Mercurial > repos > fubar > toolfactory2
changeset 3:290f552d7e05 draft default tip
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| author | fubar |
|---|---|
| date | Sat, 17 Apr 2021 22:58:34 +0000 |
| parents | 9fd3d83e1bac |
| children | |
| files | toolfactory/README.md toolfactory/rgToolFactory2.py |
| diffstat | 2 files changed, 1561 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/README.md Sat Apr 17 22:58:34 2021 +0000 @@ -0,0 +1,380 @@ +## Breaking news! Docker container at https://github.com/fubar2/toolfactory-galaxy-docker recommended as at December 2020 + +### New demonstration of planemo tool_factory command  + +## This is the original ToolFactory suitable for non-docker situations. Please use the docker container if you can because it's integrated with a Toolshed... + +# WARNING + +Install this tool to a throw-away private Galaxy or Docker container ONLY! + +Please NEVER on a public or production instance where a hostile user may +be able to gain access if they can acquire an administrative account login. + +It only runs for server administrators - the ToolFactory tool will refuse to execute for an ordinary user since +it can install new tools to the Galaxy server it executes on! This is not something you should allow other than +on a throw away instance that is protected from potentially hostile users. + +## Short Story + +Galaxy is easily extended to new applications by adding a new tool. Each new scientific computational package added as +a tool to Galaxy requires an XML document describing how the application interacts with Galaxy. +This is sometimes termed "wrapping" the package because the instructions tell Galaxy how to run the package +as a new Galaxy tool. Any tool that has been wrapped is readily available to all the users through a consistent +and easy to use interface once installed in the local Galaxy server. + +Most Galaxy tool wrappers have been manually prepared by skilled programmers, many using Planemo because it +automates much of the boilerplate and makes the process much easier. +The ToolFactory (TF) now uses Planemo under the hood for testing, but hides the command +line complexities. The user will still need appropriate skills in terms of describing the interface between +Galaxy and the new application, but will be helped by a Galaxy tool form to collect all the needed +settings, together with automated testing and uploading to a toolshed with optional local installation. + + +## ToolFactory generated tools are ordinary Galaxy tools + +A TF generated tool that passes the Planemo test is ready to publish in any Galaxy Toolshed and ready to install in any running Galaxy instance. +They are fully workflow compatible and work exactly like any hand-written tool. The user can select input files of the specified type(s) from their +history and edit each of the specified parameters. The tool form will show all the labels and help text supplied when the tool was built. When the tool +is executed, the dependent binary or script will be passed all the i/o files and parameters as specified, and will write outputs to the specified new +history datasets - just like any other Galaxy tool. + +## Models for tool command line construction + +The key to turning any software package into a Galaxy tool is the automated construction of a suitable command line. + +The TF can build a new tool that will allow the tool user to select input files from their history, set any parameters and when run will send the +new output files to the history as specified when the tool builder completed the form and built the new tool. + +That tool can contain instructions to run any Conda dependency or a system executable like bash. Whether a bash script you have written or +a Conda package like bwa, the executable will expect to find settings for input, output and parameters on a command line. + +These are often passed as "--name value" (argparse style) or in a fixed order (positional style). + +The ToolFactory allows either, or for "filter" applications that process input from STDIN and write processed output to STDOUT. + +The simplest tool model wraps a simple script or Conda dependency package requiring only input and output files, with no user supplied settings illustrated by +the Tacrev demonstration tool found in the Galaxy running in the ToolFactory docker container. It passes a user selected input file from the current history on STDIN +to a bash script. The bash script runs the unix tac utility (reverse cat) piped to the unix rev (reverse lines in a text file) utility. It's a one liner: + +`tac | rev` + +The tool building form allows zero or more Conda package name(s) and version(s) and an optional script to be executed by either a system +executable like ``bash`` or the first of any named Conda dependency package/version. Tacrev uses a tiny bash script shown above and uses the system +bash. Conda bash can be specified if it is important to use the same version consistently for the tool. + +On the tool form, the repeat section allowing zero or more input files was set to be a text file to be selected by the tool user and +in the repeat section allowing one or more outputs, a new output file with special value `STDOUT` as the positional parameter, causes the TF to +generate a command to capture STDOUT and send it to the new history file containing the reversed input text. + +By reversed, we mean really, truly reversed. + +That simple model can be made much more complicated, and can pass inputs and outputs as named or positional parameters, +to allow more complicated scripts or dependent binaries that require: + +1. Any number of input data files selected