remove bare excepts

lib/galaxy/tool_util/linters/citations.py

@@ -8,13 +8,17 @@ of the tool publish results.
 def lint_citations(tool_xml, lint_ctx):
     """Ensure tool contains at least one valid citation."""
     root = tool_xml.getroot()
+    if root is not None:
+        root_line = root.sourceline
+    else:
+        root_line = 1
     citations = root.findall("citations")
     if len(citations) > 1:
         lint_ctx.error("More than one citation section found, behavior undefined.", line=citations[1].sourceline)
         return
 
     if len(citations) == 0:
-        lint_ctx.warn("No citations found, consider adding citations to your tool.", line=root.sourceline)
+        lint_ctx.warn("No citations found, consider adding citations to your tool.", line=root_line)
         return
 
     valid_citations = 0
@@ -32,4 +36,4 @@ def lint_citations(tool_xml, lint_ctx):
         valid_citations += 1
 
     if valid_citations > 0:
-        lint_ctx.valid(f"Found {valid_citations} likely valid citations.", line=root.sourceline)
+        lint_ctx.valid(f"Found {valid_citations} likely valid citations.", line=root_line)

lib/galaxy/tool_util/linters/command.py

@@ -8,13 +8,17 @@ from supplied inputs.
 def lint_command(tool_xml, lint_ctx):
     """Ensure tool contains exactly one command and check attributes."""
     root = tool_xml.getroot()
+    if root is not None:
+        root_line = root.sourceline
+    else:
+        root_line = 1
     commands = root.findall("command")
     if len(commands) > 1:
         lint_ctx.error("More than one command tag found, behavior undefined.", line=commands[1].sourceline)
         return
 
     if len(commands) == 0:
-        lint_ctx.error("No command tag found, must specify a command template to execute.", line=root.sourceline)
+        lint_ctx.error("No command tag found, must specify a command template to execute.", line=root_line)
         return
 
     command = get_command(tool_xml)

lib/galaxy/tool_util/linters/general.py

@@ -31,7 +31,7 @@ def lint_general(tool_source, lint_ctx):
     tool_xml = getattr(tool_source, "xml_tree", None)
     try:
         tool_line = tool_xml.find("./tool").sourceline
-    except:
+    except AttributeError:
         tool_line = 0
     version = tool_source.parse_version() or ''
     parsed_version = packaging.version.parse(version)

lib/galaxy/tool_util/linters/help.py

@@ -7,15 +7,20 @@ from galaxy.util import (
 
 def lint_help(tool_xml, lint_ctx):
     """Ensure tool contains exactly one valid RST help block."""
-    # determine line to report for general problems with outputs
+    # determine line to report for general problems with help
     root = tool_xml.getroot()
+    if root is not None:
+        root_line = root.sourceline
+    else
+        root_line = 1
+
     helps = root.findall("help")
     if len(helps) > 1:
         lint_ctx.error("More than one help section found, behavior undefined.", line=helps[1].sourceline)
         return
 
     if len(helps) == 0:
-        lint_ctx.warn("No help section found, consider adding a help section to your tool.", line=root.sourceline)
+        lint_ctx.warn("No help section found, consider adding a help section to your tool.", line=root_line)
         return
 
     help = helps[0].text or ''
@@ -23,7 +28,7 @@ def lint_help(tool_xml, lint_ctx):
         lint_ctx.warn("Help section appears to be empty.", line=helps[0].sourceline)
         return
 
-    lint_ctx.valid("Tool contains help section.", line=root.sourceline)
+    lint_ctx.valid("Tool contains help section.", line=root_line)
     invalid_rst = rst_invalid(help)
 
     if "TODO" in help:

lib/galaxy/tool_util/linters/inputs.py

@@ -49,7 +49,7 @@ def lint_inputs(tool_xml, lint_ctx):
     # determine line to report for general problems with outputs
     try:
         tool_line = tool_xml.find("./tool").sourceline
-    except:
+    except AttributeError:
         tool_line = 0
     datasource = is_datasource(tool_xml)
     inputs = tool_xml.findall("./inputs//param")

lib/galaxy/tool_util/linters/outputs.py

@@ -9,7 +9,7 @@ def lint_output(tool_xml, lint_ctx):
     # determine line to report for general problems with outputs
     try:
         tool_line = tool_xml.find("./tool").sourceline
-    except:
+    except AttributeError:
         tool_line = 0
     outputs = tool_xml.findall("./outputs")
     if len(outputs) == 0:

lib/galaxy/tool_util/linters/stdio.py

@@ -7,7 +7,7 @@ def lint_stdio(tool_source, lint_ctx):
     # determine line to report for general problems with stdio
     try:
         tool_line = tool_xml.find("./tool").sourceline
-    except:
+    except AttributeError:
         tool_line = 0
     
     stdios = tool_xml.findall("./stdio") if tool_xml else []

lib/galaxy/tool_util/linters/tests.py

@@ -5,15 +5,14 @@ from ._util import is_datasource
 # Misspelled so as not be picked up by nosetests.
 def lint_tsts(tool_xml, lint_ctx):
     # determine line to report for general problems with tests
-    try:
-        tests_line = tool_xml.find("./tool").sourceline
-    except:
-        tests_line = 0
     try:
         tests_line = tool_xml.find("./tests").sourceline
-    except:
+    except AttributeError:
+        tests_line = 1
+    try:
+        tests_line = tool_xml.find("./tool").sourceline
+    except AttributeError:
         pass
-
     tests = tool_xml.findall("./tests/test")
     datasource = is_datasource(tool_xml)
     if not tests and not datasource: