# HG changeset patch # User fubar # Date 1422491312 18000 # Node ID dd6cf2ddaac7acb05200d91700316e21daa786d3 # Parent 3635f4518c4d546e72179f7e454224906277be80 Uploaded diff -r 3635f4518c4d -r dd6cf2ddaac7 README.md --- a/README.md Tue Jan 20 19:03:18 2015 -0500 +++ b/README.md Wed Jan 28 19:28:32 2015 -0500 @@ -2,14 +2,15 @@ ============= This is an upgrade to the tool factory but with added parameters -(optionally editable in the generated tool form - otherwise fixed) and multiple input files. +(optionally editable in the generated tool form - otherwise fixed) and +multiple input files. Any number of parameters up to the limit of your patience with repeat groups -These are optionally editable by the user - names cannot be changed - no overwriting $JAVA_HOME_DIR -or else permanently fixed and not editable at run time. +These are optionally editable by the user - names cannot be changed so +no overwriting $JAVA_HOME_DIR or else permanently fixed and not editable at run time. Any number of input files can be passed to your script, but of course it -has to deal with them. Both path and metadata name are supplied either in the environment (bash/sh) or -as command line parameters (python,perl,rscript) that need to be parsed and +has to deal with them. Both path and metadata name are supplied either in the environment +(bash/sh) or as command line parameters (python,perl,rscript) that need to be parsed and dealt with in the script. diff -r 3635f4518c4d -r dd6cf2ddaac7 README.txt --- a/README.txt Tue Jan 20 19:03:18 2015 -0500 +++ b/README.txt Wed Jan 28 19:28:32 2015 -0500 @@ -1,177 +1,226 @@ -# WARNING before you start +# WARNING before you start # Install this tool on a private Galaxy ONLY # Please NEVER on a public or production instance # updated august 2014 by John Chilton adding citation support # # updated august 8 2014 to fix bugs reported by Marius van den Beek -# please cite the resource at http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref +# please cite the resource at +http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref # if you use this tool in your published work. *Short Story* This is an unusual Galaxy tool capable of generating new Galaxy tools. -It works by exposing *unrestricted* and therefore extremely dangerous -scripting to all designated administrators of the host Galaxy server, allowing them to run scripts -in R, python, sh and perl over multiple selected input data sets, writing a single new data set as output. +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. + +*Differences between TF2 and the original Tool Factory* + +1. TF2 (this one) allows any number of either fixed or user-editable parameters to be defined +for the new tool. If these are editable, the user can change them but otherwise, they are passed +as fixed and invisible parameters for each execution. Obviously, there are substantial security +implications with editable parameters, but these are always sanitized by Galaxy's inbuilt +parameter sanitization so you may need to "unsanitize" characters - eg translate all "__lt__" +into "<" for certain parameters where that is needed. Please practise safe toolshed. + +2. Any number of (the same datatype) of input files may be defined. + +These changes substantially complicate the way your supplied script is supplied with +all the new and variable parameters. Examples in each scripting language are shown +in the tool help *Automated outputs in named sections* -If your script writes to the current directory path, arbitrary mix of (eg) pdfs, tabular analysis results and run logs, -the tool factory can optionally auto-generate a linked Html page with separate sections showing a thumbnail grid -for all pdfs and the log text, grouping all artifacts sharing a file name and log name prefix:: +If your script writes to the current directory path, arbitrary mix of (eg) +pdfs, tabular analysis results and run logs,the tool factory can optionally +auto-generate a linked Html page with separate sections showing a thumbnail +grid for all pdfs and the log text, grouping all artifacts sharing a file +name and log name prefix:: - eg: if "foo.log" is emitted then *all* other outputs matching foo_* will all be grouped together - eg + eg: if "foo.log" is emitted then *all* other outputs matching foo_* will + all be grouped together - eg foo_baz.pdf foo_bar.pdf and foo_zot.xls - would all be displayed and linked in the same section with foo.log's contents - to form the "Foo" section of the Html page. - Sections