Source code for planemo.autoupdate

"""Autoupdate older conda dependencies in the requirements section."""

import collections
import itertools
import re
import xml.etree.ElementTree as ET

import packaging.version
import requests
import yaml
from bioblend import toolshed
from galaxy.tool_util.deps import conda_util

import planemo.conda
from import (


[docs]def find_macros(xml_tree): """ Get macros from the XML tree """ macros = [] for macro_import in xml_tree.iter("import"): macros.append(macro_import.text) return macros
[docs]def get_requirements(xml_tree): """ Get requirements from the XML tree """ requirements = {} main_req = None for requirement in xml_tree.iter("requirement"): if requirement.attrib.get("version") == "@TOOL_VERSION@": main_req = requirement.text else: requirements[requirement.text] = { "tag": ET.tostring(requirement, encoding="unicode").strip(), "text": requirement.attrib.get("version"), } return requirements, main_req
[docs]def get_tokens(xml_tree): """ Get tokens from the XML tree """ tokens = {} for token in xml_tree.iter("token"): tokens[token.attrib["name"]] = {"tag": ET.tostring(token, encoding="unicode").strip(), "text": token.text} return tokens
[docs]def check_conda(tool_name, ctx, **kwds): """ Get the most up-to-date conda version for a tool requirement """ conda_context = planemo.conda.build_conda_context(ctx, **kwds) if not conda_context.is_conda_installed(): # check directly via Anaconda API r = requests.get("", params={"name": tool_name}) search_results = itertools.chain.from_iterable( n["versions"] for n in r.json() if n["name"] == tool_name and n["owner"] in kwds["conda_ensure_channels"] ) return sorted(search_results, key=packaging.version.parse, reverse=True)[0] target = planemo.conda.conda_util.CondaTarget(tool_name) search_results = conda_util.best_search_result(target, conda_context=conda_context) return search_results[0]["version"]
[docs]def update_xml(tool_path, xml_tree, tags_to_update, wrapper_version_token, is_macro=False): """ Write modified XML to tool_path """ def update_token(xml_text, tag, token_value): new_tag = f">{token_value}<".join(re.split(">.*<", tag)) return re.sub(tag, new_tag, xml_text) def update_requirement(xml_text, tag, requirement_value): new_tag = f'version="{requirement_value}"'.join(re.split('version=".*"', tag)) return re.sub(tag, new_tag, xml_text) with open(tool_path, "r+", newline="") as f: xml_text = for tag_to_update in tags_to_update: if tag_to_update["type"] == "token": xml_text = update_token(xml_text, tag_to_update["tag"], tag_to_update["value"]) if tag_to_update["type"] == "requirement": xml_text = update_requirement(xml_text, tag_to_update["tag"], tag_to_update["value"]) if wrapper_version_token == 0 and not is_macro: # i.e. @VERSION_SUFFIX@ not specified so update the version directly in the tool tag tool_tag = re.sub( 'version="@TOOL_VERSION@.*?"', 'version="@TOOL_VERSION@+galaxy0"', re.findall('<tool .*version="@TOOL_VERSION@.*">', xml_text)[0], ) xml_text = re.sub('<tool .*version="@TOOL_VERSION@.*">', tool_tag, xml_text) f.truncate() f.write(xml_text)
[docs]def create_requirement_dict(xml_files, skip_reqs): """ Create dict with requirements and find main requirement """ requirements = {} main_req = None for k, v in xml_files.items(): file_reqs, file_main_req = get_requirements(v) requirements[k] = {k: v for k, v in file_reqs.items() if k not in skip_reqs} if file_main_req: if main_req: error("Multiple requirements use the token @TOOL_VERSION@!") main_req = (file_main_req, k) if not main_req: error("No requirement uses the token @TOOL_VERSION@!") return requirements, main_req
