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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/home/ross/galaxy/tools/tool_makers/toolfactory/README.md Thu Jan 07 09:22:51 2021 +0000 @@ -0,0 +1,211 @@ +**Breaking news! Docker container is recommended as at August 2020** + +A Docker container can be built - see the docker directory. +It is highly recommended for isolation. It also has an integrated toolshed to allow installation of new tools back +into the Galaxy being used to generate them. + +Built from quay.io/bgruening/galaxy:20.05 but updates the +Galaxy code to the dev branch - it seems to work fine with updated bioblend>=0.14 +with planemo and the right version of gxformat2 needed by the ToolFactory (TF). + +The runclean.sh script run from the docker subdirectory of your local clone of this repository +should create a container (eventually) and serve it at localhost:8080 with a toolshed at +localhost:9009. + +Once it's up, please restart Galaxy in the container with +```docker exec [container name] supervisorctl restart galaxy: ``` +Jobs just do not seem to run properly otherwise and the next steps won't work! + +The generated container includes a workflow and 2 sample data sets for the workflow + +Load the workflow. Adjust the inputs for each as labelled. The perl example counts GC in phiX.fasta. +The python scripts use the rgToolFactory.py as their input - any text file will work but I like the +recursion. The BWA example has some mitochondrial reads and reference. Run the workflow and watch. +This should fill the history with some sample tools you can rerun and play with. +Note that each new tool will have been tested using Planemo. In the workflow, in Galaxy. +Extremely cool to watch. + +*WARNING* + + Install this tool on a throw-away private Galaxy or Docker container ONLY + Please NEVER on a public or production instance + +*Short Story* + +Galaxy is easily extended to new applications by adding a new tool. Each new scientific computational package added as +a tool to Galaxy requires some special instructions to be written. This is sometimes termed "wrapping" the package +because the instructions tell Galaxy how to run the package as a new Galaxy tool. Any tool in a Galaxy is +readily available to all the users through a consistent and easy to use interface. + +Most Galaxy tool wrappers have been manually prepared by skilled programmers, many using Planemo because it +automates much of the basic boilerplate and makes the process much easier. The ToolFactory (TF) +uses Planemo under the hood for many functions, but hides the command +line complexities from the TF user. + +*More Explanation* + +The TF is an unusual Galaxy tool, designed to allow a skilled user to make new Galaxy tools. +It appears in Galaxy just like any other tool but outputs include new Galaxy tools generated +using instructions provided by the user and the results of Planemo lint and tool testing using +small sample inputs provided by the TF user. The small samples become tests built in to the new tool. + +It offers a familiar Galaxy form driven way to define how the user of the new tool will +choose input data from their history, and what parameters the new tool user will be able to adjust. +The TF user must know, or be able to read, enough about the tool to be able to define the details of +the new Galaxy interface and the ToolFactory offers little guidance on that other than some examples. + +Tools always depend on other things. Most tools in Galaxy depend on third party +scientific packages, so TF tools usually have one or more dependencies. These can be +scientific packages such as BWA or scripting languages such as Python and are +usually managed by Conda. If the new tool relies on a system utility such as bash or awk +where the importance of version control on reproducibility is low, these can be used without +Conda management - but remember the potential risks of unmanaged dependencies on computational +reproducibility. + +The TF user can optionally supply a working script where scripting is +required and the chosen dependency is a scripting language such as Python or a system +scripting executable such as bash. Whatever the language, the script must correctly parse the command line +arguments it receives at tool execution, as they are defined by the TF user. The +text of that script is "baked in" to the new tool and will be executed each time +the new tool is run. It is highly recommended that scripts and their command lines be developed +and tested until proven to work before the TF is invoked. Galaxy as a software development +environment is actually possible, but not recommended being somewhat clumsy and inefficient. + +Tools nearly always take one or more data sets from the user's history as input. TF tools +allow the TF user to define what Galaxy datatypes the tool end user will be able to choose and what +names or positions will be used to pass them on a command line to the package or script. + +Tools often have various parameter settings. The TF allows the TF user to define how each +parameter will appear on the tool form to the end user, and what names or positions will be +used to pass them on the command line to the package. At present, parameters are limited to +simple text and number fields. Pull requests for other kinds of parameters that galaxyxml +can handle are welcomed. + +Best practice Galaxy tools have one or more automated tests. These should use small sample data sets and +specific parameter settings so when the tool is tested, the outputs can be compared with their expected +values. The TF will automatically create a test for the new tool. It will use the sample data sets +chosen by the TF user when they built the new tool. + +The TF works by exposing *unrestricted* and therefore extremely dangerous scripting +to all designated administrators of the host Galaxy server, allowing them to +run scripts in R, python, sh and perl. For this reason, a Docker container is +available to help manage the associated risks. + +*Scripting uses* + +To use a scripting language to create a new tool, you must first prepared and properly test a script. Use small sample +data sets for testing. When the script is working correctly, upload the small sample datasets +into a new history, start configuring a new ToolFactory tool, and paste the script into the script text box on the TF form. + +*Outputs* + +Once the script runs sucessfully, a new Galaxy tool that runs your script +can be generated. Select the "generate" option and supply some help text and +names. The new tool will be generated in the form of a new Galaxy datatype +*tgz* - as the name suggests, it's an archive ready to upload to a +Galaxy ToolShed as a new tool repository. + +It is also possible to run a tool to generate test outputs, then test it +using planemo. A toolshed is built in to the Docker container and configured +so a tool can be tested, sent to that toolshed, then installed in the Galaxy +where the TF is running. + +If the tool requires a command or test XML override, then planemo is +needed to generate test outputs to make a complete tool, rerun to test +and if required upload to the local toolshed and install in the Galaxy +where the TF is running. + +Once it's in a ToolShed, it can be installed into any local Galaxy server +from the server administrative interface. + +Once the new tool is installed, local users can run it - each time, the +package and/or script that was supplied when it was built will be executed with the input chosen +from the user's history, together with user supplied parameters. In other words, the tools you generate with the +ToolFactory run just like any other Galaxy tool. + +TF generated tools work as normal workflow components. + + +*Limitations* + +The TF is flexible enough to generate wrappers for many common scientific packages +but the inbuilt automation will not cope with all possible situations. Users can +supply overrides for two tool XML segments - tests and command and the BWA +example in the supplied samples workflow illustrates their use. + +*Installation* + +The Docker container is the best way to use the TF because it is preconfigured +to automate new tool testing and has a built in local toolshed where each new tool +is uploaded. If you grab the docker container, it should just work. + +If you build the container, there are some things to watch out for. Let it run for 10 minutes +or so once you build it - check with top until conda has finished fussing. Once everything quietens +down, find the container with +```docker ps``` +and use +```docker exec [containername] supervisorctl restart galaxy:``` +That colon is not a typographical mistake. +Not restarting after first boot seems to leave the job/worflow system confused and the workflow +just will not run properly until Galaxy has restarted. + +Login as admin@galaxy.org with password "password". Feel free to change it once you are logged in. +There should be a companion toolshed at localhost:9090. The history should have some sample data for +the workflow. + +Run the workflow and make sure the right dataset is selected for each of the input files. Most of the +examples use text files so should run, but the bwa example needs the right ones to work properly. + +When the workflow is finished, you will have half a dozen examples to rerun and play with. They have also +all been tested and installed so you should find them in your tool menu under "Generated Tools" + +It is easy to install without Docker, but you will need to make some +configuration changes (TODO write a configuration). You can install it most conveniently using the +administrative "Search and browse tool sheds" link. Find the Galaxy Main +toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory +repository in the Tool Maker section. Open it and review the code and select the option to install it. + +Otherwise, if not already there pending an accepted PR, +please add: +<datatype extension="tgz" type="galaxy.datatypes.binary:Binary" +mimetype="multipart/x-gzip" subclass="True" /> +to your local data_types_conf.xml. + + +*Restricted execution* + +The tool factory tool itself will then be usable ONLY by admin users - +people with IDs in admin_users. **Yes, that's right. ONLY +admin_users can run this tool** Think about it for a moment. If allowed to +run any arbitrary script on your Galaxy server, the only thing that would +impede a miscreant bent on destroying all your Galaxy data would probably +be lack of appropriate technical skills. + +**Generated tool Security** + +Once you install a generated tool, it's just +another tool - assuming the script is safe. They just run normally and their +user cannot do anything unusually insecure but please, practice safe toolshed. +Read the code before you install any tool. Especially this one - it is really scary. + +**Send Code** + +Pull requests and suggestions welcome as git issues please? + +**Attribution** + +Creating re-usable tools from scripts: The Galaxy Tool Factory +Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team +Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 + +http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref + +**Licensing** + +Copyright Ross Lazarus 2010 +ross lazarus at g mail period com + +All rights reserved. + +Licensed under the LGPL +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/home/ross/galaxy/tools/tool_makers/toolfactory/galaxy-tool-test Thu Jan 07 09:22:51 2021 +0000 @@ -0,0 +1,457 @@ +#!/usr/bin/env python + +import argparse +import datetime as dt +import json +import logging +import os +import sys +import tempfile +from collections import namedtuple +from concurrent.futures import thread, ThreadPoolExecutor + +import yaml + +from galaxy.tool_util.verify.interactor import ( + DictClientTestConfig, + GalaxyInteractorApi, + verify_tool, +) + +DESCRIPTION = """Script to quickly run a tool test against a running Galaxy instance.""" +DEFAULT_SUITE_NAME = "Galaxy Tool Tests" +ALL_TESTS = -1 +ALL_TOOLS = "*" +ALL_VERSION = "*" +LATEST_VERSION = None + + +TestReference = namedtuple("TestReference", ["tool_id", "tool_version", "test_index"]) +TestException = namedtuple("TestException", ["tool_id", "exception", "was_recorded"]) + + +class Results: + + def __init__(self, default_suitename, test_json, append=False): + self.test_json = test_json or "-" + test_results = [] + test_exceptions = [] + suitename = default_suitename + if append: + assert test_json != "-" + with open(test_json) as f: + previous_results = json.load(f) + test_results = previous_results["tests"] + if "suitename" in previous_results: + suitename = previous_results["suitename"] + self.test_results = test_results + self.test_exceptions = test_exceptions + self.suitename = suitename + + def register_result(self, result): + self.test_results.append(result) + + def register_exception(self, test_exception): + self.test_exceptions.append(test_exception) + + def already_successful(self, test_reference): + test_id = _test_id_for_reference(test_reference) + for test_result in self.test_results: + if test_result.get('id') != test_id: + continue + + has_data = test_result.get('has_data', False) + if has_data: + test_data = test_result.get("data", {}) + if 'status' in test_data and test_data['status'] == 'success': + return True + + return False + + def write(self): + tests = sorted(self.test_results, key=lambda el: el['id']) + n_passed, n_failures, n_skips = 0, 0, 0 + n_errors = len([e for e in self.test_exceptions if not e.was_recorded]) + for test in tests: + has_data = test.get('has_data', False) + if has_data: + test_data = test.get("data", {}) + if 'status' not in test_data: + raise Exception(f"Test result data {test_data} doesn't contain a status key.") + status = test_data['status'] + if status == "success": + n_passed += 1 + elif status == "error": + n_errors += 1 + elif status == "skip": + n_skips += 1 + elif status == "failure": + n_failures += 1 + report_obj = { + 'version': '0.1', + 'suitename': self.suitename, + 'results': { + 'total': n_passed + n_failures + n_skips + n_errors, + 'errors': n_errors, + 'failures': n_failures, + 'skips': n_skips, + }, + 'tests': tests, + } + if self.test_json == "-": + print(json.dumps(report_obj)) + else: + with open(self.test_json, "w") as f: + json.dump(report_obj, f) + + def info_message(self): + messages = [] + passed_tests = self._tests_with_status('success') + messages.append("Passed tool tests ({}): {}".format( + len(passed_tests), + [t["id"] for t in passed_tests] + )) + failed_tests = self._tests_with_status('failure') + messages.append("Failed tool tests ({}): {}".format( + len(failed_tests), + [t["id"] for t in failed_tests] + )) + skiped_tests = self._tests_with_status('skip') + messages.append("Skipped tool tests ({}): {}".format( + len(skiped_tests), + [t["id"] for t in skiped_tests] + )) + errored_tests = self._tests_with_status('error') + messages.append("Errored tool tests ({}): {}".format( + len(errored_tests), + [t["id"] for t in errored_tests] + )) + return "\n".join(messages) + + @property + def success_count(self): + self._tests_with_status('success') + + @property + def skip_count(self): + self._tests_with_status('skip') + + @property + def error_count(self): + return self._tests_with_status('error') + len(self.test_exceptions) + + @property + def failure_count(self): + return self._tests_with_status('failure') + + def _tests_with_status(self, status): + return [t for t in self.test_results if t.get("data", {}).get("status") == status] + + +def test_tools( + galaxy_interactor, + test_references, + results, + log=None, + parallel_tests=1, + history_per_test_case=False, + no_history_cleanup=False, + retries=0, + verify_kwds=None, +): + """Run through tool tests and write report. + + Refactor this into Galaxy in 21.01. + """ + verify_kwds = (verify_kwds or {}).copy() + tool_test_start = dt.datetime.now() + history_created = False + if history_per_test_case: + test_history = None + else: + history_created = True + test_history = galaxy_interactor.new_history(history_name=f"History for {results.suitename}") + verify_kwds.update({ + "no_history_cleanup": no_history_cleanup, + "test_history": test_history, + }) + with ThreadPoolExecutor(max_workers=parallel_tests) as executor: + try: + for test_reference in test_references: + _test_tool( + executor=executor, + test_reference=test_reference, + results=results, + galaxy_interactor=galaxy_interactor, + log=log, + retries=retries, + verify_kwds=verify_kwds, + ) + finally: + # Always write report, even if test was cancelled. + try: + executor.shutdown(wait=True) + except KeyboardInterrupt: + executor._threads.clear() + thread._threads_queues.clear() + results.write() + if log: + log.info("Report written to '%s'", os.path.abspath(results.test_json)) + log.info(results.info_message()) + log.info("Total tool test time: {}".format(dt.datetime.now() - tool_test_start)) + if history_created and not no_history_cleanup: + galaxy_interactor.delete_history(test_history) + + +def _test_id_for_reference(test_reference): + tool_id = test_reference.tool_id + tool_version = test_reference.tool_version + test_index = test_reference.test_index + + if tool_version and tool_id.endswith("/" + tool_version): + tool_id = tool_id[:-len("/" + tool_version)] + + label_base = tool_id + if tool_version: + label_base += "/" + str(tool_version) + + test_id = label_base + "-" + str(test_index) + return test_id + + +def _test_tool( + executor, + test_reference, + results, + galaxy_interactor, + log, + retries, + verify_kwds, +): + tool_id = test_reference.tool_id + tool_version = test_reference.tool_version + test_index = test_reference.test_index + # If given a tool_id with a version suffix, strip it off so we can treat tool_version + # correctly at least in client_test_config. + if tool_version and tool_id.endswith("/" + tool_version): + tool_id = tool_id[:-len("/" + tool_version)] + + test_id = _test_id_for_reference(test_reference) + + def run_test(): + run_retries = retries + job_data = None + job_exception = None + + def register(job_data_): + nonlocal job_data + job_data = job_data_ + + try: + while run_retries >= 0: + job_exception = None + try: + if log: + log.info("Executing test '%s'", test_id) + verify_tool( + tool_id, galaxy_interactor, test_index=test_index, tool_version=tool_version, + register_job_data=register, **verify_kwds + ) + if log: + log.info("Test '%s' passed", test_id) + break + except Exception as e: + if log: + log.warning("Test '%s' failed", test_id, exc_info=True) + + job_exception = e + run_retries -= 1 + finally: + if job_data is not None: + results.register_result({ + "id": test_id, + "has_data": True, + "data": job_data, + }) + if job_exception is not None: + was_recorded = job_data is not None + test_exception = TestException(tool_id, job_exception, was_recorded) + results.register_exception(test_exception) + + executor.submit(run_test) + + +def build_case_references( + galaxy_interactor, + tool_id=ALL_TOOLS, + tool_version=LATEST_VERSION, + test_index=ALL_TESTS, + page_size=0, + page_number=0, + check_against=None, + log=None, +): + test_references = [] + if tool_id == ALL_TOOLS: + tests_summary = galaxy_interactor.get_tests_summary() + for tool_id, tool_versions_dict in tests_summary.items(): + for tool_version, summary in tool_versions_dict.items(): + for test_index in range(summary["count"]): + test_reference = TestReference(tool_id, tool_version, test_index) + test_references.append(test_reference) + else: + assert tool_id + tool_test_dicts = galaxy_interactor.get_tool_tests(tool_id, tool_version=tool_version) or {} + for i, tool_test_dict in enumerate(tool_test_dicts): + this_tool_version = tool_test_dict.get("tool_version", tool_version) + this_test_index = i + if test_index == ALL_TESTS or i == test_index: + test_reference = TestReference(tool_id, this_tool_version, this_test_index) + test_references.append(test_reference) + + if check_against: + filtered_test_references = [] + for test_reference in test_references: + if check_against.already_successful(test_reference): + if log is not None: + log.debug(f"Found successful test for {test_reference}, skipping") + continue + filtered_test_references.append(test_reference) + log.info(f"Skipping {len(test_references)-len(filtered_test_references)} out of {len(test_references)} tests.") + test_references = filtered_test_references + + if page_size > 0: + slice_start = page_size * page_number + slice_end = page_size * (page_number + 1) + test_references = test_references[slice_start:slice_end] + + return test_references + + +def main(argv=None): + if argv is None: + argv = sys.argv[1:] + + args = _arg_parser().parse_args(argv) + log = setup_global_logger(__name__, verbose=args.verbose) + client_test_config_path = args.client_test_config + if client_test_config_path is not None: + log.debug(f"Reading client config path {client_test_config_path}") + with open(client_test_config_path) as f: + client_test_config = yaml.full_load(f) + else: + client_test_config = {} + + def get_option(key): + arg_val = getattr(args, key, None) + if arg_val is None and key in client_test_config: + val = client_test_config.get(key) + else: + val = arg_val + return val + + output_json_path = get_option("output_json") + galaxy_interactor_kwds = { + "galaxy_url": get_option("galaxy_url"), + "master_api_key": get_option("admin_key"), + "api_key": get_option("key"), + "keep_outputs_dir": args.output, + "download_attempts": get_option("download_attempts"), + "download_sleep": get_option("download_sleep"), + } + tool_id = args.tool_id + tool_version = args.tool_version + tools_client_test_config = DictClientTestConfig(client_test_config.get("tools")) + verbose = args.verbose + + galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds) + results = Results(args.suite_name, output_json_path, append=args.append) + check_against = None if not args.skip_successful else results + test_references = build_case_references( + galaxy_interactor, + tool_id=tool_id, + tool_version=tool_version, + test_index=args.test_index, + page_size=args.page_size, + page_number=args.page_number, + check_against=check_against, + log=log, + ) + log.debug(f"Built {len(test_references)} test references to executed.") + verify_kwds = dict( + client_test_config=tools_client_test_config, + force_path_paste=args.force_path_paste, + skip_with_reference_data=not args.with_reference_data, + quiet=not verbose, + ) + test_tools( + galaxy_interactor, + test_references, + results, + log=log, + parallel_tests=args.parallel_tests, + history_per_test_case=args.history_per_test_case, + no_history_cleanup=args.no_history_cleanup, + verify_kwds=verify_kwds, + ) + exceptions = results.test_exceptions + if exceptions: + exception = exceptions[0] + if hasattr(exception, "exception"): + exception = exception.exception + raise exception + + +def setup_global_logger(name, log_file=None, verbose=False): + formatter = logging.Formatter('%(asctime)s %(levelname)-5s - %(message)s') + console = logging.StreamHandler() + console.setFormatter(formatter) + + logger = logging.getLogger(name) + logger.setLevel(logging.DEBUG if verbose else logging.INFO) + logger.addHandler(console) + + if not log_file: + # delete = false is chosen here because it is always nice to have a log file + # ready if you need to debug. Not having the "if only I had set a log file" + # moment after the fact. + temp = tempfile.NamedTemporaryFile(prefix="ephemeris_", delete=False) + log_file = temp.name + file_handler = logging.FileHandler(log_file) + logger.addHandler(file_handler) + logger.info(f"Storing log file in: {log_file}") + return logger + + +def _arg_parser(): + parser = argparse.ArgumentParser(description=DESCRIPTION) + parser.add_argument('-u', '--galaxy-url', default="http://localhost:8080", help='Galaxy URL') + parser.add_argument('-k', '--key', default=None, help='Galaxy User API Key') + parser.add_argument('-a', '--admin-key', default=None, help='Galaxy Admin API Key') + parser.add_argument('--force_path_paste', default=False, action="store_true", help='This requires Galaxy-side config option "allow_path_paste" enabled. Allows for fetching test data locally. Only for admins.') + parser.add_argument('-t', '--tool-id', default=ALL_TOOLS, help='Tool ID') + parser.add_argument('--tool-version', default=None, help='Tool Version (if tool id supplied). Defaults to just latest version, use * to test all versions') + parser.add_argument('-i', '--test-index', default=ALL_TESTS, type=int, help='Tool Test Index (starting at 0) - by default all tests will run.') + parser.add_argument('-o', '--output', default=None, help='directory to dump outputs to') + parser.add_argument('--append', default=False, action="store_true", help="Extend a test record json (created with --output-json) with additional tests.") + parser.add_argument('--skip-successful', default=False, action="store_true", help="When used with --append, skip previously run successful tests.") + parser.add_argument('-j', '--output-json', default=None, help='output metadata json') + parser.add_argument('--verbose', default=False, action="store_true", help="Verbose logging.") + parser.add_argument('-c', '--client-test-config', default=None, help="Test config YAML to help with client testing") + parser.add_argument('--suite-name', default=DEFAULT_SUITE_NAME, help="Suite name for tool test output") + parser.add_argument('--with-reference-data', dest="with_reference_data", default=False, action="store_true") + parser.add_argument('--skip-with-reference-data', dest="with_reference_data", action="store_false", help="Skip tests the Galaxy server believes use data tables or loc files.") + parser.add_argument('--history-per-suite', dest="history_per_test_case", default=False, action="store_false", help="Create new history per test suite (all tests in same history).") + parser.add_argument('--history-per-test-case', dest="history_per_test_case", action="store_true", help="Create new history per test case.") + parser.add_argument('--no-history-cleanup', default=False, action="store_true", help="Perserve histories created for testing.") + parser.add_argument('--parallel-tests', default=1, type=int, help="Parallel tests.") + parser.add_argument('--retries', default=0, type=int, help="Retry failed tests.") + parser.add_argument('--page-size', default=0, type=int, help="If positive, use pagination and just run one 'page' to tool tests.") + parser.add_argument('--page-number', default=0, type=int, help="If page size is used, run this 'page' of tests - starts with 0.") + parser.add_argument('--download-attempts', default=1, type=int, help="Galaxy may return a transient 500 status code for download if test results are written but not yet accessible.") + parser.add_argument('--download-sleep', default=1, type=int, help="If download attempts is greater than 1, the amount to sleep between download attempts.") + return parser + + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/home/ross/galaxy/tools/tool_makers/toolfactory/rgToolFactory2.py Thu Jan 07 09:22:51 2021 +0000 @@ -0,0 +1,1037 @@ +# replace with shebang for biocontainer +# see https://github.com/fubar2/toolfactory +# +# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012 +# +# all rights reserved +# Licensed under the LGPL +# suggestions for improvement and bug fixes welcome at +# https://github.com/fubar2/toolfactory +# +# July 2020: BCC was fun and I feel like rip van winkle after 5 years. +# Decided to +# 1. Fix the toolfactory so it works - done for simplest case +# 2. Fix planemo so the toolfactory function works +# 3. Rewrite bits using galaxyxml functions where that makes sense - done + +import argparse +import copy +import logging +import os +import re +import shutil +import subprocess +import sys +import tarfile +import tempfile +import time + +from bioblend import ConnectionError +from bioblend import toolshed + +import galaxyxml.tool as gxt +import galaxyxml.tool.parameters as gxtp + +import lxml + +import yaml + +myversion = "V2.1 July 2020" +verbose = True +debug = True +toolFactoryURL = "https://github.com/fubar2/toolfactory" +ourdelim = "~~~" + +# --input_files="$intab.input_files~~~$intab.input_CL~~~ +# $intab.input_formats# ~~~$intab.input_label +# ~~~$intab.input_help" +IPATHPOS = 0 +ICLPOS = 1 +IFMTPOS = 2 +ILABPOS = 3 +IHELPOS = 4 +IOCLPOS = 5 + +# --output_files "$otab.history_name~~~$otab.history_format~~~ +# $otab.history_CL~~~$otab.history_test" +ONAMEPOS = 0 +OFMTPOS = 1 +OCLPOS = 2 +OTESTPOS = 3 +OOCLPOS = 4 + + +# --additional_parameters="$i.param_name~~~$i.param_value~~~ +# $i.param_label~~~$i.param_help~~~$i.param_type +# ~~~$i.CL~~~i$.param_CLoverride" +ANAMEPOS = 0 +AVALPOS = 1 +ALABPOS = 2 +AHELPPOS = 3 +ATYPEPOS = 4 +ACLPOS = 5 +AOVERPOS = 6 +AOCLPOS = 7 + + +foo = len(lxml.__version__) +# fug you, flake8. Say my name! +FAKEEXE = "~~~REMOVE~~~ME~~~" +# need this until a PR/version bump to fix galaxyxml prepending the exe even +# with override. + + +def timenow(): + """return current time as a string""" + return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time())) + + +def quote_non_numeric(s): + """return a prequoted string for non-numerics + useful for perl and Rscript parameter passing? + """ + try: + _ = float(s) + return s + except ValueError: + return '"%s"' % s + + +html_escape_table = { + "&": "&", + ">": ">", + "<": "<", + "#": "#", + "$": "$", +} +cheetah_escape_table = {"$": "\\$", "#": "\\#"} + + +def html_escape(text): + """Produce entities within text.""" + return "".join([html_escape_table.get(c, c) for c in text]) + + +def cheetah_escape(text): + """Produce entities within text.""" + return "".join([cheetah_escape_table.get(c, c) for c in text]) + + +def parse_citations(citations_text): + """""" + citations = [c for c in citations_text.split("**ENTRY**") if c.strip()] + citation_tuples = [] + for citation in citations: + if citation.startswith("doi"): + citation_tuples.append(("doi", citation[len("doi") :].strip())) + else: + citation_tuples.append(("bibtex", citation[len("bibtex") :].strip())) + return citation_tuples + + +class ScriptRunner: + """Wrapper for an arbitrary script + uses galaxyxml + + """ + + def __init__(self, args=None): + """ + prepare command line cl for running the tool here + and prepare elements needed for galaxyxml tool generation + """ + self.ourcwd = os.getcwd() + self.ourenv = copy.deepcopy(os.environ) + self.infiles = [x.split(ourdelim) for x in args.input_files] + self.outfiles = [x.split(ourdelim) for x in args.output_files] + self.addpar = [x.split(ourdelim) for x in args.additional_parameters] + self.args = args + self.cleanuppar() + self.lastclredirect = None + self.lastxclredirect = None + self.cl = [] + self.xmlcl = [] + self.is_positional = self.args.parampass == "positional" + if self.args.sysexe: + self.executeme = self.args.sysexe + else: + if self.args.packages: + self.executeme = self.args.packages.split(",")[0].split(":")[0].strip() + else: + self.executeme = None + aCL = self.cl.append + aXCL = self.xmlcl.append + assert args.parampass in [ + "0", + "argparse", + "positional", + ], 'args.parampass must be "0","positional" or "argparse"' + self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name) + self.tool_id = self.tool_name + self.newtool = gxt.Tool( + self.tool_name, + self.tool_id, + self.args.tool_version, + self.args.tool_desc, + FAKEEXE, + ) + self.newtarpath = "toolfactory_%s.tgz" % self.tool_name + self.tooloutdir = "./tfout" + self.repdir = "./TF_run_report_tempdir" + self.testdir = os.path.join(self.tooloutdir, "test-data") + if not os.path.exists(self.tooloutdir): + os.mkdir(self.tooloutdir) + if not os.path.exists(self.testdir): + os.mkdir(self.testdir) + if not os.path.exists(self.repdir): + os.mkdir(self.repdir) + self.tinputs = gxtp.Inputs() + self.toutputs = gxtp.Outputs() + self.testparam = [] + if self.args.script_path: + self.prepScript() + if self.args.command_override: + scos = open(self.args.command_override, "r").readlines() + self.command_override = [x.rstrip() for x in scos] + else: + self.command_override = None + if self.args.test_override: + stos = open(self.args.test_override, "r").readlines() + self.test_override = [x.rstrip() for x in stos] + else: + self.test_override = None + if self.args.cl_prefix: # DIY CL start + clp = self.args.cl_prefix.split(" ") + for c in clp: + aCL(c) + aXCL(c) + else: + if self.args.script_path: + aCL(self.executeme) + aCL(self.sfile) + aXCL(self.executeme) + aXCL("$runme") + else: + aCL(self.executeme) + aXCL(self.executeme) + self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name) + self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name) + + if self.args.parampass == "0": + self.clsimple() + else: + clsuffix = [] + xclsuffix = [] + for i, p in enumerate(self.infiles): + if p[IOCLPOS].upper() == "STDIN": + appendme = [ + p[ICLPOS], + p[ICLPOS], + p[IPATHPOS], + "< %s" % p[IPATHPOS], + ] + xappendme = [ + p[ICLPOS], + p[ICLPOS], + p[IPATHPOS], + "< $%s" % p[ICLPOS], + ] + else: + appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""] + xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""] + clsuffix.append(appendme) + xclsuffix.append(xappendme) + for i, p in enumerate(self.outfiles): + if p[OOCLPOS] == "STDOUT": + self.lastclredirect = [">", p[ONAMEPOS]] + self.lastxclredirect = [">", "$%s" % p[OCLPOS]] + else: + clsuffix.append([p[OCLPOS], p[ONAMEPOS], p[ONAMEPOS], ""]) + xclsuffix.append([p[OCLPOS], p[ONAMEPOS], "$%s" % p[ONAMEPOS], ""]) + for p in self.addpar: + clsuffix.append([p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]]) + xclsuffix.append( + [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]] + ) + clsuffix.sort() + xclsuffix.sort() + self.xclsuffix = xclsuffix + self.clsuffix = clsuffix + if self.args.parampass == "positional": + self.clpositional() + else: + self.clargparse() + + def prepScript(self): + rx = open(self.args.script_path, "r").readlines() + rx = [x.rstrip() for x in rx] + rxcheck = [x.strip() for x in rx if x.strip() > ""] + assert len(rxcheck) > 0, "Supplied script is empty. Cannot run" + self.script = "\n".join(rx) + fhandle, self.sfile = tempfile.mkstemp( + prefix=self.tool_name, suffix="_%s" % (self.executeme) + ) + tscript = open(self.sfile, "w") + tscript.write(self.script) + tscript.close() + self.escapedScript = [cheetah_escape(x) for x in rx] + self.spacedScript = [f" {x}" for x in rx if x.strip() > ""] + art = "%s.%s" % (self.tool_name, self.executeme) + artifact = open(art, "wb") + artifact.write(bytes("\n".join(self.escapedScript), "utf8")) + artifact.close() + + def cleanuppar(self): + """ positional parameters are complicated by their numeric ordinal""" + if self.args.parampass == "positional": + for i, p in enumerate(self.infiles): + assert ( + p[ICLPOS].isdigit() or p[ICLPOS].strip().upper() == "STDIN" + ), "Positional parameters must be ordinal integers - got %s for %s" % ( + p[ICLPOS], + p[ILABPOS], + ) + for i, p in enumerate(self.outfiles): + assert ( + p[OCLPOS].isdigit() or p[OCLPOS].strip().upper() == "STDOUT" + ), "Positional parameters must be ordinal integers - got %s for %s" % ( + p[OCLPOS], + p[ONAMEPOS], + ) + for i, p in enumerate(self.addpar): + assert p[ + ACLPOS + ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % ( + p[ACLPOS], + p[ANAMEPOS], + ) + for i, p in enumerate(self.infiles): + infp = copy.copy(p) + icl = infp[ICLPOS] + infp.append(icl) + if ( + infp[ICLPOS].isdigit() \ + or self.args.parampass == "0" \ + or infp[ICLPOS].strip().upper() == "STDOUT" + ): + scl = "input%d" % (i + 1) + infp[ICLPOS] = scl + self.infiles[i] = infp + for i, p in enumerate(self.outfiles): + p.append(p[OCLPOS]) # keep copy + if (p[OOCLPOS].isdigit() and self.args.parampass != "positional") or p[ + OOCLPOS + ].strip().upper() == "STDOUT": + scl = p[ONAMEPOS] + p[OCLPOS] = scl + self.outfiles[i] = p + for i, p in enumerate(self.addpar): + p.append(p[ACLPOS]) + if p[ACLPOS].isdigit(): + scl = "param%s" % p[ACLPOS] + p[ACLPOS] = scl + self.addpar[i] = p + + def clsimple(self): + """no parameters - uses < and > for i/o""" + aCL = self.cl.append + aXCL = self.xmlcl.append + + if len(self.infiles) > 0: + aCL("<") + aCL(self.infiles[0][IPATHPOS]) + aXCL("<") + aXCL("$%s" % self.infiles[0][ICLPOS]) + if len(self.outfiles) > 0: + aCL(">") + aCL(self.outfiles[0][OCLPOS]) + aXCL(">") + aXCL("$%s" % self.outfiles[0][ONAMEPOS]) + + def clpositional(self): + # inputs in order then params + aCL = self.cl.append + for (o_v, k, v, koverride) in self.clsuffix: + if " " in v: + aCL("%s" % v) + else: + aCL(v) + aXCL = self.xmlcl.append + for (o_v, k, v, koverride) in self.xclsuffix: + aXCL(v) + if self.lastxclredirect: + aXCL(self.lastxclredirect[0]) + aXCL(self.lastxclredirect[1]) + + def clargparse(self): + """argparse style""" + aCL = self.cl.append + aXCL = self.xmlcl.append + # inputs then params in argparse named form + + for (o_v, k, v, koverride) in self.xclsuffix: + if koverride > "": + k = koverride + elif len(k.strip()) == 1: + k = "-%s" % k + else: + k = "--%s" % k + aXCL(k) + aXCL(v) + for (o_v, k, v, koverride) in self.clsuffix: + if koverride > "": + k = koverride + elif len(k.strip()) == 1: + k = "-%s" % k + else: + k = "--%s" % k + aCL(k) + aCL(v) + + def getNdash(self, newname): + if self.is_positional: + ndash = 0 + else: + ndash = 2 + if len(newname) < 2: + ndash = 1 + return ndash + + def doXMLparam(self): + """flake8 made me do this...""" + for p in self.outfiles: + # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test" + newname, newfmt, newcl, test, oldcl = p + test = test.strip() + ndash = self.getNdash(newcl) + aparm = gxtp.OutputData( + name=newname, format=newfmt, num_dashes=ndash, label=newcl + ) + aparm.positional = self.is_positional + if self.is_positional: + if oldcl.upper() == "STDOUT": + aparm.positional = 9999999 + aparm.command_line_override = "> $%s" % newname + else: + aparm.positional = int(oldcl) + aparm.command_line_override = "$%s" % newname + self.toutputs.append(aparm) + ld = None + if test.strip() > "": + if test.startswith("diff"): + c = "diff" + ld = 0 + if test.split(":")[1].isdigit: + ld = int(test.split(":")[1]) + tp = gxtp.TestOutput( + name=newname, + value="%s_sample" % newname, + compare=c, + lines_diff=ld, + ) + elif test.startswith("sim_size"): + c = "sim_size" + tn = test.split(":")[1].strip() + if tn > "": + if "." in tn: + delta = None + delta_frac = min(1.0, float(tn)) + else: + delta = int(tn) + delta_frac = None + tp = gxtp.TestOutput( + name=newname, + value="%s_sample" % newname, + compare=c, + delta=delta, + delta_frac=delta_frac, + ) + self.testparam.append(tp) + for p in self.infiles: + newname = p[ICLPOS] + newfmt = p[IFMTPOS] + ndash = self.getNdash(newname) + if not len(p[ILABPOS]) > 0: + alab = p[ICLPOS] + else: + alab = p[ILABPOS] + aninput = gxtp.DataParam( + newname, + optional=False, + label=alab, + help=p[IHELPOS], + format=newfmt, + multiple=False, + num_dashes=ndash, + ) + aninput.positional = self.is_positional + self.tinputs.append(aninput) + tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname) + self.testparam.append(tparm) + for p in self.addpar: + ( + newname, + newval, + newlabel, + newhelp, + newtype, + newcl, + override, + oldcl, + ) = p + if not len(newlabel) > 0: + newlabel = newname + ndash = self.getNdash(newname) + if newtype == "text": + aparm = gxtp.TextParam( + newname, + label=newlabel, + help=newhelp, + value=newval, + num_dashes=ndash, + ) + elif newtype == "integer": + aparm = gxtp.IntegerParam( + newname, + label=newname, + help=newhelp, + value=newval, + num_dashes=ndash, + ) + elif newtype == "float": + aparm = gxtp.FloatParam( + newname, + label=newname, + help=newhelp, + value=newval, + num_dashes=ndash, + ) + else: + raise ValueError( + 'Unrecognised parameter type "%s" for\ + additional parameter %s in makeXML' + % (newtype, newname) + ) + aparm.positional = self.is_positional + if self.is_positional: + aparm.positional = int(oldcl) + self.tinputs.append(aparm) + tparm = gxtp.TestParam(newname, value=newval) + self.testparam.append(tparm) + + def doNoXMLparam(self): + """filter style package - stdin to stdout""" + if len(self.infiles) > 0: + alab = self.infiles[0][ILABPOS] + if len(alab) == 0: + alab = self.infiles[0][ICLPOS] + max1s = ( + "Maximum one input if parampass is 0 but multiple input files supplied - %s" + % str(self.infiles) + ) + assert len(self.infiles) == 1, max1s + newname = self.infiles[0][ICLPOS] + aninput = gxtp.DataParam( + newname, + optional=False, + label=alab, + help=self.infiles[0][IHELPOS], + format=self.infiles[0][IFMTPOS], + multiple=False, + num_dashes=0, + ) + aninput.command_line_override = "< $%s" % newname + aninput.positional = self.is_positional + self.tinputs.append(aninput) + tp = gxtp.TestParam(name=newname, value="%s_sample" % newname) + self.testparam.append(tp) + if len(self.outfiles) > 0: + newname = self.outfiles[0][OCLPOS] + newfmt = self.outfiles[0][OFMTPOS] + anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0) + anout.command_line_override = "> $%s" % newname + anout.positional = self.is_positional + self.toutputs.append(anout) + tp = gxtp.TestOutput( + name=newname, value="%s_sample" % newname + ) + self.testparam.append(tp) + + def makeXML(self): + """ + Create a Galaxy xml tool wrapper for the new script + Uses galaxyhtml + Hmmm. How to get the command line into correct order... + """ + if self.command_override: + self.newtool.command_override = self.command_override # config file + else: + self.newtool.command_override = self.xmlcl + cite = gxtp.Citations() + acite = gxtp.Citation(type="doi", value="10.1093/bioinformatics/bts573") + cite.append(acite) + self.newtool.citations = cite + safertext = "" + if self.args.help_text: + helptext = open(self.args.help_text, "r").readlines() + safertext = "\n".join([cheetah_escape(x) for x in helptext]) + if len(safertext.strip()) == 0: + safertext = ( + "Ask the tool author (%s) to rebuild with help text please\n" + % (self.args.user_email) + ) + if self.args.script_path: + if len(safertext) > 0: + safertext = safertext + "\n\n------\n" # transition allowed! + scr = [x for x in self.spacedScript if x.strip() > ""] + scr.insert(0, "\n\nScript::\n") + if len(scr) > 300: + scr = ( + scr[:100] \ + + [" >300 lines - stuff deleted", " ......"] \ + + scr[-100:] + ) + scr.append("\n") + safertext = safertext + "\n".join(scr) + self.newtool.help = safertext + self.newtool.version_command = f'echo "{self.args.tool_version}"' + requirements = gxtp.Requirements() + if self.args.packages: + for d in self.args.packages.split(","): + ver = "" + d = d.replace("==", ":") + d = d.replace("=", ":") + if ":" in d: + packg, ver = d.split(":") + else: + packg = d + requirements.append( + gxtp.Requirement("package", packg.strip(), ver.strip()) + ) + self.newtool.requirements = requirements + if self.args.parampass == "0": + self.doNoXMLparam() + else: + self.doXMLparam() + self.newtool.outputs = self.toutputs + self.newtool.inputs = self.tinputs + if self.args.script_path: + configfiles = gxtp.Configfiles() + configfiles.append( + gxtp.Configfile(name="runme", text="\n".join(self.escapedScript)) + ) + self.newtool.configfiles = configfiles + tests = gxtp.Tests() + test_a = gxtp.Test() + for tp in self.testparam: + test_a.append(tp) + tests.append(test_a) + self.newtool.tests = tests + self.newtool.add_comment( + "Created by %s at %s using the Galaxy Tool Factory." + % (self.args.user_email, timenow()) + ) + self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL)) + exml0 = self.newtool.export() + exml = exml0.replace(FAKEEXE, "") # temporary work around until PR accepted + if ( + self.test_override + ): # cannot do this inside galaxyxml as it expects lxml objects for tests + part1 = exml.split("<tests>")[0] + part2 = exml.split("</tests>")[1] + fixed = "%s\n%s\n%s" % (part1, self.test_override, part2) + exml = fixed + # exml = exml.replace('range="1:"', 'range="1000:"') + xf = open("%s.xml" % self.tool_name, "w") + xf.write(exml) + xf.write("\n") + xf.close() + # ready for the tarball + + def run(self): + """ + generate test outputs by running a command line + won't work if command or test override in play - planemo is the + easiest way to generate test outputs for that case so is + automagically selected + """ + scl = " ".join(self.cl) + err = None + if self.args.parampass != "0": + if os.path.exists(self.elog): + ste = open(self.elog, "a") + else: + ste = open(self.elog, "w") + if self.lastclredirect: + sto = open(self.lastclredirect[1], "wb") # is name of an output file + else: + if os.path.exists(self.tlog): + sto = open(self.tlog, "a") + else: + sto = open(self.tlog, "w") + sto.write( + "## Executing Toolfactory generated command line = %s\n" % scl + ) + sto.flush() + subp = subprocess.run( + self.cl, env=self.ourenv, shell=False, stdout=sto, stderr=ste + ) + sto.close() + ste.close() + retval = subp.returncode + else: # work around special case - stdin and write to stdout + if len(self.infiles) > 0: + sti = open(self.infiles[0][IPATHPOS], "rb") + else: + sti = sys.stdin + if len(self.outfiles) > 0: + sto = open(self.outfiles[0][ONAMEPOS], "wb") + else: + sto = sys.stdout + subp = subprocess.run( + self.cl, env=self.ourenv, shell=False, stdout=sto, stdin=sti + ) + sto.write("## Executing Toolfactory generated command line = %s\n" % scl) + retval = subp.returncode + sto.close() + sti.close() + if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0: + os.unlink(self.tlog) + if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0: + os.unlink(self.elog) + if retval != 0 and err: # problem + sys.stderr.write(err) + logging.debug("run done") + return retval + + def shedLoad(self): + """ + use bioblend to create new repository + or update existing + + """ + if os.path.exists(self.tlog): + sto = open(self.tlog, "a") + else: + sto = open(self.tlog, "w") + + ts = toolshed.ToolShedInstance( + url=self.args.toolshed_url, + key=self.args.toolshed_api_key, + verify=False, + ) + repos = ts.repositories.get_repositories() + rnames = [x.get("name", "?") for x in repos] + rids = [x.get("id", "?") for x in repos] + tfcat = "ToolFactory generated tools" + if self.tool_name not in rnames: + tscat = ts.categories.get_categories() + cnames = [x.get("name", "?").strip() for x in tscat] + cids = [x.get("id", "?") for x in tscat] + catID = None + if tfcat.strip() in cnames: + ci = cnames.index(tfcat) + catID = cids[ci] + res = ts.repositories.create_repository( + name=self.args.tool_name, + synopsis="Synopsis:%s" % self.args.tool_desc, + description=self.args.tool_desc, + type="unrestricted", + remote_repository_url=self.args.toolshed_url, + homepage_url=None, + category_ids=catID, + ) + tid = res.get("id", None) + sto.write(f"#create_repository {self.args.tool_name} tid={tid} res={res}\n") + else: + i = rnames.index(self.tool_name) + tid = rids[i] + try: + res = ts.repositories.update_repository( + id=tid, tar_ball_path=self.newtarpath, commit_message=None + ) + sto.write(f"#update res id {id} ={res}\n") + except ConnectionError: + sto.write( + "####### Is the toolshed running and the API key correct? Bioblend shed upload failed\n" + ) + sto.close() + + def eph_galaxy_load(self): + """ + use ephemeris to load the new tool from the local toolshed after planemo uploads it + """ + if os.path.exists(self.tlog): + tout = open(self.tlog, "a") + else: + tout = open(self.tlog, "w") + cll = [ + "shed-tools", + "install", + "-g", + self.args.galaxy_url, + "--latest", + "-a", + self.args.galaxy_api_key, + "--name", + self.tool_name, + "--owner", + "fubar", + "--toolshed", + self.args.toolshed_url, + "--section_label", + "ToolFactory", + ] + tout.write("running\n%s\n" % " ".join(cll)) + subp = subprocess.run( + cll, + env=self.ourenv, + cwd=self.ourcwd, + shell=False, + stderr=tout, + stdout=tout, + ) + tout.write( + "installed %s - got retcode %d\n" % (self.tool_name, subp.returncode) + ) + tout.close() + return subp.returncode + + def writeShedyml(self): + """for planemo""" + yuser = self.args.user_email.split("@")[0] + yfname = os.path.join(self.tooloutdir, ".shed.yml") + yamlf = open(yfname, "w") + odict = { + "name": self.tool_name, + "owner": yuser, + "type": "unrestricted", + "description": self.args.tool_desc, + "synopsis": self.args.tool_desc, + "category": "TF Generated Tools", + } + yaml.dump(odict, yamlf, allow_unicode=True) + yamlf.close() + + def makeTool(self): + """write xmls and input samples into place""" + self.makeXML() + if self.args.script_path: + stname = os.path.join(self.tooloutdir, "%s" % (self.sfile)) + if not os.path.exists(stname): + shutil.copyfile(self.sfile, stname) + xreal = "%s.xml" % self.tool_name + xout = os.path.join(self.tooloutdir, xreal) + shutil.copyfile(xreal, xout) + for p in self.infiles: + pth = p[IPATHPOS] + dest = os.path.join(self.testdir, "%s_sample" % p[ICLPOS]) + shutil.copyfile(pth, dest) + + def makeToolTar(self): + """move outputs into test-data and prepare the tarball""" + excludeme = "_planemo_test_report.html" + + def exclude_function(tarinfo): + filename = tarinfo.name + return None if filename.endswith(excludeme) else tarinfo + + if os.path.exists(self.tlog): + tout = open(self.tlog, "a") + else: + tout = open(self.tlog, "w") + for p in self.outfiles: + oname = p[ONAMEPOS] + tdest = os.path.join(self.testdir, "%s_sample" % oname) + if not os.path.isfile(tdest): + src = os.path.join(self.testdir, oname) + if os.path.isfile(src): + shutil.copyfile(src, tdest) + dest = os.path.join(self.repdir, "%s.sample" % (oname)) + shutil.copyfile(src, dest) + else: + tout.write( + "###Output file %s not found in testdir %s. This is normal during the first Planemo run that generates test outputs" + % (tdest, self.testdir) + ) + tf = tarfile.open(self.newtarpath, "w:gz") + tf.add( + name=self.tooloutdir, + arcname=self.tool_name, + filter=exclude_function, + ) + tf.close() + shutil.copyfile(self.newtarpath, self.args.new_tool) + + def moveRunOutputs(self): + """need to move planemo or run outputs into toolfactory collection""" + with os.scandir(self.tooloutdir) as outs: + for entry in outs: + if not entry.is_file(): + continue + if "." in entry.name: + nayme, ext = os.path.splitext(entry.name) + if ext in [".yml", ".xml", ".json", ".yaml"]: + ext = f"{ext}.txt" + else: + ext = ".txt" + ofn = "%s%s" % (entry.name.replace(".", "_"), ext) + dest = os.path.join(self.repdir, ofn) + src = os.path.join(self.tooloutdir, entry.name) + shutil.copyfile(src, dest) + with os.scandir(self.testdir) as outs: + for entry in outs: + if ( + (not entry.is_file()) \ + or entry.name.endswith("_sample") \ + or entry.name.endswith("_planemo_test_report.html") + ): + continue + if "." in entry.name: + nayme, ext = os.path.splitext(entry.name) + else: + ext = ".txt" + newname = f"{entry.name}{ext}" + dest = os.path.join(self.repdir, newname) + src = os.path.join(self.testdir, entry.name) + shutil.copyfile(src, dest) + + def planemo_test(self, genoutputs=True): + """planemo is a requirement so is available for testing but needs a + different call if in the biocontainer - see above + and for generating test outputs if command or test overrides are + supplied test outputs are sent to repdir for display + """ + xreal = "%s.xml" % self.tool_name + tool_test_path = os.path.join( + self.repdir, f"{self.tool_name}_planemo_test_report.html" + ) + if os.path.exists(self.tlog): + tout = open(self.tlog, "a") + else: + tout = open(self.tlog, "w") + if genoutputs: + dummy, tfile = tempfile.mkstemp() + cll = [ + "planemo", + "test", + "--test_data", + os.path.abspath(self.testdir), + "--test_output", + os.path.abspath(tool_test_path), + "--skip_venv", + "--galaxy_root", + self.args.galaxy_root, + "--update_test_data", + os.path.abspath(xreal), + ] + p = subprocess.run( + cll, + env=self.ourenv, + shell=False, + cwd=self.tooloutdir, + stderr=dummy, + stdout=dummy, + ) + + else: + cll = [ + "planemo", + "test", + "--test_data", + os.path.abspath(self.testdir), + "--test_output", + os.path.abspath(tool_test_path), + "--skip_venv", + "--galaxy_root", + self.args.galaxy_root, + os.path.abspath(xreal), + ] + p = subprocess.run( + cll, + shell=False, + env=self.ourenv, + cwd=self.tooloutdir, + stderr=tout, + stdout=tout, + ) + tout.close() + return p.returncode + + +def main(): + """ + This is a Galaxy wrapper. + It expects to be called by a special purpose tool.xml + + """ + parser = argparse.ArgumentParser() + a = parser.add_argument + a("--script_path", default=None) + a("--history_test", default=None) + a("--cl_prefix", default=None) + a("--sysexe", default=None) + a("--packages", default=None) + a("--tool_name", default="newtool") + a("--tool_dir", default=None) + a("--input_files", default=[], action="append") + a("--output_files", default=[], action="append") + a("--user_email", default="Unknown") + a("--bad_user", default=None) + a("--make_Tool", default="runonly") + a("--help_text", default=None) + a("--tool_desc", default=None) + a("--tool_version", default=None) + a("--citations", default=None) + a("--command_override", default=None) + a("--test_override", default=None) + a("--additional_parameters", action="append", default=[]) + a("--edit_additional_parameters", action="store_true", default=False) + a("--parampass", default="positional") + a("--tfout", default="./tfout") + a("--new_tool", default="new_tool") + a("--galaxy_url", default="http://localhost:8080") + a("--toolshed_url", default="http://localhost:9009") + # make sure this is identical to tool_sheds_conf.xml + # localhost != 127.0.0.1 so validation fails + a("--toolshed_api_key", default="fakekey") + a("--galaxy_api_key", default="fakekey") + a("--galaxy_root", default="/galaxy-central") + a("--galaxy_venv", default="/galaxy_venv") + args = parser.parse_args() + assert not args.bad_user, ( + 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy \ +admin adds %s to "admin_users" in the galaxy.yml Galaxy configuration file' + % (args.bad_user, args.bad_user) + ) + assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq" + assert ( + args.sysexe or args.packages + ), "## Tool Factory wrapper expects an interpreter \ +or an executable package in --sysexe or --packages" + args.input_files = [x.replace('"', "").replace("'", "") for x in args.input_files] + # remove quotes we need to deal with spaces in CL params + for i, x in enumerate(args.additional_parameters): + args.additional_parameters[i] = args.additional_parameters[i].replace('"', "") + r = ScriptRunner(args) + r.writeShedyml() + r.makeTool() + if args.make_Tool == "generate": + retcode = r.run() + r.moveRunOutputs() + r.makeToolTar() + else: + retcode = r.planemo_test(genoutputs=True) # this fails :( - see PR + r.moveRunOutputs() + r.makeToolTar() + retcode = r.planemo_test(genoutputs=False) + r.moveRunOutputs() + r.makeToolTar() + print(f"second planemo_test returned {retcode}") + if args.make_Tool == "gentestinstall": + r.shedLoad() + r.eph_galaxy_load() + + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/home/ross/galaxy/tools/tool_makers/toolfactory/rgToolFactory2.xml Thu Jan 07 09:22:51 2021 +0000 @@ -0,0 +1,536 @@ +<tool id="rgtf2" name="toolfactory" version="2.00" profile="16.04" > + <description>Scripts into tools v2.0</description> + <macros> + <xml name="tool_metadata"> + <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01" + help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/> + <param name="tool_desc" label="Tool Synopsis" type="text" value="" + help="Supply a brief tool description for the Galaxy tool menu entry" /> + <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true" + value="**What it Does**" + help="Supply user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" > + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <repeat name="citations" title="Citation"> + <conditional name="citation_type"> + <param name="type" type="select" display="radio" label="Citation Type"> + <option value="doi">DOI</option> + <option value="bibtex">BibTeX</option> + </param> + <when value="doi"> + <param name="doi" label="DOI" type="text" value="" + help="Supply a DOI (e.g. doi: 10.1111/j.1740-9713.2007.00258.x) to be cited when this tool is used in published research." /> + </when> + <when value="bibtex"> + <param name="bibtex" label="BibTex" type="text" area="true" + help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" > + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + </when> + </conditional> + </repeat> + </xml> + <xml name="io"> + <section name="io" title="Input and output files" expanded="true"> + <repeat name="history_inputs" title="zero or more input data files to pass as parameters to the executable." + help="USE SMALL SAMPLES for the new tool's test. Prompts will form a history item selector as input for users of this new tool"> + <param name="input_files" type="data" format="data" label="Select an input file from your history" optional="true" multiple="false" + help=""/> + <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input" + help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular"> + <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> + <column name="value" index="0"/> + </options> + </param> + <param name="input_label" type="text" value="" label="This will become the user prompt for the form so please make it informative" + help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" > + <sanitizer invalid_char=""> + <valid initial="string.printable"> <remove value='~~~'/> </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="input_help" type="text" value="" label="This will become help text on the form." + help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> <remove value='~~~'/> </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="input_CL" type="text" label="Positional: ordinal integer. Argparse: argument name. STDIN if the executable/script expects it" + help="If you will pass positional parameters, enter the integer ordinal for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value=""> + </param> + </repeat> + <repeat name="history_outputs" title="one or more new history items output by the executable to appear in the user history after the tool runs" + help="The name will become a history item for users of the new tool you are making containing one of it's outputs"> + <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false" + help="No spaces! Argparse will also use this name as --[name]"> + <sanitizer invalid_char="_"> + <valid initial="string.ascii_letters,string.digits"> + <add value="_" /> + </valid> + </sanitizer> + </param> + <param name="history_format" type="select" multiple="false" label="Select the datatype for this output" + help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular"> + <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> + <column name="value" index="0"/> + </options> + </param> + <param name="history_CL" type="text" label="Positional: ordinal integer. Use STDOUT if '>' required. Otherwise ignored if argparse because name is used" + help="If positional parameters, enter the integer ordinal expected for this parameter. If argparse, ignore unless STDOUT needed" value=""/> + <param name="history_test" type="text" label="Test pass decision criterion for this output compared to test generation" + help="Available options are diff:[lines], sim_size:[delta (integer) or delta_frac (float)" value="diff:0"/> + </repeat> + </section> + </xml> + <xml name="additparam"> + <section name="addparam" title="Executable or script settings passed on the command line other than I/O files" expanded="true"> + <param name="edit_params" type="select" display="radio" label="Make these settings on the generated tool form user editable?" + help="If no, users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing"> + <option value="yes" selected="true">Yes, allow user to edit all additional parameters on the generated tool form</option> + <option value="no">No - use the fixed values for all additional parameters - no user editing</option> + </param> + + <repeat name="additional_parameters" title="zero or more settings to be set by the tool user and passed on the command line" + help="See examples below to see how these can be parsed by scripts in the various languages"> + <param name="param_name" type="text" value="" label="Choose the name for this parameter - MUST not be blank!"> + <sanitizer invalid_char=""> + <valid initial="string.ascii_letters,string.digits"/> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="param_type" type="select" label="Select the type for this parameter"> + <option value="text" selected="true">text</option> + <option value="integer">integer</option> + <option value="float">float</option> + </param> + <param name="param_value" type="text" value="" label="Enter this parameter's default value" + help="Note that '~~~' is an internal delimiter must not appear in this text field - please work around this technical limitation" > + <sanitizer invalid_char=""> + <valid initial="string.printable"> <remove value='~~~'/> </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="param_label" type="text" value="" label="Enter this parameter's label for the form" + help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" > + <sanitizer invalid_char=""> + <valid initial="string.printable"> <remove value='~~~'/> </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="param_help" type="text" value="" label="Help for this parameter" + help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation" > + <sanitizer invalid_char=""> + <valid initial="string.printable"> <remove value='~~~'/> </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="param_CL" type="text" label="Positional ordinal | argparse argument name" + help="Using positional parameters, enter the integer ordinal for this parameter on the command line. Using Argparse style, '--' will be prepended on the CL" value="" /> + <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ~~--foo if needed" + help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="" /> + </repeat> + </section> + </xml> + </macros> + +<requirements> + <requirement type="package" version="0.4.11">galaxyxml</requirement> + <requirement type="package" version="0.14.0">bioblend</requirement> + <requirement type="package" version="0.10.6">ephemeris</requirement> + <requirement type="package" version="0.74.1">planemo</requirement> +</requirements> + + <command ><![CDATA[ +#import os +#set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1' +#if not $dev_env and ( $__user_email__ not in $__admin_users__ ): +python3 $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__ + #else: +python3 $__tool_directory__/rgToolFactory2.py + #if len(str($cl_prefix)) > 3: +--cl_prefix "$cl_prefix" + #end if + #if $cover.commover == "yes": + #if len(str($cover.command_override)) > 10: +--command_override "$commandoverride" + #end if + #if len(str($cover.test_override)) > 10: +--test_override "$testoverride" + #end if + #end if +--packages "$deps.packages" + #if $deps.usescript.choosescript == "yes": +--script_path "$runme" +--sysexe "$deps.usescript.scriptrunner" + #end if +--tool_name "$tool_name" --user_email "$__user_email__" --citations "$citeme" --parampass "$io_param.ppass.parampass" + #if str($make.makeMode.make_Tool)!="runonly": +--make_Tool "$make.makeMode.make_Tool" +--tool_desc "$make.makeMode.tool_desc" +--tool_version "$make.makeMode.tool_version" +--help_text "$helpme" +--new_tool "$new_tool" +--toolshed_api_key "$make.makeMode.toolshed_apikey" +--galaxy_api_key "$make.makeMode.galaxy_apikey" +--toolshed_url "$make.makeMode.toolshed_url" +--galaxy_url "$make.makeMode.galaxy_url" + #end if + #if $io_param.ppass.parampass != '0': + #if str($io_param.ppass.addparam.edit_params) == "yes": +--edit_additional_parameters + #end if + #for apar in $io_param.ppass.addparam.additional_parameters: +--additional_parameters "$apar.param_name~~~$apar.param_value~~~$apar.param_label~~~$apar.param_help~~~$apar.param_type~~~$apar.param_CL~~~$apar.param_CLprefixed" + #end for + #end if + #for $intab in $io_param.ppass.io.history_inputs: +--input_files "$intab.input_files~~~$intab.input_CL~~~$intab.input_formats~~~$intab.input_label~~~$intab.input_help" + #end for + #for $otab in $io_param.ppass.io.history_outputs: +--output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test" + #end for +--galaxy_root "$__root_dir__" +--tool_dir "$__tool_directory__" + #end if +]]></command> + <configfiles> + <configfile name="runme"> +$deps.usescript.dynScript + </configfile> + <configfile name="commandoverride"> +#if $cover.commover == "yes" and len(str($cover.command_override).strip()) > 1: +$cover.command_override +#end if + </configfile> + <configfile name="testoverride"> +#if $cover.commover == "yes" and len(str($cover.test_override).strip()) > 1: +$cover.test_override +#end if + </configfile> + <configfile name="helpme"> + #if $make.makeMode.make_Tool != "runonly": +${make.makeMode.help_text} + #else +$tool_name help goes here + #end if + </configfile> + <configfile name="citeme"> +#if $make.makeMode.make_Tool != "runonly": + #for $citation in $make.makeMode.citations: + #if $citation.citation_type.type == "bibtex": + **ENTRY**bibtex + ${citation.citation_type.bibtex} + #else + **ENTRY**doi + ${citation.citation_type.doi} + #end if + #end for +#end if + </configfile> + </configfiles> + <inputs> + <param name="tool_name" type="text" value="tool1" label="New tool ID and title for outputs" + help="Toolshed repository name. Choose thoughtfully to avoid namespace clashes with other tool writers. Lower case, digits and underscores only"> + <sanitizer invalid_char=""> + <valid initial="string.ascii_lowercase,string.digits"> + <add value="_"/> + </valid> + </sanitizer> + </param> + + <section name="deps" title="Dependencies, optional script and script interpreter" expanded="true"> + + <param name="packages" type="text" value="" label="Conda dependencies as package name[:version, name:version...]. These will always be available when this tool executes" + optional="false" help="Use =[ver] or :[ver] for specific version - 'bwa=0.17.0'. Default is latest. Will be used every time the tool is (re)run. Only Conda is currently supported" /> + + <conditional name="usescript"> + <param name="choosescript" type="select" display="radio" label="Supply a script for a dependency (e.g. python/R/bash) or a system executable such as Bash" + help = "For script interpreters like Python or bash, parameters and i/o specified below must match script's expectations - if you pass parameters, the script must deal with them"> + <option value="no">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option> + <option value="yes" selected="true">Yes, a script is ready to be pasted below</option> + </param> + <when value="no"> + <param name="dynScript" type="hidden" value="" /> + <param name="scriptrunner" type="hidden" value="" /> + </when> + <when value="yes"> + <param name="scriptrunner" type="text" value="" label="Interpreter for the script - eg bash or python. Can be one of the dependencies named above or a system executable" + help="Scripts are interpreted by the executable named here. Use bash for bash scripts, or a conda dependency such as R or Python for those scripts"> + <sanitizer invalid_char=""> + <valid initial="string.ascii_letters,string.digits"> + <add value="_"/> + </valid> + </sanitizer> + </param> + <param name="dynScript" type="text" area="True" value="" label="Script for executable above to interpret. It can be one of the Conda dependency names " + help="Script must handle all i/o and parameters as specified below using the parameters and passing method chosen below"> + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + </when> + </conditional> + </section> + <section name="io_param" title="Data file input, output and settings forming the executable or script command line" expanded="true"> + <conditional name="ppass"> + <param name="parampass" type="select" display="radio" label="Command line parameter passing method to use"> + <option value="argparse" selected="true">Argparse: passed in the form of --clname value</option> + <option value="positional">Positional: Passed in the order of positional ordinals ...foo.bam bar.idx zot.xls</option> + <option value="0">Tool reads selected input file from STDIN and writes STDOUT with no parameters</option> + </param> + <when value="argparse"> + <expand macro="io" /> + <expand macro="additparam" /> + </when> + <when value="positional"> + <expand macro="io" /> + <expand macro="additparam" /> + </when> + <when value="0"> + <expand macro="io"/> + </when> + </conditional> + </section> + <param name="cl_prefix" type="text" value="" label="Prefix for generated command line. Prepends generated i/o and parameter CL. Use override below to replace completely" + help="Text will replace generated executable/script elements. Sometimes required before i/o and parameters in the generated command line." /> + <conditional name="cover"> + <param name="commover" type="select" display="radio" label="Add Human wrought code to override the generated XML command and/or test section - DIY" + help = "For arbitrary and artfull command lines. All i/o and parameters must be passed. Choose No unless needed. Not for the faint of heart"> + <option value="no" selected="true">No. Use automatically generated command/test XML </option> + <option value="yes">Yes. XML needed to override autogenerated command and/or test segments will be pasted below</option> + </param> + <when value="no"> + <param name="command_override" type="hidden" value="" /> + <param name="test_override" type="hidden" value="" /> + </when> + <when value="yes"> + <param name="command_override" type="text" area="True" value="" label="Optional. Human wrought command element override XML/template - e.g. for bwa" + help="For arbitrary and artfull command lines. All i/o and parameters must be passed. Leave blank unless needed. Not for the faint of heart"> + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="test_override" type="text" area="True" value="" label="Optional. Human wrought test element override XML/template - e.g. for bwa" + help="For arbitrary and artfull scripts. Leave blank unless needed. Not for the faint of heart"> + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + </when> + </conditional> + <section name="make" title="Generate, toolshed and local Galaxy installation options" expanded="true"> + <conditional name="makeMode"> + <param name="make_Tool" type="select" display="radio" label="Choose the steps you want to run. The TF Docker container is recommended for local installation" + help="Installation in this Galaxy is optional" > + <option value="generate" >Run to generate tests only. Should fail if dependencies needed.