appear in alphabetic order and there are no limits on the number of files or sections. + would all be displayed and linked in the same section with foo.log's contents + - to form the "Foo" section of the Html page. Sections appear in alphabetic + order and there are no limits on the number of files or sections. -*Automated generation of new Galaxy tool shed tools for installation into any Galaxy* +*Automated generation of new Galaxy tools for installation into any Galaxy* -Once a script is working correctly, this tool optionally generates a new Galaxy tool, effectively -freezing the supplied script into a new, ordinary Galaxy tool that runs it over one or more input files -selected by the user. Generated tools are installed via a tool shed by an administrator and work exactly like all other Galaxy tools for your users. +Once a script is working correctly, this tool optionally generates a +new Galaxy tool, effectively freezing the supplied script into a new, +ordinary Galaxy tool that runs it over one or more input files selected by +the user. Generated tools are installed via a tool shed by an administrator +and work exactly like all other Galaxy tools for your users. -If you use the Html output option, please ensure that sanitize_all_html is set to False and -uncommented in universe_wsgi.ini - it should show:: +If you use the Html output option, please ensure that sanitize_all_html is +set to False and uncommented in universe_wsgi.ini - it should show:: # By default, all tool output served as 'text/html' will be sanitized sanitize_all_html = False -This opens potential security risks and may not be acceptable for public sites where the lack of stylesheets -may make Html pages damage onlookers' eyeballs but should still be correct. +This opens potential security risks and may not be acceptable for public +sites where the lack of stylesheets may make Html pages damage onlookers' +eyeballs but should still be correct. *More Detail* -To use the ToolFactory, you should have prepared a script to paste into a text box, -and a small test input example ready to select from your history to test your new script. -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. +To use the ToolFactory, you should have prepared a script to paste into a +text box, and a small test input example ready to select from your history +to test your new script. -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. +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. -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. +If the script fails somehow, use the "redo" button on the tool output in +your history to recreate the form complete with broken script. Fix the bug +and execute again. Rinse, wash, repeat. -Once it's in a ToolShed, it can be installed into any local Galaxy server from -the server administrative interface. +Once the script runs sucessfully, a new Galaxy tool that runs your script +can be generated. Select the "generate" option and supply some help text and +names. The new tool will be generated in the form of a new Galaxy datatype +- toolshed.gz - as the name suggests, it's an archive ready to upload to a +Galaxy ToolShed as a new tool repository. + +Once it's in a ToolShed, it can be installed into any local Galaxy server +from the server administrative interface. -Once the new tool is installed, local users can run it - each time, the script that was supplied -when it was built will be executed with the input chosen from the user's history. In other words, -the tools you generate with the ToolFactory run just like any other Galaxy tool, -but run your script every time. +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. +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 +*To fully and safely exploit the awesome power* of this tool, +Galaxy and the ToolShed, you should be a developer installing this +tool on a private/personal/scratch local instance where you are an +admin_user. Then, if you break it, you get to keep all the pieces see +https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home ** Installation ** -This is a Galaxy tool. You can install it most conveniently using the administrative "Search and browse tool sheds" link. -Find the Galaxy Main toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory repository. -Open it and review the code and select the option to install it. +This is a Galaxy tool. You can install it most conveniently using the +administrative "Search and browse tool sheds" link. Find the Galaxy Main +toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory +repository. Open it and review the code and select the option to install it. ( -If you can't get the tool that way, the xml and py files here need to be copied into a new tools -subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry pointing to the xml +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::
-If not already there (I just added it to datatypes_conf.xml.sample), please add: - +If not already there (I just added it to datatypes_conf.xml.sample), +please add: + to your local data_types_conf.xml. ) -Of course, R, python, perl etc are needed on your path if you want to test scripts using those interpreters. -Adding new ones to this tool code should be easy enough. Please make suggestions as bitbucket issues and code. -The HTML file code automatically shrinks R's bloated pdfs, and depends on ghostscript. The thumbnails require imagemagick . +Of course, R, python, perl etc are needed on your path if you want to test +scripts using those interpreters. Adding new ones to this tool code should +be easy enough. Please make suggestions as bitbucket issues and code. The +HTML file code automatically shrinks R's bloated pdfs, and depends on +ghostscript. The thumbnails require imagemagick . * 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. +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. +*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 avaailable. +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. +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 +*What you do* You paste and run your script, you fix the syntax errors and +eventually it runs. You can use the redo button and edit the script before trying to rerun it as you debug - it works pretty well. -Once the script works on some test data, you can -generate a toolshed compatible gzip file -containing your script ready to run as an ordinary Galaxy tool in a -repository on your local toolshed. That means safe and largely automated installation in any -production Galaxy configured to use your toolshed. +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 fucking code before you install any tool. -Especially this one - it is really scary. +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 fucking code before you install any tool. Especially this one - +it is really scary. If you opt for an HTML output, you get all the script outputs arranged -as a single Html history item - all output files are linked, thumbnails for all the pdfs. -Ugly but really inexpensive. +as a single Html history item - all output files are linked, thumbnails for +all the pdfs. Ugly but really inexpensive. -Patches and suggestions welcome as bitbucket issues please? +Patches and suggestions welcome as bitbucket issues please? copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012 all rights reserved -Licensed under the LGPL if you want to improve it, feel free https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home +Licensed under the LGPL if you want to improve it, feel free +https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home -Material for our more enthusiastic and voracious readers continues below - we salute you. +Material for our more enthusiastic and voracious readers continues below - +we salute you. -**Motivation** Simple transformation, filtering or reporting scripts get written, run and lost every day in most busy labs -- even ours where Galaxy is in use. This 'dark script matter' is pervasive and generally not reproducible. +**Motivation** Simple transformation, filtering or reporting scripts get +written, run and lost every day in most busy labs - even ours where Galaxy is +in use. This 'dark script matter' is pervasive and generally not reproducible. -**Benefits** For our group, this allows Galaxy to fill that important dark script gap - all those "small" bioinformatics -tasks. Once a user has a working R (or python or perl) script that does something Galaxy cannot currently do (eg transpose a -tabular file) and takes parameters the way Galaxy supplies them (see example below), they: +**Benefits** For our group, this allows Galaxy to fill that important dark +script gap - all those "small" bioinformatics tasks. Once a user has a working +R (or python or perl) script that does something Galaxy cannot currently do +(eg transpose a tabular file) and takes parameters the way Galaxy supplies +them (see example below), they: 1. Install the tool factory on a personal private instance 2. Upload a