# HG changeset patch
# User iuc
# Date 1606053301 0
# Node ID 97f70f7ed0771fbd503220bfa3c509bb516d5878
# Parent  f067504aa92a77dc8e8be5edd5577e0ad6607162
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"

diff -r f067504aa92a -r 97f70f7ed077 idr_download_by_ids.py
--- a/idr_download_by_ids.py	Thu Nov 05 23:29:40 2020 +0000
+++ b/idr_download_by_ids.py	Sun Nov 22 13:55:01 2020 +0000
@@ -1,4 +1,5 @@
 import argparse
+import json
 import os
 import sys
 import tarfile
@@ -112,8 +113,22 @@
     image_ids,
     channel=None, z_stack=0, frame=0,
     coord=(0, 0), width=0, height=0, region_spec='rectangle',
-    skip_failed=False, download_tar=False, omero_host='idr.openmicroscopy.org', omero_secured=True, omero_username='public', omero_password='public'
+    skip_failed=False, download_tar=False, omero_host='idr.openmicroscopy.org', omero_secured=False, config_file=None
 ):
+
+    if config_file is None:  # IDR connection
+        omero_username = 'public'
+        omero_password = 'public'
+    else:  # other omero instance
+        with open(config_file) as f:
+            cfg = json.load(f)
+            omero_username = cfg['username']
+            omero_password = cfg['password']
+
+            if omero_username == "" or omero_password == "":
+                omero_username = 'public'
+                omero_password = 'public'
+
     # basic argument sanity checks and adjustments
     prefix = 'image-'
     # normalize image ids by stripping off prefix if it exists
@@ -358,13 +373,10 @@
         '-oh', '--omero-host', type=str, default="idr.openmicroscopy.org"
     )
     p.add_argument(
-        '--omero-secured', action='store_false'
+        '--omero-secured', action='store_true', default=True
     )
     p.add_argument(
-        '-u', '--omero-username', type=str, default="public"
-    )
-    p.add_argument(
-        '-p', '--omero-password', type=str, default="public"
+        '-cf', '--config-file', dest='config_file', default=None
     )
     args = p.parse_args()
     if not args.image_ids:
diff -r f067504aa92a -r 97f70f7ed077 idr_download_by_ids.xml
--- a/idr_download_by_ids.xml	Thu Nov 05 23:29:40 2020 +0000
+++ b/idr_download_by_ids.xml	Sun Nov 22 13:55:01 2020 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
-<tool id="idr_download_by_ids" name="IDR Download" version="0.43" profile="18.09">
-    <description>- download images from the Image Data Resource using image IDs</description>
+<tool id="idr_download_by_ids" name="IDR/OMERO Download" version="0.43" profile="18.09">
+    <description>- download images from any OMERO instance using image IDs</description>
     <macros>
         <xml name="region_spec" token_pos="upper-left corner">
             <param name="x_coord" type="integer" value="0" min="0"
@@ -22,12 +22,14 @@
     <command detect_errors="exit_code"><![CDATA[
         
         #if $omero_instance_type.omero_instance == "priv":
+            ## the user wants to use a non-public OMERO instance
+            ## check if credentials are set in the user-preferences, if not warn the user and exit
             #set $username = $__user__.extra_preferences.get('omero_account|username', "")
             #set $password = $__user__.extra_preferences.get('omero_account|password', "")
 
-            #if $username == "" or $password =="":
-                echo "OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information"  &&
-                exit 1
+            #if $omero_instance_type.galaxy_test_param != 'true' and ($username == "" or $password ==""):
+                echo "OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" 1>&2 &&
+                exit 1 &&
             #end if
         #end if
         
@@ -51,13 +53,28 @@
         $skip_failed
         $download_tar
         #if $omero_instance_type.omero_instance =='priv':
-            -h '$omero_host'
-            $omero_secured
-            -u '$username'
-            -p '$password'
+            -oh '$omero_instance_type.omero_host'
+            $omero_instance_type.omero_secured
+            -cf '$credentials'
         #end if
         2> >(tee -a $out_log >&2)
     ]]></command>
+    <configfiles>
+        <configfile name="credentials"><![CDATA[
+#if $omero_instance_type.omero_instance =='priv' and $omero_instance_type.galaxy_test_param == 'true':
+    ## as a test for a private instance we actually use a public instance, but with credentials
+    #set $username = 'public'
+    #set $password = 'public'
+#else:
+    #set $username = $__user__.extra_preferences.get('omero_account|username', "")
+    #set $password = $__user__.extra_preferences.get('omero_account|password', "")
+#end if
+{
+    "username": "$username",
+    "password": "$password"
+}
+        ]]></configfile>
+    </configfiles>
 <inputs>
         <conditional name="omero_instance_type">
             <param name="omero_instance" type="select" label="Which OMERO instance to connect?"
@@ -68,13 +85,13 @@
             </param>
             <when value="priv">
                 <param name="omero_host" type="text" label="OMERO host URL">
-                    <validator type="regex" message="Enter a valid host location, for example, your.omero.server">
-                        [.A-Za-z0-9_-]
-                    </validator>
+                    <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator>
+                    <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
                 </param>
-                <param name="omero_secured" type="boolean" label="Seured connection?" checked="true" truevalue="--omero-secured" falsevalue=""
+                <param name="omero_secured" type="boolean" label="Secured connection?" checked="true" truevalue="--omero-secured" falsevalue=""
                         help="Select Yes if your OMERO instance is running with SSL, otherwise select No">
                 </param>
+                <param name="galaxy_test_param" type="hidden" value="false" />
             </when>
             <when value="idr" />
         </conditional>
@@ -300,6 +317,51 @@
                     </assert_contents>
             </output>
         </test>
+        <test>
+            <conditional name="omero_instance_type">
+                 <param name="omero_instance" value="priv" />
+                 <param name="omero_host" value="idr.openmicroscopy.org" />
+                 <param name="omero_secured" value="true" />
+                 <param name="galaxy_test_param" value="true" />
+            </conditional>
+            <param name="source" value="dataset" />
+            <param name="id_spec" value="ids.txt" />
+            <param name="channel" value="PCNT" />
+            <conditional name="clip_image">
+                <param name="select" value="--rectangle" />
+                <param name="x_coord" value="3" />
+                <param name="y_coord" value="3" />
+                <param name="width" value="5" />
+                <param name="height" value="5" />
+            </conditional>
+            <param name="frame" value="0" />
+            <param name="download_tar" value="false" />
+            <output_collection name="output_file" type="list">
+                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test0.tiff"/>
+            </output_collection>
+        </test>
+        <test expect_failure="true">
+            <conditional name="omero_instance_type">
+                 <param name="omero_instance" value="priv" />
+                 <param name="omero_host" value="idr.openmicroscopy.org" />
+                 <param name="omero_secured" value="true" />
+            </conditional>
+            <param name="source" value="dataset" />
+            <param name="id_spec" value="ids.txt" />
+            <param name="channel" value="PCNT" />
+            <conditional name="clip_image">
+                <param name="select" value="--rectangle" />
+                <param name="x_coord" value="3" />
+                <param name="y_coord" value="3" />
+                <param name="width" value="5" />
+                <param name="height" value="5" />
+            </conditional>
+            <param name="frame" value="0" />
+            <param name="download_tar" value="false" />
+            <assert_stderr>
+                <has_text text="OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" />
+            </assert_stderr >
+        </test>
     </tests>
     <help><![CDATA[
 Download image data from the IDR_ (Image Data Resource) - a public repository