# HG changeset patch # User fubar # Date 1623205681 0 # Node ID 807b8d103f18bf98e15dffef67d9f4b16ab0fc31 # Parent 36d46b20095a1f0955d0c63cf288fecfe055c7e9 Uploaded diff -r 36d46b20095a -r 807b8d103f18 toolfactory/LICENSE --- a/toolfactory/LICENSE Sun Apr 18 02:14:13 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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Docker container at https://github.com/fubar2/toolfactory-galaxy-docker recommended as at December 2020 - -### New demonstration of planemo tool_factory command ![Planemo ToolFactory demonstration](images/lintplanemo-2021-01-08_18.02.45.mkv?raw=false "Demonstration inside Planemo") - -## 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 - -![IHello example ToolFactory tool form](files/hello_toolfactory_form.png?raw=true "Part of the Hello world example ToolFactory tool form") - - -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. - -![How it works](files/TFasIDE.png?raw=true "Overview of the ToolFactory as an Integrated Development Environment") - -## 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. -``` - - - - - Planemo advanced tool building sample bwa mem mapper as a ToolFactory demo - - bwa - samtools - - - tempsam -samtools view -Sb tempsam > temporary_bam_file.bam -samtools sort -o "\$BAMOUT" temporary_bam_file.bam - -]]> - - - - - - - - - - - - - - - - - tempsam - samtools view -Sb tempsam > temporary_bam_file.bam - samtools sort -o "$BAMOUT" temporary_bam_file.bam - -]]> - - -``` - - - -## 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: - -``` - -``` - -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 - diff -r 36d46b20095a -r 807b8d103f18 toolfactory/ToolFactory.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/ToolFactory.py Wed Jun 09 02:28:01 2021 +0000 @@ -0,0 +1,897 @@ +# 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 +# +# April 2021: Refactored into two tools - generate and test/install +# as part of GTN tutorial development and biocontainer adoption +# The tester runs planemo on a non-tested archive, creates the test outputs +# and returns a new proper tool with test. + + + +import argparse +import copy +import fcntl +import json +import os +import re +import rpyc +import shlex +import shutil +import subprocess +import sys +import tarfile +import tempfile +import time + +from bioblend import galaxy + +import galaxyxml.tool as gxt +import galaxyxml.tool.parameters as gxtp + +import lxml.etree as ET + +import yaml + +myversion = "V2.3 April 2021" +verbose = True +debug = True +toolFactoryURL = "https://github.com/fubar2/toolfactory" +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())) + + +cheetah_escape_table = {"$": "\\$", "#": "\\#"} + + +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 Tool_Factory: + """Wrapper for an arbitrary script + uses galaxyxml + + """ + + def __init__(self, args=None): # noqa + """ + prepare command line cl for running the tool here + and prepare elements needed for galaxyxml tool generation + """ + self.ourcwd = os.getcwd() + self.collections = [] + if len(args.collection) > 0: + try: + self.collections = [ + json.loads(x) for x in args.collection if len(x.strip()) > 1 + ] + except Exception: + print( + f"--collections parameter {str(args.collection)} is malformed - should be a dictionary" + ) + try: + self.infiles = [ + json.loads(x) for x in args.input_files if len(x.strip()) > 1 + ] + except Exception: + print( + f"--input_files parameter {str(args.input_files)} is malformed - should be a dictionary" + ) + try: + self.outfiles = [ + json.loads(x) for x in args.output_files if len(x.strip()) > 1 + ] + except Exception: + print( + f"--output_files parameter {args.output_files} is malformed - should be a dictionary" + ) + assert (len(self.outfiles) + len(self.collections)) > 0, 'No outfiles or output collections specified. The Galaxy job runner will fail without an output of some sort' + try: + self.addpar = [ + json.loads(x) for x in args.additional_parameters if len(x.strip()) > 1 + ] + except Exception: + print( + f"--additional_parameters {args.additional_parameters} is malformed - should be a dictionary" + ) + try: + self.selpar = [ + json.loads(x) for x in args.selecttext_parameters if len(x.strip()) > 1 + ] + except Exception: + print( + f"--selecttext_parameters {args.selecttext_parameters} is malformed - should be a dictionary" + ) + self.args = args + self.cleanuppar() + self.lastxclredirect = None + self.xmlcl = [] + self.is_positional = self.args.parampass == "positional" + if self.args.sysexe: + if " " in self.args.sysexe: + self.executeme = self.args.sysexe.split(" ") + else: + self.executeme = [ + self.args.sysexe, + ] + else: + if self.args.packages: + self.executeme = [ + self.args.packages.split(",")[0].split(":")[0].strip(), + ] + else: + self.executeme = None + 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.tooloutdir = "./tfout" + self.repdir = "./toolgen" + self.newtarpath = os.path.join(self.tooloutdir, "%s_not_tested.toolshed.gz" % self.tool_name) + 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.script_path: + for ex in self.executeme: + aXCL(ex) + aXCL("$runme") + else: + for ex in self.executeme: + aXCL(ex) + + if self.args.parampass == "0": + self.clsimple() + else: + if self.args.parampass == "positional": + self.prepclpos() + self.clpositional() + else: + self.prepargp() + self.clargparse() + + def clsimple(self): + """no parameters or repeats - uses < and > for i/o""" + aXCL = self.xmlcl.append + if len(self.infiles) > 0: + aXCL("<") + aXCL("$%s" % self.infiles[0]["infilename"]) + if len(self.outfiles) > 0: + aXCL(">") + aXCL("$%s" % self.outfiles[0]["name"]) + if self.args.cl_user_suffix: # DIY CL end + clp = shlex.split(self.args.cl_user_suffix) + for c in clp: + aXCL(c) + + def prepargp(self): + xclsuffix = [] + for i, p in enumerate(self.infiles): + nam = p["infilename"] + if p["origCL"].strip().upper() == "STDIN": + xappendme = [ + nam, + nam, + "< $%s" % nam, + ] + else: + rep = p["repeat"] == "1" + over = "" + if rep: + over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for' + xappendme = [p["CL"], "$%s" % p["CL"], over] + xclsuffix.append(xappendme) + for i, p in enumerate(self.outfiles): + if p["origCL"].strip().upper() == "STDOUT": + self.lastxclredirect = [">", "$%s" % p["name"]] + else: + xclsuffix.append([p["name"], "$%s" % p["name"], ""]) + for p in self.addpar: + nam = p["name"] + rep = p["repeat"] == "1" + if rep: + over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for' + else: + over = p["override"] + xclsuffix.append([p["CL"], '"$%s"' % nam, over]) + for p in self.selpar: + xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]]) + self.xclsuffix = xclsuffix + + def prepclpos(self): + xclsuffix = [] + for i, p in enumerate(self.infiles): + if p["origCL"].strip().upper() == "STDIN": + xappendme = [ + "999", + p["infilename"], + "< $%s" % p["infilename"], + ] + else: + xappendme = [p["CL"], "$%s" % p["infilename"], ""] + xclsuffix.append(xappendme) + for i, p in enumerate(self.outfiles): + if p["origCL"].strip().upper() == "STDOUT": + self.lastxclredirect = [">", "$%s" % p["name"]] + else: + xclsuffix.append([p["CL"], "$%s" % p["name"], ""]) + for p in self.addpar: + nam = p["name"] + rep = p["repeat"] == "1" # repeats make NO sense + if rep: + print( + f"### warning. Repeats for {nam} ignored - not permitted in positional parameter command lines!" + ) + over = p["override"] + xclsuffix.append([p["CL"], '"$%s"' % nam, over]) + for p in self.selpar: + xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]]) + xclsuffix.sort() + self.xclsuffix = xclsuffix + + 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[0]) + ) + tscript = open(self.sfile, "w") + tscript.write(self.script) + tscript.close() + self.spacedScript = [f" {x}" for x in rx if x.strip() > ""] + rx.insert(0, "#raw") + rx.append("#end raw") + self.escapedScript = rx + art = "%s.%s" % (self.tool_name, self.executeme[0]) + artifact = open(art, "wb") + artifact.write(bytes(self.script, "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["CL"].isdigit() or p["CL"].strip().upper() == "STDIN" + ), "Positional parameters must be ordinal integers - got %s for %s" % ( + p["CL"], + p["label"], + ) + for i, p in enumerate(self.outfiles): + assert ( + p["CL"].isdigit() or p["CL"].strip().upper() == "STDOUT" + ), "Positional parameters must be ordinal integers - got %s for %s" % ( + p["CL"], + p["name"], + ) + for i, p in enumerate(self.addpar): + assert p[ + "CL" + ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % ( + p["CL"], + p["name"], + ) + for i, p in enumerate(self.infiles): + infp = copy.copy(p) + infp["origCL"] = infp["CL"] + if self.args.parampass in ["positional", "0"]: + infp["infilename"] = infp["label"].replace(" ", "_") + else: + infp["infilename"] = infp["CL"] + self.infiles[i] = infp + for i, p in enumerate(self.outfiles): + outfp = copy.copy(p) + outfp["origCL"] = outfp["CL"] # keep copy + self.outfiles[i] = outfp + for i, p in enumerate(self.addpar): + addp = copy.copy(p) + addp["origCL"] = addp["CL"] + self.addpar[i] = addp + + def clpositional(self): + # inputs in order then params + aXCL = self.xmlcl.append + for (k, v, koverride) in self.xclsuffix: + aXCL(v) + if self.lastxclredirect: + for cl in self.lastxclredirect: + aXCL(cl) + if self.args.cl_user_suffix: # DIY CL end + clp = shlex.split(self.args.cl_user_suffix) + for c in clp: + aXCL(c) + + def clargparse(self): + """argparse style""" + aXCL = self.xmlcl.append + # inputs then params in argparse named form + + for (k, v, koverride) in self.xclsuffix: + if koverride > "": + k = koverride + aXCL(k) + else: + if len(k.strip()) == 1: + k = "-%s" % k + else: + k = "--%s" % k + aXCL(k) + aXCL(v) + if self.lastxclredirect: + for cl in self.lastxclredirect: + aXCL(cl) + if self.args.cl_user_suffix: # DIY CL end + clp = shlex.split(self.args.cl_user_suffix) + for c in clp: + aXCL(c) + + def getNdash(self, newname): + if self.is_positional: + ndash = 0 + else: + ndash = 2 + if len(newname) < 2: + ndash = 1 + return ndash + + def doXMLparam(self): # noqa + """Add all needed elements to tool""" + for p in self.outfiles: + newname = p["name"] + newfmt = p["format"] + newcl = p["CL"] + test = p["test"] + oldcl = p["origCL"] + test = test.strip() + ndash = self.getNdash(newcl) + aparm = gxtp.OutputData( + name=newname, format=newfmt, num_dashes=ndash, label=newname + ) + 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.strip().