by the user from existing history data +2. Any number of output data files written to the user's history +3. Any number of user supplied parameters. These can be passed as command line arguments to the script or the dependency package. Either +positional or named (argparse) style command line parameter passing can be used. + +More complex models can be seen in the Sedtest, Pyrevpos and Pyrevargparse tools illustrating positional and argparse parameter passing. + +The most complex demonstration is the Planemo advanced tool tutorial BWA tool. There is one version using a command-override to implement +exactly the same command structure in the Planemo tutorial. A second version uses a bash script and positional parameters to achieve the same +result. Some tool builders may find the bash version more familiar and cleaner but the choice is yours. + +## Overview + + + + +Steps in building a new Galaxy tool are all conducted through Galaxy running in the docker container: + +1. Login to the Galaxy running in the container at http://localhost:8080 using an admin account. They are specified in config/galaxy.yml and + in the documentation at + and the ToolFactory will error out and refuse to run for non-administrative tool builders as a minimal protection from opportunistic hostile use. + +2. Start the TF and fill in the form, providing sample inputs and parameter values to suit the Conda package being wrapped. + +3. Execute the tool to create a new XML tool wrapper using the sample inputs and parameter settings for the inbuilt tool test. Planemo runs twice. + firstly to generate the test outputs and then to perform a proper test. The completed toolshed archive is written to the history + together with the planemo test report. Optionally the new tool archive can be uploaded + to the toolshed running in the same container (http://localhost:9009) and then installed inside the Galaxy in the container for further testing. + +4. If the test fails, rerun the failed history job and correct errors on the tool form before rerunning until everything works correctly. + + + +## Planning and building new Galaxy tool wrappers. + +It is best to have all the required planning done to wrap any new script or binary before firing up the TF. +Conda is the only current dependency manager supported. Before starting, at the very least, the tool builder will need +to know the required software package name in Conda and the version to use, how the command line for +the package must be constructed, and there must be sample inputs in the working history for each of the required data inputs +for the package, together with values for every parameter to suit these sample inputs. These are required on the TF form +for preparing the inbuilt tool test. That test is run using Planemo, as part of the tool generation process. + +A new tool is specified by filling in the usual Galaxy tool form. + +The form starts with a new tool name. Most tools will need dependency packages and versions +for the executable. Only Conda is currently supported. + +If a script is needed, it can be pasted into a text box and the interpreter named. Available system executables +can be used such as bash, or an interpreter such as python, perl or R can be nominated as conda dependencies +to ensure reproducible analyses. + +The tool form will be generated from the input data and the tool builder supplied parameters. The command line for the +executable is built using positional or argparse (named e.g. --input_file /foo/baz) style +parameters and is completely dependent on the executable. These can include: + +1. Any number of input data sets needed by the executable. Each appears to the tool user on the run form and is included +on the command line for the executable. The tool builder must supply a small representative sample for each one as +an input for the automated tool test. + +2. Any number of output data sets generated by the package can be added to the command line and will appear in +the user's history at the end of the job + +3. Any number of text or numeric parameters. Each will appear to the tool user on the run form and are included +on the command line to the executable. The tool builder must supply a suitable representative value for each one as +the value to be used for the automated tool test. + +Once the form is completed, executing the TF will build a new XML tool wrapper +including a functional test based on the sample settings and data. + +If the Planemo test passes, the tool can be optionally uploaded to the local Galaxy used in the image for more testing. + +A local toolshed runs inside the container to allow an automated installation, although any toolshed and any accessible +Galaxy can be specified for this process by editing the default URL and API keys to provide appropriate credentials. + +## Generated Tool Dependency management + +Conda is used for all dependency management although tools that use system utilities like sed, bash or awk +may be available on job execution nodes. Sed and friends are available as Conda (conda-forge) dependencies if necessary. +Versioned Conda dependencies are always baked-in to the tool and will be used for reproducible calculation. + +## Requirements + +These are all managed automagically. The TF relies on galaxyxml to generate tool xml and uses ephemeris and +bioblend to load tools to the toolshed and to Galaxy. Planemo is used for testing and runs in a biocontainer currently at +https://quay.io/fubar2/planemo-biocontainer + +## Caveats + +This docker image requires privileged mode so exposes potential security risks if hostile tool builders gain access. +Please, do not run it in any situation where that is a problem - never, ever on a public facing Galaxy server. +On a laptop or workstation should be fine in a non-hostile environment. + + +## Example generated XML + +For the bwa-mem example, a supplied bash script is included as a configfile and so has escaped characters. +``` +<tool name="bwatest" id="bwatest" version="0.01"> + <!