small test data set -3. Paste the script into the 'script' text box and iteratively run the insecure tool on test data until it works right - -there is absolutely no reason to do this anywhere other than on a personal private instance. +3. Paste the script into the 'script' text box and iteratively run the +insecure tool on test data until it works right - there is absolutely no +reason to do this anywhere other than on a personal private instance. -4. Once it works right, set the 'Generate toolshed gzip' option and run it again. +4. Once it works right, set the 'Generate toolshed gzip' option and run +it again. -5. A toolshed style gzip appears ready to upload and install like any other Toolshed entry. +5. A toolshed style gzip appears ready to upload and install like any other +Toolshed entry. 6. Upload the new tool to the toolshed -7. Ask the local admin to check the new tool to confirm it's not evil and install it in the local production galaxy +7. Ask the local admin to check the new tool to confirm it's not evil and +install it in the local production galaxy **Simple examples on the tool form** -A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file, -does something (transpose in this case) and writes the results to a new tabular file:: +A simple Rscript "filter" showing how the command line parameters can be +handled, takes an input file, does something (transpose in this case) and +writes the results to a new tabular file:: # transpose a tabular input file and write as a tabular output file ourargs = commandArgs(TRUE) @@ -181,11 +230,13 @@ outp = t(inp) write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F) -Calculate a multiple test adjusted p value from a column of p values - for this script to be useful, -it needs the right column for the input to be specified in the code for the -given input file type(s) specified when the tool is generated :: +Calculate a multiple test adjusted p value from a column of p values - +for this script to be useful, it needs the right column for the input to be +specified in the code for the given input file type(s) specified when the +tool is generated :: - # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use + # use p.adjust - assumes a HEADER row and column 1 - please fix for any + real use column = 1 # adjust if necessary for some other kind of input fdrmeth = 'BH' ourargs = commandArgs(TRUE) @@ -198,23 +249,28 @@ q = data.frame(q) names(q) = newval outp = cbind(inp,newval=q) - write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T) + write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T) -Another Rscript example without any input file - generates a random heatmap pdf - you must make sure the option to create an HTML output file is -turned on for this to work. The heatmap will be presented as a thumbnail linked to the pdf in the resulting HTML page:: +Another Rscript example without any input file - generates a random heatmap +pdf - you must make sure the option to create an HTML output file is +turned on for this to work. The heatmap will be presented as a thumbnail +linked to the pdf in the resulting HTML page:: # note this script takes NO input or output because it generates random data - foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100)) + 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( "heattest.pdf" ) heatmap(bar,main='Random Heatmap') dev.off() -A Python example that reverses each row of a tabular file. You'll need to remove the leading spaces for this to work if cut -and pasted into the script box. Note that you can already do this in Galaxy by setting up the cut columns tool with the -correct number of columns in reverse order,but this script will work for any number of columns so is completely generic:: +A Python example that reverses each row of a tabular file. You'll need +to remove the leading spaces for this to work if cut and pasted into the +script box. Note that you can already do this in Galaxy by setting up the +cut columns tool with the correct number of columns in reverse order,but +this script will work for any number of columns so is completely generic:: # reverse order of columns in a tabular file import sys @@ -232,22 +288,39 @@ Galaxy as an IDE for developing API scripts -If you need to develop Galaxy API scripts and you like to live dangerously, please read on. +If you need to develop Galaxy API scripts and you like to live dangerously, +please read on. Galaxy as an IDE? -Amazingly enough, blend-lib API scripts run perfectly