# HG changeset patch
# User rhohensinner
# Date 1626700305 0
# Node ID d2be2eb8350f501f305de21a04c4981799637fdc
# Parent  0641ea2f75b1d8db8fecf8d9ec375aa0bdc1b4c1
"planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"

diff -r 0641ea2f75b1 -r d2be2eb8350f irods_upload.py
--- a/irods_upload.py	Fri Jul 02 09:40:25 2021 +0000
+++ b/irods_upload.py	Mon Jul 19 13:11:45 2021 +0000
@@ -9,9 +9,10 @@
 import os
 import shutil
 import sys
-sys.path.append("/home/richard/galaxy/lib")
+import main
 from json import dump, load, loads
-
+global python_path
+sys.path = python_path
 from galaxy.datatypes import sniff
 from galaxy.datatypes.registry import Registry
 from galaxy.datatypes.upload_util import handle_upload, UploadProblemException
@@ -307,6 +308,7 @@
         print('usage: upload.py <root> <datatypes_conf> <json paramfile> <output spec> ...', file=sys.stderr)
         sys.exit(1)
 
+    sys.path.append(argv[5])
     output_paths = parse_outputs(sys.argv[4:])
 
     registry = Registry()
diff -r 0641ea2f75b1 -r d2be2eb8350f main.py
--- a/main.py	Fri Jul 02 09:40:25 2021 +0000
+++ b/main.py	Mon Jul 19 13:11:45 2021 +0000
@@ -4,7 +4,6 @@
 
 # general imports
 import os, sys, json
-import irods_upload
 
 from shutil import copyfile
 from datetime import datetime
@@ -24,6 +23,7 @@
 session_success = False
 selection_success = False
 iRODSCredentials = {"host": "", "port": "", "user": "", "pw": "", "zone": ""}
+python_path = []
 
 
 ########################################################################################################################
@@ -440,6 +440,7 @@
         arg2 = params["galaxy_datatypes"]
         arg3 = os.path.abspath(fileParams.name)
         arg4 = params["job_id"] + ":" + params["out_dir"] + ":" + params["out_file"]
+        arg5 = params["galaxy_root"] + "/lib/galaxy"
 
         # copy sample registry.xml to working directory
         copyfile(reg_file, params["galaxy_datatypes"])
@@ -460,7 +461,9 @@
             if upload_file != "":
                 break
                 
-        os.system("python " +  upload_file + " " + arg1 + " " + arg2 + " " + arg3 + " " + arg4)
+        global python_path
+        python_path = sys.path
+        os.system(params["galaxy_root"] + "/.venv/bin/python " +  upload_file + " " + arg1 + " " + arg2 + " " + arg3 + " " + arg4)
     # close connection
     session.cleanup()
 # -------------------------------------------------------------------------------------------------------------------- #
diff -r 0641ea2f75b1 -r d2be2eb8350f tug_download.xml
--- a/tug_download.xml	Fri Jul 02 09:40:25 2021 +0000
+++ b/tug_download.xml	Mon Jul 19 13:11:45 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="irods_download" name="iRODS Download" version="0.2" workflow_compatible="false">
+<tool id="irods_download" name="iRODS Download" version="0.3" workflow_compatible="false">
 	<description>Download your files from iRODS into Galaxy</description>
 	<requirements>
 		<requirement type="package" version="0.8.2">python-irodsclient</requirement>
diff -r 0641ea2f75b1 -r d2be2eb8350f tug_upload.xml
--- a/tug_upload.xml	Fri Jul 02 09:40:25 2021 +0000
+++ b/tug_upload.xml	Mon Jul 19 13:11:45 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="irods_upload" name="iRODS Upload" version="0.2" workflow_compatible="false">
+<tool id="irods_upload" name="iRODS Upload" version="0.3" workflow_compatible="false">
 	<description>Upload your files to iRODS from Galaxy</description>
 	<requirements>
 		<requirement type="package" version="0.8.2">python-irodsclient</requirement>