tool_factory_2: toolfactory/rgToolFactory2.py comparison

comparison toolfactory/rgToolFactory2.py @ 113:6873c211b250 draft

Uploaded

author	fubar
date	Tue, 01 Dec 2020 09:03:34 +0000
parents	5509dc4c1cf2
children	e0cf315853cf

comparison

equal deleted inserted replaced

-:5509dc4c1cf2
+:6873c211b250
 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)  # make tests directory
+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 = []
 aCL(self.executeme)
 aCL(self.sfile)
 aXCL(self.executeme)
 aXCL("$runme")
 else:
-aCL(self.executeme)  # this little CL will just run
+aCL(self.executeme)
 aXCL(self.executeme)
 self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name)
 self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name)
 if self.args.parampass == "0":
 xclsuffix.append(xappendme)
 for i, p in enumerate(self.outfiles):
 if p[OOCLPOS] == "STDOUT":
 self.lastclredirect = [">", p[ONAMEPOS]]
 self.lastxclredirect = [">", "$%s" % p[OCLPOS]]
-else: #   for (o_v, k, v, koverride) in self.xclsuffix:
+else:
 clsuffix.append([p[ONAMEPOS], p[ONAMEPOS], p[ONAMEPOS], ""])
 xclsuffix.append([p[ONAMEPOS], p[ONAMEPOS], "$%s" % p[ONAMEPOS], ""])
 for p in self.addpar:
 clsuffix.append([p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]])
 xclsuffix.append(
 infp[ICLPOS] = scl
 self.infiles[i] = infp
 for i, p in enumerate(
 self.outfiles
 ):
-if self.args.parampass == "positional" and p[OCLPOS] != "STDOUT":
+if self.args.parampass == "positional" and p[OCLPOS].upper() != "STDOUT":
 assert p[
 OCLPOS
 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
 p[OCLPOS],
 p[ONAMEPOS],
 )
 p.append(p[OCLPOS]) # keep copy
-if p[OOCLPOS].isdigit() or p[OOCLPOS] == "STDOUT":
+if p[OOCLPOS].isdigit() or p[OOCLPOS].upper() == "STDOUT":
 scl = p[ONAMEPOS]
 p[OCLPOS] = scl
 self.outfiles[i] = p
 for i, p in enumerate(self.addpar):
 if self.args.parampass == "positional":
 for (o_v, k, v, koverride) in self.xclsuffix:
 aXCL(v)
 if self.lastxclredirect:
 aXCL(self.lastxclredirect[0])
 aXCL(self.lastxclredirect[1])
-if os.path.exists(self.tlog):
-tout = open(self.tlog, "a")
-else:
-tout = open(self.tlog, "w")
-tout.write(f" #### clpositional: self.clsuffix = {self.clsuffix} and self.xclsuffix = {self.xclsuffix}")
-tout.close()
 def clargparse(self):
 """argparse style"""
 aCL = self.cl.append
 k = "-%s" % k
 else:
 k = "--%s" % k
 aCL(k)
 aCL(v)
-if os.path.exists(self.tlog):
-tout = open(self.tlog, "a")
-else:
-tout = open(self.tlog, "w")
-tout.write(f" #### clargparse: self.clsuffix = {self.clsuffix} and self.xclsuffix = {self.xclsuffix}")
-tout.close()
 def getNdash(self, newname):
 if self.is_positional:
 ndash = 0
 test = test.strip()
 ndash = self.getNdash(newcl)
 aparm = gxtp.OutputData(name=newname, format=newfmt, num_dashes=ndash, label=newcl)
 aparm.positional = self.is_positional
 if self.is_positional:
-if oldcl == "STDOUT":
+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.newtool.version_command = None  # do not want
 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
-ver = ""
 requirements.append(
 gxtp.Requirement("package", packg.strip(), ver.strip())
 )
 self.newtool.requirements = requirements
 if self.args.parampass == "0":
 def prun(container, tout, cl, user="biodocker"):
 rlog = container.exec_run(cl, user=user)
 slogl = str(rlog).split("\\n")
 slog = "\n".join(slogl)
 tout.write(f"## got rlog {slog} from {cl}\n")
 if os.path.exists(self.tlog):
 tout = open(self.tlog, "a")
 else:
 tout = open(self.tlog, "w")
 planemoimage = "quay.io/fubar2/planemo-biocontainer"
 client = docker.from_env()
 tvol = client.volumes.create()
 tvolname = tvol.name
 destdir = "/toolfactory/ptest"
 imrep = os.path.join(destdir, repname)
-# need to keep the container running so sleep a while - we stop and destroy it when we are done
+# need to keep the container running so keep it open with tail -f.
+# will stop and destroy it when we are done
 container = client.containers.run(
 planemoimage,
-"sleep 30m",
+"tail -f /galaxy-central/CITATION",
 detach=True,
 user="biodocker",
 volumes={f"{tvolname}": {"bind": "/toolfactory", "mode": "rw"}},
 )
 cl = f"mkdir -p {destdir}"
 prun(container, tout, cl, user="root")
+# that's how hard it is to get root on a biodocker container :(
 cl = f"rm -rf {destdir}/*"
 prun(container, tout, cl, user="root")
 ptestpath = os.path.join(destdir, "tfout", xreal)
 self.copy_to_container(self.tooloutdir, destdir, container)
 cl = "chown -R biodocker /toolfactory"
 prun(container, tout, cl, user="root")
 rlog = container.exec_run(f"ls -la {destdir}")
 ptestcl = f"planemo test  --update_test_data  --no_cleanup --test_data {destdir}/tfout/test-data --galaxy_root /home/biodocker/galaxy-central {ptestpath}"
 try:
 rlog = container.exec_run(ptestcl)
+# fails because test outputs missing but updates the test-data directory
 except:
 e = sys.exc_info()[0]
 tout.write(f"#### error: {e} from {ptestcl}\n")
-# fails - used to generate test outputs
 cl = f"planemo test  --test_output {imrep} --no_cleanup --test_data {destdir}/tfout/test-data --galaxy_root /home/biodocker/galaxy-central {ptestpath}"
 try:
 prun(container, tout, cl)
 except:
 pass
 tout.write(f"No output from run to shutil.copytree in {src}\n")
 tout.close()
 container.stop()
 container.remove()
 tvol.remove()
-# shutil.rmtree(testouts)
+# shutil.rmtree(testouts) leave for debugging
 def shedLoad(self):
 """
-{'deleted': False,
+use bioblend to create new repository
-'description': 'Tools for manipulating data',
+or update existing
-'id': '175812cd7caaf439',
-'model_class': 'Category',
-'name': 'Text Manipulation',
-'url': '/api/categories/175812cd7caaf439'}]
 """
 if os.path.exists(self.tlog):
 sto = open(self.tlog, "a")
 else:
 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")
+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")
+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"
+"####### Is the toolshed running and the API key correct? Bioblend shed upload failed\n"
 )
 sto.close()
 def eph_galaxy_load(self):
-"""load the new tool from the local toolshed after planemo uploads it"""
+"""
+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 = [
 a("--galaxy_api_key", default="fakekey")
 a("--galaxy_root", default="/galaxy-central")
 a("--galaxy_venv", default="/galaxy_venv")
 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'
+'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

Mercurial > repos > fubar > tool_factory_2

comparison toolfactory/rgToolFactory2.py @ 113:6873c211b250 draft