well *inside* Galaxy when pasted into a Tool Factory form. No need to generate a new tool. Galaxy+Tool_Factory = IDE I think we need a new t-shirt. Seriously, it is actually quite useable. +Amazingly enough, blend-lib API scripts run perfectly well *inside* +Galaxy when pasted into a Tool Factory form. No need to generate a new +tool. Galaxy+Tool_Factory = IDE I think we need a new t-shirt. Seriously, +it is actually quite useable. Why bother - what's wrong with Eclipse -Nothing. But, compared with developing API scripts in the usual way outside Galaxy, you get persistence and other framework benefits plus at absolutely no extra charge, a ginormous security problem if you share the history or any outputs because they contain the api script with key so development servers only please! +Nothing. But, compared with developing API scripts in the usual way outside +Galaxy, you get persistence and other framework benefits plus at absolutely +no extra charge, a ginormous security problem if you share the history or +any outputs because they contain the api script with key so development +servers only please! Workflow Fire up the Tool Factory in Galaxy. -Leave the input box empty, set the interpreter to python, paste and run an api script - eg working example (substitute the url and key) below. +Leave the input box empty, set the interpreter to python, paste and run an +api script - eg working example (substitute the url and key) below. -It took me a few iterations to develop the example below because I know almost nothing about the API. I started with very simple code from one of the samples and after each run, the (edited..) api script is conveniently recreated using the redo button on the history output item. So each successive version of the developing api script you run is persisted - ready to be edited and rerun easily. It is ''very'' handy to be able to add a line of code to the script and run it, then view the output to (eg) inspect dicts returned by API calls to help move progressively deeper iteratively. +It took me a few iterations to develop the example below because I know +almost nothing about the API. I started with very simple code from one of the +samples and after each run, the (edited..) api script is conveniently recreated +using the redo button on the history output item. So each successive version +of the developing api script you run is persisted - ready to be edited and +rerun easily. It is ''very'' handy to be able to add a line of code to the +script and run it, then view the output to (eg) inspect dicts returned by +API calls to help move progressively deeper iteratively. -Give the below a whirl on a private clone (install the tool factory from the main toolshed) and try adding complexity with few rerun/edit/rerun cycles. +Give the below a whirl on a private clone (install the tool factory from +the main toolshed) and try adding complexity with few rerun/edit/rerun cycles. Eg tool factory api script import sys @@ -258,16 +331,17 @@ libs = gi.libraries.get_libraries() res = [] # libs looks like -# u'url': u'/galaxy/api/libraries/441d8112651dc2f3', u'id': u'441d8112651dc2f3', u'name':.... u'Demonstration sample RNA data', -for lib in libs: +# u'url': u'/galaxy/api/libraries/441d8112651dc2f3', u'id': +u'441d8112651dc2f3', u'name':.... u'Demonstration sample RNA data', +for lib in libs: res.append('%s:\n' % lib['name']) res.append(str(gi.libraries.show_library(lib['id'],contents=True))) outf=open(sys.argv[2],'w') outf.write('\n'.join(res)) outf.close() -**Attribution** -Creating re-usable tools from scripts: The Galaxy Tool Factory +**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 diff -r 3635f4518c4d -r dd6cf2ddaac7 getlocalrpackages.py --- a/getlocalrpackages.py Tue Jan 20 19:03:18 2015 -0500 +++ b/getlocalrpackages.py Wed Jan 28 19:28:32 2015 -0500 @@ -20,9 +20,13 @@ fver = [x.split(os.path.sep)[-4:-1] for x in fpaths] # >>> foo.split(os.path.sep)[-4:-1] # ['fubar', 'package_r_3_1_1', '63cdb9b2234c'] - res = [['%s rev %s owner %s' % (x[1],x[2],x[0]),fpaths[i],False] for i,x in enumerate(fver)] - res.insert(0,['Use default (system) interpreter','system',False]) - if len(res) > 1: + if len(fpaths) > 0: + res = [['%s rev %s owner %s' % (x[1],x[2],x[0]),fpaths[i],False] for i,x in enumerate(fver)] + res.insert(0,['Use default (system) interpreter','system',False]) + else: + res = [['Use default (system) interpreter','system',False], + ['**WARNING** NO package env.sh files found - is the "locate" system command working? Are