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, + ) + else: + c = test + tp = gxtp.TestOutput( + name=newname, + value="%s_sample" % newname, + compare=c, + ) + self.testparam.append(tp) + for p in self.infiles: + newname = p["infilename"] + newfmt = p["format"] + ndash = self.getNdash(newname) + reps = p.get("repeat", "0") == "1" + if not len(p["label"]) > 0: + alab = p["CL"] + else: + alab = p["label"] + aninput = gxtp.DataParam( + newname, + optional=False, + label=alab, + help=p["help"], + format=newfmt, + multiple=False, + num_dashes=ndash, + ) + aninput.positional = self.is_positional + if self.is_positional: + if p["origCL"].upper() == "STDIN": + aninput.positional = 9999998 + aninput.command_line_override = "> $%s" % newname + else: + aninput.positional = int(p["origCL"]) + aninput.command_line_override = "$%s" % newname + if reps: + repe = gxtp.Repeat( + name=f"R_{newname}", title=f"Add as many {alab} as needed" + ) + repe.append(aninput) + self.tinputs.append(repe) + tparm = gxtp.TestRepeat(name=f"R_{newname}") + tparm2 = gxtp.TestParam(newname, value="%s_sample" % newname) + tparm.append(tparm2) + self.testparam.append(tparm) + else: + self.tinputs.append(aninput) + tparm = gxtp.TestParam(newname, value="%s_sample" % newname) + self.testparam.append(tparm) + for p in self.addpar: + newname = p["name"] + newval = p["value"] + newlabel = p["label"] + newhelp = p["help"] + newtype = p["type"] + newcl = p["CL"] + oldcl = p["origCL"] + reps = p["repeat"] == "1" + 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=newlabel, + help=newhelp, + value=newval, + num_dashes=ndash, + ) + elif newtype == "float": + aparm = gxtp.FloatParam( + newname, + label=newlabel, + help=newhelp, + value=newval, + num_dashes=ndash, + ) + elif newtype == "boolean": + aparm = gxtp.BooleanParam( + newname, + label=newlabel, + 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) + if reps: + repe = gxtp.Repeat( + name=f"R_{newname}", title=f"Add as many {newlabel} as needed" + ) + repe.append(aparm) + self.tinputs.append(repe) + tparm = gxtp.TestRepeat(name=f"R_{newname}") + tparm2 = gxtp.TestParam(newname, value=newval) + tparm.append(tparm2) + self.testparam.append(tparm) + else: + self.tinputs.append(aparm) + tparm = gxtp.TestParam(newname, value=newval) + self.testparam.append(tparm) + for p in self.selpar: + newname = p["name"] + newval = p["value"] + newlabel = p["label"] + newhelp = p["help"] + newtype = p["type"] + newcl = p["CL"] + if not len(newlabel) > 0: + newlabel = newname + ndash = self.getNdash(newname) + if newtype == "selecttext": + newtext = p["texts"] + aparm = gxtp.SelectParam( + newname, + label=newlabel, + help=newhelp, + num_dashes=ndash, + ) + for i in range(len(newval)): + anopt = gxtp.SelectOption( + value=newval[i], + text=newtext[i], + ) + aparm.append(anopt) + aparm.positional = self.is_positional + if self.is_positional: + aparm.positional = int(newcl) + self.tinputs.append(aparm) + tparm = gxtp.TestParam(newname, value=newval) + self.testparam.append(tparm) + else: + raise ValueError( + 'Unrecognised parameter type "%s" for\ + selecttext parameter %s in makeXML' + % (newtype, newname) + ) + for p in self.collections: + newkind = p["kind"] + newname = p["name"] + newlabel = p["label"] + newdisc = p["discover"] + collect = gxtp.OutputCollection(newname, label=newlabel, type=newkind) + disc = gxtp.DiscoverDatasets( + pattern=newdisc, directory=f"{newname}", visible="false" + ) + collect.append(disc) + self.toutputs.append(collect) + try: + tparm = gxtp.TestOutputCollection(newname) # broken until PR merged. + self.testparam.append(tparm) + except Exception: + print( + "#### WARNING: Galaxyxml version does not have the PR merged yet - tests for collections must be over-ridden until then!" + ) + + def doNoXMLparam(self): + """filter style package - stdin to stdout""" + if len(self.infiles) > 0: + alab = self.infiles[0]["label"] + if len(alab) == 0: + alab = self.infiles[0]["infilename"] + 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]["infilename"] + aninput = gxtp.DataParam( + newname, + optional=False, + label=alab, + help=self.infiles[0]["help"], + format=self.infiles[0]["format"], + multiple=False, + num_dashes=0, + ) + aninput.command_line_override = "< $%s" % newname + aninput.positional = True + 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]["name"] + newfmt = self.outfiles[0]["format"] + 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): # noqa + """ + 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}"' + std = gxtp.Stdios() + std1 = gxtp.Stdio() + std.append(std1) + self.newtool.stdios = std + requirements = gxtp.Requirements() + if self.args.packages: + try: + for d in self.args.packages.split(","): + ver = None + packg = None + d = d.replace("==", ":") + d = d.replace("=", ":") + if ":" in d: + packg, ver = d.split(":") + ver = ver.strip() + packg = packg.strip() + else: + packg = d.strip() + ver = None + if ver == "": + ver = None + if packg: + requirements.append( + gxtp.Requirement("package", packg.strip(), ver) + ) + except Exception: + print( + "### malformed packages string supplied - cannot parse =", + self.args.packages, + ) + sys.exit(2) + 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("")[0] + part2 = exml.split("")[1] + fixed = "%s\n%s\n%s" % (part1, "\n".join(self.test_override), part2) + exml = fixed + with open("%s.xml" % self.tool_name, "w") as xf: + xf.write(exml) + xf.write("\n") + with open(self.args.untested_tool_out, 'w') as outf: + outf.write(exml) + outf.write('\n') + # galaxy history item + + 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""" + if self.args.parampass == 0: + self.doNoXMLparam() + else: + self.makeXML() + if self.args.script_path: + stname = os.path.join(self.tooloutdir, 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["name"] + dest = os.path.join(self.testdir, "%s_sample" % p["infilename"]) + shutil.copyfile(pth, dest) + dest = os.path.join( + self.repdir, "%s_sample.%s" % (p["infilename"], p["format"]) + ) + shutil.copyfile(pth, dest) + + def makeToolTar(self, report_fail=False): + """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 + + for p in self.outfiles: + oname = p["name"] + tdest = os.path.join(self.testdir, "%s_sample" % oname) + src = os.path.join(self.testdir, oname) + if not os.path.isfile(tdest): + if os.path.isfile(src): + shutil.copyfile(src, tdest) + dest = os.path.join(self.repdir, "%s.sample.%s" % (oname,p['format'])) + shutil.copyfile(src, dest) + else: + if report_fail: + print( + "###Tool may have failed - output file %s not found in testdir after planemo run %s." + % (tdest, self.testdir) + ) + tf = tarfile.open(self.newtarpath, "w:gz") + tf.add( + name=self.tooloutdir, + arcname=self.tool_name, + filter=exclude_function, + ) + shutil.copy(self.newtarpath, os.path.join(self.tooloutdir, f"{self.tool_name}_untested.toolshed.gz")) + tf.close() + + +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_user_suffix", 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("--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("--selecttext_parameters", action="append", default=[]) + a("--edit_additional_parameters", action="store_true", default=False) + a("--parampass", default="positional") + a("--tfout", default="./tfout") + a("--galaxy_root", default="/galaxy-central") + a("--galaxy_venv", default="/galaxy_venv") + a("--collection", action="append", default=[]) + a("--include_tests", default=False, action="store_true") + a("--install_flag", action = "store_false", default=True) + a("--admin_only", default=False, action="store_true") + a("--untested_tool_out", default=None) + a("--local_tools", default="tools") # relative to $__root_dir__ + a("--tool_conf_path", default="config/tool_conf.xml") # relative to $__root_dir__ + args = parser.parse_args() + if args.admin_only: + assert not args.bad_user, ( + 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy \ +admin adds %s to "admin_users" in the galaxy.yml Galaxy configuration file' + % (args.bad_user, args.bad_user) + ) + assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq" + tf = Tool_Factory(args) + tf.writeShedyml() + tf.makeTool() + tf.makeToolTar() + if args.install_flag: # always true except during toolfactory test - only works if the appliance rpyc server is running + try: + conn = rpyc.connect("planemo-server", port=9999, config={'sync_request_timeout':1200}) + except ConnectionRefusedError: + print('### Remote rpyc server not available - cannot install new tool %s. This only works in the ToolFactory Appliance with the server running' % args.tool_name) + sys.exit(1) + res = conn.root.tool_updater(galaxy_root=args.galaxy_root, + tool_conf_path=args.tool_conf_path, new_tool_archive_path=os.path.abspath(tf.newtarpath), + new_tool_name=tf.tool_name, local_tool_dir=args.local_tools) + conn.close() + # code all moved to the server. No need for rsync other than there now. + +if __name__ == "__main__": + main() diff -r 36d46b20095a -r 807b8d103f18 toolfactory/ToolFactory.