</option> + <option value="gentest" selected="true">Test with planemo after generating.</option> + <option value="gentestinstall">Install in Galaxy after generation and testing. URLs and matching API keys are required for this step! </option> + </param> + <when value="generate"> + <param name="galaxy_apikey" value="" type="hidden" ></param> + <param name="toolshed_apikey" value="" type="hidden" ></param> + <param name="galaxy_url" value="" type="hidden" ></param> + <param name="toolshed_url" value="" type="hidden" ></param> + <expand macro="tool_metadata" /> + </when> + <when value="gentest"> + <param name="galaxy_apikey" value="" type="hidden" ></param> + <param name="toolshed_apikey" value="" type="hidden" ></param> + <param name="galaxy_url" value="" type="hidden" ></param> + <param name="toolshed_url" value="" type="hidden" ></param> + <expand macro="tool_metadata" /> + </when> + <when value="gentestinstall"> + <param name="galaxy_url" type="text" value="http://localhost:8080" label="URL for the Galaxy server where the new tool should be installed" + help="Default is localhost"> + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="galaxy_apikey" type="text" value="fakekey" label="API key for the Galaxy to install the new tool" + help="Cut and paste from the admin user properties screen"> + <sanitizer> + <valid initial="string.ascii_letters,string.digits"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="toolshed_url" type="text" value="http://localhost:9009" label="URL for the Toolshed where the new tool should be installed" + help="Default value is localhost:9009"> + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="toolshed_apikey" type="text" value="fakekey" label="API key for the local toolshed to use when installing the tool" + help="Cut and paste from the admin user properties screen"> + <sanitizer> + <valid initial="string.ascii_letters,string.digits"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <expand macro="tool_metadata" /> + </when> + </conditional> + </section> + </inputs> + <outputs> + + <data format="tgz" name="new_tool" label="${tool_name}_toolshed.tgz" > + <filter>makeMode['make_Tool'] != "runonly"</filter> + </data> + + <collection name="TF_run_report" type="list" label="${tool_name} outputs"> + <discover_datasets pattern="__name_and_ext__" directory="TF_run_report_tempdir" /> + </collection> + </outputs> +<tests> +<test> + <param name="user_email" value="admin@galaxy.org"/> + <param name="input_files" value="input1_sample" /> + <param name="input_CL" value="1" /> + <param name="input_formats" value="txt" /> + <param name="input_label" value="input" /> + <param name="input_help" value="help" /> + <param name="tool_name" value="pyrevpos" /> + <param name="parampass" value="positional" /> + <param name="make_Tool" value="generate" /> + <param name="tool_version" value="0.01" /> + <param name="tool_desc" value="positional reverse" /> + <param name="help_text" value="help text goes here" /> + <param name="packages" value="python"/> + <param name="history_name" value="output2" /> + <param name="history_format" value="txt" /> + <param name="history_CL" value="2" /> + <param name="dynScript" value="import sys; inp = sys.argv[1]; outp = sys.argv[2]; inlist = open(inp,'r').readlines(); o = open(outp,'w'); rs = [''.join(list(reversed(x.rstrip()))) for x in inlist]; o.write('\n'.join(rs)); o.close()"/> + <param name="choosescript" value="yes" /> + <param name="script_path" value="$runme"/> + <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" /> +</test> +</tests> +<help> + +.. class:: warningmark + +**Details and attribution** +(see GTF_) + +**Local Admins ONLY** +Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool. + +**If you find a bug** +Please raise an issue, or even better, submit a pull request fixing it, on the github repository GTF_ + +**What it does** +This tool optionally generates normal workflow compatible first class Galaxy tools + +Generated tools can run existing binary packages that become requirements, existing scripts, or new scripts pasted into this tool form. +Pasted scripts are written so they are part of the new tool and cannot be adjusted by the downstream user. +Binary packages are managed by the dependency subsystem - conda usually, so anything in bioconda or conda_forge is available for example. + +Any number of parameters can be built into the new tool form for passing in to the script or executable at runtime. +These can be editable by the downstream user or baked in. + +When you run this tool, your executable or script and supplied parameter values will be run to produce a canonical +set of outputs - these are used to construct a test for the new tool. + +If tool generation is required, a new tarball compatible with any Galaxy toolshed is created. +It can be unpacked in your galaxy/tools directory and manually added to tool_conf.xml, or +installed into any toolshed from where it can be installed into your Galaxy. + + +.. class:: warningmark + +**Note to system administrators** +This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances. +Admin_users will have the power to do anything they want as the Galaxy user if you install this tool. + +.. class:: warningmark + +**Use on public servers** is STRONGLY discouraged for obvious reasons + +The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation. +We recommend that you follow the good code hygiene practices associated with safe toolshed practices. + +Here's a sample python script that can be cut and pasted into the tool form, suitable for positional parameter passing: + +:: + + # reverse order of text by row + import sys + inp = sys.argv[1] + outp = sys.argv[2] + i = open(inp,'r').readlines() + o = open(outp,'w') + for row in i: + rs = row.rstrip() + rs = list(rs) + rs.reverse() + o.write(''.join(rs)) + o.write('\n') + o.close() + +With argparse style parameters: + +:: + + # reverse order of text by row + import argparse + parser = argparse.ArgumentParser() + a = parser.add_argument + a('--infile',default='') + a('--outfile',default=None) + args = parser.parse_args() + inp = args.infile + outp = args.outfile + i = open(inp,'r').readlines() + o = open(outp,'w') + for row in i: + rs = row.rstrip() + rs = list(rs) + rs.reverse() + o.write(''.join(rs)) + o.write('\n') + o.close() + + + +Paper_ + +*Licensing* + +Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012 +All rights reserved. +Licensed under the LGPL_ + +.. _LGPL: http://www.gnu.org/copyleft/lesser.html +.. _GTF: https://github.com/fubar2/toolfactory +.. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573 + + +</help> +<citations> + <citation type="doi">10.1093/bioinformatics/bts573</citation> +</citations> +</tool> + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/home/ross/galaxy/tools/tool_makers/toolfactory/test-data/input1_sample Thu Jan 07 09:22:51 2021 +0000 @@ -0,0 +1,166 @@ +*WARNING before you start* + + Install this tool on a private Galaxy ONLY + Please NEVER on a public or production instance + +Updated august 2014 by John Chilton adding citation support + +Updated august 8 2014 to fix bugs reported by Marius van den Beek + +Please cite the resource at +http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref +if you use this tool in your published work. + +**Short Story** + +This is an unusual Galaxy tool capable of generating new Galaxy tools. +It works by exposing *unrestricted* and therefore extremely dangerous scripting +to all designated administrators of the host Galaxy server, allowing them to +run scripts in R, python, sh and perl over multiple selected input data sets, +writing a single new data set as output. + +*You have a working r/python/perl/bash script or any executable with positional or argparse style parameters* + +It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool. + + +**Automated generation of new Galaxy tools for installation into any Galaxy** + +A test is generated using small sample test data inputs and parameter settings you supply. +Once the test case outputs have been produced, they can be used to build a +new Galaxy tool. The supplied script or executable is baked as a requirement +into a new, ordinary Galaxy tool, fully workflow compatible out of the box. +Generated tools are installed via a tool shed by an administrator +and work exactly like all other Galaxy tools for your users. + +**More Detail** + +To use the ToolFactory, you should have prepared a script to paste into a +text box, or have a package in mind and a small test input example ready to select from your history +to test your new script. + +```planemo test rgToolFactory2.xml --galaxy_root ~/galaxy --test_data ~/galaxy/tools/tool_makers/toolfactory/test-data``` works for me + +There is an example in each scripting language on the Tool Factory form. You +can just cut and paste these to try it out - remember to select the right +interpreter please. You'll also need to create a small test data set using +the Galaxy history add new data tool. + +If the script fails somehow, use the "redo" button on the tool output in +your history to recreate the form complete with broken script. Fix the bug +and execute again. Rinse, wash, repeat. + +Once the script runs sucessfully, a new Galaxy tool that runs your script +can be generated. Select the "generate" option and supply some help text and +names. The new tool will be generated in the form of a new Galaxy datatype +*toolshed.gz* - as the name suggests, it's an archive ready to upload to a +Galaxy ToolShed as a new tool repository. + +Once it's in a ToolShed, it can be installed into any local Galaxy server +from the server administrative interface. + +Once the new tool is installed, local users can run it - each time, the script +that was supplied when it was built will be executed with the input chosen +from the user's history. In other words, the tools you generate with the +ToolFactory run just like any other Galaxy tool,but run your script every time. + +Tool factory tools are perfect for workflow components. One input, one output, +no variables. + +*To fully and safely exploit the awesome power* of this tool, +Galaxy and the ToolShed, you should be a developer installing this +tool on a private/personal/scratch local instance where you are an +admin_user. Then, if you break it, you get to keep all the pieces see +https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home + +**Installation** +This is a Galaxy tool. You can install it most conveniently using the +administrative "Search and browse tool sheds" link. Find the Galaxy Main +toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory +repository. Open it and review the code and select the option to install it. + +If you can't get the tool that way, the xml and py files here need to be +copied into a new tools +subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry +pointing to the xml +file - something like:: + + <section name="Tool building tools" id="toolbuilders"> + <tool file="toolfactory/rgToolFactory.xml"/> + </section> + +If not already there, +please add: +<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" +mimetype="multipart/x-gzip" subclass="True" /> +to your local data_types_conf.xml. + + +**Restricted execution** + +The tool factory tool itself will then be usable ONLY by admin users - +people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY +admin_users can run this tool** Think about it for a moment. If allowed to +run any arbitrary script on your Galaxy server, the only thing that would +impede a miscreant bent on destroying all your Galaxy data would probably +be lack of appropriate technical skills. + +**What it does** + +This is a tool factory for simple scripts in python, R and +perl currently. Functional tests are automatically generated. How cool is that. + +LIMITED to simple scripts that read one input from the history. Optionally can +write one new history dataset, and optionally collect any number of outputs +into links on an autogenerated HTML index page for the user to navigate - +useful if the script writes images and output files - pdf outputs are shown +as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and +imagemagik need to be available. + +Generated tools can be edited and enhanced like any Galaxy tool, so start +small and build up since a generated script gets you a serious leg up to a +more complex one. + +**What you do** + +You paste and run your script, you fix the syntax errors and +eventually it runs. You can use the redo button and edit the script before +trying to rerun it as you debug - it works pretty well. + +Once the script works on some test data, you can generate a toolshed compatible +gzip file containing your script ready to run as an ordinary Galaxy tool in +a repository on your local toolshed. That means safe and largely automated +installation in any production Galaxy configured to use your toolshed. + +**Generated tool Security** + +Once you install a generated tool, it's just +another tool - assuming the script is safe. They just run normally and their +user cannot do anything unusually insecure but please, practice safe toolshed. +Read the code before you install any tool. Especially this one - it is really scary. + +**Send Code** + +Patches and suggestions welcome as bitbucket issues please? + +**Attribution** + +Creating re-usable tools from scripts: The Galaxy Tool Factory +Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team +Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 + +http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref + +**Licensing** + +Copyright Ross Lazarus 2010 +ross lazarus at g mail period com + +All rights reserved. + +Licensed under the LGPL + +**Obligatory screenshot** + +http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/home/ross/galaxy/tools/tool_makers/toolfactory/test-data/output2_sample Thu Jan 07 09:22:51 2021 +0000 @@ -0,0 +1,165 @@ +*trats uoy erofeb GNINRAW* + +YLNO yxalaG etavirp a no loot siht llatsnI +ecnatsni noitcudorp ro cilbup a no REVEN esaelP + +troppus noitatic gnidda notlihC nhoJ yb 4102 tsugua detadpU + +keeB ned nav suiraM yb detroper sgub xif ot 4102 8 tsugua detadpU + +ta ecruoser eht etic esaelP +fer=epytyek&JWYdwMrWs1hQzcl=yekji?375stb/tnirper/igc/gro.slanruojdrofxo.scitamrofnioib//:ptth +.krow dehsilbup ruoy ni loot siht esu uoy fi + +**yrotS trohS** + +.sloot yxalaG wen gnitareneg fo elbapac loot yxalaG lausunu na si sihT +gnitpircs suoregnad ylemertxe erofereht dna *detcirtsernu* gnisopxe yb skrow tI +ot meht gniwolla ,revres yxalaG tsoh eht fo srotartsinimda detangised lla ot +,stes atad tupni detceles elpitlum revo lrep dna hs ,nohtyp ,R ni stpircs nur +.tuptuo sa tes atad wen elgnis a gnitirw + +*sretemarap elyts esrapgra ro lanoitisop htiw elbatucexe yna ro tpircs hsab/lrep/nohtyp/r gnikrow a evah uoY* + +.loot yxalaG a gnisu ,setunim ni loot yxalaG yranidro na otni denrut eb nac tI + + +**yxalaG yna otni noitallatsni rof sloot yxalaG wen fo noitareneg detamotuA** + +.ylppus uoy sgnittes retemarap dna stupni atad tset elpmas llams gnisu detareneg si tset A +a dliub ot desu eb nac yeht ,decudorp neeb evah stuptuo esac tset eht ecnO +tnemeriuqer a sa dekab si elbatucexe ro tpircs deilppus ehT .loot yxalaG wen +.xob eht fo tuo elbitapmoc wolfkrow ylluf ,loot yxalaG yranidro ,wen a otni +rotartsinimda na yb dehs loot a aiv dellatsni era sloot detareneG +.sresu ruoy rof sloot yxalaG rehto lla ekil yltcaxe krow dna + +**liateD eroM** + +a otni etsap ot tpircs a deraperp evah dluohs uoy ,yrotcaFlooT eht esu oT +yrotsih ruoy morf tceles ot ydaer elpmaxe tupni tset llams a dna dnim ni egakcap a evah ro ,xob txet +.tpircs wen ruoy tset ot + +em rof skrow ```atad-tset/yrotcafloot/srekam_loot/sloot/yxalag/~ atad_tset-- yxalag/~ toor_yxalag-- lmx.2yrotcaFlooTgr tset omenalp``` + +uoY .mrof yrotcaF looT eht no egaugnal gnitpircs hcae ni elpmaxe na si erehT +thgir eht tceles ot rebmemer - tuo ti yrt ot eseht etsap dna tuc tsuj nac +gnisu tes atad tset llams a etaerc ot deen osla ll'uoY .esaelp reterpretni +.loot atad wen dda yrotsih yxalaG eht + +ni tuptuo loot eht no nottub "oder" eht esu ,wohemos sliaf tpircs eht fI +gub eht xiF .tpircs nekorb htiw etelpmoc mrof eht etaercer ot yrotsih ruoy +.taeper ,hsaw ,esniR .niaga etucexe dna + +tpircs ruoy snur taht loot yxalaG wen a ,yllufssecus snur tpircs eht ecnO +dna txet pleh emos ylppus dna noitpo "etareneg" eht tceleS .detareneg eb nac +epytatad yxalaG wen a fo mrof eht ni detareneg eb lliw loot wen ehT .seman +a ot daolpu ot ydaer evihcra na s'ti ,stseggus eman eht sa - *zg.dehsloot* +.yrotisoper loot wen a sa dehSlooT yxalaG + +revres yxalaG lacol yna otni dellatsni eb nac ti ,dehSlooT a ni s'ti ecnO +.ecafretni evitartsinimda revres eht morf + +tpircs eht ,emit hcae - ti nur nac sresu lacol ,dellatsni si loot wen eht ecnO +nesohc tupni eht htiw detucexe eb lliw tliub saw ti nehw deilppus saw taht +eht htiw etareneg uoy sloot eht ,sdrow rehto nI .yrotsih s'resu eht morf +.emit yreve tpircs ruoy nur tub,loot yxalaG rehto yna ekil tsuj nur yrotcaFlooT + +,tuptuo eno ,tupni enO .stnenopmoc wolfkrow rof tcefrep era sloot yrotcaf looT +.selbairav on + +,loot siht fo *rewop emosewa eht tiolpxe ylefas dna ylluf oT* +siht gnillatsni repoleved a eb dluohs uoy ,dehSlooT eht dna yxalaG +na era uoy erehw ecnatsni lacol hctarcs/lanosrep/etavirp a no loot +ees seceip eht lla peek ot teg uoy ,ti kaerb uoy fi ,nehT .resu_nimda +emoH/ikiw/yrotcaflootyxalag/rabuf/gro.tekcubtib//:sptth + +**noitallatsnI** +eht gnisu yltneinevnoc tsom ti llatsni nac uoY .loot yxalaG a si sihT +niaM yxalaG eht dniF .knil "sdehs loot esworb dna hcraeS" evitartsinimda +yrotcafloot eht rof hcraes dna /ude.usp.xb.2g.dehsloot//:sptth ta dehsloot +.ti llatsni ot noitpo eht tceles dna edoc eht weiver dna ti nepO .yrotisoper + +eb ot deen ereh selif yp dna lmx eht ,yaw taht loot eht teg t'nac uoy fI +sloot wen a otni deipoc +yrtne wen a sdeen lmx.fnoc_loot ruoY yrotcafloot/sloot sa hcus yrotceridbus +lmx eht ot gnitniop +::ekil gnihtemos - elif + +>"sredliubloot"=di "sloot gnidliub looT"=eman noitces< +>/"lmx.yrotcaFlooTgr/yrotcafloot"=elif loot< +>noitces/< + +,ereht ydaerla ton fI +:dda esaelp +"yraniB:yranib.sepytatad.yxalag"=epyt "zg.dehsloot"=noisnetxe epytatad< +>/ "eurT"=ssalcbus "pizg-x/trapitlum"=epytemim +.lmx.fnoc_sepyt_atad lacol ruoy ot + + +**noitucexe detcirtseR** + +- sresu nimda yb YLNO elbasu eb neht lliw flesti loot yrotcaf loot ehT +YLNO .thgir s'taht ,seY** ini.igsw_esrevinu ni sresu_nimda ni sDI htiw elpoep +ot dewolla fI .tnemom a rof ti tuoba knihT **loot siht nur nac sresu_nimda +dluow taht gniht ylno eht ,revres yxalaG ruoy no tpircs yrartibra yna nur +ylbaborp dluow atad yxalaG ruoy lla gniyortsed no tneb tnaercsim a edepmi +.slliks lacinhcet etairporppa fo kcal eb + +**seod ti tahW** + +dna R ,nohtyp ni stpircs elpmis rof yrotcaf loot a si sihT +.taht si looc woH .detareneg yllacitamotua era stset lanoitcnuF .yltnerruc lrep + +nac yllanoitpO .yrotsih eht morf tupni eno daer taht stpircs elpmis ot DETIMIL +stuptuo fo rebmun yna tcelloc yllanoitpo dna ,tesatad yrotsih wen eno etirw +- etagivan ot resu eht rof egap xedni LMTH detarenegotua na no sknil otni +nwohs era stuptuo fdp - selif tuptuo dna segami setirw tpircs eht fi lufesu +dna taht os tpircstsohg htiw knurhs era s'fdp detaolb s'R dna slianbmuht sa +.elbaliava eb ot deen kigamegami + +trats os ,loot yxalaG yna ekil decnahne dna detide eb nac sloot detareneG +a ot pu gel suoires a uoy steg tpircs detareneg a ecnis pu dliub dna llams +.eno xelpmoc erom + +**od uoy tahW** + +dna srorre xatnys eht xif uoy ,tpircs ruoy nur dna etsap uoY +erofeb tpircs eht tide dna nottub oder eht esu nac uoY .snur ti yllautneve +.llew ytterp skrow ti - gubed uoy sa ti nurer ot gniyrt + +elbitapmoc dehsloot a etareneg nac uoy ,atad tset emos no skrow tpircs eht ecnO +ni loot yxalaG yranidro na sa nur ot ydaer tpircs ruoy gniniatnoc elif pizg +detamotua ylegral dna efas snaem tahT .dehsloot lacol ruoy no yrotisoper a +.dehsloot ruoy esu ot derugifnoc yxalaG noitcudorp yna ni noitallatsni + +**ytiruceS loot detareneG** + +tsuj s'ti ,loot detareneg a llatsni uoy ecnO +rieht dna yllamron nur tsuj yehT .efas si tpircs eht gnimussa - loot rehtona +.dehsloot efas ecitcarp ,esaelp tub erucesni yllausunu gnihtyna od tonnac resu +.yracs yllaer si ti - eno siht yllaicepsE .loot yna llatsni uoy erofeb edoc eht daeR + +**edoC dneS** + +?esaelp seussi tekcubtib sa emoclew snoitseggus dna sehctaP + +**noitubirttA** + +yrotcaF looT yxalaG ehT :stpircs morf sloot elbasu-er gnitaerC +maeT yxalaG ehT ;nnameiZ kraM ;ipsaK ynotnA ;surazaL ssoR +375stb/scitamrofnioib/3901.01 :iod ;2102 scitamrofnioiB + +fer=epytyek&JWYdwMrWs1hQzcl=yekji?375stb/tnirper/igc/gro.slanruojdrofxo.scitamrofnioib//:ptth + +**gnisneciL** + +0102 surazaL ssoR thgirypoC +moc doirep liam g ta surazal ssor + +.devreser sthgir llA + +LPGL eht rednu desneciL + +**tohsneercs yrotagilbO** + +gnp.looTtpircScimanyd/segami/989ef2308adf/crs/rekamlootyxalag/rabuf/gro.tekcubtib//:ptth
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/home/ross/galaxy/tools/tool_makers/toolfactory/test-data/pyrevpos.python Thu Jan 07 09:22:51 2021 +0000 @@ -0,0 +1,13 @@ +# reverse order of text by row +import sys +inp = sys.argv[1] +outp = sys.argv[2] +i = open(inp,'r').readlines() +o = open(outp,'w') +for row in i: + rs = row.rstrip() + rs = list(rs) + rs.reverse() + o.write(''.join(rs)) +o.close() +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/home/ross/galaxy/tools/tool_makers/toolfactory/test-data/test1_log.txt Thu Jan 07 09:22:51 2021 +0000 @@ -0,0 +1,1 @@ +## Executing Toolfactory generated command line = python /tmp/pyrevposq5dmcdy1.python /tmp/tmpqrksf8sd/files/5/b/9/dataset_5b952a86-87df-44ad-a415-ea549f3f0cee.dat output2
Binary file home/ross/galaxy/tools/tool_makers/toolfactory/test-data/toolfactory_pyrevpos_tgz_sample has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/home/ross/galaxy/tools/tool_makers/toolfactory/testtf.sh Thu Jan 07 09:22:51 2021 +0000 @@ -0,0 +1,2 @@ +planemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/toolfactory &>foo +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/home/ross/galaxy/tools/tool_makers/toolfactory/whoosh.sh Thu Jan 07 09:22:51 2021 +0000 @@ -0,0 +1,16 @@ +# using the galaxy venv this seems to work +. /galaxy_venv/bin/activate +python scripts/tool_shed/build_ts_whoosh_index.py -c config/tool_shed.yml --config-section tool_shed +# eeesh. /etc/galaxy is where the actual galaxy.yml lives - despite other configs being where they might be expected +# fix tool_shed.yml to 0.0.0.0 and admin email +# add tgz to datatypes :( +# need to source a venv in /export/tool_deps/toolfactorydeps/0.01/fubar/toolfactorydeps/9e9428fe9134/env.sh +# as nothing was done by the setup_virtualenv step apparently. +# gcc and friends for planemo pip installation +# File "/galaxy-central/lib/galaxy/tool_util/verify/interactor.py", line 595, in <listcomp> +# test_user = [user for user in all_users if user["email"] == email][0] +# add local to tool_sheds_conf.xml +# <tool_sheds> +# <tool_shed name="local" url="http://localhost:9009"/> +# mercurial > 5.5!! +
--- a/toolfactory/.planemo.yml Tue Jan 05 00:34:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -## Planemo Global Configuration File. -## Everything in this file is completely optional - these values can all be -## configured via command line options for the corresponding commands. - -## Specify a default galaxy_root for test and server commands here. -galaxy_root: /galaxy-central -## Username used with toolshed(s). -shed_username: galaxy -sheds: - # For each tool shed you wish to target, uncomment key or both email and - # password. - toolshed: - #key: "<TODO>" - #email: "<TODO>" - #password: "<TODO>" - testtoolshed: - #key: "<TODO>" - #email: "<TODO>" - #password: "<TODO>" - local: - key: "fakekey" - email: "admin@galaxy.org" - password: "password"
--- a/toolfactory/.shed.yml Tue Jan 05 00:34:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -name: toolfactory -owner: fubar -description: ToolFactory - tool to make Galaxy tools ready for the toolshed -homepage_url: https://github.com/fubar2/toolfactory -long_description: | - ToolFactory - turn executable packages and R/python/perl/bash scripts into ordinary Galaxy tools - - Creating re-usable tools from scripts: The Galaxy Tool Factory Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team - Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 -remote_repository_url: https://github.com/fubar2/toolfactory -type: tool_dependency_definition -categories: -- Tool Generators
--- a/toolfactory/LICENSE Tue Jan 05 00:34:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,504 +0,0 @@ -GNU LESSER GENERAL PUBLIC LICENSE - Version 2.1, February 1999 - - Copyright (C) 1991, 1999 Free Software Foundation, Inc. - 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - -(This is the first released version of the Lesser GPL. It also counts - as the successor of the GNU Library Public License, version 2, hence - the version number 2.1.) - - Preamble - - The licenses for most software are designed to take away your -freedom to share and change it. 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--- a/toolfactory/README.md Tue Jan 05 00:34:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,380 +0,0 @@ -## Breaking news! Docker container at https://github.com/fubar2/toolfactory-galaxy-docker recommended as at December 2020 - -## This is the original ToolFactory suitable for non-docker situations. Please use the docker container if you can because it's integrated with a Toolshed... - -# WARNING - -Install this tool to a throw-away private Galaxy or Docker container ONLY! - -Please NEVER on a public or production instance where a hostile user may -be able to gain access if they can acquire an administrative account login. - -It only runs for server administrators - the ToolFactory tool will refuse to execute for an ordinary user since -it can install new tools to the Galaxy server it executes on! This is not something you should allow other than -on a throw away instance that is protected from potentially hostile users. - -## Short Story - -Galaxy is easily extended to new applications by adding a new tool. Each new scientific computational package added as -a tool to Galaxy requires an XML document describing how the application interacts with Galaxy. -This is sometimes termed "wrapping" the package because the instructions tell Galaxy how to run the package -as a new Galaxy tool. Any tool that has been wrapped is readily available to all the users through a consistent -and easy to use interface once installed in the local Galaxy server. - -Most Galaxy tool wrappers have been manually prepared by skilled programmers, many using Planemo because it -automates much of the boilerplate and makes the process much easier. -The ToolFactory (TF) now uses Planemo under the hood for testing, but hides the command -line complexities. The user will still need appropriate skills in terms of describing the interface between -Galaxy and the new application, but will be helped by a Galaxy tool form to collect all the needed -settings, together with automated testing and uploading to a toolshed with optional local installation. - - -## ToolFactory generated tools are ordinary Galaxy tools - -A TF generated tool that passes the Planemo test is ready to publish in any Galaxy Toolshed and ready to install in any running Galaxy instance. -They are fully workflow compatible and work exactly like any hand-written tool. The user can select input files of the specified type(s) from their -history and edit each of the specified parameters. The tool form will show all the labels and help text supplied when the tool was built. When the tool -is executed, the dependent binary or script will be passed all the i/o files and parameters as specified, and will write outputs to the specified new -history datasets - just like any other Galaxy tool. - -## Models for tool command line construction - -The key to turning any software package into a Galaxy tool is the automated construction of a suitable command line. - -The TF can build a new tool that will allow the tool user to select input files from their history, set any parameters and when run will send the -new output files to the history as specified when the tool builder completed the form and built the new tool. - -That tool can contain instructions to run any Conda dependency or a system executable like bash. Whether a bash script you have written or -a Conda package like bwa, the executable will expect to find settings for input, output and parameters on a command line. - -These are often passed as "--name value" (argparse style) or in a fixed order (positional style). - -The ToolFactory allows either, or for "filter" applications that process input from STDIN and write processed output to STDOUT. - -The simplest tool model wraps a simple script or Conda dependency package requiring only input and output files, with no user supplied settings illustrated by -the Tacrev demonstration tool found in the Galaxy running in the ToolFactory docker container. It passes a user selected input file from the current history on STDIN -to a bash script. The bash script runs the unix tac utility (reverse cat) piped to the unix rev (reverse lines in a text file) utility. It's a one liner: - -`tac | rev` - -The tool building form allows zero or more Conda package name(s) and version(s) and an optional script to be executed by either a system -executable like ``bash`` or the first of any named Conda dependency package/version. Tacrev uses a tiny bash script shown above and uses the system -bash. Conda bash can be specified if it is important to use the same version consistently for the tool. - -On the tool form, the repeat section allowing zero or more input files was set to be a text file to be selected by the tool user and -in the repeat section allowing one or more outputs, a new output file with special value `STDOUT` as the positional parameter, causes the TF to -generate a command to capture STDOUT and send it to the new history file containing the reversed input text. - -By reversed, we mean really, truly reversed. - -That simple model can be made much more complicated, and can pass inputs and outputs as named or positional parameters, -to allow more complicated scripts or dependent binaries that require: - -1. Any number of input data files selected by the user from existing history data -2. Any number of output data files written to the user's history -3. Any number of user supplied parameters. These can be passed as command line arguments to the script or the dependency package. Either -positional or named (argparse) style command line parameter passing can be used. - -More complex models can be seen in the Sedtest, Pyrevpos and Pyrevargparse tools illustrating positional and argparse parameter passing. - -The most complex demonstration is the Planemo advanced tool tutorial BWA tool. There is one version using a command-override to implement -exactly the same command structure in the Planemo tutorial. A second version uses a bash script and positional parameters to achieve the same -result. Some tool builders may find the bash version more familiar and cleaner but the choice is yours. - -## Overview - - - - -Steps in building a new Galaxy tool are all conducted through Galaxy running in the docker container: - -1. Login to the Galaxy running in the container at http://localhost:8080 using an admin account. They are specified in config/galaxy.yml and - in the documentation at - and the ToolFactory will error out and refuse to run for non-administrative tool builders as a minimal protection from opportunistic hostile use. - -2. Start the TF and fill in the form, providing sample inputs and parameter values to suit the Conda package being wrapped. - -3. Execute the tool to create a new XML tool wrapper using the sample inputs and parameter settings for the inbuilt tool test. Planemo runs twice. - firstly to generate the test outputs and then to perform a proper test. The completed toolshed archive is written to the history - together with the planemo test report. Optionally the new tool archive can be uploaded - to the toolshed running in the same container (http://localhost:9009) and then installed inside the Galaxy in the container for further testing. - -4. If the test fails, rerun the failed history job and correct errors on the tool form before rerunning until everything works correctly. - - - - - -## Planning and building new Galaxy tool wrappers. - -It is best to have all the required planning done to wrap any new script or binary before firing up the TF. -Conda is the only current dependency manager supported. Before starting, at the very least, the tool builder will need -to know the required software package name in Conda and the version to use, how the command line for -the package must be constructed, and there must be sample inputs in the working history for each of the required data inputs -for the package, together with values for every parameter to suit these sample inputs. These are required on the TF form -for preparing the inbuilt tool test. That test is run using Planemo, as part of the tool generation process. - -A new tool is specified by filling in the usual Galaxy tool form. - -The form starts with a new tool name. Most tools will need dependency packages and versions -for the executable. Only Conda is currently supported. - -If a script is needed, it can be pasted into a text box and the interpreter named. Available system executables -can be used such as bash, or an interpreter such as python, perl or R can be nominated as conda dependencies -to ensure reproducible analyses. - -The tool form will be generated from the input data and the tool builder supplied parameters. The command line for the -executable is built using positional or argparse (named e.g. --input_file /foo/baz) style -parameters and is completely dependent on the executable. These can include: - -1. Any number of input data sets needed by the executable. Each appears to the tool user on the run form and is included -on the command line for the executable. The tool builder must supply a small representative sample for each one as -an input for the automated tool test. - -2. Any number of output data sets generated by the package can be added to the command line and will appear in -the user's history at the end of the job - -3. Any number of text or numeric parameters. Each will appear to the tool user on the run form and are included -on the command line to the executable. The tool builder must supply a suitable representative value for each one as -the value to be used for the automated tool test. - -Once the form is completed, executing the TF will build a new XML tool wrapper -including a functional test based on the sample settings and data. - -If the Planemo test passes, the tool can be optionally uploaded to the local Galaxy used in the image for more testing. - -A local toolshed runs inside the container to allow an automated installation, although any toolshed and any accessible -Galaxy can be specified for this process by editing the default URL and API keys to provide appropriate credentials. - -## Generated Tool Dependency management - -Conda is used for all dependency management although tools that use system utilities like sed, bash or awk -may be available on job execution nodes. Sed and friends are available as Conda (conda-forge) dependencies if necessary. -Versioned Conda dependencies are always baked-in to the tool and will be used for reproducible calculation. - -## Requirements - -These are all managed automagically. The TF relies on galaxyxml to generate tool xml and uses ephemeris and -bioblend to load tools to the toolshed and to Galaxy. Planemo is used for testing and runs in a biocontainer currently at -https://quay.io/fubar2/planemo-biocontainer - -## Caveats - -This docker image requires privileged mode so exposes potential security risks if hostile tool builders gain access. -Please, do not run it in any situation where that is a problem - never, ever on a public facing Galaxy server. -On a laptop or workstation should be fine in a non-hostile environment. - - -## Example generated XML - -For the bwa-mem example, a supplied bash script is included as a configfile and so has escaped characters. -``` -<tool name="bwatest" id="bwatest" version="0.01"> - <!--Cite: Creating re-usable tools from scripts doi:10.1093/bioinformatics/bts573--> - <!--Source in git at: https://github.com/fubar2/toolfactory--> - <!--Created by admin@galaxy.org at 30/11/2020 07:12:10 using the Galaxy Tool Factory.--> - <description>Planemo advanced tool building sample bwa mem mapper as a ToolFactory demo</description> - <requirements> - <requirement version="0.7.15" type="package">bwa</requirement> - <requirement version="1.3" type="package">samtools</requirement> - </requirements> - <configfiles> - <configfile name="runme"><![CDATA[ -REFFILE=\$1 -FASTQ=\$2 -BAMOUT=\$3 -rm -f "refalias" -ln -s "\$REFFILE" "refalias" -bwa index -a is "refalias" -bwa mem -t "2" -v 1 "refalias" "\$FASTQ" > tempsam -samtools view -Sb tempsam > temporary_bam_file.bam -samtools sort -o "\$BAMOUT" temporary_bam_file.bam - -]]></configfile> - </configfiles> - <version_command/> - <command><![CDATA[bash -$runme -$input1 -$input2 -$bam_output]]></command> - <inputs> - <param optional="false" label="Reference sequence for bwa to map the fastq reads against" help="" format="fasta" multiple="false" type="data" name="input1" argument="input1"/> - <param optional="false" label="Reads as fastqsanger to align to the reference sequence" help="" format="fastqsanger" multiple="false" type="data" name="input2" argument="input2"/> - </inputs> - <outputs> - <data name="bam_output" format="bam" label="bam_output" hidden="false"/> - </outputs> - <tests> - <test> - <output name="bam_output" value="bam_output_sample" compare="sim_size" format="bam" delta_frac="0.1"/> - <param name="input1" value="input1_sample"/> - <param name="input2" value="input2_sample"/> - </test> - </tests> - <help><![CDATA[ - -**What it Does** - -Planemo advanced tool building sample bwa mem mapper - -Reimagined as a bash script for a ToolFactory demonstration - - ------- - -Script:: - - REFFILE=$1 - FASTQ=$2 - BAMOUT=$3 - rm -f "refalias" - ln -s "$REFFILE" "refalias" - bwa index -a is "refalias" - bwa mem -t "2" -v 1 "refalias" "$FASTQ" > tempsam - samtools view -Sb tempsam > temporary_bam_file.bam - samtools sort -o "$BAMOUT" temporary_bam_file.bam - -]]></help> -</tool> - -``` - - - -## More Explanation - -The TF is an unusual Galaxy tool, designed to allow a skilled user to make new Galaxy tools. -It appears in Galaxy just like any other tool but outputs include new Galaxy tools generated -using instructions provided by the user and the results of Planemo lint and tool testing using -small sample inputs provided by the TF user. The small samples become tests built in to the new tool. - -It offers a familiar Galaxy form driven way to define how the user of the new tool will -choose input data from their history, and what parameters the new tool user will be able to adjust. -The TF user must know, or be able to read, enough about the tool to be able to define the details of -the new Galaxy interface and the ToolFactory offers little guidance on that other than some examples. - -Tools always depend on other things. Most tools in Galaxy depend on third party -scientific packages, so TF tools usually have one or more dependencies. These can be -scientific packages such as BWA or scripting languages such as Python and are -managed by Conda. If the new tool relies on a system utility such as bash or awk -where the importance of version control on reproducibility is low, these can be used without -Conda management - but remember the potential risks of unmanaged dependencies on computational -reproducibility. - -The TF user can optionally supply a working script where scripting is -required and the chosen dependency is a scripting language such as Python or a system -scripting executable such as bash. Whatever the language, the script must correctly parse the command line -arguments it receives at tool execution, as they are defined by the TF user. The -text of that script is "baked in" to the new tool and will be executed each time -the new tool is run. It is highly recommended that scripts and their command lines be developed -and tested until proven to work before the TF is invoked. Galaxy as a software development -environment is actually possible, but not recommended being somewhat clumsy and inefficient. - -Tools nearly always take one or more data sets from the user's history as input. TF tools -allow the TF user to define what Galaxy datatypes the tool end user will be able to choose and what -names or positions will be used to pass them on a command line to the package or script. - -Tools often have various parameter settings. The TF allows the TF user to define how each -parameter will appear on the tool form to the end user, and what names or positions will be -used to pass them on the command line to the package. At present, parameters are limited to -simple text and number fields. Pull requests for other kinds of parameters that galaxyxml -can handle are welcomed. - -Best practice Galaxy tools have one or more automated tests. These should use small sample data sets and -specific parameter settings so when the tool is tested, the outputs can be compared with their expected -values. The TF will automatically create a test for the new tool. It will use the sample data sets -chosen by the TF user when they built the new tool. - -The TF works by exposing *unrestricted* and therefore extremely dangerous scripting -to all designated administrators of the host Galaxy server, allowing them to -run scripts in R, python, sh and perl. For this reason, a Docker container is -available to help manage the associated risks. - -## Scripting uses - -To use a scripting language to create a new tool, you must first prepared and properly test a script. Use small sample -data sets for testing. When the script is working correctly, upload the small sample datasets -into a new history, start configuring a new ToolFactory tool, and paste the script into the script text box on the TF form. - -### Outputs - -The TF will generate the new tool described on the TF form, and test it -using planemo. Optionally if a local toolshed is running, it can be used to -install the new tool back into the generating Galaxy. - -A toolshed is built in to the Docker container and configured -so a tool can be tested, sent to that toolshed, then installed in the Galaxy -where the TF is running using the default toolshed and Galaxy URL and API keys. - -Once it's in a ToolShed, it can be installed into any local Galaxy server -from the server administrative interface. - -Once the new tool is installed, local users can run it - each time, the -package and/or script that was supplied when it was built will be executed with the input chosen -from the user's history, together with user supplied parameters. In other words, the tools you generate with the -TF run just like any other Galaxy tool. - -TF generated tools work as normal workflow components. - - -## Limitations - -The TF is flexible enough to generate wrappers for many common scientific packages -but the inbuilt automation will not cope with all possible situations. Users can -supply overrides for two tool XML segments - tests and command and the BWA -example in the supplied samples workflow illustrates their use. It does not deal with -repeated elements or conditional parameters such as allowing a user to choose to see "simple" -or "advanced" parameters (yet) and there will be plenty of packages it just -won't cover - but it's a quick and efficient tool for the other 90% of cases. Perfect for -that bash one liner you need to get that workflow functioning correctly for this -afternoon's demonstration! - -## Installation - -The Docker container https://github.com/fubar2/toolfactory-galaxy-docker/blob/main/README.md -is the best way to use the TF because it is preconfigured -to automate new tool testing and has a built in local toolshed where each new tool -is uploaded. If you grab the docker container, it should just work after a restart and you -can run a workflow to generate all the sample tools. Running the samples and rerunning the ToolFactory -jobs that generated them allows you to add fields and experiment to see how things work. - -It can be installed like any other tool from the Toolshed, but you will need to make some -configuration changes (TODO write a configuration). You can install it most conveniently using the -administrative "Search and browse tool sheds" link. Find the Galaxy Main -toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory -repository in the Tool Maker section. Open it and review the code and select the option to install it. - -If not already there please add: - -``` -<datatype extension="tgz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /> -``` - -to your local config/data_types_conf.xml. - - -## Restricted execution - -The tool factory tool itself will ONLY run for admin users - -people with IDs in config/galaxy.yml "admin_users". - -*ONLY admin_users can run this tool* - -That doesn't mean it's safe to install on a shared or exposed instance - please don't. - -## Generated tool Security - -Once you install a generated tool, it's just -another tool - assuming the script is safe. They just run normally and their -user cannot do anything unusually insecure but please, practice safe toolshed. -Read the code before you install any tool. Especially this one - it is really scary. - -## Attribution - -Creating re-usable tools from scripts: The Galaxy Tool Factory -Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team -Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 - -http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref -
--- a/toolfactory/install_tf_demos.py Tue Jan 05 00:34:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,47 +0,0 @@ -import argparse -import os -import subprocess -import sys -import urllib.request - -from bioblend import galaxy - -WF = "https://drive.google.com/uc?export=download&id=13xE8o7tucHGNA0qYkEP98FfUGl2wdOU5" -HIST = ( - "https://drive.google.com/uc?export=download&id=1V0ZN9ZBuqcGJvt2AP7s3g0q11uYEhdDB" -) -WF_FILE = "tf_workflow.ga" -HIST_FILE = "tf_history.tgz" - - -def _parser(): - parser = argparse.ArgumentParser() - parser.add_argument( - "-g", "--galaxy", help="URL of target galaxy", default="http://localhost:9090" - ) - parser.add_argument("-a", "--key", help="Galaxy admin key", default=None) - return parser - - -def main(): - """ - load the planemo tool_factory demonstration history and tool generating workflow - fails in planemo served galaxies because there seems to be no user in trans? - """ - args = _parser().parse_args() - urllib.request.urlretrieve(WF, WF_FILE) - urllib.request.urlretrieve(HIST, HIST_FILE) - assert args.key, "Need an administrative key for the target Galaxy supplied please" - wfp = os.path.abspath(WF_FILE) - hp = os.path.abspath(HIST_FILE) - gi = galaxy.GalaxyInstance( - url=args.galaxy, key=args.key, email="planemo@galaxyproject.org" - ) - x = gi.workflows.import_workflow_from_local_path(WF_FILE, publish=True) - print(f"installed {WF_FILE} Returned = {x}\n") - x = gi.histories.import_history(file_path=HIST_FILE) - print(f"installed {HIST_FILE} Returned = {x}\n") - - -if __name__ == "__main__": - main()
--- a/toolfactory/rgToolFactory2.py Tue Jan 05 00:34:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1021 +0,0 @@ -# replace with shebang for biocontainer -# see https://github.com/fubar2/toolfactory -# -# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012 -# -# all rights reserved -# Licensed under the LGPL -# suggestions for improvement and bug fixes welcome at -# https://github.com/fubar2/toolfactory -# -# July 2020: BCC was fun and I feel like rip van winkle after 5 years. -# Decided to -# 1. Fix the toolfactory so it works - done for simplest case -# 2. Fix planemo so the toolfactory function works -# 3. Rewrite bits using galaxyxml functions where that makes sense - done - -import argparse -import copy -import logging -import os -import re -import shutil -import subprocess -import sys -import tarfile -import tempfile -import time - -from bioblend import ConnectionError -from bioblend import toolshed - -import galaxyxml.tool as gxt -import galaxyxml.tool.parameters as gxtp - -import lxml - -import yaml - -myversion = "V2.1 July 2020" -verbose = True -debug = True -toolFactoryURL = "https://github.com/fubar2/toolfactory" -ourdelim = "~~~" - -# --input_files="$intab.input_files~~~$intab.input_CL~~~ -# $intab.input_formats# ~~~$intab.input_label -# ~~~$intab.input_help" -IPATHPOS = 0 -ICLPOS = 1 -IFMTPOS = 2 -ILABPOS = 3 -IHELPOS = 4 -IOCLPOS = 5 - -# --output_files "$otab.history_name~~~$otab.history_format~~~ -# $otab.history_CL~~~$otab.history_test" -ONAMEPOS = 0 -OFMTPOS = 1 -OCLPOS = 2 -OTESTPOS = 3 -OOCLPOS = 4 - - -# --additional_parameters="$i.param_name~~~$i.param_value~~~ -# $i.param_label~~~$i.param_help~~~$i.param_type -# ~~~$i.CL~~~i$.param_CLoverride" -ANAMEPOS = 0 -AVALPOS = 1 -ALABPOS = 2 -AHELPPOS = 3 -ATYPEPOS = 4 -ACLPOS = 5 -AOVERPOS = 6 -AOCLPOS = 7 - - -foo = len(lxml.__version__) -# fug you, flake8. Say my name! -FAKEEXE = "~~~REMOVE~~~ME~~~" -# need this until a PR/version bump to fix galaxyxml prepending the exe even -# with override. - - -def timenow(): - """return current time as a string""" - return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time())) - - -def quote_non_numeric(s): - """return a prequoted string for non-numerics - useful for perl and Rscript parameter passing? - """ - try: - _ = float(s) - return s - except ValueError: - return '"%s"' % s - - -html_escape_table = { - "&": "&", - ">": ">", - "<": "<", - "#": "#", - "$": "$", -} -cheetah_escape_table = {"$": "\\$", "#": "\\#"} - - -def html_escape(text): - """Produce entities within text.""" - return "".join([html_escape_table.get(c, c) for c in text]) - - -def cheetah_escape(text): - """Produce entities within text.""" - return "".join([cheetah_escape_table.get(c, c) for c in text]) - - -def html_unescape(text): - """Revert entities within text. Multiple character targets so use replace""" - t = text.replace("&", "&") - t = t.replace(">", ">") - t = t.replace("<", "<") - t = t.replace("\\$", "$") - t = t.replace("$", "$") - t = t.replace("#", "#") - return t - - -def parse_citations(citations_text): - """""" - citations = [c for c in citations_text.split("**ENTRY**") if c.strip()] - citation_tuples = [] - for citation in citations: - if citation.startswith("doi"): - citation_tuples.append(("doi", citation[len("doi") :].strip())) - else: - citation_tuples.append( - ("bibtex", citation[len("bibtex") :].strip()) - ) - return citation_tuples - - -class ScriptRunner: - """Wrapper for an arbitrary script - uses galaxyxml - - """ - - def __init__(self, args=None): - """ - prepare command line cl for running the tool here - and prepare elements needed for galaxyxml tool generation - """ - self.ourcwd = os.getcwd() - self.ourenv = copy.deepcopy(os.environ) - self.infiles = [x.split(ourdelim) for x in args.input_files] - self.outfiles = [x.split(ourdelim) for x in args.output_files] - self.addpar = [x.split(ourdelim) for x in args.additional_parameters] - self.args = args - self.cleanuppar() - self.lastclredirect = None - self.lastxclredirect = None - self.cl = [] - self.xmlcl = [] - self.is_positional = self.args.parampass == "positional" - if self.args.sysexe: - self.executeme = self.args.sysexe - else: - if self.args.packages: - self.executeme = ( - self.args.packages.split(",")[0].split(":")[0].strip() - ) - else: - self.executeme = None - aCL = self.cl.append - aXCL = self.xmlcl.append - assert args.parampass in [ - "0", - "argparse", - "positional", - ], 'args.parampass must be "0","positional" or "argparse"' - self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name) - self.tool_id = self.tool_name - self.newtool = gxt.Tool( - self.tool_name, - self.tool_id, - self.args.tool_version, - self.args.tool_desc, - FAKEEXE, - ) - self.newtarpath = "toolfactory_%s.tgz" % self.tool_name - self.tooloutdir = "./tfout" - self.repdir = "./TF_run_report_tempdir" - self.testdir = os.path.join(self.tooloutdir, "test-data") - if not os.path.exists(self.tooloutdir): - os.mkdir(self.tooloutdir) - if not os.path.exists(self.testdir): - os.mkdir(self.testdir) - if not os.path.exists(self.repdir): - os.mkdir(self.repdir) - self.tinputs = gxtp.Inputs() - self.toutputs = gxtp.Outputs() - self.testparam = [] - if self.args.script_path: - self.prepScript() - if self.args.command_override: - scos = open(self.args.command_override, "r").readlines() - self.command_override = [x.rstrip() for x in scos] - else: - self.command_override = None - if self.args.test_override: - stos = open(self.args.test_override, "r").readlines() - self.test_override = [x.rstrip() for x in stos] - else: - self.test_override = None - if self.args.cl_prefix: # DIY CL start - clp = self.args.cl_prefix.split(" ") - for c in clp: - aCL(c) - aXCL(c) - else: - if self.args.script_path: - aCL(self.executeme) - aCL(self.sfile) - aXCL(self.executeme) - aXCL("$runme") - else: - aCL(self.executeme) - aXCL(self.executeme) - self.elog = os.path.join( - self.repdir, "%s_error_log.txt" % self.tool_name - ) - self.tlog = os.path.join( - self.repdir, "%s_runner_log.txt" % self.tool_name - ) - - if self.args.parampass == "0": - self.clsimple() - else: - clsuffix = [] - xclsuffix = [] - for i, p in enumerate(self.infiles): - if p[IOCLPOS].upper() == "STDIN": - appendme = [ - p[ICLPOS], - p[ICLPOS], - p[IPATHPOS], - "< %s" % p[IPATHPOS], - ] - xappendme = [ - p[ICLPOS], - p[ICLPOS], - p[IPATHPOS], - "< $%s" % p[ICLPOS], - ] - else: - appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""] - xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""] - clsuffix.append(appendme) - xclsuffix.append(xappendme) - for i, p in enumerate(self.outfiles): - if p[OOCLPOS] == "STDOUT": - self.lastclredirect = [">", p[ONAMEPOS]] - self.lastxclredirect = [">", "$%s" % p[OCLPOS]] - else: - clsuffix.append([p[OCLPOS], p[ONAMEPOS], p[ONAMEPOS], ""]) - xclsuffix.append( - [p[OCLPOS], p[ONAMEPOS], "$%s" % p[ONAMEPOS], ""] - ) - for p in self.addpar: - clsuffix.append( - [p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]] - ) - xclsuffix.append( - [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]] - ) - clsuffix.sort() - xclsuffix.sort() - self.xclsuffix = xclsuffix - self.clsuffix = clsuffix - if self.args.parampass == "positional": - self.clpositional() - else: - self.clargparse() - - def prepScript(self): - rx = open(self.args.script_path, "r").readlines() - rx = [x.rstrip() for x in rx] - rxcheck = [x.strip() for x in rx if x.strip() > ""] - assert len(rxcheck) > 0, "Supplied script is empty. Cannot run" - self.script = "\n".join(rx) - fhandle, self.sfile = tempfile.mkstemp( - prefix=self.tool_name, suffix="_%s" % (self.executeme) - ) - tscript = open(self.sfile, "w") - tscript.write(self.script) - tscript.close() - self.escapedScript = [cheetah_escape(x) for x in rx] - self.spacedScript = [f" {x}" for x in rx if x.strip() > ""] - art = "%s.%s" % (self.tool_name, self.executeme) - artifact = open(art, "wb") - artifact.write(bytes("\n".join(self.escapedScript), "utf8")) - artifact.close() - - def cleanuppar(self): - """ positional parameters are complicated by their numeric ordinal""" - if self.args.parampass == "positional": - for i, p in enumerate(self.infiles): - assert ( - p[ICLPOS].isdigit() or p[ICLPOS].strip().upper() == "STDIN" - ), "Positional parameters must be ordinal integers - got %s for %s" % ( - p[ICLPOS], - p[ILABPOS], - ) - for i, p in enumerate(self.outfiles): - assert ( - p[OCLPOS].isdigit() - or p[OCLPOS].strip().upper() == "STDOUT" - ), "Positional parameters must be ordinal integers - got %s for %s" % ( - p[OCLPOS], - p[ONAMEPOS], - ) - for i, p in enumerate(self.addpar): - assert p[ - ACLPOS - ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % ( - p[ACLPOS], - p[ANAMEPOS], - ) - for i, p in enumerate(self.infiles): - infp = copy.copy(p) - icl = infp[ICLPOS] - infp.append(icl) - if ( - infp[ICLPOS].isdigit() - or self.args.parampass == "0" - or infp[ICLPOS].strip().upper() == "STDOUT" - ): - scl = "input%d" % (i + 1) - infp[ICLPOS] = scl - self.infiles[i] = infp - for i, p in enumerate(self.outfiles): - p.append(p[OCLPOS]) # keep copy - if ( - p[OOCLPOS].isdigit() and self.args.parampass != "positional" - ) or p[OOCLPOS].strip().upper() == "STDOUT": - scl = p[ONAMEPOS] - p[OCLPOS] = scl - self.outfiles[i] = p - for i, p in enumerate(self.addpar): - p.append(p[ACLPOS]) - if p[ACLPOS].isdigit(): - scl = "param%s" % p[ACLPOS] - p[ACLPOS] = scl - self.addpar[i] = p - - def clsimple(self): - """no parameters - uses < and > for i/o""" - aCL = self.cl.append - aXCL = self.xmlcl.append - - if len(self.infiles) > 0: - aCL("<") - aCL(self.infiles[0][IPATHPOS]) - aXCL("<") - aXCL("$%s" % self.infiles[0][ICLPOS]) - if len(self.outfiles) > 0: - aCL(">") - aCL(self.outfiles[0][OCLPOS]) - aXCL(">") - aXCL("$%s" % self.outfiles[0][ONAMEPOS]) - - def clpositional(self): - # inputs in order then params - aCL = self.cl.append - for (o_v, k, v, koverride) in self.clsuffix: - if " " in v: - aCL("%s" % v) - else: - aCL(v) - aXCL = self.xmlcl.append - for (o_v, k, v, koverride) in self.xclsuffix: - aXCL(v) - if self.lastxclredirect: - aXCL(self.lastxclredirect[0]) - aXCL(self.lastxclredirect[1]) - - def clargparse(self): - """argparse style""" - aCL = self.cl.append - aXCL = self.xmlcl.append - # inputs then params in argparse named form - - for (o_v, k, v, koverride) in self.xclsuffix: - if koverride > "": - k = koverride - elif len(k.strip()) == 1: - k = "-%s" % k - else: - k = "--%s" % k - aXCL(k) - aXCL(v) - for (o_v, k, v, koverride) in self.clsuffix: - if koverride > "": - k = koverride - elif len(k.strip()) == 1: - k = "-%s" % k - else: - k = "--%s" % k - aCL(k) - aCL(v) - - def getNdash(self, newname): - if self.is_positional: - ndash = 0 - else: - ndash = 2 - if len(newname) < 2: - ndash = 1 - return ndash - - def doXMLparam(self): - """flake8 made me do this...""" - for ( - p - ) in ( - self.outfiles - ): # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test" - newname, newfmt, newcl, test, oldcl = p - test = test.strip() - ndash = self.getNdash(newcl) - aparm = gxtp.OutputData( - name=newname, format=newfmt, num_dashes=ndash, label=newcl - ) - aparm.positional = self.is_positional - if self.is_positional: - if oldcl.upper() == "STDOUT": - aparm.positional = 9999999 - aparm.command_line_override = "> $%s" % newname - else: - aparm.positional = int(oldcl) - aparm.command_line_override = "$%s" % newname - self.toutputs.append(aparm) - ld = None - if test.strip() > "": - if test.startswith("diff"): - c = "diff" - ld = 0 - if test.split(":")[1].isdigit: - ld = int(test.split(":")[1]) - tp = gxtp.TestOutput( - name=newname, - value="%s_sample" % newname, - format=newfmt, - compare=c, - lines_diff=ld, - ) - elif test.startswith("sim_size"): - c = "sim_size" - tn = test.split(":")[1].strip() - if tn > "": - if "." in tn: - delta = None - delta_frac = min(1.0, float(tn)) - else: - delta = int(tn) - delta_frac = None - tp = gxtp.TestOutput( - name=newname, - value="%s_sample" % newname, - format=newfmt, - compare=c, - delta=delta, - delta_frac=delta_frac, - ) - self.testparam.append(tp) - for p in self.infiles: - newname = p[ICLPOS] - newfmt = p[IFMTPOS] - ndash = self.getNdash(newname) - if not len(p[ILABPOS]) > 0: - alab = p[ICLPOS] - else: - alab = p[ILABPOS] - aninput = gxtp.DataParam( - newname, - optional=False, - label=alab, - help=p[IHELPOS], - format=newfmt, - multiple=False, - num_dashes=ndash, - ) - aninput.positional = self.is_positional - self.tinputs.append(aninput) - tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname) - self.testparam.append(tparm) - for p in self.addpar: - ( - newname, - newval, - newlabel, - newhelp, - newtype, - newcl, - override, - oldcl, - ) = p - if not len(newlabel) > 0: - newlabel = newname - ndash = self.getNdash(newname) - if newtype == "text": - aparm = gxtp.TextParam( - newname, - label=newlabel, - help=newhelp, - value=newval, - num_dashes=ndash, - ) - elif newtype == "integer": - aparm = gxtp.IntegerParam( - newname, - label=newname, - help=newhelp, - value=newval, - num_dashes=ndash, - ) - elif newtype == "float": - aparm = gxtp.FloatParam( - newname, - label=newname, - help=newhelp, - value=newval, - num_dashes=ndash, - ) - else: - raise ValueError( - 'Unrecognised parameter type "%s" for\ - additional parameter %s in makeXML' - % (newtype, newname) - ) - aparm.positional = self.is_positional - if self.is_positional: - aparm.positional = int(oldcl) - self.tinputs.append(aparm) - tparm = gxtp.TestParam(newname, value=newval) - self.testparam.append(tparm) - - def doNoXMLparam(self): - """filter style package - stdin to stdout""" - if len(self.infiles) > 0: - alab = self.infiles[0][ILABPOS] - if len(alab) == 0: - alab = self.infiles[0][ICLPOS] - max1s = ( - "Maximum one input if parampass is 0 but multiple input files supplied - %s" - % str(self.infiles) - ) - assert len(self.infiles) == 1, max1s - newname = self.infiles[0][ICLPOS] - aninput = gxtp.DataParam( - newname, - optional=False, - label=alab, - help=self.infiles[0][IHELPOS], - format=self.infiles[0][IFMTPOS], - multiple=False, - num_dashes=0, - ) - aninput.command_line_override = "< $%s" % newname - aninput.positional = self.is_positional - self.tinputs.append(aninput) - tp = gxtp.TestParam(name=newname, value="%s_sample" % newname) - self.testparam.append(tp) - if len(self.outfiles) > 0: - newname = self.outfiles[0][OCLPOS] - newfmt = self.outfiles[0][OFMTPOS] - anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0) - anout.command_line_override = "> $%s" % newname - anout.positional = self.is_positional - self.toutputs.append(anout) - tp = gxtp.TestOutput( - name=newname, value="%s_sample" % newname, format=newfmt - ) - self.testparam.append(tp) - - def makeXML(self): - """ - Create a Galaxy xml tool wrapper for the new script - Uses galaxyhtml - Hmmm. How to get the command line into correct order... - """ - if self.command_override: - self.newtool.command_override = ( - self.command_override - ) # config file - else: - self.newtool.command_override = self.xmlcl - if self.args.help_text: - helptext = open(self.args.help_text, "r").readlines() - safertext = "\n".join([cheetah_escape(x) for x in helptext]) - if self.args.script_path: - scr = [x for x in self.spacedScript if x.strip() > ""] - scr.insert(0, "\n------\n\n\nScript::\n") - if len(scr) > 300: - scr = ( - scr[:100] - + [" >300 lines - stuff deleted", " ......"] - + scr[-100:] - ) - scr.append("\n") - safertext = safertext + "\n".join(scr) - self.newtool.help = safertext - else: - self.newtool.help = ( - "Please ask the tool author (%s) for help \ - as none was supplied at tool generation\n" - % (self.args.user_email) - ) - self.newtool.version_command = None # do not want - requirements = gxtp.Requirements() - if self.args.packages: - for d in self.args.packages.split(","): - ver = "" - d = d.replace("==", ":") - d = d.replace("=", ":") - if ":" in d: - packg, ver = d.split(":") - else: - packg = d - requirements.append( - gxtp.Requirement("package", packg.strip(), ver.strip()) - ) - self.newtool.requirements = requirements - if self.args.parampass == "0": - self.doNoXMLparam() - else: - self.doXMLparam() - self.newtool.outputs = self.toutputs - self.newtool.inputs = self.tinputs - if self.args.script_path: - configfiles = gxtp.Configfiles() - configfiles.append( - gxtp.Configfile( - name="runme", text="\n".join(self.escapedScript) - ) - ) - self.newtool.configfiles = configfiles - tests = gxtp.Tests() - test_a = gxtp.Test() - for tp in self.testparam: - test_a.append(tp) - tests.append(test_a) - self.newtool.tests = tests - self.newtool.add_comment( - "Created by %s at %s using the Galaxy Tool Factory." - % (self.args.user_email, timenow()) - ) - self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL)) - self.newtool.add_comment( - "Cite: Creating re-usable tools from scripts doi:10.1093/bioinformatics/bts573" - ) - exml0 = self.newtool.export() - exml = exml0.replace( - FAKEEXE, "" - ) # temporary work around until PR accepted - if ( - self.test_override - ): # cannot do this inside galaxyxml as it expects lxml objects for tests - part1 = exml.split("<tests>")[0] - part2 = exml.split("</tests>")[1] - fixed = "%s\n%s\n%s" % (part1, self.test_override, part2) - exml = fixed - # exml = exml.replace('range="1:"', 'range="1000:"') - xf = open("%s.xml" % self.tool_name, "w") - xf.write(exml) - xf.write("\n") - xf.close() - # ready for the tarball - - def run(self): - """ - generate test outputs by running a command line - won't work if command or test override in play - planemo is the - easiest way to generate test outputs for that case so is - automagically selected - """ - scl = " ".join(self.cl) - err = None - if self.args.parampass != "0": - if os.path.exists(self.elog): - ste = open(self.elog, "a") - else: - ste = open(self.elog, "w") - if self.lastclredirect: - sto = open( - self.lastclredirect[1], "wb" - ) # is name of an output file - else: - if os.path.exists(self.tlog): - sto = open(self.tlog, "a") - else: - sto = open(self.tlog, "w") - sto.write( - "## Executing Toolfactory generated command line = %s\n" - % scl - ) - sto.flush() - subp = subprocess.run( - self.cl, env=self.ourenv, shell=False, stdout=sto, stderr=ste - ) - sto.close() - ste.close() - retval = subp.returncode - else: # work around special case - stdin and write to stdout - if len(self.infiles) > 0: - sti = open(self.infiles[0][IPATHPOS], "rb") - else: - sti = sys.stdin - if len(self.outfiles) > 0: - sto = open(self.outfiles[0][ONAMEPOS], "wb") - else: - sto = sys.stdout - subp = subprocess.run( - self.cl, env=self.ourenv, shell=False, stdout=sto, stdin=sti - ) - sto.write( - "## Executing Toolfactory generated command line = %s\n" % scl - ) - retval = subp.returncode - sto.close() - sti.close() - if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0: - os.unlink(self.tlog) - if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0: - os.unlink(self.elog) - if retval != 0 and err: # problem - sys.stderr.write(err) - logging.debug("run done") - return retval - - def shedLoad(self): - """ - use bioblend to create new repository - or update existing - - """ - if os.path.exists(self.tlog): - sto = open(self.tlog, "a") - else: - sto = open(self.tlog, "w") - - ts = toolshed.ToolShedInstance( - url=self.args.toolshed_url, - key=self.args.toolshed_api_key, - verify=False, - ) - repos = ts.repositories.get_repositories() - rnames = [x.get("name", "?") for x in repos] - rids = [x.get("id", "?") for x in repos] - tfcat = "ToolFactory generated tools" - if self.tool_name not in rnames: - tscat = ts.categories.get_categories() - cnames = [x.get("name", "?").strip() for x in tscat] - cids = [x.get("id", "?") for x in tscat] - catID = None - if tfcat.strip() in cnames: - ci = cnames.index(tfcat) - catID = cids[ci] - res = ts.repositories.create_repository( - name=self.args.tool_name, - synopsis="Synopsis:%s" % self.args.tool_desc, - description=self.args.tool_desc, - type="unrestricted", - remote_repository_url=self.args.toolshed_url, - homepage_url=None, - category_ids=catID, - ) - tid = res.get("id", None) - sto.write( - f"#create_repository {self.args.tool_name} tid={tid} res={res}\n" - ) - else: - i = rnames.index(self.tool_name) - tid = rids[i] - try: - res = ts.repositories.update_repository( - id=tid, tar_ball_path=self.newtarpath, commit_message=None - ) - sto.write(f"#update res id {id} ={res}\n") - except ConnectionError: - sto.write( - "####### Is the toolshed running and the API key correct? Bioblend shed upload failed\n" - ) - sto.close() - - def eph_galaxy_load(self): - """ - use ephemeris to load the new tool from the local toolshed after planemo uploads it - """ - if os.path.exists(self.tlog): - tout = open(self.tlog, "a") - else: - tout = open(self.tlog, "w") - cll = [ - "shed-tools", - "install", - "-g", - self.args.galaxy_url, - "--latest", - "-a", - self.args.galaxy_api_key, - "--name", - self.tool_name, - "--owner", - "fubar", - "--toolshed", - self.args.toolshed_url, - "--section_label", - "ToolFactory", - ] - tout.write("running\n%s\n" % " ".join(cll)) - subp = subprocess.run( - cll, - env=self.ourenv, - cwd=self.ourcwd, - shell=False, - stderr=tout, - stdout=tout, - ) - tout.write( - "installed %s - got retcode %d\n" - % (self.tool_name, subp.returncode) - ) - tout.close() - return subp.returncode - - def writeShedyml(self): - """for planemo""" - yuser = self.args.user_email.split("@")[0] - yfname = os.path.join(self.tooloutdir, ".shed.yml") - yamlf = open(yfname, "w") - odict = { - "name": self.tool_name, - "owner": yuser, - "type": "unrestricted", - "description": self.args.tool_desc, - "synopsis": self.args.tool_desc, - "category": "TF Generated Tools", - } - yaml.dump(odict, yamlf, allow_unicode=True) - yamlf.close() - - def makeTool(self): - """write xmls and input samples into place""" - self.makeXML() - if self.args.script_path: - stname = os.path.join(self.tooloutdir, "%s" % (self.sfile)) - if not os.path.exists(stname): - shutil.copyfile(self.sfile, stname) - xreal = "%s.xml" % self.tool_name - xout = os.path.join(self.tooloutdir, xreal) - shutil.copyfile(xreal, xout) - for p in self.infiles: - pth = p[IPATHPOS] - dest = os.path.join(self.testdir, "%s_sample" % p[ICLPOS]) - shutil.copyfile(pth, dest) - - def makeToolTar(self): - """move outputs into test-data and prepare the tarball""" - excludeme = "_planemo_test_report.html" - - def exclude_function(tarinfo): - filename = tarinfo.name - return None if filename.endswith(excludeme) else tarinfo - - if os.path.exists(self.tlog): - tout = open(self.tlog, "a") - else: - tout = open(self.tlog, "w") - for p in self.outfiles: - oname = p[ONAMEPOS] - tdest = os.path.join(self.testdir, "%s_sample" % oname) - if not os.path.isfile(tdest): - src = os.path.join(self.testdir, oname) - if os.path.isfile(src): - shutil.copyfile(src, tdest) - dest = os.path.join(self.repdir, "%s.sample" % (oname)) - shutil.copyfile(src, dest) - else: - tout.write( - "###Output file %s not found in testdir %s. This is normal during the first Planemo run that generates test outputs" - % (tdest, self.testdir) - ) - tf = tarfile.open(self.newtarpath, "w:gz") - tf.add( - name=self.tooloutdir, - arcname=self.tool_name, - filter=exclude_function, - ) - tf.close() - shutil.copyfile(self.newtarpath, self.args.new_tool) - - def moveRunOutputs(self): - """need to move planemo or run outputs into toolfactory collection""" - with os.scandir(self.tooloutdir) as outs: - for entry in outs: - if not entry.is_file(): - continue - if "." in entry.name: - nayme, ext = os.path.splitext(entry.name) - if ext in [".yml", ".xml", ".json", ".yaml"]: - ext = f"{ext}.txt" - else: - ext = ".txt" - ofn = "%s%s" % (entry.name.replace(".", "_"), ext) - dest = os.path.join(self.repdir, ofn) - src = os.path.join(self.tooloutdir, entry.name) - shutil.copyfile(src, dest) - with os.scandir(self.testdir) as outs: - for entry in outs: - if ( - (not entry.is_file()) - or entry.name.endswith("_sample") - or entry.name.endswith("_planemo_test_report.html") - ): - continue - if "." in entry.name: - nayme, ext = os.path.splitext(entry.name) - else: - ext = ".txt" - newname = f"{entry.name}{ext}" - dest = os.path.join(self.repdir, newname) - src = os.path.join(self.testdir, entry.name) - shutil.copyfile(src, dest) - - -def main(): - """ - This is a Galaxy wrapper. - It expects to be called by a special purpose tool.xml - - """ - parser = argparse.ArgumentParser() - a = parser.add_argument - a("--script_path", default=None) - a("--history_test", default=None) - a("--cl_prefix", default=None) - a("--sysexe", default=None) - a("--packages", default=None) - a("--tool_name", default="newtool") - a("--tool_dir", default=None) - a("--input_files", default=[], action="append") - a("--output_files", default=[], action="append") - a("--user_email", default="Unknown") - a("--bad_user", default=None) - a("--make_Tool", default="runonly") - a("--help_text", default=None) - a("--tool_desc", default=None) - a("--tool_version", default=None) - a("--citations", default=None) - a("--command_override", default=None) - a("--test_override", default=None) - a("--additional_parameters", action="append", default=[]) - a("--edit_additional_parameters", action="store_true", default=False) - a("--parampass", default="positional") - a("--tfout", default="./tfout") - a("--new_tool", default="new_tool") - a("--galaxy_url", default="http://localhost:8080") - a("--toolshed_url", default="http://localhost:9009") - # make sure this is identical to tool_sheds_conf.xml - # localhost != 127.0.0.1 so validation fails - a("--toolshed_api_key", default="fakekey") - a("--galaxy_api_key", default="fakekey") - a("--galaxy_root", default="/galaxy-central") - a("--galaxy_venv", default="/galaxy_venv") - args = parser.parse_args() - assert not args.bad_user, ( - 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy \ -admin adds %s to "admin_users" in the galaxy.yml Galaxy configuration file' - % (args.bad_user, args.bad_user) - ) - assert ( - args.tool_name - ), "## Tool Factory expects a tool name - eg --tool_name=DESeq" - assert ( - args.sysexe or args.packages - ), "## Tool Factory wrapper expects an interpreter \ -or an executable package in --sysexe or --packages" - args.input_files = [ - x.replace('"', "").replace("'", "") for x in args.input_files - ] - # remove quotes we need to deal with spaces in CL params - for i, x in enumerate(args.additional_parameters): - args.additional_parameters[i] = args.additional_parameters[i].replace( - '"', "" - ) - r = ScriptRunner(args) - r.writeShedyml() - r.makeTool() - if args.make_Tool == "generate": - retcode = r.run() - r.moveRunOutputs() - r.makeToolTar() - else: - retcode = r.planemo_test(genoutputs=True) # this fails :( - see PR - r.moveRunOutputs() - r.makeToolTar() - retcode = r.planemo_test(genoutputs=False) - r.moveRunOutputs() - r.makeToolTar() - print(f"second planemo_test returned {retcode}") - if args.make_Tool == "gentestinstall": - r.shedLoad() - r.eph_galaxy_load() - - -if __name__ == "__main__": - main()
--- a/toolfactory/rgToolFactory2.xml Tue Jan 05 00:34:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,536 +0,0 @@ -<tool id="rgtf2" name="toolfactory" version="2.00" profile="16.04" > - <description>Scripts into tools v2.0</description> - <macros> - <xml name="tool_metadata"> - <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01" - help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/> - <param name="tool_desc" label="Tool Synopsis" type="text" value="" - help="Supply a brief tool description for the Galaxy tool menu entry" /> - <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true" - value="**What it Does**" - help="Supply user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" > - <sanitizer> - <valid initial="string.printable"> - </valid> - <mapping initial="none"/> - </sanitizer> - </param> - <repeat name="citations" title="Citation"> - <conditional name="citation_type"> - <param name="type" type="select" display="radio" label="Citation Type"> - <option value="doi">DOI</option> - <option value="bibtex">BibTeX</option> - </param> - <when value="doi"> - <param name="doi" label="DOI" type="text" value="" - help="Supply a DOI (e.g. doi: 10.1111/j.1740-9713.2007.00258.x) to be cited when this tool is used in published research." /> - </when> - <when value="bibtex"> - <param name="bibtex" label="BibTex" type="text" area="true" - help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" > - <sanitizer> - <valid initial="string.printable"> - </valid> - <mapping initial="none"/> - </sanitizer> - </param> - </when> - </conditional> - </repeat> - </xml> - <xml name="io"> - <section name="io" title="Input and output files" expanded="true"> - <repeat name="history_inputs" title="zero or more input data files to pass as parameters to the executable." - help="USE SMALL SAMPLES for the new tool's test. Prompts will form a history item selector as input for users of this new tool"> - <param name="input_files" type="data" format="data" label="Select an input file from your history" optional="true" multiple="false" - help=""/> - <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input" - help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular"> - <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> - <column name="value" index="0"/> - </options> - </param> - <param name="input_label" type="text" value="" label="This will become the user prompt for the form so please make it informative" - help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" > - <sanitizer invalid_char=""> - <valid initial="string.printable"> <remove value='~~~'/> </valid> - <mapping initial="none"/> - </sanitizer> - </param> - <param name="input_help" type="text" value="" label="This will become help text on the form." - help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation"> - <sanitizer invalid_char=""> - <valid initial="string.printable"> <remove value='~~~'/> </valid> - <mapping initial="none"/> - </sanitizer> - </param> - <param name="input_CL" type="text" label="Positional: ordinal integer. Argparse: argument name. STDIN if the executable/script expects it" - help="If you will pass positional parameters, enter the integer ordinal for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value=""> - </param> - </repeat> - <repeat name="history_outputs" title="one or more new history items output by the executable to appear in the user history after the tool runs" - help="The name will become a history item for users of the new tool you are making containing one of it's outputs"> - <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false" - help="No spaces! Argparse will also use this name as --[name]"> - <sanitizer invalid_char="_"> - <valid initial="string.ascii_letters,string.digits"> - <add value="_" /> - </valid> - </sanitizer> - </param> - <param name="history_format" type="select" multiple="false" label="Select the datatype for this output" - help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular"> - <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> - <column name="value" index="0"/> - </options> - </param> - <param name="history_CL" type="text" label="Positional: ordinal integer. Use STDOUT if '>' required. Otherwise ignored if argparse because name is used" - help="If positional parameters, enter the integer ordinal expected for this parameter. If argparse, ignore unless STDOUT needed" value=""/> - <param name="history_test" type="text" label="Test pass decision criterion for this output compared to test generation" - help="Available options are diff:[lines], sim_size:[delta (integer) or delta_frac (float)" value="diff:0"/> - </repeat> - </section> - </xml> - <xml name="additparam"> - <section name="addparam" title="Executable or script settings passed on the command line other than I/O files" expanded="true"> - <param name="edit_params" type="select" display="radio" label="Make these settings on the generated tool form user editable?" - help="If no, users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing"> - <option value="yes" selected="true">Yes, allow user to edit all additional parameters on the generated tool form</option> - <option value="no">No - use the fixed values for all additional parameters - no user editing</option> - </param> - - <repeat name="additional_parameters" title="zero or more settings to be set by the tool user and passed on the command line" - help="See examples below to see how these can be parsed by scripts in the various languages"> - <param name="param_name" type="text" value="" label="Choose the name for this parameter - MUST not be blank!"> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"/> - <mapping initial="none"/> - </sanitizer> - </param> - <param name="param_type" type="select" label="Select the type for this parameter"> - <option value="text" selected="true">text</option> - <option value="integer">integer</option> - <option value="float">float</option> - </param> - <param name="param_value" type="text" value="" label="Enter this parameter's default value" - help="Note that '~~~' is an internal delimiter must not appear in this text field - please work around this technical limitation" > - <sanitizer invalid_char=""> - <valid initial="string.printable"> <remove value='~~~'/> </valid> - <mapping initial="none"/> - </sanitizer> - </param> - <param name="param_label" type="text" value="" label="Enter this parameter's label for the form" - help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" > - <sanitizer invalid_char=""> - <valid initial="string.printable"> <remove value='~~~'/> </valid> - <mapping initial="none"/> - </sanitizer> - </param> - <param name="param_help" type="text" value="" label="Help for this parameter" - help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation" > - <sanitizer invalid_char=""> - <valid initial="string.printable"> <remove value='~~~'/> </valid> - <mapping initial="none"/> - </sanitizer> - </param> - <param name="param_CL" type="text" label="Positional ordinal | argparse argument name" - help="Using positional parameters, enter the integer ordinal for this parameter on the command line. Using Argparse style, '--' will be prepended on the CL" value="" /> - <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ~~--foo if needed" - help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="" /> - </repeat> - </section> - </xml> - </macros> - -<requirements> - <requirement type="package" version="0.4.11">galaxyxml</requirement> - <requirement type="package" version="0.14.0">bioblend</requirement> - <requirement type="package" version="0.10.6">ephemeris</requirement> - <requirement type="package" version="0.74.1">planemo</requirement> -</requirements> - - <command ><![CDATA[ -#import os -#set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1' -#if not $dev_env and ( $__user_email__ not in $__admin_users__ ): -python3 $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__ - #else: -python3 $__tool_directory__/rgToolFactory2.py - #if len(str($cl_prefix)) > 3: ---cl_prefix "$cl_prefix" - #end if - #if $cover.commover == "yes": - #if len(str($cover.command_override)) > 10: ---command_override "$commandoverride" - #end if - #if len(str($cover.test_override)) > 10: ---test_override "$testoverride" - #end if - #end if ---packages "$deps.packages" - #if $deps.usescript.choosescript == "yes": ---script_path "$runme" ---sysexe "$deps.usescript.scriptrunner" - #end if ---tool_name "$tool_name" --user_email "$__user_email__" --citations "$citeme" --parampass "$io_param.ppass.parampass" - #if str($make.makeMode.make_Tool)!="runonly": ---make_Tool "$make.makeMode.make_Tool" ---tool_desc "$make.makeMode.tool_desc" ---tool_version "$make.makeMode.tool_version" ---help_text "$helpme" ---new_tool "$new_tool" ---toolshed_api_key "$make.makeMode.toolshed_apikey" ---galaxy_api_key "$make.makeMode.galaxy_apikey" ---toolshed_url "$make.makeMode.toolshed_url" ---galaxy_url "$make.makeMode.galaxy_url" - #end if - #if $io_param.ppass.parampass != '0': - #if str($io_param.ppass.addparam.edit_params) == "yes": ---edit_additional_parameters - #end if - #for apar in $io_param.ppass.addparam.additional_parameters: ---additional_parameters "$apar.param_name~~~$apar.param_value~~~$apar.param_label~~~$apar.param_help~~~$apar.param_type~~~$apar.param_CL~~~$apar.param_CLprefixed" - #end for - #end if - #for $intab in $io_param.ppass.io.history_inputs: ---input_files "$intab.input_files~~~$intab.input_CL~~~$intab.input_formats~~~$intab.input_label~~~$intab.input_help" - #end for - #for $otab in $io_param.ppass.io.history_outputs: ---output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test" - #end for ---galaxy_root "$__root_dir__" ---tool_dir "$__tool_directory__" - #end if -]]></command> - <configfiles> - <configfile name="runme"> -$deps.usescript.dynScript - </configfile> - <configfile name="commandoverride"> -#if $cover.commover == "yes" and len(str($cover.command_override).strip()) > 1: -$cover.command_override -#end if - </configfile> - <configfile name="testoverride"> -#if $cover.commover == "yes" and len(str($cover.test_override).strip()) > 1: -$cover.test_override -#end if - </configfile> - <configfile name="helpme"> - #if $make.makeMode.make_Tool != "runonly": -${make.makeMode.help_text} - #else -$tool_name help goes here - #end if - </configfile> - <configfile name="citeme"> -#if $make.makeMode.make_Tool != "runonly": - #for $citation in $make.makeMode.citations: - #if $citation.citation_type.type == "bibtex": - **ENTRY**bibtex - ${citation.citation_type.bibtex} - #else - **ENTRY**doi - ${citation.citation_type.doi} - #end if - #end for -#end if - </configfile> - </configfiles> - <inputs> - <param name="tool_name" type="text" value="tool1" label="New tool ID and title for outputs" - help="Toolshed repository name. Choose thoughtfully to avoid namespace clashes with other tool writers. Lower case, digits and underscores only"> - <sanitizer invalid_char=""> - <valid initial="string.ascii_lowercase,string.digits"> - <add value="_"/> - </valid> - </sanitizer> - </param> - - <section name="deps" title="Dependencies, optional script and script interpreter" expanded="true"> - - <param name="packages" type="text" value="" label="Conda dependencies as package name[:version, name:version...]. These will always be available when this tool executes" - optional="false" help="Use =[ver] or :[ver] for specific version - 'bwa=0.17.0'. Default is latest. Will be used every time the tool is (re)run. Only Conda is currently supported" /> - - <conditional name="usescript"> - <param name="choosescript" type="select" display="radio" label="Supply a script for a dependency (e.g. python/R/bash) or a system executable such as Bash" - help = "For script interpreters like Python or bash, parameters and i/o specified below must match script's expectations - if you pass parameters, the script must deal with them"> - <option value="no">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option> - <option value="yes" selected="true">Yes, a script is ready to be pasted below</option> - </param> - <when value="no"> - <param name="dynScript" type="hidden" value="" /> - <param name="scriptrunner" type="hidden" value="" /> - </when> - <when value="yes"> - <param name="scriptrunner" type="text" value="" label="Interpreter for the script - eg bash or python. Can be one of the dependencies named above or a system executable" - help="Scripts are interpreted by the executable named here. Use bash for bash scripts, or a conda dependency such as R or Python for those scripts"> - <sanitizer invalid_char=""> - <valid initial="string.ascii_letters,string.digits"> - <add value="_"/> - </valid> - </sanitizer> - </param> - <param name="dynScript" type="text" area="True" value="" label="Script for executable above to interpret. It can be one of the Conda dependency names " - help="Script must handle all i/o and parameters as specified below using the parameters and passing method chosen below"> - <sanitizer> - <valid initial="string.printable"> - </valid> - <mapping initial="none"/> - </sanitizer> - </param> - </when> - </conditional> - </section> - <section name="io_param" title="Data file input, output and settings forming the executable or script command line" expanded="true"> - <conditional name="ppass"> - <param name="parampass" type="select" display="radio" label="Command line parameter passing method to use"> - <option value="argparse" selected="true">Argparse: passed in the form of --clname value</option> - <option value="positional">Positional: Passed in the order of positional ordinals ...foo.bam bar.idx zot.xls</option> - <option value="0">Tool reads selected input file from STDIN and writes STDOUT with no parameters</option> - </param> - <when value="argparse"> - <expand macro="io" /> - <expand macro="additparam" /> - </when> - <when value="positional"> - <expand macro="io" /> - <expand macro="additparam" /> - </when> - <when value="0"> - <expand macro="io"/> - </when> - </conditional> - </section> - <param name="cl_prefix" type="text" value="" label="Prefix for generated command line. Prepends generated i/o and parameter CL. Use override below to replace completely" - help="Text will replace generated executable/script elements. Sometimes required before i/o and parameters in the generated command line." /> - <conditional name="cover"> - <param name="commover" type="select" display="radio" label="Add Human wrought code to override the generated XML command and/or test section - DIY" - help = "For arbitrary and artfull command lines. All i/o and parameters must be passed. Choose No unless needed. Not for the faint of heart"> - <option value="no" selected="true">No. Use automatically generated command/test XML </option> - <option value="yes">Yes. XML needed to override autogenerated command and/or test segments will be pasted below</option> - </param> - <when value="no"> - <param name="command_override" type="hidden" value="" /> - <param name="test_override" type="hidden" value="" /> - </when> - <when value="yes"> - <param name="command_override" type="text" area="True" value="" label="Optional. Human wrought command element override XML/template - e.g. for bwa" - help="For arbitrary and artfull command lines. All i/o and parameters must be passed. Leave blank unless needed. Not for the faint of heart"> - <sanitizer> - <valid initial="string.printable"> - </valid> - <mapping initial="none"/> - </sanitizer> - </param> - <param name="test_override" type="text" area="True" value="" label="Optional. Human wrought test element override XML/template - e.g. for bwa" - help="For arbitrary and artfull scripts. Leave blank unless needed. Not for the faint of heart"> - <sanitizer> - <valid initial="string.printable"> - </valid> - <mapping initial="none"/> - </sanitizer> - </param> - </when> - </conditional> - <section name="make" title="Generate, toolshed and local Galaxy installation options" expanded="true"> - <conditional name="makeMode"> - <param name="make_Tool" type="select" display="radio" label="Choose the steps you want to run. The TF Docker container is recommended for local installation" - help="Installation in this Galaxy is optional" > - <option value="generate" >Run to generate tests only. Should fail if dependencies needed.