any interpreters installed?','system',True]] + if len(res) > 2: res[1][2] = True # selected if more than one # return a triplet - user_sees,value,selected - all unselected if False return res diff -r 3635f4518c4d -r dd6cf2ddaac7 rgToolFactory2.py --- a/rgToolFactory2.py Tue Jan 20 19:03:18 2015 -0500 +++ b/rgToolFactory2.py Wed Jan 28 19:28:32 2015 -0500 @@ -8,6 +8,8 @@ # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home # # January 2015 +# unified all setups by passing the script on the cl rather than via a PIPE - no need for treat_bash_special so removed +# # in the process of building a complex tool # added ability to choose one of the current toolshed package_r or package_perl or package_python dependencies and source that package # add that package to tool_dependencies @@ -120,6 +122,16 @@ """ return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) +def quote_non_numeric(s): + """return a prequoted string for non-numerics + useful for perl and Rscript parameter passing? + """ + try: + res = float(s) + return s + except ValueError: + return '"%s"' % s + html_escape_table = { "&": "&", ">": ">", @@ -154,12 +166,9 @@ return citation_tuples def shell_source(script): - """need a way to source a Galaxy tool interpreter env.sh so we can use that dependency - package - see http://pythonwise.blogspot.fr/2010/04/sourcing-shell-script.html - Sometime you want to emulate the action of "source" in bash, - settings some environment variables. Here is a way to do it. - Note that we have to finesse the automagic exports using nulls as newlines for env""" + """need a way to source a Galaxy tool interpreter env.sh to point at the right dependency package + This based on the idea in http://pythonwise.blogspot.fr/2010/04/sourcing-shell-script.html + Note that we have to finesse any wierdly quoted newlines in automagic exports using nulls (env -0) as newlines""" pipe = subprocess.Popen("env -i ; . %s ; env -0" % script, stdout=subprocess.PIPE, shell=True) output = pipe.communicate()[0] outl = output.split('\0') @@ -176,7 +185,7 @@ """ - def __init__(self,opts=None,treatbashSpecial=True): + def __init__(self,opts=None): """ cleanup inputs, setup some outputs @@ -313,7 +322,6 @@ self.useIM = cmd_exists('convert') self.useGS = cmd_exists('gs') self.temp_warned = False # we want only one warning if $TMP not set - self.treatbashSpecial = treatbashSpecial if opts.output_dir: # simplify for the tool tarball os.chdir(opts.output_dir) self.thumbformat = 'png' @@ -380,7 +388,7 @@ value = html_unescape(psplit[1]) a('%s="%s"' % (param,value)) if (self.opts.interpreter == 'Rscript'): - # pass params on command line + # pass params on command line as expressions which the script evaluates - see sample if self.opts.input_tab: a('INPATHS="%s"' % self.infile_paths) a('INNAMES="%s"' % self.infile_names) @@ -391,23 +399,21 @@ psplit = p.split(',') param = html_unescape(psplit[0]) value = html_unescape(psplit[1]) - a('%s="%s"' % (param,value)) + a('%s=%s' % (param,quote_non_numeric(value))) if (self.opts.interpreter == 'perl'): - # pass params on command line + # pass positional params on command line - perl script needs to discombobulate the path/name lists if self.opts.input_tab: a('%s' % self.infile_paths) a('%s' % self.infile_names) if self.opts.output_tab: a('%s' % self.opts.output_tab) for p in opts.additional_parameters: + # followed by any additional name=value parameter pairs p = p.replace('"','') psplit = p.split(',') param = html_unescape(psplit[0]) value = html_unescape(psplit[1]) - if (value.find(' ') <> -1): - a('%s="%s"' % (param,value)) - else: - a('%s=%s' % (param,value)) + a('%s=%s' % (param,quote_non_numeric(value))) if self.opts.interpreter == 'sh' or self.opts.interpreter == 'bash': # more is better - now move all params into environment AND drop on to command line. self.cl.insert(0,'env') @@ -423,19 +429,16 @@ psplit = p.split(',') param = html_unescape(psplit[0]) value = html_unescape(psplit[1]) - if (value.find(' ') <> -1): - a('%s="%s"' % (param,value)) - self.cl.insert(4+i,'%s="%s"' % (param,value)) - else: - a('%s=%s' % (param,value)) - self.cl.insert(4+i,'%s=%s' % (param,value)) - self.interp_owner = None - self.interp_pack = None - self.interp_revision = None - self.interp_version = None + a('%s=%s' % (param,quote_non_numeric(value))) + self.cl.insert(4+i,'%s=%s' % (param,quote_non_numeric(value))) + self.interpreter_owner = 'SYSTEM' + self.interpreter_pack = 'SYSTEM' + self.interpreter_name = 'SYSTEM' + self.interpreter_version = 