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/ToolFactory.xml Wed Jun 09 02:28:01 2021 +0000 @@ -0,0 +1,487 @@ + + Scripts into tools v2.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + galaxyxml + bioblend + rpyc + + + 0: +--cl_user_suffix "$cl_suffix" + #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 + #if $deps.packages > "": + --packages "$deps.packages" + #end if + #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 "$io_param.ppass.parampass" +--tool_desc "$tool_desc" +--tool_version "$tool_version" +--help_text "$helpme" + #if $io_param.ppass.parampass != '0': + #for $apar in $io_param.ppass.addparam.additional_parameters: + #if $apar.ap_type.param_type=="selecttext": +--selecttext_parameters '{"name":"$apar.param_name", "label":"$apar.param_label", "help":"$apar.param_help", +"type":"$apar.ap_type.param_type","CL":"$apar.param_CL","override":"$apar.param_CLprefixed","value": [ + #for $i,$st in enumerate($apar.ap_type.selectTexts): + "$st.select_value" + #if ($i < (len($apar.ap_type.selectTexts)-1)): + , + #end if + #end for + ], "texts": [ + #for $i,$st in enumerate($apar.ap_type.selectTexts): + "$st.select_text" + #if ($i < (len($apar.ap_type.selectTexts)-1)): + , + #end if + + #end for + ] + }' + #else: +--additional_parameters '{"name": "$apar.param_name", "value": "$apar.ap_type.param_value", "label": "$apar.param_label", "help": "$apar.param_help", +"type": "$apar.ap_type.param_type","CL": "$apar.param_CL","override": "$apar.param_CLprefixed", "repeat": "$apar.param_repeat"}' + #end if + #end for + #end if + #for $intab in $io_param.ppass.io.history_inputs: +--input_files '{"name": "$intab.input_files", "CL": "$intab.input_CL", "format": "$intab.input_formats", "label": "$intab.input_label", "help": "$intab.input_help", "repeat": "$intab.input_repeat"}' + #end for + #for $otab in $io_param.ppass.io.history_outputs: +--output_files '{"name": "$otab.history_name", "format": "$otab.history_format", "CL": "$otab.history_CL", "test": "$otab.history_test"}' + #end for + #for $collect in $io_param.ppass.io.collection_outputs: +--collection '{"name": "$collect.name", "kind": "$collect.kind", "discover": "$collect.discover", "label": "$collect.label"}' + #end for +--untested_tool_out "$generated_xml" +#if $install == "0": +--install_flag +#end if +--galaxy_root "$__root_dir__" +--tool_dir "$__tool_directory__" +--admin_only + #end if +]]> + + +$deps.usescript.dynScript + + +#if $cover.commover == "yes" and len(str($cover.command_override).strip()) > 1: +$cover.command_override +#end if + + +#if $cover.commover == "yes" and len(str($cover.test_override).strip()) > 1: +$cover.test_override +#end if + + +${help_text} + + + +#for $citation in $citations: + #if $citation.citation_type.type == "bibtex": + **ENTRY**bibtex + ${citation.citation_type.bibtex} + #else + **ENTRY**doi + ${citation.citation_type.doi} + #end if +#end for + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**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. + +A new tarball compatible with any Galaxy toolshed is created in your history, however, it does not have the test prepared. +There is a separate tool you can run to update the archive after testing with Planemo + +If the configuration in job_conf.xml allows tools to write to [galaxy_root]/tools, the new tool will be installed so you can view and test it locally. + +.. 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 - allowing potentially malicious users to install and run any code they like is asking for trouble. + +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. + + +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: https://academic.oup.com/bioinformatics/article/28/23/3139/192853 + + + + + 10.1093/bioinformatics/bts573 + + + + diff -r 36d46b20095a -r 807b8d103f18 toolfactory/ToolFactoryDemosApril30.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/ToolFactoryDemosApril30.ga Wed Jun 09 02:28:01 2021 +0000 @@ -0,0 +1,965 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "ToolFactory - make, test and install demonstration tools", + "steps": { + "0": { + "annotation": "", + "content_id": "rgtf2", + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "new_tool", + "type": "toolshed.gz" + } + ], + "position": { + "bottom": -152.39999389648438, + "height": 102.60000610351562, + "left": 252.5, + "right": 452.5, + "top": -255, + "width": 200, + "x": 252.5, + "y": -255 + }, + "post_job_actions": {}, + "tool_id": "rgtf2", + "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"dbb99db2a98811ebbc9e0242ac1b0004\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_prefix\": \"\", \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"bash\", \"dynScript\": \"echo \\\"Hello $1\\\"\"}}, \"help_text\": \"**What it Does**\", \"install\": \"false\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"Hello_output\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"say_hello_to\", \"ap_type\": {\"param_type\": \"text\", \"__current_case__\": 0, \"param_value\": \"\"}, \"param_label\": \"Say hello to\", \"param_help\": \"\", \"param_CL\": \"1\", \"param_CLprefixed\": \"\", \"param_repeat\": \"false\"}]}}}, \"make\": {\"makeMode\": {\"__current_case__\": 1, \"citations\": [], \"galaxy_apikey\": \"fakekey\", \"galaxy_url\": \"http://localhost:8080\", \"help_text\": \"**What it Does**\\nToolFactory demonstration - hello world in Galaxy\", \"make_Tool\": \"gentest\", \"tool_desc\": \"Says hello\", \"tool_version\": \"0.01\", \"toolshed_apikey\": \"fakekey\", \"toolshed_url\": \"http://localhost:9009\"}}, \"run_test\": \"true\", \"tool_desc\": \"\", \"tool_name\": \"hello_toolshed\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "f07cf7c8-4a96-4c4f-bd7b-d43c30642369", + "workflow_outputs": [ + { + "label": null, + "output_name": "new_tool", + "uuid": "5e1e49e0-ed56-4c7a-95fe-2f66aa4d7165" + } + ] + }, + "1": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "bwa-mem-fastq1.fq" + } + ], + "label": "bwa-mem-fastq1.fq", + "name": "Input dataset", + "outputs": [], + "position": { + "bottom": 353.1999969482422, + "height": 82.19999694824219, + "left": 252.5, + "right": 452.5, + "top": 271, + "width": 200, + "x": 252.5, + "y": 271 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "e1c43d57-ee0e-42ea-aed7-d86c595d06e7", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "ecd799ad-b7be-4b58-87ea-050884620d99" + } + ] + }, + "2": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "bwa-mem-mt-genome.fa" + } + ], + "label": "bwa-mem-mt-genome.fa", + "name": "Input dataset", + "outputs": [], + "position": { + "bottom": 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"input_connections": {}, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "new_tool", + "type": "toolshed.gz" + } + ], + "position": { + "bottom": -313.3999938964844, + "height": 102.60000610351562, + "left": 1086.5, + "right": 1286.5, + "top": -416, + "width": 200, + "x": 1086.5, + "y": -416 + }, + "post_job_actions": {}, + "tool_id": "rgtf2", + "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"bash\", \"dynScript\": \"echo \\\"You chose $1\\\"\"}}, \"help_text\": \"**What it Does**\\nDemonstrates select parameters generated by ToolFactory forms\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"select_out\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"choose\", \"ap_type\": {\"param_type\": \"selecttext\", \"__current_case__\": 4, \"selectTexts\": [{\"__index__\": 0, \"select_text\": \"one\", \"select_value\": \"won\"}, {\"__index__\": 1, \"select_text\": \"two\", \"select_value\": \"too\"}, {\"__index__\": 2, \"select_text\": \"three\", \"select_value\": \"free\"}]}, \"param_label\": \"Choose\", \"param_help\": \"\", \"param_CL\": \"1\", \"param_CLprefixed\": \"\", \"param_repeat\": \"false\"}]}}}, \"run_test\": \"true\", \"tool_desc\": \"ToolFactory select demonstration\", \"tool_name\": \"select_test\", \"tool_version\": \"0.01\", \"__page__\": null, 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+ "annotation": "", + "content_id": "rgtf2", + "errors": null, + "id": 10, + "input_connections": {}, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "new_tool", + "type": "toolshed.gz" + } + ], + "position": { + "bottom": -313.3999938964844, + "height": 102.60000610351562, + "left": 1364.5, + "right": 1564.5, + "top": -416, + "width": 200, + "x": 1364.5, + "y": -416 + }, + "post_job_actions": {}, + "tool_id": "rgtf2", + "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"r-base\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"Rscript\", \"dynScript\": \"# demo\\nargs = commandArgs(trailingOnly=TRUE)\\nif (length(args)==0) {\\n n_plots = 3 \\n} else {\\n n_plots = as.integer(args[1]) }\\ndir.create('plots')\\nfor (i in 1:n_plots) {\\n foo = runif(100)\\n bar = rnorm(100)\\n bar = foo + 0.05*bar\\n pdf(paste('plots/yet',i,\\\"anotherplot.pdf\\\",sep='_'))\\n plot(foo,bar,main=paste(\\\"Foo by Bar plot #\\\",i),col=\\\"maroon\\\", pch=3,cex=0.6)\\n dev.off()\\n foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))\\n bar = as.matrix(foo)\\n pdf(paste('plots/yet',i,\\\"anotherheatmap.pdf\\\",sep='_'))\\n heatmap(bar,main='Random Heatmap')\\n dev.off()\\n}\\n\"}}, \"help_text\": \"**What it Does**\\nToolFactory demonstration of a collection to hide lots of outputs from a tool in a single history item to avoid clutter.