| Previous changeset 111:223b78754735 (2020-11-29) Next changeset 113:6873c211b250 (2020-12-01) |
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modified:
toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml |
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| diff -r 223b78754735 -r 5509dc4c1cf2 toolfactory/rgToolFactory2.py --- a/toolfactory/rgToolFactory2.py Sun Nov 29 07:51:53 2020 +0000 +++ b/toolfactory/rgToolFactory2.py Sun Nov 29 10:34:48 2020 +0000 |
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| b'@@ -14,16 +14,11 @@\n # 2. Fix planemo so the toolfactory function works\n # 3. Rewrite bits using galaxyxml functions where that makes sense - done\n #\n-# removed all the old complications including making the new tool use this same script\n-# galaxyxml now generates the tool xml https://github.com/hexylena/galaxyxml\n-# No support for automatic HTML file creation from arbitrary outputs\n-# essential problem is to create two command lines - one for the tool xml and a different\n-# one to run the executable with the supplied test data and settings\n-# Be simpler to write the tool, then run it with planemo and soak up the test outputs.\n-# well well. sh run_tests.sh --id rgtf2 --report_file tool_tests_tool_conf.html functional.test_toolbox\n-# does the needful. Use GALAXY_TEST_SAVE /foo to save outputs - only the tar.gz - not the rest sadly\n-# GALAXY_TEST_NO_CLEANUP GALAXY_TEST_TMP_DIR=wherever\n-# planemo test --engine docker_galaxy --test_data ./test-data/ --docker_extra_volume ./test-data rgToolFactory2.xml\n+# uses planemo in a biodocker sort of image as a requirement\n+# otherwise planemo seems to leak dependencies back into the\n+# calling venv. Hilarity ensues.\n+\n+\n \n import argparse\n import copy\n@@ -58,10 +53,6 @@\n debug = True\n toolFactoryURL = "https://github.com/fubar2/toolfactory"\n ourdelim = "~~~"\n-ALOT = 10000000 # srsly. command or test overrides use read() so just in case\n-STDIOXML = """<stdio>\n-<exit_code range="100:" level="debug" description="shite happens" />\n-</stdio>"""\n \n # --input_files="$intab.input_files~~~$intab.input_CL~~~$intab.input_formats\\\n #~~~$intab.input_label~~~$intab.input_help"\n@@ -263,12 +254,12 @@\n clsuffix.append(appendme)\n xclsuffix.append(xappendme)\n for i, p in enumerate(self.outfiles):\n- if p[OCLPOS] == "STDOUT":\n+ if p[OOCLPOS] == "STDOUT":\n self.lastclredirect = [">", p[ONAMEPOS]]\n self.lastxclredirect = [">", "$%s" % p[OCLPOS]]\n- else:\n- clsuffix.append([p[OOCLPOS], p[OCLPOS], p[ONAMEPOS], ""])\n- xclsuffix.append([p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS], ""])\n+ else: # for (o_v, k, v, koverride) in self.xclsuffix:\n+ clsuffix.append([p[ONAMEPOS], p[ONAMEPOS], p[ONAMEPOS], ""])\n+ xclsuffix.append([p[ONAMEPOS], p[ONAMEPOS], "$%s" % p[ONAMEPOS], ""])\n for p in self.addpar:\n clsuffix.append([p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]])\n xclsuffix.append(\n@@ -296,7 +287,7 @@\n tscript.write(self.script)\n tscript.close()\n self.escapedScript = [cheetah_escape(x) for x in rx]\n- self.spacedScript = [f" {x}" for x in rx]\n+ self.spacedScript = [f" {x}" for x in rx if x.strip() > ""]\n art = "%s.%s" % (self.tool_name, self.executeme)\n artifact = open(art, "wb")\n artifact.write(bytes(\'\\n\'.join(self.escapedScript),\'utf8\'))\n@@ -330,7 +321,7 @@\n p[ONAMEPOS],\n )\n p.append(p[OCLPOS]) # keep copy\n- if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT":\n+ if p[OOCLPOS].isdigit() or p[OOCLPOS] == "STDOUT":\n scl = p[ONAMEPOS]\n p[OCLPOS] = scl\n self.outfiles[i] = p\n@@ -378,12 +369,20 @@\n if self.lastxclredirect:\n aXCL(self.lastxclredirect[0])\n aXCL(self.lastxclredirect[1])\n+ if os.path.exists(self.tlog):\n+ tout = open(self.tlog, "a")\n+ else:\n+ tout = open(self.tlog, "w")\n+ tout.write(f" #### clpositional: self.clsuffix = {self.clsuffix} and self.xclsuffix = {self.xclsuffix}")\n+ tout.close()\n+\n \n def clargparse(self):\n """argparse style"""\n aCL = self.cl.append\n aXCL = self.xmlcl.append\n # inputs then params in argparse named form\n+\n for (o_v, k, v, kover'..b' = os.path.join(self.testdir, self.newtarpath)\n- shutil.copyfile(src, dest)\n- else:\n- tout.write(\n- "No toolshed archive found after first ephemeris test - not a good sign"\n- )\n- ephouts = os.path.join(jobdir, "working", "tfout", "test-data")\n- with os.scandir(ephouts) as outs:\n- for entry in outs:\n- if not entry.is_file():\n- continue\n- dest = os.path.join(self.tooloutdir, entry.name)\n- src = os.path.join(ephouts, entry.name)\n- shutil.copyfile(src, dest)\n- else:\n- subp = subprocess.run(\n- cll,\n- env=self.ourenv,\n- cwd=self.ourcwd,\n- shell=False,\n- stderr=tout,\n- stdout=tout,\n- )\n- tout.write("eph_test Ran %s got %d" % (" ".join(cll), subp.returncode))\n- tout.close()\n- return subp.returncode\n-\n- def planemo_test_biocontainer(self, genoutputs=True):\n- """planemo is a requirement so is available for testing but testing in a biocontainer\n- requires some fiddling to use the hacked galaxy-central .venv\n-\n- Planemo runs:\n- python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file\n- /export/galaxy-central/database/job_working_directory/000/17/working/TF_run_report_tempdir/tacrev_planemo_test_report.html\n- --with-xunit --xunit-file /tmp/tmpt90p7f9h/xunit.xml --with-structureddata\n- --structured-data-file\n- /export/galaxy-central/database/job_working_directory/000/17/working/tfout/tool_test_output.json functional.test_toolbox\n-\n-\n- for the planemo-biocontainer,\n- planemo test --conda_dependency_resolution --skip_venv --galaxy_root /galthrow/ rgToolFactory2.xml\n-\n- """\n- xreal = "%s.xml" % self.tool_name\n- tool_test_path = os.path.join(\n- self.repdir, f"{self.tool_name}_planemo_test_report.html"\n- )\n- if os.path.exists(self.tlog):\n- tout = open(self.tlog, "a")\n- else:\n- tout = open(self.tlog, "w")\n- if genoutputs:\n- dummy, tfile = tempfile.mkstemp()\n- cll = [\n- ".",\n- os.path.join(self.args.galaxy_root, ".venv", "bin", "activate"),\n- "&&",\n- "planemo",\n- "test",\n- "--test_data",\n- self.testdir,\n- "--test_output",\n- tool_test_path,\n- "--skip_venv",\n- "--galaxy_root",\n- self.args.galaxy_root,\n- "--update_test_data",\n- xreal,\n- ]\n- subp = subprocess.run(\n- cll,\n- env=self.ourenv,\n- shell=False,\n- cwd=self.tooloutdir,\n- stderr=dummy,\n- stdout=dummy,\n- )\n-\n- else:\n- cll = [\n- ".",\n- os.path.join(self.args.galaxy_root, ".venv", "bin", "activate"),\n- "&&",\n- "planemo",\n- "test",\n- "--test_data",\n- os.path.self.testdir,\n- "--test_output",\n- os.path.tool_test_path,\n- "--skip_venv",\n- "--galaxy_root",\n- self.args.galaxy_root,\n- xreal,\n- ]\n- subp = subprocess.run(\n- cll,\n- env=self.ourenv,\n- shell=False,\n- cwd=self.tooloutdir,\n- stderr=tout,\n- stdout=tout,\n- )\n- tout.close()\n- return subp.returncode\n-\n def writeShedyml(self):\n """for planemo"""\n yuser = self.args.user_email.split("@")[0]\n' |
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| diff -r 223b78754735 -r 5509dc4c1cf2 toolfactory/rgToolFactory2.xml --- a/toolfactory/rgToolFactory2.xml Sun Nov 29 07:51:53 2020 +0000 +++ b/toolfactory/rgToolFactory2.xml Sun Nov 29 10:34:48 2020 +0000 |
| [ |
| @@ -241,8 +241,8 @@ optional="false" help="Use :[ver] for specific version - 'bwa:0.17.0'. Default is latest. Will be used every time the tool is (re)run. Only Conda is currently supported" /> <conditional name="usescript"> - <param name="choosescript" type="select" display="radio" label="Supply a script to either a dependency (e.g. python/R/bash) or a system executable such as Bash" - help = "For script interpreters like Python or bash. Parameters and i/o specified below must match script's expectations - if you pass parameters, the script must deal with them"> + <param name="choosescript" type="select" display="radio" label="Supply a script for a dependency (e.g. python/R/bash) or a system executable such as Bash" + help = "For script interpreters like Python or bash, parameters and i/o specified below must match script's expectations - if you pass parameters, the script must deal with them"> <option value="no">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option> <option value="yes" selected="true">Yes, a script is ready to be pasted below</option> </param> @@ -251,7 +251,7 @@ <param name="scriptrunner" type="hidden" value="" /> </when> <when value="yes"> - <param name="scriptrunner" type="text" value="" label="Interpreter for the script pasted below - eg bash or python. Can be one of the dependencies named above or a system executable" + <param name="scriptrunner" type="text" value="" label="Interpreter for the script - eg bash or python. Can be one of the dependencies named above or a system executable" help="Scripts are interpreted by the executable named here. Use bash for bash scripts, or a conda dependency such as R or Python for those scripts"> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> @@ -259,7 +259,7 @@ </valid> </sanitizer> </param> - <param name="dynScript" type="text" area="True" value="" label="Script for executable below to interpret. It can be one of the Conda dependency names " + <param name="dynScript" type="text" area="True" value="" label="Script for executable above to interpret. It can be one of the Conda dependency names " help="Script must handle all i/o and parameters as specified below using the parameters and passing method chosen below"> <sanitizer> <valid initial="string.printable"> |