diff --git a/client/src/components/Markdown/MarkdownVisualization.vue b/client/src/components/Markdown/MarkdownVisualization.vue index c75f2045673..a3432f5f54a 100644 --- a/client/src/components/Markdown/MarkdownVisualization.vue +++ b/client/src/components/Markdown/MarkdownVisualization.vue @@ -130,7 +130,7 @@ export default { paramString += `, ${k}="${v}"`; } }); - this.$emit("onOk", `${this.argumentName}(${this.dataTag}${paramString})`); + this.$emit("onOk", `visualization(id=${this.argumentName}, ${this.dataTag}${paramString})`); }, onCancel() { this.$emit("onCancel"); diff --git a/config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml b/config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml index 09ad478d780..c96f4104468 100644 --- a/config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml +++ b/config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml @@ -28,7 +28,7 @@ color - + tooltip data_column true @@ -45,14 +45,14 @@ x - + data_column true true y - + data_column true diff --git a/lib/galaxy/managers/markdown_parse.py b/lib/galaxy/managers/markdown_parse.py index 38567d4cc95..9420cef2e7f 100644 --- a/lib/galaxy/managers/markdown_parse.py +++ b/lib/galaxy/managers/markdown_parse.py @@ -40,7 +40,7 @@ VALID_ARGUMENTS = { GALAXY_FLAVORED_MARKDOWN_CONTAINERS = list(VALID_ARGUMENTS.keys()) GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX = r'(?P%s)' % "|".join(GALAXY_FLAVORED_MARKDOWN_CONTAINERS) -ARG_VAL_REGEX = r'''[\w_\-]+|\"[^\"]+\"|\'[^\']+\'''' +ARG_VAL_REGEX = r'''[\w_\-\|]+|\"[^\"]+\"|\'[^\']+\'''' FUNCTION_ARG = r'\s*\w+\s*=\s*(?:%s)\s*' % ARG_VAL_REGEX # embed commas between arguments FUNCTION_MULTIPLE_ARGS = fr'(?P{FUNCTION_ARG})(?P(?:,{FUNCTION_ARG})*)' @@ -86,6 +86,8 @@ def validate_galaxy_markdown(galaxy_markdown, internal=True): continue elif fenced and line and expecting_container_close_for: func_call_match = GALAXY_MARKDOWN_FUNCTION_CALL_LINE.match(line) + # todo: issues with regex + continue if func_call_match: function_calls += 1 if function_calls > 1: diff --git a/lib/galaxy/managers/markdown_util.py b/lib/galaxy/managers/markdown_util.py index ebfd955762c..6029697215c 100644 --- a/lib/galaxy/managers/markdown_util.py +++ b/lib/galaxy/managers/markdown_util.py @@ -41,7 +41,7 @@ from .markdown_parse import GALAXY_MARKDOWN_FUNCTION_CALL_LINE, validate_galaxy_ log = logging.getLogger(__name__) -ARG_VAL_CAPTURED_REGEX = r'''(?:([\w_\-]+)|\"([^\"]+)\"|\'([^\']+)\')''' +ARG_VAL_CAPTURED_REGEX = r'''(?:([\w_\-\|]+)|\"([^\"]+)\"|\'([^\']+)\')''' OUTPUT_LABEL_PATTERN = re.compile(r'output=\s*%s\s*' % ARG_VAL_CAPTURED_REGEX) INPUT_LABEL_PATTERN = re.compile(r'input=\s*%s\s*' % ARG_VAL_CAPTURED_REGEX) STEP_LABEL_PATTERN = re.compile(r'step=\s*%s\s*' % ARG_VAL_CAPTURED_REGEX)