# HG changeset patch # User fubar_too # Date 1625118727 0 # Node ID 7596aa302d6081fbecdd2c36cded1aac54a6f537 # Parent 312eb2aaf31386f515fcf8c17b3a2955170d8ae5 Uploaded diff -r 312eb2aaf313 -r 7596aa302d60 toolfactory/LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/LICENSE Thu Jul 01 05:52:07 2021 +0000 @@ -0,0 +1,504 @@ +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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See the GNU + Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public + License along with this library; if not, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 + USA + +Also add information on how to contact you by electronic and paper mail. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the library, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the + library `Frob' (a library for tweaking knobs) written by James Random + Hacker. + + {signature of Ty Coon}, 1 April 1990 + Ty Coon, President of Vice + +That's all there is to it! diff -r 312eb2aaf313 -r 7596aa302d60 toolfactory/README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/README.md Thu Jul 01 05:52:07 2021 +0000 @@ -0,0 +1,378 @@ +## Breaking news! Completely refactored + +### New demonstration of planemo tool_factory command ![Planemo ToolFactory demonstration](images/lintplanemo-2021-01-08_18.02.45.mkv?raw=false "Demonstration inside Planemo") + +# 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 312eb2aaf313 -r 7596aa302d60 toolfactory/ToolFactory.py --- a/toolfactory/ToolFactory.py Mon Jun 21 04:18:59 2021 +0000 +++ b/toolfactory/ToolFactory.py Thu Jul 01 05:52:07 2021 +0000 @@ -851,7 +851,7 @@ a("--bad_user", default=None) a("--help_text", default=None) a("--tool_desc", default=None) - a("--tool_version", default=None) + a("--tool_version", default="0.01") a("--citations", default=None) a("--command_override", default=None) a("--test_override", default=None) diff -r 312eb2aaf313 -r 7596aa302d60 toolfactory/ToolFactory.xml --- a/toolfactory/ToolFactory.xml Mon Jun 21 04:18:59 2021 +0000 +++ b/toolfactory/ToolFactory.xml Thu Jul 01 05:52:07 2021 +0000 @@ -143,12 +143,8 @@ -
- - - - +
+ @@ -363,7 +359,6 @@ -
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"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 312eb2aaf313 -r 7596aa302d60 toolfactory/test-data/output2_sample --- a/toolfactory/test-data/output2_sample Mon Jun 21 04:18:59 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,165 +0,0 @@ -*trats uoy erofeb GNINRAW* - -YLNO yxalaG etavirp a no loot siht llatsnI -ecnatsni noitcudorp ro cilbup a no REVEN esaelP - -troppus noitatic gnidda notlihC nhoJ yb 4102 tsugua detadpU - -keeB ned nav suiraM yb detroper sgub xif ot 4102 8 tsugua detadpU - -ta ecruoser eht etic esaelP -fer=epytyek&JWYdwMrWs1hQzcl=yekji?375stb/tnirper/igc/gro.slanruojdrofxo.scitamrofnioib//:ptth -.krow dehsilbup ruoy ni loot siht esu uoy fi - -**yrotS trohS** - -.sloot yxalaG wen gnitareneg fo elbapac loot yxalaG lausunu na si sihT -gnitpircs suoregnad ylemertxe erofereht dna *detcirtsernu* gnisopxe yb skrow tI -ot meht gniwolla ,revres yxalaG tsoh eht fo srotartsinimda detangised lla ot -,stes atad tupni detceles elpitlum revo lrep dna hs ,nohtyp ,R ni stpircs nur -.tuptuo sa tes atad wen elgnis a gnitirw - -*sretemarap elyts esrapgra ro lanoitisop htiw elbatucexe yna ro tpircs hsab/lrep/nohtyp/r gnikrow a evah uoY* - -.loot yxalaG a gnisu ,setunim ni loot yxalaG yranidro na otni denrut eb nac tI - - -**yxalaG yna otni noitallatsni rof sloot yxalaG wen fo noitareneg detamotuA** - -.ylppus uoy sgnittes