[docs]def create_token_dict(ctx, xml_files, main_req, **kwds): """ Create dict with relevant tokens and check conda requirements for main """ tokens = {} current_main_req, updated_main_req = None, None xml_to_update = collections.defaultdict(list) for k, v in xml_files.items(): tokens[k] = get_tokens(v) # check if it is @TOOL_VERSION@ and if so do check_conda if "@TOOL_VERSION@" in tokens[k]: current_main_req = tokens[k]["@TOOL_VERSION@"]["text"] updated_main_req = check_conda(main_req[0], ctx, **kwds) if current_main_req: xml_to_update[k].append( {"type": "token", "tag": tokens[k]["@TOOL_VERSION@"]["tag"], "value": updated_main_req} ) return tokens, xml_to_update, current_main_req, updated_main_req
[docs]def perform_required_update( ctx, xml_files, tool_path, requirements, tokens, xml_to_update, wrapper_version_token, **kwds ): """ Carry out the update, if requirements are out-of-date """ # check all requirements for k, v in requirements.items(): for req in v: req_check = check_conda(req, ctx, **kwds) # print(req_check, v[req]['text']) if req_check != v[req]["text"]: xml_to_update[k].append({"type": "requirement", "tag": v[req]["tag"], "value": req_check}) # check all tokens, if wrapper_version_token exists if wrapper_version_token: for k, v in tokens.items(): if wrapper_version_token in v: xml_to_update[k].append({"type": "token", "tag": v[wrapper_version_token]["tag"], "value": 0}) # finally, update each file separately for k, v in xml_files.items(): update_xml(k, v, xml_to_update[k], wrapper_version_token, is_macro=(k != tool_path)) info(f"Tool {tool_path} successfully updated.") return set(xml_files)
[docs]def autoupdate_tool(ctx, tool_path, modified_files, **kwds): """ Autoupdate an XML file """ modified_files = modified_files or set() # create a dict of all files that need editing - wrapper plus macros xml_files = {tool_path: ET.parse(tool_path)} # get name of token which defines the wrapper version; if just an integer, None versions = xml_files[tool_path].getroot().attrib.get("version") if versions: versions = versions.split("+galaxy") if versions[0] != "@TOOL_VERSION@": error("Tool version does not contain @TOOL_VERSION@ as required by autoupdate.") return elif len(versions) == 1: wrapper_version_token = None else: if versions[1][0] == versions[1][-1] == "@": wrapper_version_token = versions[1] else: wrapper_version_token = 0 # assume an int else: wrapper_version_token = None # add macros to xml_files for macro in find_macros(xml_files[tool_path]): macro_path = "/".join(tool_path.split("/")[:-1] + [macro]) xml_files[macro_path] = ET.parse(macro_path) requirements, main_req = create_requirement_dict(xml_files, kwds.get("skip_requirements", "").split(",")) tokens, xml_to_update, current_main_req, updated_main_req = create_token_dict(ctx, xml_files, main_req, **kwds) if current_main_req == updated_main_req and not (modified_files & set(xml_files)): info(f"No updates required or made to {tool_path}.") return # end here if no update needed if kwds.get("dry_run"): error( f"Update required to {tool_path}! Tool main requirement has version {current_main_req}, newest conda version is {updated_main_req}" ) return else: info(f"Updating {tool_path.split('/')[-1]} from version {current_main_req} to {updated_main_req}") return perform_required_update( ctx, xml_files, tool_path, requirements, tokens, xml_to_update, wrapper_version_token, **kwds )
def _update_wf(config, workflow_id, instance=False): """ Recursively update a workflow, including subworkflows """ wf = config.user_gi.make_get_request( f"{config.user_gi.url}/workflows/{workflow_id}", params={"instance": instance} ).json() for step in wf.get("steps", {}).values(): if step["type"] == "subworkflow": # update subworkflows before the main workflow _update_wf(config, step["workflow_id"], instance=True) config.user_gi.workflows.refactor_workflow(wf["id"], actions=[{"action_type": "upgrade_all_steps"}])
