Improve logging. Improve sphinx index.

CHANGELOG.md

@@ -1,5 +1,10 @@
 # Change Log
 
+## Unreleased
+
+### Changes
+- Some log levels have been adjusted ([#689](../../pull/689))
+
 ## Version 1.8.7
 
 ### Improvements

docs/source/conf.py

@@ -66,6 +66,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = []
+html_static_path = ['static']
+html_css_files = ['custom.css']
 
 autoclass_content = 'both'

docs/source/index.rst

@@ -43,4 +43,3 @@ Indices and tables
 
 * :ref:`genindex`
 * :ref:`modindex`
-* :ref:`search`

docs/source/static/custom.css

@@ -0,0 +1,10 @@
+.indextable.genindextable td {
+  padding-right: 10px
+}
+.indextable.genindextable li {
+  word-break: break-word;
+}
+.indextable.genindextable a:before {
+  content: "\2022\00A0";
+}
+

girder_annotation/girder_large_image_annotation/models/annotation.py

@@ -938,7 +938,7 @@ def _similarElementStructure(self, a, b, parentKey=None):  # noqa
         return True
 
     def validate(self, doc):
-        starttime = time.time()
+        startTime = lastTime = time.time()
         try:
             # This block could just use the json validator:
             #   jsonschema.validate(doc.get('annotation'),
@@ -951,7 +951,7 @@ def validate(self, doc):
             annot['elements'] = []
             self.validatorAnnotation.validate(annot)
             lastValidatedElement = None
-            for element in elements:
+            for idx, element in enumerate(elements):
                 if isinstance(element.get('id'), ObjectId):
                     element['id'] = str(element['id'])
                 # Handle elements with large arrays by checking that a
@@ -972,10 +972,15 @@ def validate(self, doc):
                     lastValidatedElement = element
                 if key:
                     element[key] = keydata
+                if time.time() - lastTime > 10:
+                    logger.info('Validated %s of %d elements in %5.3fs',
+                                idx + 1, len(elements), time.time() - startTime)
+                    lastTime = time.time()
             annot['elements'] = elements
         except jsonschema.ValidationError as exp:
             raise ValidationException(exp)
-        logger.debug('Validated in %5.3fs' % (time.time() - starttime))
+        if time.time() - startTime > 10:
+            logger.info('Validated in %5.3fs' % (time.time() - startTime))
         elementIds = [entry['id'] for entry in
                       doc['annotation'].get('elements', []) if 'id' in entry]
         if len(set(elementIds)) != len(elementIds):

girder_annotation/girder_large_image_annotation/models/annotationelement.py

@@ -440,7 +440,7 @@ def updateElements(self, annotation):
 
         :param annotation: the annotation to save elements for.  Modified.
         """
-        startTime = time.time()
+        startTime = lastTime = time.time()
         elements = annotation['annotation'].get('elements', [])
         if not len(elements):
             return
@@ -464,10 +464,11 @@ def updateElements(self, annotation):
                 if 'id' not in entry['element']:
                     entry['element']['id'] = str(res.inserted_ids[pos])
             # If the whole insert is slow, log information about it.
-            if time.time() - startTime > 10:
+            if time.time() - lastTime > 10:
                 logger.info('insert %d elements in %4.2fs (prep time %4.2fs), done %d/%d' % (
                     len(entries), time.time() - chunkStartTime, prepTime,
                     chunk + len(entries), len(elements)))
+                lastTime = time.time()
         if time.time() - startTime > 10:
             logger.info('inserted %d elements in %4.2fs' % (
                 len(elements), time.time() - startTime))