'SYSTEM' + self.interpreter_revision = 'SYSTEM' if opts.envshpath <> 'system': # need to parse out details for our tool_dependency try: # fragile - depends on common naming convention as at jan 2015 = package_[interp]_v0_v1_v2... = version v0.v1.v2.. is in play - + # this ONLY happens at tool generation by an admin - the generated tool always uses the default of system so path is from local env.sh packdetails = opts.envshpath.split(os.path.sep)[-4:-1] # eg ['fubar', 'package_r_3_1_1', '63cdb9b2234c'] self.interpreter_owner = packdetails[0] self.interpreter_pack = packdetails[1] @@ -631,7 +634,7 @@ else: tooldepcontent = self.toolhtmldepinterpskel % readme_dict else: - tooldepcontent = self.emptytoolhtmldepskel % readme_dictls -l + tooldepcontent = self.emptytoolhtmldepskel % readme_dict depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w') depf.write(tooldepcontent) depf.write('\n') @@ -860,50 +863,44 @@ def run(self): """ - scripts must be small enough not to fill the pipe! + Some devteam tools have this defensive stderr read so I'm keeping with the faith + Feel free to update. """ if self.opts.envshpath <> 'system': shell_source(self.opts.envshpath) - if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']: - retval = self.runBash() - else: - if self.opts.output_dir: - ste = open(self.elog,'w') - sto = open(self.tlog,'w') - sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl)) - sto.flush() - p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,cwd=self.opts.output_dir) - else: - p = subprocess.Popen(self.cl,shell=False) + # this only happens at tool generation - the generated tool relies on the dependencies all being set up + # at toolshed installation by sourcing local env.sh + if self.opts.output_dir: + ste = open(self.elog,'wb') + sto = open(self.tlog,'wb') + s = ' '.join(self.cl) + sto.write('## Executing Toolfactory generated command line = %s\n' % s) + sto.flush() + p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,cwd=self.opts.output_dir) retval = p.wait() - if self.opts.output_dir: - sto.close() - ste.close() - err = open(self.elog,'r').readlines() - if retval <> 0 and err: # problem - print >> sys.stderr,err - if self.opts.make_HTML: - self.makeHtml() - return retval - - def runBash(self): - """ - cannot use - for bash so use self.sfile - """ + sto.close() + ste.close() + tmp_stderr = open( self.elog, 'rb' ) + err = '' + buffsize = 1048576 + try: + while True: + err += tmp_stderr.read( buffsize ) + if not err or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + else: + p = subprocess.Popen(self.cl,shell=False) + retval = p.wait() if self.opts.output_dir: - s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl) - sto = open(self.tlog,'w') - sto.write(s) - sto.flush() - p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir) - else: - p = subprocess.Popen(self.cl,shell=False) - retval = p.wait() - if self.opts.output_dir: - sto.close() + if retval <> 0 and err: # problem + print >> sys.stderr,err if self.opts.make_HTML: self.makeHtml() return retval + def main(): diff -r 3635f4518c4d -r dd6cf2ddaac7 rgToolFactory2.xml --- a/rgToolFactory2.xml Tue Jan 20 19:03:18 2015 -0500 +++ b/rgToolFactory2.xml Wed Jan 28 19:28:32 2015 -0500 @@ -1,4 +1,4 @@ - + Scripts into tools ghostscript diff -r 3635f4518c4d -r dd6cf2ddaac7 test-data/tf2_test.html --- a/test-data/tf2_test.html Tue Jan 20 19:03:18 2015 -0500 +++ b/test-data/tf2_test.html Wed Jan 28 19:28:32 2015 -0500 @@ -8,18 +8,18 @@
-
Galaxy Tool "tf2_test" run at 15/01/2015 11:06:33

+
Galaxy Tool "tf2_test" run at 29/01/2015 11:24:54

tf2 log output
tf2_test_error.log is empty
Other log output
-/tmp/tmp5bLHi4/job_working_directory/000/2/dataset_3_files/tf2_test_runner.log is empty
+/tmp/tmpdRM3H0/job_working_directory/000/2/dataset_3_files/tf2_test_runner.log is empty
All output files available for downloading
- +
Output File Name (click to view)Size
tf2_test.python0 B
tf2_test_error.log0 B
tf2_test_runner.log216 B
tf2_test_runner.log226 B

diff -r 3635f4518c4d -r dd6cf2ddaac7 test-data/tf2_test.toolshed.gz Binary file test-data/tf2_test.toolshed.gz has changed diff -r 3635f4518c4d -r dd6cf2ddaac7 tool_test_output.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_test_output.html Wed Jan 28 19:28:32 2015 -0500 @@ -0,0 +1,356 @@ + + + + + + + Tool Test Results (powered by Planemo) + + + + + + + + + + + + + + +
+
+
+ + +
+
+ +

Overview

+
+
+
+

Tests

+

The remainder of this contains a description for each test executed to run these jobs.

+
+
+
+ + + + + + +