\\nAs many random plots as you want.\\nViewable inside the resulting history collection\\nScript is responsible for writing all the appropriate outputs into a directory called the same name as the collection as shown here.\\nVery handy for things not useful downstream but useful for the user to 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{ + "label": null, + "output_name": "new_tool", + "uuid": "4d769d8b-370c-444e-9245-2b2fa719ca99" + } + ] + }, + "11": { + "annotation": "", + "content_id": "rgtf2", + "errors": null, + "id": 11, + "input_connections": {}, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "new_tool", + "type": "toolshed.gz" + } + ], + "position": { + "bottom": -293, + "height": 123, + "left": 1642.5, + "right": 1842.5, + "top": -416, + "width": 200, + "x": 1642.5, + "y": -416 + }, + "post_job_actions": {}, + "tool_id": "rgtf2", + "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"bash\", \"dynScript\": \"# pathetic attempt at a malicious script in Galaxy\\n# it fails because the job execution environment gives write access to few places\\necho \\\"ls -la\\\"\\nls -la\\ncd /\\necho \\\"ls -la after changing to /\\\"\\nls -la\\ntouch \\\"foo_was.here\\\"\\necho \\\"ls -la in root after touch foo_was.here - foo_was_not.here more like it\\\"\\nls -la\\n\"}}, \"help_text\": \"**What it Does**\\nShows what you can't do with a bash script\\nCheck the tool stderr - it isn't captured but should be. 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is sensible.\\nPlease don't expose this anywhere.\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"SBCL Lisp script to execute\", \"input_help\": \"Provide a script in lisp to be interpreted by SBCL\", \"input_CL\": \"1\", \"input_repeat\": \"false\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"lisp_out\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": []}}}, \"run_test\": \"true\", \"tool_desc\": \"ToolFactory demonstration using Lisp for the nostalgic.\", \"tool_name\": \"lisp_demo\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "0241fb8d-f8c7-43c2-953c-95a45d4af735", + "workflow_outputs": [ + { + "label": null, + "output_name": "new_tool", + "uuid": "789a7cc9-bea5-45d2-ae2e-7026265fc835" + } + ] + }, + "22": { + "annotation": "", + "content_id": "rgtf2", + "errors": null, + "id": 22, + "input_connections": { + "io_param|ppass|io|history_inputs_0|input_files": { + "id": 9, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "new_tool", + "type": "toolshed.gz" + } + ], + "position": { + "bottom": -100.60000610351562, + "height": 154.39999389648438, + "left": 1642.5, + "right": 1842.5, + "top": -255, + "width": 200, + "x": 1642.5, + "y": -255 + }, + "post_job_actions": {}, + "tool_id": "rgtf2", + "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"dbb99db2a98811ebbc9e0242ac1b0004\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_prefix\": \"\", \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"planemo\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"bash\", \"dynScript\": \"cp $1 foo.tar.gz\\ntar -xvf foo.tar.gz\\nTOOLNAME=`find . -name \\\"*.xml\\\"`\\necho \\\"TOOLNAME = $TOOLNAME\\\"\\nplanemo test --test_output $2 $TOOLNAME\"}}, \"help_text\": \"**What it Does**\", \"install\": \"false\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"tgz\"], \"input_label\": \"ToolFactory toolshed archive from the history to test\", \"input_help\": \"\", \"input_CL\": \"1\", \"input_repeat\": \"false\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"planemo_test_output\", \"history_format\": \"txt\", \"history_CL\": \"2\", \"history_test\": \"sim_size:0.05\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": []}}}, \"make\": {\"makeMode\": {\"__current_case__\": 1, \"citations\": [], \"galaxy_apikey\": \"\", \"galaxy_url\": \"\", \"help_text\": \"**What it Does**\\n\\nRuns planemo test on a ToolFactory or other toolshed archive\", \"make_Tool\": \"gentest\", \"tool_desc\": \"Tests a ToolFactory tool\", \"tool_version\": \"0.01\", \"toolshed_apikey\": \"\", \"toolshed_url\": \"\"}}, \"run_test\": \"true\", \"tool_desc\": \"\", \"tool_name\": \"planemo_test\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "2d826252-a3fc-4e99-8791-2908926cda10", + "workflow_outputs": [ + { + "label": null, + "output_name": "new_tool", + "uuid": "659cabcf-e7db-4b61-8e3c-097a1d25c336" + } + ] + } + }, + "tags": [], + "uuid": "308d4b95-f04f-49b0-8674-f0ddf0587850", + "version": 1 +} diff -r 36d46b20095a -r 807b8d103f18 toolfactory/rgToolFactory2.py --- a/toolfactory/rgToolFactory2.py Sun Apr 18 02:14:13 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1149 +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 json -import logging -import os -import re -import shlex -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 = "V2.2 February 2021" -verbose = True -debug = True -toolFactoryURL = "https://github.com/fubar2/toolfactory" -foo = len(lxml.__version__) -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())) - - -cheetah_escape_table = {"$": "\\$", "#": "\\#"} - - -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): # noqa - """ - prepare command line cl for running the tool here - and prepare elements needed for galaxyxml tool generation - """ - self.ourcwd = os.getcwd() - self.collections = [] - if len(args.collection) > 0: - try: - self.collections = [ - json.loads(x) for x in args.collection if len(x.strip()) > 1 - ] - except Exception: - print( - f"--collections parameter {str(args.collection)} is malformed - should be a dictionary" - ) - try: - self.infiles = [ - json.loads(x) for x in args.input_files if len(x.strip()) > 1 - ] - except Exception: - print( - f"--input_files parameter {str(args.input_files)} is malformed - should be a dictionary" - ) - try: - self.outfiles = [ - json.loads(x) for x in args.output_files if len(x.strip()) > 1 - ] - except Exception: - print( - f"--output_files parameter {args.output_files} is malformed - should be a dictionary" - ) - try: - self.addpar = [ - json.loads(x) for x in args.additional_parameters if len(x.strip()) > 1 - ] - except Exception: - print( - f"--additional_parameters {args.additional_parameters} is malformed - should be a dictionary" - ) - try: - self.selpar = [ - json.loads(x) for x in args.selecttext_parameters if len(x.strip()) > 1 - ] - except Exception: - print( - f"--selecttext_parameters {args.selecttext_parameters} is malformed - should be a dictionary" - ) - 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: - if ' ' in self.args.sysexe: - self.executeme = self.args.sysexe.split(' ') - else: - 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 = "%s_toolshed.gz" % 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.script_path: - for ex in self.executeme: - aCL(ex) - aXCL(ex) - aCL(self.sfile) - aXCL("$runme") - else: - for ex in self.executeme: - aCL(ex) - aXCL(ex) - - self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name) - self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name) - if self.args.parampass == "0": - self.clsimple() - else: - if self.args.parampass == "positional": - self.prepclpos() - self.clpositional() - else: - self.prepargp() - self.clargparse() - if self.args.cl_suffix: # DIY CL end - clp = shlex.split(self.args.cl_suffix) - for c in clp: - aCL(c) - aXCL(c) - - def clsimple(self): - """no parameters or repeats - uses < and > for i/o""" - aCL = self.cl.append - aXCL = self.xmlcl.append - if len(self.infiles) > 0: - aCL("<") - aCL(self.infiles[0]["infilename"]) - aXCL("<") - aXCL("$%s" % self.infiles[0]["infilename"]) - if len(self.outfiles) > 0: - aCL(">") - aCL(self.outfiles[0]["name"]) - aXCL(">") - aXCL("$%s" % self.outfiles[0]["name"]) - - def prepargp(self): - clsuffix = [] - xclsuffix = [] - for i, p in enumerate(self.infiles): - nam = p["infilename"] - if p["origCL"].strip().upper() == "STDIN": - appendme = [ - nam, - nam, - "< %s" % nam, - ] - xappendme = [ - nam, - nam, - "< $%s" % nam, - ] - else: - rep = p["repeat"] == "1" - over = "" - if rep: - over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for' - appendme = [p["CL"], p["CL"], ""] - xappendme = [p["CL"], "$%s" % p["CL"], over] - clsuffix.append(appendme) - xclsuffix.append(xappendme) - for i, p in enumerate(self.outfiles): - if p["origCL"].strip().upper() == "STDOUT": - self.lastclredirect = [">", p["name"]] - self.lastxclredirect = [">", "$%s" % p["name"]] - else: - clsuffix.append([p["name"], p["name"], ""]) - xclsuffix.append([p["name"], "$%s" % p["name"], ""]) - for p in self.addpar: - nam = p["name"] - rep = p["repeat"] == "1" - if rep: - over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for' - else: - over = p["override"] - clsuffix.append([p["CL"], nam, over]) - xclsuffix.append([p["CL"], nam, over]) - for p in self.selpar: - clsuffix.append([p["CL"], p["name"], p["override"]]) - xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]]) - self.xclsuffix = xclsuffix - self.clsuffix = clsuffix - - def prepclpos(self): - clsuffix = [] - xclsuffix = [] - for i, p in enumerate(self.infiles): - if p["origCL"].strip().upper() == "STDIN": - appendme = [ - "999", - p["infilename"], - "< $%s" % p["infilename"], - ] - xappendme = [ - "999", - p["infilename"], - "< $%s" % p["infilename"], - ] - else: - appendme = [p["CL"], p["infilename"], ""] - xappendme = [p["CL"], "$%s" % p["infilename"], ""] - clsuffix.append(appendme) - xclsuffix.append(xappendme) - for i, p in enumerate(self.outfiles): - if p["origCL"].strip().upper() == "STDOUT": - self.lastclredirect = [">", p["name"]] - self.lastxclredirect = [">", "$%s" % p["name"]] - else: - clsuffix.append([p["CL"], p["name"], ""]) - xclsuffix.append([p["CL"], "$%s" % p["name"], ""]) - for p in self.addpar: - nam = p["name"] - rep = p["repeat"] == "1" # repeats make NO sense - if rep: - print(f'### warning. Repeats for {nam} ignored - not permitted in positional parameter command lines!') - over = p["override"] - clsuffix.append([p["CL"], nam, over]) - xclsuffix.append([p["CL"], '"$%s"' % nam, over]) - for p in self.selpar: - clsuffix.append([p["CL"], p["name"], p["override"]]) - xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]]) - clsuffix.sort() - xclsuffix.sort() - self.xclsuffix = xclsuffix - self.clsuffix = clsuffix - - 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[0]) - ) - 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[0]) - 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["CL"].isdigit() or p["CL"].strip().upper() == "STDIN" - ), "Positional parameters must be ordinal integers - got %s for %s" % ( - p["CL"], - p["label"], - ) - for i, p in enumerate(self.outfiles): - assert ( - p["CL"].isdigit() or p["CL"].strip().upper() == "STDOUT" - ), "Positional parameters must be ordinal integers - got %s for %s" % ( - p["CL"], - p["name"], - ) - for i, p in enumerate(self.addpar): - assert p[ - "CL" - ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % ( - p["CL"], - p["name"], - ) - for i, p in enumerate(self.infiles): - infp = copy.copy(p) - infp["origCL"] = infp["CL"] - if self.args.parampass in ["positional", "0"]: - infp["infilename"] = infp["label"].replace(" ", "_") - else: - infp["infilename"] = infp["CL"] - self.infiles[i] = infp - for i, p in enumerate(self.outfiles): - p["origCL"] = p["CL"] # keep copy - self.outfiles[i] = p - for i, p in enumerate(self.addpar): - p["origCL"] = p["CL"] - self.addpar[i] = p - - def clpositional(self): - # inputs in order then params - aCL = self.cl.append - for (k, v, koverride) in self.clsuffix: - if " " in v: - aCL("%s" % v) - else: - aCL(v) - aXCL = self.xmlcl.append - for (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 (k, v, koverride) in self.xclsuffix: - if koverride > "": - k = koverride - aXCL(k) - else: - if len(k.strip()) == 1: - k = "-%s" % k - else: - k = "--%s" % k - aXCL(k) - aXCL(v) - for (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) - if self.lastxclredirect: - aXCL(self.lastxclredirect[0]) - aXCL(self.lastxclredirect[1]) - - def getNdash(self, newname): - if self.is_positional: - ndash = 0 - else: - ndash = 2 - if len(newname) < 2: - ndash = 1 - return ndash - - def doXMLparam(self): - """Add all needed elements to tool""" # noqa - for p in self.outfiles: - newname = p["name"] - newfmt = p["format"] - newcl = p["CL"] - test = p["test"] - oldcl = p["origCL"] - test = test.strip() - ndash = self.getNdash(newcl) - aparm = gxtp.OutputData( - name=newname, format=newfmt, num_dashes=ndash, label=newname - ) - 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, - ) - else: - c = test - tp = gxtp.TestOutput( - name=newname, - value="%s_sample" % newname, - compare=c, - ) - self.testparam.append(tp) - for p in self.infiles: - newname = p["infilename"] - newfmt = p["format"] - ndash = self.getNdash(newname) - reps = p.get("repeat", "0") == "1" - if not len(p["label"]) > 0: - alab = p["CL"] - else: - alab = p["label"] - aninput = gxtp.DataParam( - newname, - optional=False, - label=alab, - help=p["help"], - format=newfmt, - multiple=False, - num_dashes=ndash, - ) - aninput.positional = self.is_positional - if self.is_positional: - if p["origCL"].upper() == "STDIN": - aninput.positional = 9999998 - aninput.command_line_override = "> $%s" % newname - else: - aninput.positional = int(p["origCL"]) - aninput.command_line_override = "$%s" % newname - if reps: - repe = gxtp.Repeat(name=f"R_{newname}", title=f"Add as many {alab} as needed") - repe.append(aninput) - self.tinputs.append(repe) - tparm = gxtp.TestRepeat(name=f"R_{newname}") - tparm2 = gxtp.TestParam(newname, value="%s_sample" % newname) - tparm.append(tparm2) - self.testparam.append(tparm) - else: - self.tinputs.append(aninput) - tparm = gxtp.TestParam(newname, value="%s_sample" % newname) - self.testparam.append(tparm) - for p in self.addpar: - newname = p["name"] - newval = p["value"] - newlabel = p["label"] - newhelp = p["help"] - newtype = p["type"] - newcl = p["CL"] - oldcl = p["origCL"] - reps = p["repeat"] == "1" - 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=newlabel, - help=newhelp, - value=newval, - num_dashes=ndash, - ) - elif newtype == "float": - aparm = gxtp.FloatParam( - newname, - label=newlabel, - help=newhelp, - value=newval, - num_dashes=ndash, - ) - elif newtype == "boolean": - aparm = gxtp.BooleanParam( - newname, - label=newlabel, - 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) - if reps: - repe = gxtp.Repeat(name=f"R_{newname}", title=f"Add as many {newlabel} as needed") - repe.append(aparm) - self.tinputs.append(repe) - tparm = gxtp.TestRepeat(name=f"R_{newname}") - tparm2 = gxtp.TestParam(newname, value=newval) - tparm.append(tparm2) - self.testparam.append(tparm) - else: - self.tinputs.append(aparm) - tparm = gxtp.TestParam(newname, value=newval) - self.testparam.append(tparm) - for p in self.selpar: - newname = p["name"] - newval = p["value"] - newlabel = p["label"] - newhelp = p["help"] - newtype = p["type"] - newcl = p["CL"] - if not len(newlabel) > 0: - newlabel = newname - ndash = self.getNdash(newname) - if newtype == "selecttext": - newtext = p["texts"] - aparm = gxtp.SelectParam( - newname, - label=newlabel, - help=newhelp, - num_dashes=ndash, - ) - for i in range(len(newval)): - anopt = gxtp.SelectOption( - value=newval[i], - text=newtext[i], - ) - aparm.append(anopt) - aparm.positional = self.is_positional - if self.is_positional: - aparm.positional = int(newcl) - self.tinputs.append(aparm) - tparm = gxtp.TestParam(newname, value=newval) - self.testparam.append(tparm) - else: - raise ValueError( - 'Unrecognised parameter type "%s" for\ - selecttext parameter %s in makeXML' - % (newtype, newname) - ) - for p in self.collections: - newkind = p["kind"] - newname = p["name"] - newlabel = p["label"] - newdisc = p["discover"] - collect = gxtp.OutputCollection(newname, label=newlabel, type=newkind) - disc = gxtp.DiscoverDatasets( - pattern=newdisc, directory=f"{newname}", visible="false" - ) - collect.append(disc) - self.toutputs.append(collect) - try: - tparm = gxtp.TestOutputCollection(newname) # broken until PR merged. - self.testparam.append(tparm) - except Exception: - print("#### WARNING: Galaxyxml version does not have the PR merged yet - tests for collections must be over-ridden until then!") - - def doNoXMLparam(self): - """filter style package - stdin to stdout""" - if len(self.infiles) > 0: - alab = self.infiles[0]["label"] - if len(alab) == 0: - alab = self.infiles[0]["infilename"] - 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]["infilename"] - aninput = gxtp.DataParam( - newname, - optional=False, - label=alab, - help=self.infiles[0]["help"], - format=self.infiles[0]["format"], - multiple=False, - num_dashes=0, - ) - aninput.command_line_override = "< $%s" % newname - aninput.positional = True - 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]["name"] - newfmt = self.outfiles[0]["format"] - 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): # noqa - """ - 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}"' - std = gxtp.Stdios() - std1 = gxtp.Stdio() - std.append(std1) - self.newtool.stdios = std - 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("")[0] - part2 = exml.split("")[1] - fixed = "%s\n%s\n%s" % (part1, "\n".join(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, 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]["name"], "rb") - else: - sti = sys.stdin - if len(self.outfiles) > 0: - sto = open(self.outfiles[0]["name"], "wb") - else: - sto = sys.stdout - subp = subprocess.run( - self.cl, 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, - 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""" - if self.args.parampass == 0: - self.doNoXMLparam() - else: - self.makeXML() - if self.args.script_path: - stname = os.path.join(self.tooloutdir, 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["name"] - dest = os.path.join(self.testdir, "%s_sample" % p["infilename"]) - shutil.copyfile(pth, dest) - dest = os.path.join(self.repdir, "%s_sample" % p["infilename"]) - shutil.copyfile(pth, dest) - - def makeToolTar(self, report_fail=False): - """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["name"] - tdest = os.path.join(self.testdir, "%s_sample" % oname) - src = os.path.join(self.testdir, oname) - if not os.path.isfile(tdest): - if os.path.isfile(src): - shutil.copyfile(src, tdest) - dest = os.path.join(self.repdir, "%s.sample" % (oname)) - shutil.copyfile(src, dest) - else: - if report_fail: - tout.write( - "###Tool