retemarap dna stupni atad tset elpmas llams gnisu detareneg si tset A -a dliub ot desu eb nac yeht ,decudorp neeb evah stuptuo esac tset eht ecnO -tnemeriuqer a sa dekab si elbatucexe ro tpircs deilppus ehT .loot yxalaG wen -.xob eht fo tuo elbitapmoc wolfkrow ylluf ,loot yxalaG yranidro ,wen a otni -rotartsinimda na yb dehs loot a aiv dellatsni era sloot detareneG -.sresu ruoy rof sloot yxalaG rehto lla ekil yltcaxe krow dna - -**liateD eroM** - -a otni etsap ot tpircs a deraperp evah dluohs uoy ,yrotcaFlooT eht esu oT -yrotsih ruoy morf tceles ot ydaer elpmaxe tupni tset llams a dna dnim ni egakcap a evah ro ,xob txet -.tpircs wen ruoy tset ot - -em rof skrow ```atad-tset/yrotcafloot/srekam_loot/sloot/yxalag/~ atad_tset-- yxalag/~ toor_yxalag-- lmx.2yrotcaFlooTgr tset omenalp``` - -uoY .mrof yrotcaF looT eht no egaugnal gnitpircs hcae ni elpmaxe na si erehT -thgir eht tceles ot rebmemer - tuo ti yrt ot eseht etsap dna tuc tsuj nac -gnisu tes atad tset llams a etaerc ot deen osla ll'uoY .esaelp reterpretni -.loot atad wen dda yrotsih yxalaG eht - -ni tuptuo loot eht no nottub "oder" eht esu ,wohemos sliaf tpircs eht fI -gub eht xiF .tpircs nekorb htiw etelpmoc mrof eht etaercer ot yrotsih ruoy -.taeper ,hsaw ,esniR .niaga etucexe dna - -tpircs ruoy snur taht loot yxalaG wen a ,yllufssecus snur tpircs eht ecnO -dna txet pleh emos ylppus dna noitpo "etareneg" eht tceleS .detareneg eb nac -epytatad yxalaG wen a fo mrof eht ni detareneg eb lliw loot wen ehT .seman -a ot daolpu ot ydaer evihcra na s'ti ,stseggus eman eht sa - *zg.dehsloot* -.yrotisoper loot wen a sa dehSlooT yxalaG - -revres yxalaG lacol yna otni dellatsni eb nac ti ,dehSlooT a ni s'ti ecnO -.ecafretni evitartsinimda revres eht morf - -tpircs eht ,emit hcae - ti nur nac sresu lacol ,dellatsni si loot wen eht ecnO -nesohc tupni eht htiw detucexe eb lliw tliub saw ti nehw deilppus saw taht -eht htiw etareneg uoy sloot eht ,sdrow rehto nI .yrotsih s'resu eht morf -.emit yreve tpircs ruoy nur tub,loot yxalaG rehto yna ekil tsuj nur yrotcaFlooT - -,tuptuo eno ,tupni enO .stnenopmoc wolfkrow rof tcefrep era sloot yrotcaf looT -.selbairav on - -,loot siht fo *rewop emosewa eht tiolpxe ylefas dna ylluf oT* -siht gnillatsni repoleved a eb dluohs uoy ,dehSlooT eht dna yxalaG -na era uoy erehw ecnatsni lacol hctarcs/lanosrep/etavirp a no loot -ees seceip eht lla peek ot teg uoy ,ti kaerb uoy fi ,nehT .resu_nimda -emoH/ikiw/yrotcaflootyxalag/rabuf/gro.tekcubtib//:sptth - -**noitallatsnI** -eht gnisu yltneinevnoc tsom ti llatsni nac uoY .loot yxalaG a si sihT -niaM yxalaG eht dniF .knil "sdehs loot esworb dna hcraeS" evitartsinimda -yrotcafloot eht rof hcraes dna /ude.usp.xb.2g.dehsloot//:sptth ta dehsloot -.ti llatsni ot noitpo eht tceles dna edoc eht weiver dna ti nepO .yrotisoper - -eb ot deen ereh selif yp dna lmx eht ,yaw taht loot eht teg t'nac uoy fI -sloot wen a otni deipoc -yrtne wen a sdeen lmx.fnoc_loot ruoY yrotcafloot/sloot sa hcus yrotceridbus -lmx eht ot gnitniop -::ekil gnihtemos - elif - ->"sredliubloot"=di "sloot gnidliub looT"=eman noitces< ->/"lmx.yrotcaFlooTgr/yrotcafloot"=elif loot< ->noitces/< - -,ereht ydaerla ton fI -:dda esaelp -"yraniB:yranib.sepytatad.yxalag"=epyt "zg.dehsloot"=noisnetxe epytatad< ->/ "eurT"=ssalcbus "pizg-x/trapitlum"=epytemim -.lmx.fnoc_sepyt_atad lacol ruoy ot - - -**noitucexe detcirtseR** - -- sresu nimda yb YLNO elbasu eb neht lliw flesti loot yrotcaf loot ehT -YLNO .thgir s'taht ,seY** ini.igsw_esrevinu ni sresu_nimda ni sDI htiw elpoep -ot dewolla fI .tnemom a rof ti tuoba knihT **loot siht nur nac