</option> - <option value="gentest" selected="true">Test with planemo after generating.</option> - <option value="gentestinstall">Install in Galaxy after generation and testing. URLs and matching API keys are required for this step! </option> - </param> - <when value="generate"> - <param name="galaxy_apikey" value="" type="hidden" ></param> - <param name="toolshed_apikey" value="" type="hidden" ></param> - <param name="galaxy_url" value="" type="hidden" ></param> - <param name="toolshed_url" value="" type="hidden" ></param> - <expand macro="tool_metadata" /> - </when> - <when value="gentest"> - <param name="galaxy_apikey" value="" type="hidden" ></param> - <param name="toolshed_apikey" value="" type="hidden" ></param> - <param name="galaxy_url" value="" type="hidden" ></param> - <param name="toolshed_url" value="" type="hidden" ></param> - <expand macro="tool_metadata" /> - </when> - <when value="gentestinstall"> - <param name="galaxy_url" type="text" value="http://localhost:8080" label="URL for the Galaxy server where the new tool should be installed" - help="Default is localhost"> - <sanitizer> - <valid initial="string.printable"> - </valid> - <mapping initial="none"/> - </sanitizer> - </param> - <param name="galaxy_apikey" type="text" value="fakekey" label="API key for the Galaxy to install the new tool" - help="Cut and paste from the admin user properties screen"> - <sanitizer> - <valid initial="string.letters,string.digits"> - </valid> - <mapping initial="none"/> - </sanitizer> - </param> - <param name="toolshed_url" type="text" value="http://localhost:9009" label="URL for the Toolshed where the new tool should be installed" - help="Default value is localhost:9009"> - <sanitizer> - <valid initial="string.printable"> - </valid> - <mapping initial="none"/> - </sanitizer> - </param> - <param name="toolshed_apikey" type="text" value="fakekey" label="API key for the local toolshed to use when installing the tool" - help="Cut and paste from the admin user properties screen"> - <sanitizer> - <valid initial="string.letters,string.digits"> - </valid> - <mapping initial="none"/> - </sanitizer> - </param> - <expand macro="tool_metadata" /> - </when> - </conditional> - </section> - </inputs> - <outputs> - - <data format="tgz" name="new_tool" label="${tool_name}_toolshed.tgz" > - <filter>makeMode['make_Tool'] != "runonly"</filter> - </data> - - <collection name="TF_run_report" type="list" label="${tool_name} outputs"> - <discover_datasets pattern="__name_and_ext__" directory="TF_run_report_tempdir" /> - </collection> - </outputs> -<tests> -<test> - <param name="user_email" value="admin@galaxy.org"/> - <param name="input_files" value="input1_sample" /> - <param name="input_CL" value="1" /> - <param name="input_formats" value="txt" /> - <param name="input_label" value="input" /> - <param name="input_help" value="help" /> - <param name="tool_name" value="pyrevpos" /> - <param name="parampass" value="positional" /> - <param name="make_Tool" value="generate" /> - <param name="tool_version" value="0.01" /> - <param name="tool_desc" value="positional reverse" /> - <param name="help_text" value="help text goes here" /> - <param name="packages" value="python"/> - <param name="history_name" value="output2" /> - <param name="history_format" value="txt" /> - <param name="history_CL" value="2" /> - <param name="dynScript" value="import sys; inp = sys.argv[1]; outp = sys.argv[2]; inlist = open(inp,'r').readlines(); o = open(outp,'w'); rs = [''.join(list(reversed(x.rstrip()))) for x in inlist]; o.write('\n'.join(rs)); o.close()"/> - <param name="choosescript" value="yes" /> - <param name="script_path" value="$runme"/> - <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" /> -</test> -</tests> -<help> - -.. class:: warningmark - -**Details and attribution** -(see GTF_) - -**Local Admins ONLY** -Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool. - -**If you find a bug** -Please raise an issue, or even better, submit a pull request fixing it, on the github repository GTF_ - -**What it does** -This tool optionally generates normal workflow compatible first class Galaxy tools - -Generated tools can run existing binary packages that become requirements, existing scripts, or new scripts pasted into this tool form. -Pasted scripts are written so they are part of the new tool and cannot be adjusted by the downstream user. -Binary packages are managed by the dependency subsystem - conda usually, so anything in bioconda or conda_forge is available for example. - -Any number of parameters can be built into the new tool form for passing in to the script or executable at runtime. -These can be editable by the downstream user or baked in. - -When you run this tool, your executable or script and supplied parameter values will be run to produce a canonical -set of outputs - these are used to construct a test for the new tool. - -If tool generation is required, a new tarball compatible with any Galaxy toolshed is created. -It can be unpacked in your galaxy/tools directory and manually added to tool_conf.xml, or -installed into any toolshed from where it can be installed into your Galaxy. - - -.. class:: warningmark - -**Note to system administrators** -This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances. -Admin_users will have the power to do anything they want as the Galaxy user if you install this tool. - -.. class:: warningmark - -**Use on public servers** is STRONGLY discouraged for obvious reasons - -The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation. -We recommend that you follow the good code hygiene practices associated with safe toolshed practices. - -Here's a sample python script that can be cut and pasted into the tool form, suitable for positional parameter passing: - -:: - - # reverse order of text by row - import sys - inp = sys.argv[1] - outp = sys.argv[2] - i = open(inp,'r').readlines() - o = open(outp,'w') - for row in i: - rs = row.rstrip() - rs = list(rs) - rs.reverse() - o.write(''.join(rs)) - o.write('\n') - o.close() - -With argparse style parameters: - -:: - - # reverse order of text by row - import argparse - parser = argparse.ArgumentParser() - a = parser.add_argument - a('--infile',default='') - a('--outfile',default=None) - args = parser.parse_args() - inp = args.infile - outp = args.outfile - i = open(inp,'r').readlines() - o = open(outp,'w') - for row in i: - rs = row.rstrip() - rs = list(rs) - rs.reverse() - o.write(''.join(rs)) - o.write('\n') - o.close() - - - -Paper_ - -*Licensing* - -Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012 -All rights reserved. -Licensed under the LGPL_ - -.. _LGPL: http://www.gnu.org/copyleft/lesser.html -.. _GTF: https://github.com/fubar2/toolfactory -.. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573 - - -</help> -<citations> - <citation type="doi">10.1093/bioinformatics/bts573</citation> -</citations> -</tool> - -
--- a/toolfactory/test-data/input1_sample Tue Jan 05 00:34:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,166 +0,0 @@ -*WARNING before you start* - - Install this tool on a private Galaxy ONLY - Please NEVER on a public or production instance - -Updated august 2014 by John Chilton adding citation support - -Updated august 8 2014 to fix bugs reported by Marius van den Beek - -Please cite the resource at -http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref -if you use this tool in your published work. - -**Short Story** - -This is an unusual Galaxy tool capable of generating new Galaxy tools. -It works by exposing *unrestricted* and therefore extremely dangerous scripting -to all designated administrators of the host Galaxy server, allowing them to -run scripts in R, python, sh and perl over multiple selected input data sets, -writing a single new data set as output. - -*You have a working r/python/perl/bash script or any executable with positional or argparse style parameters* - -It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool. - - -**Automated generation of new Galaxy tools for installation into any Galaxy** - -A test is generated using small sample test data inputs and parameter settings you supply. -Once the test case outputs have been produced, they can be used to build a -new Galaxy tool. The supplied script or executable is baked as a requirement -into a new, ordinary Galaxy tool, fully workflow compatible out of the box. -Generated tools are installed via a tool shed by an administrator -and work exactly like all other Galaxy tools for your users. - -**More Detail** - -To use the ToolFactory, you should have prepared a script to paste into a -text box, or have a package in mind and a small test input example ready to select from your history -to test your new script. - -```planemo test rgToolFactory2.xml --galaxy_root ~/galaxy --test_data ~/galaxy/tools/tool_makers/toolfactory/test-data``` works for me - -There is an example in each scripting language on the Tool Factory form. You -can just cut and paste these to try it out - remember to select the right -interpreter please. You'll also need to create a small test data set using -the Galaxy history add new data tool. - -If the script fails somehow, use the "redo" button on the tool output in -your history to recreate the form complete with broken script. Fix the bug -and execute again. Rinse, wash, repeat. - -Once the script runs sucessfully, a new Galaxy tool that runs your script -can be generated. Select the "generate" option and supply some help text and -names. The new tool will be generated in the form of a new Galaxy datatype -*toolshed.gz* - as the name suggests, it's an archive ready to upload to a -Galaxy ToolShed as a new tool repository. - -Once it's in a ToolShed, it can be installed into any local Galaxy server -from the server administrative interface. - -Once the new tool is installed, local users can run it - each time, the script -that was supplied when it was built will be executed with the input chosen -from the user's history. In other words, the tools you generate with the -ToolFactory run just like any other Galaxy tool,but run your script every time. - -Tool factory tools are perfect for workflow components. One input, one output, -no variables. - -*To fully and safely exploit the awesome power* of this tool, -Galaxy and the ToolShed, you should be a developer installing this -tool on a private/personal/scratch local instance where you are an -admin_user. Then, if you break it, you get to keep all the pieces see -https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home - -**Installation** -This is a Galaxy tool. You can install it most conveniently using the -administrative "Search and browse tool sheds" link. Find the Galaxy Main -toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory -repository. Open it and review the code and select the option to install it. - -If you can't get the tool that way, the xml and py files here need to be -copied into a new tools -subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry -pointing to the xml -file - something like:: - - <section name="Tool building tools" id="toolbuilders"> - <tool file="toolfactory/rgToolFactory.xml"/> - </section> - -If not already there, -please add: -<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" -mimetype="multipart/x-gzip" subclass="True" /> -to your local data_types_conf.xml. - - -**Restricted execution** - -The tool factory tool itself will then be usable ONLY by admin users - -people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY -admin_users can run this tool** Think about it for a moment. If allowed to -run any arbitrary script on your Galaxy server, the only thing that would -impede a miscreant bent on destroying all your Galaxy data would probably -be lack of appropriate technical skills. - -**What it does** - -This is a tool factory for simple scripts in python, R and -perl currently. Functional tests are automatically generated. How cool is that. - -LIMITED to simple scripts that read one input from the history. Optionally can -write one new history dataset, and optionally collect any number of outputs -into links on an autogenerated HTML index page for the user to navigate - -useful if the script writes images and output files - pdf outputs are shown -as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and -imagemagik need to be available. - -Generated tools can be edited and enhanced like any Galaxy tool, so start -small and build up since a generated script gets you a serious leg up to a -more complex one. - -**What you do** - -You paste and run your script, you fix the syntax errors and -eventually it runs. You can use the redo button and edit the script before -trying to rerun it as you debug - it works pretty well. - -Once the script works on some test data, you can generate a toolshed compatible -gzip file containing your script ready to run as an ordinary Galaxy tool in -a repository on your local toolshed. That means safe and largely automated -installation in any production Galaxy configured to use your toolshed. - -**Generated tool Security** - -Once you install a generated tool, it's just -another tool - assuming the script is safe. They just run normally and their -user cannot do anything unusually insecure but please, practice safe toolshed. -Read the code before you install any tool. Especially this one - it is really scary. - -**Send Code** - -Patches and suggestions welcome as bitbucket issues please? - -**Attribution** - -Creating re-usable tools from scripts: The Galaxy Tool Factory -Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team -Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 - -http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref - -**Licensing** - -Copyright Ross Lazarus 2010 -ross lazarus at g mail period com - -All rights reserved. - -Licensed under the LGPL - -**Obligatory screenshot** - -http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png -
--- a/toolfactory/test-data/output2_sample Tue Jan 05 00:34:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,165 +0,0 @@ -*trats uoy erofeb GNINRAW* - -YLNO yxalaG etavirp a no loot siht llatsnI -ecnatsni noitcudorp ro cilbup a no REVEN esaelP - -troppus noitatic gnidda notlihC nhoJ yb 4102 tsugua detadpU - -keeB ned nav suiraM yb detroper sgub xif ot 4102 8 tsugua detadpU - -ta ecruoser eht etic esaelP -fer=epytyek&JWYdwMrWs1hQzcl=yekji?375stb/tnirper/igc/gro.slanruojdrofxo.scitamrofnioib//:ptth -.krow dehsilbup ruoy ni loot siht esu uoy fi - -**yrotS trohS** - -.sloot yxalaG wen gnitareneg fo elbapac loot yxalaG lausunu na si sihT -gnitpircs suoregnad ylemertxe erofereht dna *detcirtsernu* gnisopxe yb skrow tI -ot meht gniwolla ,revres yxalaG tsoh eht fo srotartsinimda detangised lla ot -,stes atad tupni detceles elpitlum revo lrep dna hs ,nohtyp ,R ni stpircs nur -.tuptuo sa tes atad wen elgnis a gnitirw - -*sretemarap elyts esrapgra ro lanoitisop htiw elbatucexe yna ro tpircs hsab/lrep/nohtyp/r gnikrow a evah uoY* - -.loot yxalaG a gnisu ,setunim ni loot yxalaG yranidro na otni denrut eb nac tI - - -**yxalaG yna otni noitallatsni rof sloot yxalaG wen fo noitareneg detamotuA** - -.ylppus uoy sgnittes retemarap dna stupni atad tset elpmas llams gnisu detareneg si tset A -a dliub ot desu eb nac yeht ,decudorp neeb evah stuptuo esac tset eht ecnO -tnemeriuqer a sa dekab si elbatucexe ro tpircs deilppus ehT .loot yxalaG wen -.xob eht fo tuo elbitapmoc wolfkrow ylluf ,loot yxalaG yranidro ,wen a otni -rotartsinimda na yb dehs loot a aiv dellatsni era sloot detareneG -.sresu ruoy rof sloot yxalaG rehto lla ekil yltcaxe krow dna - -**liateD eroM** - -a otni etsap ot tpircs a deraperp evah dluohs uoy ,yrotcaFlooT eht esu oT -yrotsih ruoy morf tceles ot ydaer elpmaxe tupni tset llams a dna dnim ni egakcap a evah ro ,xob txet -.tpircs wen ruoy tset ot - -em rof skrow ```atad-tset/yrotcafloot/srekam_loot/sloot/yxalag/~ atad_tset-- yxalag/~ toor_yxalag-- lmx.2yrotcaFlooTgr tset omenalp``` - -uoY .mrof yrotcaF looT eht no egaugnal gnitpircs hcae ni elpmaxe na si erehT -thgir eht tceles ot rebmemer - tuo ti yrt ot eseht etsap dna tuc tsuj nac -gnisu tes atad tset llams a etaerc ot deen osla ll'uoY .esaelp reterpretni -.loot atad wen dda yrotsih yxalaG eht - -ni tuptuo loot eht no nottub "oder" eht esu ,wohemos sliaf tpircs eht fI -gub eht xiF .tpircs nekorb htiw etelpmoc mrof eht etaercer ot yrotsih ruoy -.taeper ,hsaw ,esniR .niaga etucexe dna - -tpircs ruoy snur taht loot yxalaG wen a ,yllufssecus snur tpircs eht ecnO -dna txet pleh emos ylppus dna noitpo "etareneg" eht tceleS .detareneg eb nac -epytatad yxalaG wen a fo mrof eht ni detareneg eb lliw loot wen ehT .seman -a ot daolpu ot ydaer evihcra na s'ti ,stseggus eman eht sa - *zg.dehsloot* -.yrotisoper loot wen a sa dehSlooT yxalaG - -revres yxalaG lacol yna otni dellatsni eb nac ti ,dehSlooT a ni s'ti ecnO -.ecafretni evitartsinimda revres eht morf - -tpircs eht ,emit hcae - ti nur nac sresu lacol ,dellatsni si loot wen eht ecnO -nesohc tupni eht htiw detucexe eb lliw tliub saw ti nehw deilppus saw taht -eht htiw etareneg uoy sloot eht ,sdrow rehto nI .yrotsih s'resu eht morf -.emit yreve tpircs ruoy nur tub,loot yxalaG rehto yna ekil tsuj nur yrotcaFlooT - -,tuptuo eno ,tupni enO .stnenopmoc wolfkrow rof tcefrep era sloot yrotcaf looT -.selbairav on - -,loot siht fo *rewop emosewa eht tiolpxe ylefas dna ylluf oT* -siht gnillatsni repoleved a eb dluohs uoy ,dehSlooT eht dna yxalaG -na era uoy erehw ecnatsni lacol hctarcs/lanosrep/etavirp a no loot -ees seceip eht lla peek ot teg uoy ,ti kaerb uoy fi ,nehT .resu_nimda -emoH/ikiw/yrotcaflootyxalag/rabuf/gro.tekcubtib//:sptth - -**noitallatsnI** -eht gnisu yltneinevnoc tsom ti llatsni nac uoY .loot yxalaG a si sihT -niaM yxalaG eht dniF .knil "sdehs loot esworb dna hcraeS" evitartsinimda -yrotcafloot eht rof hcraes dna /ude.usp.xb.2g.dehsloot//:sptth ta dehsloot -.ti llatsni ot noitpo eht tceles dna edoc eht weiver dna ti nepO .yrotisoper - -eb ot deen ereh selif yp dna lmx eht ,yaw taht loot eht teg t'nac uoy fI -sloot wen a otni deipoc -yrtne wen a sdeen lmx.fnoc_loot ruoY yrotcafloot/sloot sa hcus yrotceridbus -lmx eht ot gnitniop -::ekil gnihtemos - elif - ->"sredliubloot"=di "sloot gnidliub looT"=eman noitces< ->/"lmx.yrotcaFlooTgr/yrotcafloot"=elif loot< ->noitces/< - -,ereht ydaerla ton fI -:dda esaelp -"yraniB:yranib.sepytatad.yxalag"=epyt "zg.dehsloot"=noisnetxe epytatad< ->/ "eurT"=ssalcbus "pizg-x/trapitlum"=epytemim -.lmx.fnoc_sepyt_atad lacol ruoy ot - - -**noitucexe detcirtseR** - -- sresu nimda yb YLNO elbasu eb neht lliw flesti loot yrotcaf loot ehT -YLNO .thgir s'taht ,seY** ini.igsw_esrevinu ni sresu_nimda ni sDI htiw elpoep -ot dewolla fI .tnemom a rof ti tuoba knihT **loot siht nur nac sresu_nimda -dluow taht gniht ylno eht ,revres yxalaG ruoy no tpircs yrartibra yna nur -ylbaborp dluow atad yxalaG ruoy lla gniyortsed no tneb tnaercsim a edepmi -.slliks lacinhcet etairporppa fo kcal eb - -**seod ti tahW** - -dna R ,nohtyp ni stpircs elpmis rof yrotcaf loot a si sihT -.taht si looc woH .detareneg yllacitamotua era stset lanoitcnuF .yltnerruc lrep - -nac yllanoitpO .yrotsih eht morf tupni eno daer taht stpircs elpmis ot DETIMIL -stuptuo fo rebmun yna tcelloc yllanoitpo dna ,tesatad yrotsih wen eno etirw -- etagivan ot resu eht rof egap xedni LMTH detarenegotua na no sknil otni -nwohs era stuptuo fdp - selif tuptuo dna segami setirw tpircs eht fi lufesu -dna taht os tpircstsohg htiw knurhs era s'fdp detaolb s'R dna slianbmuht sa -.elbaliava eb ot deen kigamegami - -trats os ,loot yxalaG yna ekil decnahne dna detide eb nac sloot detareneG -a ot pu gel suoires a uoy steg tpircs detareneg a ecnis pu dliub dna llams -.eno xelpmoc erom - -**od uoy tahW** - -dna srorre xatnys eht xif uoy ,tpircs ruoy nur dna etsap uoY -erofeb tpircs eht tide dna nottub oder eht esu nac uoY .snur ti yllautneve -.llew ytterp skrow ti - gubed uoy sa ti nurer ot gniyrt - -elbitapmoc dehsloot a etareneg nac uoy ,atad tset emos no skrow tpircs eht ecnO -ni loot yxalaG yranidro na sa nur ot ydaer tpircs ruoy gniniatnoc elif pizg -detamotua ylegral dna efas snaem tahT .dehsloot lacol ruoy no yrotisoper a -.dehsloot ruoy esu ot derugifnoc yxalaG noitcudorp yna ni noitallatsni - -**ytiruceS loot detareneG** - -tsuj s'ti ,loot detareneg a llatsni uoy ecnO -rieht dna yllamron nur tsuj yehT .efas si tpircs eht gnimussa - loot rehtona -.dehsloot efas ecitcarp ,esaelp tub erucesni yllausunu gnihtyna od tonnac resu -.yracs yllaer si ti - eno siht yllaicepsE .loot yna llatsni uoy erofeb edoc eht daeR - -**edoC dneS** - -?esaelp seussi tekcubtib sa emoclew snoitseggus dna sehctaP - -**noitubirttA** - -yrotcaF looT yxalaG ehT :stpircs morf sloot elbasu-er gnitaerC -maeT yxalaG ehT ;nnameiZ kraM ;ipsaK ynotnA ;surazaL ssoR -375stb/scitamrofnioib/3901.01 :iod ;2102 scitamrofnioiB - -fer=epytyek&JWYdwMrWs1hQzcl=yekji?375stb/tnirper/igc/gro.slanruojdrofxo.scitamrofnioib//:ptth - -**gnisneciL** - -0102 surazaL ssoR thgirypoC -moc doirep liam g ta surazal ssor - -.devreser sthgir llA - -LPGL eht rednu desneciL - -**tohsneercs yrotagilbO** - -gnp.looTtpircScimanyd/segami/989ef2308adf/crs/rekamlootyxalag/rabuf/gro.tekcubtib//:ptth
--- a/toolfactory/test-data/pyrevpos.python Tue Jan 05 00:34:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -# reverse order of text by row -import sys -inp = sys.argv[1] -outp = sys.argv[2] -i = open(inp,'r').readlines() -o = open(outp,'w') -for row in i: - rs = row.rstrip() - rs = list(rs) - rs.reverse() - o.write(''.join(rs)) -o.close() -
--- a/toolfactory/test-data/test1_log.txt Tue Jan 05 00:34:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -## Executing Toolfactory generated command line = python /tmp/pyrevposq5dmcdy1.python /tmp/tmpqrksf8sd/files/5/b/9/dataset_5b952a86-87df-44ad-a415-ea549f3f0cee.dat output2
--- a/toolfactory/whoosh.sh Tue Jan 05 00:34:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -# using the galaxy venv this seems to work -. /galaxy_venv/bin/activate -python scripts/tool_shed/build_ts_whoosh_index.py -c config/tool_shed.yml --config-section tool_shed -# eeesh. /etc/galaxy is where the actual galaxy.yml lives - despite other configs being where they might be expected -# fix tool_shed.yml to 0.0.0.0 and admin email -# add tgz to datatypes :( -# need to source a venv in /export/tool_deps/toolfactorydeps/0.01/fubar/toolfactorydeps/9e9428fe9134/env.sh -# as nothing was done by the setup_virtualenv step apparently. -# gcc and friends for planemo pip installation -# File "/galaxy-central/lib/galaxy/tool_util/verify/interactor.py", line 595, in <listcomp> -# test_user = [user for user in all_users if user["email"] == email][0] -# add local to tool_sheds_conf.xml -# <tool_sheds> -# <tool_shed name="local" url="http://localhost:9009"/> -# mercurial > 5.5!! -