may have failed - output file %s not found in testdir after planemo run %s." - % (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: - _, ext = os.path.splitext(entry.name) - if ext in [".tgz", ".json"]: - continue - if ext in [".yml", ".xml", ".yaml"]: - newname = f"{entry.name.replace('.','_')}.txt" - else: - newname = entry.name - else: - newname = f"{entry.name}.txt" - dest = os.path.join(self.repdir, newname) - src = os.path.join(self.tooloutdir, entry.name) - shutil.copyfile(src, dest) - if self.args.include_tests: - with os.scandir(self.testdir) as outs: - for entry in outs: - if (not entry.is_file()) or entry.name.endswith( - "_planemo_test_report.html" - ): - continue - if "." in entry.name: - _, ext = os.path.splitext(entry.name) - if ext in [".tgz", ".json"]: - continue - if ext in [".yml", ".xml", ".yaml"]: - newname = f"{entry.name.replace('.','_')}.txt" - else: - newname = entry.name - else: - newname = f"{entry.name}.txt" - dest = os.path.join(self.repdir, newname) - src = os.path.join(self.testdir, entry.name) - shutil.copyfile(src, dest) - - def planemo_test_once(self): - """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") - cll = [ - "planemo", - "test", - "--galaxy_python_version", - self.args.python_version, - "--test_data", - os.path.abspath(self.testdir), - "--test_output", - os.path.abspath(tool_test_path), - "--galaxy_root", - self.args.galaxy_root, - "--update_test_data", - os.path.abspath(xreal), - ] - p = subprocess.run( - cll, - shell=False, - 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_suffix", 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("--selecttext_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") - a("--collection", action="append", default=[]) - a("--include_tests", default=False, action="store_true") - a("--python_version", default="3.9") - 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" - r = ScriptRunner(args) - r.writeShedyml() - r.makeTool() - if args.make_Tool == "generate": - r.run() - r.moveRunOutputs() - r.makeToolTar() - else: - r.planemo_test_once() - r.moveRunOutputs() - r.makeToolTar(report_fail=True) - if args.make_Tool == "gentestinstall": - r.shedLoad() - r.eph_galaxy_load() - - -if __name__ == "__main__": - main() diff -r 36d46b20095a -r 807b8d103f18 toolfactory/rgToolFactory2.xml --- a/toolfactory/rgToolFactory2.xml Sun Apr 18 02:14:13 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,612 +0,0 @@ - - Scripts into tools v2.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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- - - - - galaxyxml - planemo - quay.io/biocontainers/mulled-v2-0a86ccf22d71945a175383bcea5edd6b51c25ed0:55f1b8132a10ad91f0016ba9f4c692627ca2d25b-0 - - - 0: ---cl_suffix "$cl_suffix" - #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: - #if $apar.ap_type.param_type=="selecttext": ---selecttext_parameters '{"name":"$apar.param_name", "label":"$apar.param_label", "help":"$apar.param_help", -"type":"$apar.ap_type.param_type","CL":"$apar.param_CL","override":"$apar.param_CLprefixed","value": [ - #for $i,$st in enumerate($apar.ap_type.selectTexts): - "$st.select_value" - #if ($i < (len($apar.ap_type.selectTexts)-1)): - , - #end if - #end for - ], "texts": [ - #for $i,$st in enumerate($apar.ap_type.selectTexts): - "$st.select_text" - #if ($i < (len($apar.ap_type.selectTexts)-1)): - , - #end if - - #end for - ] - }' - #else: ---additional_parameters '{"name": "$apar.param_name", "value": "$apar.ap_type.param_value", "label": "$apar.param_label", "help": "$apar.param_help", -"type": "$apar.ap_type.param_type","CL": "$apar.param_CL","override": "$apar.param_CLprefixed", "repeat": "$apar.param_repeat"}' - #end if - #end for - #end if - #for $intab in $io_param.ppass.io.history_inputs: ---input_files '{"name": "$intab.input_files", "CL": "$intab.input_CL", "format": "$intab.input_formats", "label": "$intab.input_label", "help": "$intab.input_help", "repeat": "$intab.input_repeat"}' - #end for - #for $otab in $io_param.ppass.io.history_outputs: ---output_files '{"name": "$otab.history_name", "format": "$otab.history_format", "CL": "$otab.history_CL", "test": "$otab.history_test"}' - #end for - #for $collect in $io_param.ppass.io.collection_outputs: ---collection '{"name": "$collect.name", "kind": "$collect.kind", "discover": "$collect.discover", "label": "$collect.label"}' - #end for ---galaxy_root "$__root_dir__" ---tool_dir "$__tool_directory__" - #end if -]]> - - -$deps.usescript.dynScript - - -#if $cover.commover == "yes" and len(str($cover.command_override).strip()) > 1: -$cover.command_override -#end if - - -#if $cover.commover == "yes" and len(str($cover.test_override).strip()) > 1: -$cover.test_override -#end if - - - #if $make.makeMode.make_Tool != "runonly": -${make.makeMode.help_text} - #else -$tool_name help goes here - #end if - - -#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 - - - - - - - - - - - -
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- - - - - makeMode['make_Tool'] != "runonly" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -.. 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() - -R script to draw some plots - use a collection. - -:: - - - \# note this script takes NO input because it generates random data - dir.create('plots') - for (i in 1:10) { - foo = runif(100) - bar = rnorm(100) - bar = foo + 0.05*bar - pdf(paste('plots/yet',i,"anotherplot.pdf",sep='_')) - plot(foo,bar,main=paste("Foo by Bar plot \#",i),col="maroon", pch=3,cex=0.6) - dev.off() - foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100)) - bar = as.matrix(foo) - pdf(paste('plots/yet',i,"anotherheatmap.pdf",sep='_')) - heatmap(bar,main='Random Heatmap') - dev.off() - } - - - -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: https://academic.oup.com/bioinformatics/article/28/23/3139/192853 - - - - - 10.1093/bioinformatics/bts573 - - - - diff -r 36d46b20095a -r 807b8d103f18 toolfactory/test-data/generated_xml_sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/test-data/generated_xml_sample Wed Jun 09 02:28:01 2021 +0000 @@ -0,0 +1,53 @@ + + + + positional reverse + + python + + + + + + + + + + + + + + + + + + + + + + + 10.1093/bioinformatics/bts573 + + + diff -r 36d46b20095a -r 807b8d103f18 toolfactory/test-data/input1_sample --- a/toolfactory/test-data/input1_sample Sun Apr 18 02:14:13 2021 +0000 +++ b/toolfactory/test-data/input1_sample Wed Jun 09 02:28:01 2021 +0000 @@ -1,166 +1,982 @@ -*WARNING before you start* +# 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 +# +# April 2021: Refactored into two tools - generate and test/install +# as part of GTN tutorial development and biocontainer adoption +# The tester runs planemo on a non-tested archive, creates the test outputs +# and returns a new proper tool with test. + + + +import argparse +import copy +import fcntl +import json +import os +import re +import shlex +import shutil +import subprocess +import sys +import tarfile +import tempfile +import time + +from bioblend import galaxy + +import galaxyxml.tool as gxt +import galaxyxml.tool.parameters as gxtp - 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 +import lxml.etree as ET + +import yaml + +myversion = "V2.3 April 2021" +verbose = True +debug = True +toolFactoryURL = "https://github.com/fubar2/toolfactory" +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())) + -Updated august 8 2014 to fix bugs reported by Marius van den Beek +cheetah_escape_table = {"$": "\\$", "#": "\\#"} + + +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 -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. +class Locker: + """ + multiple instances of the TF may try to update tool_conf.xml so use a simple lockfile + to prevent overwriting mix ups. + """ + def __enter__ (self): + lockfile = "/tmp/.toolfactory_lockfile.lck" + if not os.path.exists(lockfile): + try: + os.utime(lockfile, None) + except OSError: + open(lockfile, 'a').close() + self.fp = open(lockfile) + fcntl.flock(self.fp.fileno(), fcntl.LOCK_EX) -**Short Story** + def __exit__ (self, _type, value, tb): + fcntl.flock(self.fp.fileno(), fcntl.LOCK_UN) + self.fp.close() + + +class Tool_Conf_Updater: + + """# update config/tool_conf.xml with a new tool unpacked in /tools + # requires highly insecure docker settings - like write to tool_conf.xml and to tools ! + # if in a container possibly not so courageous. + # Fine on your own laptop but security red flag for most production instances + Note potential race condition for tool_conf.xml update - uses a file lock. + """ -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. + def __init__( + self, args, tool_conf_path, new_tool_archive_path, new_tool_name, local_tool_dir, run_test + ): + self.args = args + self.tool_conf_path = os.path.join(args.galaxy_root, tool_conf_path) + self.tool_dir = os.path.join(args.galaxy_root, local_tool_dir,'TFtools') + self.out_section = "ToolFactory Generated Tools" + tff = tarfile.open(new_tool_archive_path, "r:*") + flist = tff.getnames() + ourdir = os.path.commonpath(flist) # eg pyrevpos + self.tool_id = ourdir # they are the same for TF tools + ourxml = [x for x in flist if x.lower().endswith(".xml")] + tff.extractall() + tff.close() + self.run_rsync(ourdir, self.tool_dir) + with Locker(): + self.update_toolconf(ourdir, ourxml) -*You have a working r/python/perl/bash script or any executable with positional or argparse style parameters* + def run_rsync(self, srcf, dstf): + src = os.path.abspath(srcf) + dst = os.path.abspath(dstf) + if os.path.isdir(src): + cll = ["rsync", "-r", src, dst] + else: + cll = ["rsync", src, dst] + subprocess.run( + cll, + capture_output=False, + encoding="utf8", + shell=False, + ) -It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool. + def update_toolconf(self, ourdir, ourxml): # path is relative to tools + localconf = "./local_tool_conf.xml" + self.run_rsync(self.tool_conf_path, localconf) + tree = ET.parse(localconf) + root = tree.getroot() + hasTF = False + TFsection = None + for e in root.findall("section"): + if e.attrib["name"] == self.out_section: + hasTF = True + TFsection = e + if not hasTF: + TFsection = ET.Element("section", {"id":self.out_section, "name":self.out_section}) + root.insert(0, TFsection) # at the top! + our_tools = TFsection.findall("tool") + conf_tools = [x.attrib["file"] for x in our_tools] + for xml in ourxml: # may be > 1 + if xml not in conf_tools: # new + ET.SubElement(TFsection, "tool", {"file": os.path.join('TFtools', xml)}) + newconf = f"{self.tool_id}_conf" + tree.write(newconf, pretty_print=True) + self.run_rsync(newconf, self.tool_conf_path) + + -**Automated generation of new Galaxy tools for installation into any Galaxy** +class Tool_Factory: + """Wrapper for an arbitrary script + uses galaxyxml + + """ -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. + def __init__(self, args=None): # noqa + """ + prepare command line cl for running the tool here + and prepare elements needed for galaxyxml tool generation + """ + self.ourcwd = os.getcwd() + self.collections = [] + if len(args.collection) > 0: + try: + self.collections = [ + json.loads(x) for x in args.collection if len(x.strip()) > 1 + ] + except Exception: + print( + f"--collections parameter {str(args.collection)} is malformed - should be a dictionary" + ) + try: + self.infiles = [ + json.loads(x) for x in args.input_files if len(x.strip()) > 1 + ] + except Exception: + print( + f"--input_files parameter {str(args.input_files)} is malformed - should be a dictionary" + ) + try: + self.outfiles = [ + json.loads(x) for x in args.output_files if len(x.strip()) > 1 + ] + except Exception: + print( + f"--output_files parameter {args.output_files} is malformed - should be a dictionary" + ) + try: + self.addpar = [ + json.loads(x) for x in args.additional_parameters if len(x.strip()) > 1 + ] + except Exception: + print( + f"--additional_parameters {args.additional_parameters} is malformed - should be a dictionary" + ) + try: + self.selpar = [ + json.loads(x) for x in args.selecttext_parameters if len(x.strip()) > 1 + ] + except Exception: + print( + f"--selecttext_parameters {args.selecttext_parameters} is malformed - should be a dictionary" + ) + self.args = args + self.cleanuppar() + self.lastxclredirect = None + self.xmlcl = [] + self.is_positional = self.args.parampass == "positional" + if self.args.sysexe: + if " " in self.args.sysexe: + self.executeme = self.args.sysexe.split(" ") + else: + self.executeme = [ + self.args.sysexe, + ] + else: + if self.args.packages: + self.executeme = [ + self.args.packages.split(",")[0].split(":")[0].strip(), + ] + else: + self.executeme = None + 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.tooloutdir = "./tfout" + self.repdir = "./toolgen" + self.newtarpath = os.path.join(self.tooloutdir, "%s_not_tested.toolshed.gz" % self.tool_name) + 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.script_path: + for ex in self.executeme: + aXCL(ex) + aXCL("$runme") + else: + for ex in self.executeme: + aXCL(ex) -**More Detail** + if self.args.parampass == "0": + self.clsimple() + else: + if self.args.parampass == "positional": + self.prepclpos() + self.clpositional() + else: + self.prepargp() + self.clargparse() -To use the ToolFactory, you should have prepared a script to paste into a -text box, or have a package in mind and a small test input example ready to select from your history -to test your new script. - -```planemo test rgToolFactory2.xml --galaxy_root ~/galaxy --test_data ~/galaxy/tools/tool_makers/toolfactory/test-data``` works for me + def clsimple(self): + """no parameters or repeats - uses < and > for i/o""" + aXCL = self.xmlcl.append + if len(self.infiles) > 0: + aXCL("<") + aXCL("$%s" % self.infiles[0]["infilename"]) + if len(self.outfiles) > 0: + aXCL(">") + aXCL("$%s" % self.outfiles[0]["name"]) + if self.args.cl_user_suffix: # DIY CL end + clp = shlex.split(self.args.cl_user_suffix) + for c in clp: + aXCL(c) -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. + def prepargp(self): + xclsuffix = [] + for i, p in enumerate(self.infiles): + nam = p["infilename"] + if p["origCL"].strip().upper() == "STDIN": + xappendme = [ + nam, + nam, + "< $%s" % nam, + ] + else: + rep = p["repeat"] == "1" + over = "" + if rep: + over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for' + xappendme = [p["CL"], "$%s" % p["CL"], over] + xclsuffix.append(xappendme) + for i, p in enumerate(self.outfiles): + if p["origCL"].strip().upper() == "STDOUT": + self.lastxclredirect = [">", "$%s" % p["name"]] + else: + xclsuffix.append([p["name"], "$%s" % p["name"], ""]) + for p in self.addpar: + nam = p["name"] + rep = p["repeat"] == "1" + if rep: + over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for' + else: + over = p["override"] + xclsuffix.append([p["CL"], '"$%s"' % nam, over]) + for p in self.selpar: + xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]]) + self.xclsuffix = xclsuffix -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. + def prepclpos(self): + xclsuffix = [] + for i, p in enumerate(self.infiles): + if p["origCL"].strip().upper() == "STDIN": + xappendme = [ + "999", + p["infilename"], + "< $%s" % p["infilename"], + ] + else: + xappendme = [p["CL"], "$%s" % p["infilename"], ""] + xclsuffix.append(xappendme) + for i, p in enumerate(self.outfiles): + if p["origCL"].strip().upper() == "STDOUT": + self.lastxclredirect = [">", "$%s" % p["name"]] + else: + xclsuffix.append([p["CL"], "$%s" % p["name"], ""]) + for p in self.addpar: + nam = p["name"] + rep = p["repeat"] == "1" # repeats make NO sense + if rep: + print( + f"### warning. Repeats for {nam} ignored - not permitted in positional parameter command lines!" + ) + over = p["override"] + xclsuffix.append([p["CL"], '"$%s"' % nam, over]) + for p in self.selpar: + xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]]) + xclsuffix.sort() + self.xclsuffix = xclsuffix + + 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[0]) + ) + tscript = open(self.sfile, "w") + tscript.write(self.script) + tscript.close() + self.spacedScript = [f" {x}" for x in rx if x.strip() > ""] + rx.insert(0, "#raw") + rx.append("#end raw") + self.escapedScript = rx + art = "%s.%s" % (self.tool_name, self.executeme[0]) + artifact = open(art, "wb") + artifact.write(bytes(self.script, "utf8")) + artifact.close() -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. + 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["CL"].isdigit() or p["CL"].strip().upper() == "STDIN" + ), "Positional parameters must be ordinal integers - got %s for %s" % ( + p["CL"], + p["label"], + ) + for i, p in enumerate(self.outfiles): + assert ( + p["CL"].isdigit() or p["CL"].strip().upper() == "STDOUT" + ), "Positional parameters must be ordinal integers - got %s for %s" % ( + p["CL"], + p["name"], + ) + for i, p in enumerate(self.addpar): + assert p[ + "CL" + ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % ( + p["CL"], + p["name"], + ) + for i, p in enumerate(self.infiles): + infp = copy.copy(p) + infp["origCL"] = infp["CL"] + if self.args.parampass in ["positional", "0"]: + infp["infilename"] = infp["label"].replace(" ", "_") + else: + infp["infilename"] = infp["CL"] + self.infiles[i] = infp + for i, p in enumerate(self.outfiles): + outfp = copy.copy(p) + outfp["origCL"] = outfp["CL"] # keep copy + self.outfiles[i] = outfp + for i, p in enumerate(self.addpar): + addp = copy.copy(p) + addp["origCL"] = addp["CL"] + self.addpar[i] = addp -Once it's in a ToolShed, it can be installed into any local Galaxy server -from the server administrative interface. + def clpositional(self): + # inputs in order then params + aXCL = self.xmlcl.append + for (k, v, koverride) in self.xclsuffix: + aXCL(v) + if self.lastxclredirect: + for cl in self.lastxclredirect: + aXCL(cl) + if self.args.cl_user_suffix: # DIY CL end + clp = shlex.split(self.args.cl_user_suffix) + for c in clp: + aXCL(c) + + def clargparse(self): + """argparse style""" + aXCL = self.xmlcl.append + # inputs then params in argparse named form + + for (k, v, koverride) in self.xclsuffix: + if koverride > "": + k = koverride + aXCL(k) + else: + if len(k.strip()) == 1: + k = "-%s" % k + else: + k = "--%s" % k + aXCL(k) + aXCL(v) + if self.lastxclredirect: + for cl in self.lastxclredirect: + aXCL(cl) + if self.args.cl_user_suffix: # DIY CL end + clp = shlex.split(self.args.cl_user_suffix) + for c in clp: + aXCL(c) + + def getNdash(self, newname): + if self.is_positional: + ndash = 0 + else: + ndash = 2 + if len(newname) < 2: + ndash = 1 + return ndash -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 + def doXMLparam(self): # noqa + """Add all needed elements to tool""" + for p in self.outfiles: + newname = p["name"] + newfmt = p["format"] + newcl = p["CL"] + test = p["test"] + oldcl = p["origCL"] + test = test.strip() + ndash = self.getNdash(newcl) + aparm = gxtp.OutputData( + name=newname, format=newfmt, num_dashes=ndash, label=newname + ) + 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, + ) + else: + c = test + tp = gxtp.TestOutput( + name=newname, + value="%s_sample" % newname, + compare=c, + ) + self.testparam.append(tp) + for p in self.infiles: + newname = p["infilename"] + newfmt = p["format"] + ndash = self.getNdash(newname) + reps = p.get("repeat", "0") == "1" + if not len(p["label"]) > 0: + alab = p["CL"] + else: + alab = p["label"] + aninput = gxtp.DataParam( + newname, + optional=False, + label=alab, + help=p["help"], + format=newfmt, + multiple=False, + num_dashes=ndash, + ) + aninput.positional = self.is_positional + if self.is_positional: + if p["origCL"].upper() == "STDIN": + aninput.positional = 9999998 + aninput.command_line_override = "> $%s" % newname + else: + aninput.positional = int(p["origCL"]) + aninput.command_line_override = "$%s" % newname + if reps: + repe = gxtp.Repeat( + name=f"R_{newname}", title=f"Add as many {alab} as needed" + ) + repe.append(aninput) + self.tinputs.append(repe) + tparm = gxtp.TestRepeat(name=f"R_{newname}") + tparm2 = gxtp.TestParam(newname, value="%s_sample" % newname) + tparm.append(tparm2) + self.testparam.append(tparm) + else: + self.tinputs.append(aninput) + tparm = gxtp.TestParam(newname, value="%s_sample" % newname) + self.testparam.append(tparm) + for p in self.addpar: + newname = p["name"] + newval = p["value"] + newlabel = p["label"] + newhelp = p["help"] + newtype = p["type"] + newcl = p["CL"] + oldcl = p["origCL"] + reps = p["repeat"] == "1" + 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=newlabel, + help=newhelp, + value=newval, + num_dashes=ndash, + ) + elif newtype == "float": + aparm = gxtp.FloatParam( + newname, + label=newlabel, + help=newhelp, + value=newval, + num_dashes=ndash, + ) + elif newtype == "boolean": + aparm = gxtp.BooleanParam( + newname, + label=newlabel, + 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) + if reps: + repe = gxtp.Repeat( + name=f"R_{newname}", title=f"Add as many {newlabel} as needed" + ) + repe.append(aparm) + self.tinputs.append(repe) + tparm = gxtp.TestRepeat(name=f"R_{newname}") + tparm2 = gxtp.TestParam(newname, value=newval) + tparm.append(tparm2) + self.testparam.append(tparm) + else: + self.tinputs.append(aparm) + tparm = gxtp.TestParam(newname, value=newval) + self.testparam.append(tparm) + for p in self.selpar: + newname = p["name"] + newval = p["value"] + newlabel = p["label"] + newhelp = p["help"] + newtype = p["type"] + newcl = p["CL"] + if not len(newlabel) > 0: + newlabel = newname + ndash = self.getNdash(newname) + if newtype == "selecttext": + newtext = p["texts"] + aparm = gxtp.SelectParam( + newname, + label=newlabel, + help=newhelp, + num_dashes=ndash, + ) + for i in range(len(newval)): + anopt = gxtp.SelectOption( + value=newval[i], + text=newtext[i], + ) + aparm.append(anopt) + aparm.positional = self.is_positional + if self.is_positional: + aparm.positional = int(newcl) + self.tinputs.append(aparm) + tparm = gxtp.TestParam(newname, value=newval) + self.testparam.append(tparm) + else: + raise ValueError( + 'Unrecognised parameter type "%s" for\ + selecttext parameter %s in makeXML' + % (newtype, newname) + ) + for p in self.collections: + newkind = p["kind"] + newname = p["name"] + newlabel = p["label"] + newdisc = p["discover"] + collect = gxtp.OutputCollection(newname, label=newlabel, type=newkind) + disc = gxtp.DiscoverDatasets( + pattern=newdisc, directory=f"{newname}", visible="false" + ) + collect.append(disc) + self.toutputs.append(collect) + try: + tparm = gxtp.TestOutputCollection(newname) # broken until PR merged. + self.testparam.append(tparm) + except Exception: + print( + "#### WARNING: Galaxyxml version does not have the PR merged yet - tests for collections must be over-ridden until then!" + ) -**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. + def doNoXMLparam(self): + """filter style package - stdin to stdout""" + if len(self.infiles) > 0: + alab = self.infiles[0]["label"] + if len(alab) == 0: + alab = self.infiles[0]["infilename"] + 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]["infilename"] + aninput = gxtp.DataParam( + newname, + optional=False, + label=alab, + help=self.infiles[0]["help"], + format=self.infiles[0]["format"], + multiple=False, + num_dashes=0, + ) + aninput.command_line_override = "< $%s" % newname + aninput.positional = True + 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]["name"] + newfmt = self.outfiles[0]["format"] + 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) -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:: + def makeXML(self): # noqa + """ + 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}"' + std = gxtp.Stdios() + std1 = gxtp.Stdio() + std.append(std1) + self.newtool.stdios = std + requirements = gxtp.Requirements() + if self.args.packages: + try: + for d in self.args.packages.split(","): + ver = None + packg = None + d = d.replace("==", ":") + d = d.replace("=", ":") + if ":" in d: + packg, ver = d.split(":") + ver = ver.strip() + packg = packg.strip() + else: + packg = d.strip() + ver = None + if ver == "": + ver = None + if packg: + requirements.append( + gxtp.Requirement("package", packg.strip(), ver) + ) + except Exception: + print( + "### malformed packages string supplied - cannot parse =", + self.args.packages, + ) + sys.exit(2) + 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("")[0] + part2 = exml.split("")[1] + fixed = "%s\n%s\n%s" % (part1, "\n".join(self.test_override), part2) + exml = fixed + # exml = exml.replace('range="1:"', 'range="1000:"') + with open("%s.xml" % self.tool_name, "w") as xf: + xf.write(exml) + xf.write("\n") + with open(self.args.untested_tool_out, 'w') as outf: + outf.write(exml) + outf.write('\n') + # ready for the tarball -
- -
+ 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() -If not already there, -please add: - -to your local data_types_conf.xml. + def makeTool(self): + """write xmls and input samples into place""" + if self.args.parampass == 0: + self.doNoXMLparam() + else: + self.makeXML() + if self.args.script_path: + stname = os.path.join(self.tooloutdir, 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) + #xout = os.path.join(self.repdir, xreal) + #shutil.copyfile(xreal, xout) + for p in self.infiles: + pth = p["name"] + dest = os.path.join(self.testdir, "%s_sample" % p["infilename"]) + shutil.copyfile(pth, dest) + dest = os.path.join( + self.repdir, "%s_sample.%s" % (p["infilename"], p["format"]) + ) + shutil.copyfile(pth, dest) + + def makeToolTar(self, report_fail=False): + """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 + + for p in self.outfiles: + oname = p["name"] + tdest = os.path.join(self.testdir, "%s_sample" % oname) + src = os.path.join(self.testdir, oname) + if not os.path.isfile(tdest): + if os.path.isfile(src): + shutil.copyfile(src, tdest) + dest = os.path.join(self.repdir, "%s.sample.%s" % (oname,p['format'])) + shutil.copyfile(src, dest) + else: + if report_fail: + print( + "###Tool may have failed - output file %s not found in testdir after planemo run %s." + % (tdest, self.testdir) + ) + tf = tarfile.open(self.newtarpath, "w:gz") + tf.add( + name=self.tooloutdir, + arcname=self.tool_name, + filter=exclude_function, + ) + shutil.copy(self.newtarpath, os.path.join(self.tooloutdir, f"{self.tool_name}_untested.toolshed.gz")) + tf.close() -**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. +def main(): + """ + This is a Galaxy wrapper. + It expects to be called by a special purpose tool.xml -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** + """ + parser = argparse.ArgumentParser() + a = parser.add_argument + a("--script_path", default=None) + a("--history_test", default=None) + a("--cl_user_suffix", 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("--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("--selecttext_parameters", action="append", default=[]) + a("--edit_additional_parameters", action="store_true", default=False) + a("--parampass", default="positional") + a("--tfout", default="./tfout") + a("--galaxy_root", default="/galaxy-central") + a("--galaxy_venv", default="/galaxy_venv") + a("--collection", action="append", default=[]) + a("--include_tests", default=False, action="store_true") + a("--install", default="1") + a("--admin_only", default=False, action="store_true") + a("--untested_tool_out", default=None) + a("--local_tools", default="tools") # relative to $__root_dir__ + a("--tool_conf_path", default="config/tool_conf.xml") # relative to $__root_dir__ + args = parser.parse_args() + if args.admin_only: + 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" + r = Tool_Factory(args) + r.writeShedyml() + r.makeTool() + r.makeToolTar() + if args.install == "1": + TCU = Tool_Conf_Updater( + args=args, + local_tool_dir=args.local_tools, + new_tool_archive_path=r.newtarpath, + tool_conf_path=args.tool_conf_path, + new_tool_name=r.tool_name, + run_test = args.run_test + ) -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 - +if __name__ == "__main__": + main() diff -r 36d46b20095a -r 807b8d103f18 toolfactory/test-data/pyrevpos_not_tested.toolshed_sample Binary file toolfactory/test-data/pyrevpos_not_tested.toolshed_sample has changed diff -r 36d46b20095a -r 807b8d103f18 toolfactory/test-data/test1_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/test-data/test1_log.txt Wed Jun 09 02:28:01 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