sresu_nimda -dluow taht gniht ylno eht ,revres yxalaG ruoy no tpircs yrartibra yna nur -ylbaborp dluow atad yxalaG ruoy lla gniyortsed no tneb tnaercsim a edepmi -.slliks lacinhcet etairporppa fo kcal eb - -**seod ti tahW** - -dna R ,nohtyp ni stpircs elpmis rof yrotcaf loot a si sihT -.taht si looc woH .detareneg yllacitamotua era stset lanoitcnuF .yltnerruc lrep - -nac yllanoitpO .yrotsih eht morf tupni eno daer taht stpircs elpmis ot DETIMIL -stuptuo fo rebmun yna tcelloc yllanoitpo dna ,tesatad yrotsih wen eno etirw -- etagivan ot resu eht rof egap xedni LMTH detarenegotua na no sknil otni -nwohs era stuptuo fdp - selif tuptuo dna segami setirw tpircs eht fi lufesu -dna taht os tpircstsohg htiw knurhs era s'fdp detaolb s'R dna slianbmuht sa -.elbaliava eb ot deen kigamegami - -trats os ,loot yxalaG yna ekil decnahne dna detide eb nac sloot detareneG -a ot pu gel suoires a uoy steg tpircs detareneg a ecnis pu dliub dna llams -.eno xelpmoc erom - -**od uoy tahW** - -dna srorre xatnys eht xif uoy ,tpircs ruoy nur dna etsap uoY -erofeb tpircs eht tide dna nottub oder eht esu nac uoY .snur ti yllautneve -.llew ytterp skrow ti - gubed uoy sa ti nurer ot gniyrt - -elbitapmoc dehsloot a etareneg nac uoy ,atad tset emos no skrow tpircs eht ecnO -ni loot yxalaG yranidro na sa nur ot ydaer tpircs ruoy gniniatnoc elif pizg -detamotua ylegral dna efas snaem tahT .dehsloot lacol ruoy no yrotisoper a -.dehsloot ruoy esu ot derugifnoc yxalaG noitcudorp yna ni noitallatsni - -**ytiruceS loot detareneG** - -tsuj s'ti ,loot detareneg a llatsni uoy ecnO -rieht dna yllamron nur tsuj yehT .efas si tpircs eht gnimussa - loot rehtona -.dehsloot efas ecitcarp ,esaelp tub erucesni yllausunu gnihtyna od tonnac resu -.yracs yllaer si ti - eno siht yllaicepsE .loot yna llatsni uoy erofeb edoc eht daeR - -**edoC dneS** - -?esaelp seussi tekcubtib sa emoclew snoitseggus dna sehctaP - -**noitubirttA** - -yrotcaF looT yxalaG ehT :stpircs morf sloot elbasu-er gnitaerC -maeT yxalaG ehT ;nnameiZ kraM ;ipsaK ynotnA ;surazaL ssoR -375stb/scitamrofnioib/3901.01 :iod ;2102 scitamrofnioiB - -fer=epytyek&JWYdwMrWs1hQzcl=yekji?375stb/tnirper/igc/gro.slanruojdrofxo.scitamrofnioib//:ptth - -**gnisneciL** - -0102 surazaL ssoR thgirypoC -moc doirep liam g ta surazal ssor - -.devreser sthgir llA - -LPGL eht rednu desneciL - -**tohsneercs yrotagilbO** - -gnp.looTtpircScimanyd/segami/989ef2308adf/crs/rekamlootyxalag/rabuf/gro.tekcubtib//:ptth diff -r 312eb2aaf313 -r 7596aa302d60 toolfactory/test-data/pyrevpos.python --- a/toolfactory/test-data/pyrevpos.python Mon Jun 21 04:18:59 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -# reverse order of text by row -import sys -inp = sys.argv[1] -outp = sys.argv[2] -i = open(inp,'r').readlines() -o = open(outp,'w') -for row in i: - rs = row.rstrip() - rs = list(rs) - rs.reverse() - o.write(''.join(rs)) -o.close() - diff -r 312eb2aaf313 -r 7596aa302d60 toolfactory/test-data/pyrevpos_not_tested.toolshed_sample Binary file toolfactory/test-data/pyrevpos_not_tested.toolshed_sample has changed diff -r 312eb2aaf313 -r 7596aa302d60 toolfactory/test-data/test1_log.txt --- a/toolfactory/test-data/test1_log.txt Mon Jun 21 04:18:59 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -## Executing Toolfactory generated command line = python /tmp/pyrevposq5dmcdy1.python /tmp/tmpqrksf8sd/files/5/b/9/dataset_5b952a86-87df-44ad-a415-ea549f3f0cee.dat output2 diff -r 312eb2aaf313 -r 7596aa302d60 toolfactory/test-data/toolfactory_pyrevpos_tgz_sample Binary file toolfactory/test-data/toolfactory_pyrevpos_tgz_sample has changed