Mercurial > repos > fubar > tool_factory_2
changeset 76:46db8143adb7 draft
Uploaded
| author | fubar |
|---|---|
| date | Mon, 16 Nov 2020 02:42:49 +0000 |
| parents | 25dd9364a32a |
| children | 1fa49a9a4ec5 |
| files | toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml |
| diffstat | 2 files changed, 50 insertions(+), 20 deletions(-) [+] |
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--- a/toolfactory/rgToolFactory2.py Sat Nov 14 23:35:27 2020 +0000 +++ b/toolfactory/rgToolFactory2.py Mon Nov 16 02:42:49 2020 +0000 @@ -24,6 +24,8 @@ import argparse +import datetime +import json import logging import os import re @@ -179,6 +181,7 @@ self.args.tool_desc, FAKEEXE, ) + self.newtarpath = "toolfactory_%s.tgz" % self.tool_name self.tooloutdir = "tfout" self.repdir = "TF_run_report_tempdir" self.testdir = os.path.join(self.tooloutdir, "test-data") @@ -815,8 +818,9 @@ tout.close() return p.returncode - def eph_test(self): - """""" + def eph_test(self, genoutputs=True): + """problem getting jobid - ephemeris upload is the job before the one we want - but depends on how many inputs + """ if os.path.exists(self.tlog): tout = open(self.tlog, "a") else: @@ -833,10 +837,41 @@ "--owner", "fubar", ] - p = subprocess.run( - cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout - ) - tout.write("eph_test Ran %s got %d" % (" ".join(cll), p.returncode)) + if genoutputs: + dummy, tfile = tempfile.mkstemp() + p = subprocess.run( + cll, shell=False, stderr=dummy, stdout=dummy + ) + + with open('tool_test_output.json','rb') as f: + s = json.loads(f.read()) + print('read %s' % s) + cl = s['tests'][0]['data']['job']['command_line'].split() + n = cl.index('--script_path') + jobdir = cl[n+1] + jobdir = jobdir.replace('"','') + jobdir = jobdir.split('/configs')[0] + print('jobdir=%s' % jobdir) + + #"/home/ross/galthrow/database/jobs_directory/000/649/configs/tmptfxu51gs\" + src = os.path.join(jobdir,'working',self.newtarpath) + if os.path.exists(src): + dest = os.path.join(self.testdir, self.newtarpath) + shutil.copyfile(src, dest) + else: + tout.write('No toolshed archive found after first ephemeris test - not a good sign') + ephouts = os.path.join(jobdir,'working','tfout','test-data') + with os.scandir(ephouts) as outs: + for entry in outs: + if not entry.is_file(): + continue + dest = os.path.join(self.tooloutdir, entry.name) + src = os.path.join(ephouts, entry.name) + shutil.copyfile(src, dest) + else: + p = subprocess.run( + cll, shell=False, stderr=tout, stdout=tout) + tout.write("eph_test Ran %s got %d" % (" ".join(cll), p.returncode)) tout.close() return p.returncode @@ -940,7 +975,6 @@ "### problem - output file %s not found in tooloutdir %s" % (src, self.tooloutdir) ) - self.newtarpath = "toolfactory_%s.tgz" % self.tool_name tf = tarfile.open(self.newtarpath, "w:gz") tf.add(name=self.tooloutdir, arcname=self.tool_name, filter=exclude_function) tf.close() @@ -962,6 +996,7 @@ shutil.copyfile(src, dest) + def main(): """ This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as: @@ -976,7 +1011,7 @@ a("--cl_prefix", default=None) a("--sysexe", default=None) a("--packages", default=None) - a("--tool_name", default=None) + a("--tool_name", default="newtool") a("--tool_dir", default=None) a("--input_files", default=[], action="append") a("--output_files", default=[], action="append") @@ -996,15 +1031,11 @@ a("--new_tool", default="new_tool") a("--galaxy_url", default="http://localhost:8080") a( - "--toolshed_url", default="http://localhost:9009" - ) # make sure this is NOT 127.0.0.1 - it won't work if tool_sheds_conf.xml has localhost - # a("--galaxy_api_key", default="1e62ddad74fe9bf112859f4e9efea48b") - # a("--toolshed_api_key", default="9154c91f2a162bf12fda15764f43846c") - + "--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") - 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 configuration file' @@ -1031,9 +1062,8 @@ r.makeToolTar() retcode = r.planemo_test(genoutputs=False) r.moveRunOutputs() + print(f"second planemo_test returned {retcode}") if args.make_Tool == "gentestinstall": - retcode = r.planemo_shedload() # r.shedLoad() - print(f"planemo_shedload returned {retcode}") r.eph_galaxy_load()
--- a/toolfactory/rgToolFactory2.xml Sat Nov 14 23:35:27 2020 +0000 +++ b/toolfactory/rgToolFactory2.xml Mon Nov 16 02:42:49 2020 +0000 @@ -132,8 +132,8 @@ </macros> <requirements> - <requirement type="package" >galaxyxml</requirement> - <requirement type="package" >bioblend</requirement> + <requirement type="package">galaxyxml</requirement> + <requirement type="package">bioblend</requirement> <requirement type="package">planemo</requirement> <container type="docker">quay.io/fubar2/toolfactorybiocontainer</container> </requirements> @@ -142,9 +142,9 @@ #import os #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1' #if not $dev_env and ( $__user_email__ not in $__admin_users__ ): -rgToolFactory2.py --bad_user $__user_email__ +python3 $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__ #else: -rgToolFactory2.py +python3 $__tool_directory__/rgToolFactory2.py #if len(str($cl_prefix)) > 3: --cl_prefix "$cl_prefix" #end if