--- a/toolfactory/.shed.yml	Fri May 21 02:05:27 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-name: toolfactory
-owner: fubar
-description: ToolFactory - tool to make Galaxy tools ready for the toolshed
-homepage_url: https://github.com/fubar2/toolfactory
-long_description: |
-    ToolFactory - turn executable packages and R/python/perl/bash scripts into ordinary Galaxy tools
-
-    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
-remote_repository_url: https://github.com/fubar2/toolfactory
-type: tool_dependency_definition
-categories:
-- Tool Generators

--- a/toolfactory/ToolFactory.py	Fri May 21 02:05:27 2021 +0000
+++ b/toolfactory/ToolFactory.py	Mon May 24 02:37:52 2021 +0000
@@ -20,6 +20,7 @@
 import json
 import os
 import re
+import rpyc
 import shlex
 import shutil
 import subprocess
@@ -70,101 +71,6 @@
             citation_tuples.append(("bibtex", citation[len("bibtex") :].strip()))
     return citation_tuples
 
-class Locker:
-    """
-    multiple instances of the TF may try to update tool_conf.xml so use a simple lockfile
-    to prevent overwriting mix ups.
-    """
-    def __enter__ (self):
-        lockfile = "/tmp/.toolfactory_lockfile.lck"
-        if not os.path.exists(lockfile):
-            try:
-                os.utime(lockfile, None)
-            except OSError:
-                open(lockfile, 'a').close()
-        self.fp = open(lockfile)
-        fcntl.flock(self.fp.fileno(), fcntl.LOCK_EX)
-
-    def __exit__ (self, _type, value, tb):
-        fcntl.flock(self.fp.fileno(), fcntl.LOCK_UN)
-        self.fp.close()
-
-
-class Tool_Conf_Updater:
-
-    """# update config/tool_conf.xml with a new tool unpacked in /tools
-    # requires highly insecure docker settings - like write to tool_conf.xml and to tools !
-    # if in a container possibly not so courageous.
-    # Fine on your own laptop but security red flag for most production instances
-    Note potential race condition for tool_conf.xml update - uses a file lock.
-    """
-
-    def __init__(
-        self, args, tool_conf_path, new_tool_archive_path, new_tool_name, local_tool_dir
-    ):
-        self.args = args
-        self.tool_conf_path = os.path.join(args.galaxy_root, tool_conf_path)
-        self.tool_dir = os.path.join(args.galaxy_root, local_tool_dir,'TFtools')
-        self.out_section = "ToolFactory Generated Tools"
-        tff = tarfile.open(new_tool_archive_path, "r:*")
-        flist = tff.getnames()
-        ourdir = os.path.commonpath(flist)  # eg pyrevpos
-        self.tool_id = ourdir  # they are the same for TF tools
-        ourxml = [x for x in flist if x.lower().endswith(".xml")]
-        tff.extractall()
-        tff.close()
-        try:
-            self.run_rsync(ourdir, self.tool_dir)
-            with Locker():
-                self.update_toolconf(ourdir, ourxml)
-        except Exception:
-            print('Cannot install the new tool. This is only possible in the ToolFactory appliance at https://github.com/fubar2/toolfactory-galaxy-server')
-
-    def run_rsync(self, srcf, dstf):
-        src = os.path.abspath(srcf)
-        dst = os.path.abspath(dstf)
-        if os.path.isdir(src):
-            cll = ["rsync", "-r", src, dst]
-        else:
-            cll = ["rsync", src, dst]
-        subprocess.run(
-            cll,
-            capture_output=False,
-            encoding="utf8",
-            shell=False,
-        )
-
-
-    def update_toolconf(self, ourdir, ourxml):  # path is relative to tools
-
-        def sortchildrenby(parent, attr):
-            parent[:] = sorted(parent, key=lambda child: child.get(attr))
-
-        localconf = "./local_tool_conf.xml"
-        self.run_rsync(self.tool_conf_path, localconf)
-        tree = ET.parse(localconf)
-        root = tree.getroot()
-        hasTF = False
-        TFsection = None
-        for e in root.findall("section"):
-            if e.attrib["name"] == self.out_section:
-                hasTF = True
-                TFsection = e
-        if not hasTF:
-            TFsection = ET.Element("section", {"id":self.out_section, "name":self.out_section})
-            root.insert(0, TFsection)  # at the top!
-        our_tools = TFsection.findall("tool")
-        conf_tools = [x.attrib["file"] for x in our_tools]
-        for xml in ourxml:  # may be > 1
-            if xml not in conf_tools:  # new
-                ET.SubElement(TFsection, "tool", {"file": os.path.join('TFtools', xml)})
-        sortchildrenby(TFsection,"file")
-        newconf = f"{self.tool_id}_conf"
-        tree.write(newconf, pretty_print=True)
-        self.run_rsync(newconf, self.tool_conf_path)
-
-
-
 
 class Tool_Factory:
     """Wrapper for an arbitrary script
@@ -978,13 +884,14 @@
     r.makeTool()
     r.makeToolTar()
     if args.install:
-        TCU = Tool_Conf_Updater(
-            args=args,
-            local_tool_dir=args.local_tools,
-            new_tool_archive_path=r.newtarpath,
-            tool_conf_path=args.tool_conf_path,
-            new_tool_name=r.tool_name
-        )
+            try:
+                conn = rpyc.connect("planemo-server", port=9999, config={'sync_request_timeout':1200})
+            except ConnectionRefusedError:
+                print('### no remote rpyc server found on port 9999 - this only works in the ToolFactory Appliance with that server running...')
+                sys.exit(1)
+            res = conn.root.tool_updater(galaxy_root=args.galaxy_root,
+                tool_conf_path=args.tool_conf_path, new_tool_archive_path=os.path.abspath(r.newtarpath),
+                new_tool_name=r.tool_name, local_tool_dir=args.local_tools)
 
 if __name__ == "__main__":
     main()

--- a/toolfactory/ToolFactory.xml	Fri May 21 02:05:27 2021 +0000
+++ b/toolfactory/ToolFactory.xml	Mon May 24 02:37:52 2021 +0000
@@ -189,7 +189,7 @@
 <requirements>
      <requirement type="package" version="0.4.14">galaxyxml</requirement>
      <requirement type="package" version="0.15.0">bioblend</requirement>
-     <requirement type="package" version="3.2.3">rsync</requirement>
+     <requirement type="package" version="5.0.1">rpyc</requirement>
 </requirements>
 
 <command detect_errors="exit_code"><![CDATA[

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/test-data/output2_sample	Mon May 24 02:37:52 2021 +0000
@@ -0,0 +1,165 @@
+*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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/test-data/pyrevpos.python	Mon May 24 02:37:52 2021 +0000
@@ -0,0 +1,13 @@
+# 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() 
+

Binary file toolfactory/test-data/pyrevpos_not_tested.toolshed_sample has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/test-data/test1_log.txt	Mon May 24 02:37:52 2021 +0000
@@ -0,0 +1,1 @@
+## Executing Toolfactory generated command line = python /tmp/pyrevposq5dmcdy1.python /tmp/tmpqrksf8sd/files/5/b/9/dataset_5b952a86-87df-44ad-a415-ea549f3f0cee.dat output2

Binary file toolfactory/test-data/toolfactory_pyrevpos_tgz_sample has changed