repositories._get(params={"tool_ids": tool_id})
-    except Exception:
-        return (f"The ToolShed returned an error when searching for the most recent version of {tool_id}", {})
+        repo = ts.repositories.get_repositories(name, owner)[0]
+        repos = ts.repositories._get(url=f'{ts.repositories._make_url()}/{repo["id"]}/metadata')
+    except Exception as e:
+        return (f"The ToolShed returned an error when searching for the most recent version of {tool_id}: {e}", {})
     if len(repos) == 0:
         return (f"The tool {tool_id} is not in the toolshed (may have been tagged as invalid).", {})
     else:
         return ("", repos)
 
 
+def assert_valid_tool_id_in_tool_shed(tool_id: str, ts: ToolShedInstance) -> Optional[str]:
+    if "/repos" not in tool_id:
+        return None
+    warning_msg, repos = find_repos_from_tool_id(tool_id, ts)
+    if warning_msg:
+        return warning_msg
+    for repo in repos.values():
+        tools = repo.get("tools", [])
+        for tool in tools:
+            if tool_id == tool.get("guid"):
+                return None
+    return f"The tool {tool_id} is not in the toolshed (may have been tagged as invalid)."
+
+
 def _lint_tool_ids(path: str, lint_context: WorkflowLintContext) -> None:
     def _lint_tool_ids_steps(lint_context: WorkflowLintContext, wf_dict: Dict, ts: ToolShedInstance) -> bool:
         """Returns whether a single tool_id was invalid"""
         failed = False
         steps = wf_dict.get("steps", {})
         for step in steps.values():
             if step.get("type", "tool") == "tool" and not step.get("run", {}).get("class") == "GalaxyWorkflow":
-                warning_msg, _ = find_repos_from_tool_id(step["tool_id"], ts)
-                if warning_msg != "":
+                warning_msg = assert_valid_tool_id_in_tool_shed(step["tool_id"], ts)
+                if warning_msg:
                     lint_context.error(warning_msg)
                     failed = True
             elif step.get("type") == "subworkflow":  # GA SWF
@@ -519,5 +535,5 @@ def _lint_tool_ids_steps(lint_context: WorkflowLintContext, wf_dict: Dict, ts: T
     ts = toolshed.ToolShedInstance(url=MAIN_TOOLSHED_URL)
     failed = _lint_tool_ids_steps(lint_context, workflow_dict, ts)
     if not failed:
-        lint_context.valid("All tools_id appear to be valid.")
+        lint_context.valid("All tool ids appear to be valid.")
     return None