[docs]def outdated_tools(ctx, wf_dict, ts): def check_tool_step(step, ts): # return a dict with current and newest tool version, in case they don't match if not step["tool_id"].startswith(AUTOUPDATE_TOOLSHED_URL[8:]): return {} # assume a built in tool try: repos = ts.repositories._get(params={"tool_ids": step["tool_id"]}) except Exception: ctx.log(f"The ToolShed returned an error when searching for the most recent version of {step['tool_id']}") return {} base_id = "/".join(step["tool_id"].split("/")[:-1]) tool_ids_found = { tool["guid"] for repo in repos.values() if type(repo) == dict for tool in repo.get("tools", []) } updated_tool_id = sorted( {tool_id for tool_id in tool_ids_found if f"{base_id}/" in tool_id}, key=lambda n: packaging.version.parse(n), )[-1] if step["tool_id"] != updated_tool_id: return {base_id: {"current": step["tool_id"], "updated": updated_tool_id}} else: return {} outdated_tool_dict = {} steps = wf_dict["steps"].values() if type(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": outdated_tool_dict.update(check_tool_step(step, ts)) elif step.get("type") == "subworkflow": # GA SWF outdated_tool_dict.update(outdated_tools(ctx, step["subworkflow"], ts)) elif step.get("run", {}).get("class") == "GalaxyWorkflow": # gxformat2 SWF outdated_tool_dict.update(outdated_tools(ctx, step["run"], ts)) else: continue return outdated_tool_dict
[docs]def get_tools_to_update(ctx, workflow, tools_to_skip): # before we run the autoupdate, we check the tools against the toolshed to see if there # are any new versions. This saves spinning up Galaxy and installing the tools if there # is nothing to do, and also allows us to collect a list of the tools which need updating with open(workflow.path) as f: wf_dict = yaml.load(f, Loader=yaml.SafeLoader) ts = toolshed.ToolShedInstance(url=AUTOUPDATE_TOOLSHED_URL) tools_to_update = outdated_tools(ctx, wf_dict, ts) return {tool: versions for tool, versions in tools_to_update.items() if tool not in tools_to_skip}
[docs]def autoupdate_wf(ctx, config, wf): workflow_id = config.workflow_id_for_runnable(wf) _update_wf(config, workflow_id) return config.user_gi.workflows.export_workflow_dict(workflow_id)
[docs]def fix_workflow_ga(original_wf, updated_wf): # the Galaxy refactor action can't do everything right now... some manual fixes here # * bump release number if present # * order steps numerically, leave everything else sorted as in the original workflow # * recurse over subworkflows edited_wf = original_wf.copy() updated_wf_steps = collections.OrderedDict(sorted(updated_wf["steps"].items(), key=lambda item: int(item[0]))) edited_wf["steps"] = updated_wf_steps # check release; bump if it exists if edited_wf.get("release"): release = [int(n) for n in edited_wf["release"].split(".")] release[-1] += 1 edited_wf["release"] = ".".join([str(n) for n in release]) # iterate over the steps for step in edited_wf["steps"]: # recurse over subworkflows if edited_wf["steps"][step].get("type") == "subworkflow": edited_wf["steps"][step]["subworkflow"] = fix_workflow_ga( edited_wf["steps"][step]["subworkflow"], updated_wf["steps"][step]["subworkflow"] ) return edited_wf
[docs]def fix_workflow_gxformat2(original_wf, updated_wf): # does the same as fix_workflow_ga for gxformat2 edited_wf = original_wf.copy() # check release; bump if it exists if edited_wf.get("release"): release = [int(n) for n in edited_wf["release"].split(".")] release[-1] += 1 edited_wf["release"] = ".".join([str(n) for n in release]) # iterate over the steps for step_index, step in enumerate(edited_wf["steps"]): # recurse over subworkflows if step.get("run", {}).get("class") == "GalaxyWorkflow": # subworkflow step["run"] = fix_workflow_gxformat2( step["run"], updated_wf["steps"][str(step_index + len(original_wf["inputs"]))]["subworkflow"] ) # fix tool_id and content_id to march tool_version elif updated_wf["steps"][str(step_index + len(original_wf["inputs"]))]["type"] == "tool": if ( updated_wf["steps"][str(step_index + len(original_wf["inputs"]))] .get("tool_id", "") .startswith(AUTOUPDATE_TOOLSHED_URL[8:]) ): step["tool_version"] = updated_wf["steps"][str(step_index + len(original_wf["inputs"]))]["tool_version"] step["tool_id"] = updated_wf["steps"][str(step_index + len(original_wf["inputs"]))]["tool_id"] step["content_id"] = updated_wf["steps"][str(step_index + len(original_wf["inputs"]))]["content_id"] return edited_wf