diff --git a/lib/galaxy/interfaces/root.py b/lib/galaxy/interfaces/root.py index cd0cb3d4407..36591bb0f21 100644 --- a/lib/galaxy/interfaces/root.py +++ b/lib/galaxy/interfaces/root.py @@ -8,7 +8,6 @@ from galaxy import util, datatypes, jobs, web, util import common from cgi import escape, FieldStorage import urllib -import traceback log = logging.getLogger( __name__ ) @@ -509,6 +508,7 @@ class Universe(common.Root): tool_params["tool_id"] = 'fix_errors' tool_params["runtool_btn"] = 'T' tool_params["input"] = id + tool_params["ext"] = data.ext # send methods selected repair_methods = data.datatype.repair_methods( data ) methods = [] @@ -519,7 +519,7 @@ class Universe(common.Root): trans.response.send_redirect(url) else: history = trans.app.model.History.get( data.history_id ) - return trans.fill_template('dataset_errors.tmpl', data=data, history=history) + return trans.fill_template('dataset/validation.tmpl', data=data, history=history) # ---- Debug methods ---------------------------------------------------- diff --git a/templates/dataset/validation.tmpl b/templates/dataset/validation.tmpl new file mode 100644 index 00000000000..62488639374 --- /dev/null +++ b/templates/dataset/validation.tmpl @@ -0,0 +1,44 @@ + + + + +Galaxy + + + + + + + +
+
Dataset Errors: $data.name
+
+
+ + + + + +
Name:$data.name
Info:$data.info
Errors:$len($data.validation_errors)
+ #if len($data.validation_errors) > 0: + + + #for count in range(min(len($data.validation_errors),10)): + + #end for + #if $data.datatype.repair_methods($data): + #for $option, $description in $data.datatype.repair_methods($data): + + #end for + + #end if +
Displaying the first 10 errors:
$data.validation_errors[count].message
$description
+ #end if +
+
+
+ + + + + \ No newline at end of file diff --git a/templates/history.tmpl b/templates/history.tmpl index cc932d040a5..a579113bf68 100644 --- a/templates/history.tmpl +++ b/templates/history.tmpl @@ -199,10 +199,14 @@ main();">
Info: $data.display_info
- #if $len($data.validation_errors)>0 + #if $len($data.validation_errors)>1
There are $len($data.validation_errors) possibles errors in this dataset (view).
+ #elif $len($data.validation_errors)==1 +
+ There is 1 possible error in this dataset (view). +
#end if
#if $data.ext in [ "bed", "interval", "tabular", "txt", "text", "axt", "maf", "fasta", "gff", "gmaj.zip" ]: diff --git a/tools/validation/fix_errors.py b/tools/validation/fix_errors.py index 60e18ef22d5..9315049ecbc 100644 --- a/tools/validation/fix_errors.py +++ b/tools/validation/fix_errors.py @@ -15,12 +15,13 @@ from galaxy import util def main(): options, args = doc_optparse.parse( __doc__ ) - + methods = [] try: if options.methods: methods = options.methods.split(",") - ext = options.ext except: - doc_optparse.exception() + pass + + ext = options.ext in_file = open(args[0], "r") error_file = open(args[1], "r") diff --git a/tools/validation/fix_errors.xml b/tools/validation/fix_errors.xml index 50c3095d200..5da2ec06e2e 100644 --- a/tools/validation/fix_errors.xml +++ b/tools/validation/fix_errors.xml @@ -4,12 +4,13 @@ in data validation - fix_errors.py $input $errorsfile $output -m $methods + fix_errors.py $input $errorsfile $output -x $ext --methods=$methods +