--Cite: Creating re-usable tools from scripts doi:10.1093/bioinformatics/bts573--> + <!--Source in git at: https://github.com/fubar2/toolfactory--> + <!--Created by admin@galaxy.org at 30/11/2020 07:12:10 using the Galaxy Tool Factory.--> + <description>Planemo advanced tool building sample bwa mem mapper as a ToolFactory demo</description> + <requirements> + <requirement version="0.7.15" type="package">bwa</requirement> + <requirement version="1.3" type="package">samtools</requirement> + </requirements> + <configfiles> + <configfile name="runme"><![CDATA[ +REFFILE=\$1 +FASTQ=\$2 +BAMOUT=\$3 +rm -f "refalias" +ln -s "\$REFFILE" "refalias" +bwa index -a is "refalias" +bwa mem -t "2" -v 1 "refalias" "\$FASTQ" > tempsam +samtools view -Sb tempsam > temporary_bam_file.bam +samtools sort -o "\$BAMOUT" temporary_bam_file.bam + +]]></configfile> + </configfiles> + <version_command/> + <command><![CDATA[bash +$runme +$input1 +$input2 +$bam_output]]></command> + <inputs> + <param optional="false" label="Reference sequence for bwa to map the fastq reads against" help="" format="fasta" multiple="false" type="data" name="input1" argument="input1"/> + <param optional="false" label="Reads as fastqsanger to align to the reference sequence" help="" format="fastqsanger" multiple="false" type="data" name="input2" argument="input2"/> + </inputs> + <outputs> + <data name="bam_output" format="bam" label="bam_output" hidden="false"/> + </outputs> + <tests> + <test> + <output name="bam_output" value="bam_output_sample" compare="sim_size" format="bam" delta_frac="0.1"/> + <param name="input1" value="input1_sample"/> + <param name="input2" value="input2_sample"/> + </test> + </tests> + <help><![CDATA[ + +**What it Does** + +Planemo advanced tool building sample bwa mem mapper + +Reimagined as a bash script for a ToolFactory demonstration + + +------ + +Script:: + + REFFILE=$1 + FASTQ=$2 + BAMOUT=$3 + rm -f "refalias" + ln -s "$REFFILE" "refalias" + bwa index -a is "refalias" + bwa mem -t "2" -v 1 "refalias" "$FASTQ" > tempsam + samtools view -Sb tempsam > temporary_bam_file.bam + samtools sort -o "$BAMOUT" temporary_bam_file.bam + +]]></help> +</tool> + +``` + + + +## More Explanation + +The TF is an unusual Galaxy tool, designed to allow a skilled user to make new Galaxy tools. +It appears in Galaxy just like any other tool but outputs include new Galaxy tools generated +using instructions provided by the user and the results of Planemo lint and tool testing using +small sample inputs provided by the TF user. The small samples become tests built in to the new tool. + +It offers a familiar Galaxy form driven way to define how the user of the new tool will +choose input data from their history, and what parameters the new tool user will be able to adjust. +The TF user must know, or be able to read, enough about the tool to be able to define the details of +the new Galaxy interface and the ToolFactory offers little guidance on that other than some examples. + +Tools always depend on other things. Most tools in Galaxy depend on third party +scientific packages, so TF tools usually have one or more dependencies. These can be +scientific packages such as BWA or scripting languages such as Python and are +managed by Conda. If the new tool relies on a system utility such as bash or awk +where the importance of version control on reproducibility is low, these can be used without +Conda management - but remember the potential risks of unmanaged dependencies on computational +reproducibility. + +The TF user can optionally supply a working script where scripting is +required and the chosen dependency is a scripting language such as Python or a system +scripting executable such as bash. Whatever the language, the script must correctly parse the command line +arguments it receives at tool execution, as they are defined by the TF user. The +text of that script is "baked in" to the new tool and will be executed each time +the new tool is run. It is highly recommended that scripts and their command lines be developed +and tested until proven to work before the TF is invoked. Galaxy as a software development +environment is actually possible, but not recommended being somewhat clumsy and inefficient. + +Tools nearly always take one or more data sets from the user's history as input. TF tools +allow the TF user to define what Galaxy datatypes the tool end user will be able to choose and what +names or positions will be used to pass them on a command line to the package or script. + +Tools often have various parameter settings. The TF allows the TF user to define how each +parameter will appear on the tool form to the end user, and what names or positions will be +used to pass them on the command line to the package. At present, parameters are limited to +simple text and number fields. Pull requests for other kinds of parameters that galaxyxml +can handle are welcomed. + +Best practice Galaxy tools have one or more automated tests. These should use small sample data sets and +specific parameter settings so when the tool is tested, the outputs can be compared with their expected +values. The TF will automatically create a test for the new tool. It will use the sample data sets +chosen by the TF user when they built the new tool. + +The TF works by exposing *unrestricted* and therefore extremely dangerous scripting +to all designated administrators of the host Galaxy server, allowing them to +run scripts in R, python, sh and perl. For this reason, a Docker container is +available to help manage the associated risks. + +## Scripting uses + +To use a scripting language to create a new tool, you must first prepared and properly test a script. Use small sample +data sets for testing. When the script is working correctly, upload the small sample datasets +into a new history, start configuring a new ToolFactory tool, and paste the script into the script text box on the TF form. + +### Outputs + +The TF will generate the new tool described on the TF form, and test it +using planemo. Optionally if a local toolshed is running, it can be used to +install the new tool back into the generating Galaxy. + +A toolshed is built in to the Docker container and configured +so a tool can be tested, sent to that toolshed, then installed in the Galaxy +where the TF is running using the default toolshed and Galaxy URL and API keys. + +Once it's in a ToolShed, it can be installed into any local Galaxy server +from the server administrative interface. + +Once the new tool is installed, local users can run it - each time, the +package and/or script that was supplied when it was built will be executed with the input chosen +from the user's history, together with user supplied parameters. In other words, the tools you generate with the +TF run just like any other Galaxy tool. + +TF generated tools work as normal workflow components. + + +## Limitations + +The TF is flexible enough to generate wrappers for many common scientific packages +but the inbuilt automation will not cope with all possible situations. Users can +supply overrides for two tool XML segments - tests and command and the BWA +example in the supplied samples workflow illustrates their use. It does not deal with +repeated elements or conditional parameters such as allowing a user to choose to see "simple" +or "advanced" parameters (yet) and there will be plenty of packages it just +won't cover - but it's a quick and efficient tool for the other 90% of cases. Perfect for +that bash one liner you need to get that workflow functioning correctly for this +afternoon's demonstration! + +## Installation + +The Docker container https://github.com/fubar2/toolfactory-galaxy-docker/blob/main/README.md +is the best way to use the TF because it is preconfigured +to automate new tool testing and has a built in local toolshed where each new tool +is uploaded. If you grab the docker container, it should just work after a restart and you +can run a workflow to generate all the sample tools. Running the samples and rerunning the ToolFactory +jobs that generated them allows you to add fields and experiment to see how things work. + +It can be installed like any other tool from the Toolshed, but you will need to make some +configuration changes (TODO write a configuration). You can install it most conveniently using the +administrative "Search and browse tool sheds" link. Find the Galaxy Main +toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory +repository in the Tool Maker section. Open it and review the code and select the option to install it. + +If not already there please add: + +``` +<datatype extension="tgz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /> +``` + +to your local config/data_types_conf.xml. + + +## Restricted execution + +The tool factory tool itself will ONLY run for admin users - +people with IDs in config/galaxy.yml "admin_users". + +*ONLY admin_users can run this tool* + +That doesn't mean it's safe to install on a shared or exposed instance - please don't. + +## Generated tool Security + +Once you install a generated tool, it's just +another tool - assuming the script is safe. They just run normally and their +user cannot do anything unusually insecure but please, practice safe toolshed. +Read the code before you install any tool. Especially this one - it is really scary. + +## Attribution + +Creating re-usable tools from scripts: The Galaxy Tool Factory +Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team +Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 + +http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/rgToolFactory2.py Sat Apr 17 22:58:34 2021 +0000 @@ -0,0 +1,1181 @@ +# 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("<tests>")[0] + part2 = exml.split("</tests>")[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, + "--conda_auto_init", + "--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 set_planemo_galaxy_root(self, galaxyroot='/galaxy-central', config_path=".planemo.yml"): + # bug in planemo - bogus '--dev-wheels' passed to run_tests.sh as at april 2021 - need a fiddled copy so it is ignored until fixed + CONFIG_TEMPLATE = """## Planemo Global Configuration File. +## Everything in this file is completely optional - these values can all be +## configured via command line options for the corresponding commands. + +## Specify a default galaxy_root for test and server commands here. +galaxy_root: %s +## Username used with toolshed(s). +#shed_username: "<TODO>" +sheds: + # For each tool shed you wish to target, uncomment key or both email and + # password. + toolshed: + #key: "<TODO>" + #email: "<TODO>" + #password: "<TODO>" + testtoolshed: + #key: "<TODO>" + #email: "<TODO>" + #password: "<TODO>" + local: + #key: "<TODO>" + #email: "<TODO>" + #password: "<TODO>" +""" + if not os.path.exists(config_path): + with open(config_path, "w") as f: + f.write(CONFIG_TEMPLATE % galaxyroot) + + +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()