Merge pull request #413 from DigitalSlideArchive/name-template

Name template option

devops/wsi_deid/girder.local.conf

@@ -22,6 +22,7 @@ cache_memcached_password = None
 enabled = True
 
 [wsi_deid]
+name_template = "{tokenId}"
 redact_macro_square = False
 always_redact_label = False
 edit_metadata = False

docs/CUSTOMIZING.rst

@@ -332,7 +332,6 @@ If ``InputFileName`` is added to the list of export fields in the ``upload_metad
   import_text_association_columns = ["SurgPathNum", "First_Name", "Last_Name", "Date_of_Birth"]
   ...
 
-
 Choosing Custom Metadata To Add to Exported Images
 ++++++++++++++++++++++++++++++++++++++++++++++++++
 
@@ -354,7 +353,6 @@ If the setting is absent or set to ``None``, then all metadata from the upload f
   upload_metadata_add_to_images = None
   ...
 
-
 Creating New TokenIDs for Refiling Images
 +++++++++++++++++++++++++++++++++++++++++
 
@@ -371,6 +369,18 @@ For example, if the specified pattern is ``0123#@@1###``, a randomly generated T
   new_token_pattern = "####@@#####"
   ...
 
+Naming Images Based on Database Values
+++++++++++++++++++++++++++++++++++++++
+
+By default, images filed based on database lookup are named based on their ``tokenId`` and a unique image number.  This can be changed to include data from the database lookup, if it is exists.  The ``name_template`` specifies how this is done; the default is ``{tokenId}``.  You can include, for instance, a tumor record number by changing it to ``{tokenId}_{tumor_record_number}``.  Note that if all fields are not present, it will default to the tokenId.
+
+.. code-block:: python
+
+  [wsi_deid]
+  ...
+  name_templaye = "{tokenId}"
+  ...
+
 An Example to Allow All Import Files
 ++++++++++++++++++++++++++++++++++++
 

wsi_deid/__init__.py

@@ -1,6 +1,7 @@
 import json
 import os
 import re
+import string
 
 import girder
 import PIL.Image
@@ -143,6 +144,26 @@ def validateNewTokenPattern(doc):
         doc['value'] = None
 
 
+@setting_utilities.validator({
+    PluginSettings.WSI_DEID_BASE + 'name_template',
+})
+def validateStringTemplate(doc):
+    if doc.get('value', None) is not None:
+        doc['value'] = re.sub(
+            r'\{tokenid\}', '{tokenId}', str(doc['value']).strip(),
+            flags=re.IGNORECASE)
+        try:
+            names = [fn for _, fn, _, _ in string.Formatter().parse(doc['value']) if fn is not None]
+        except Exception:
+            names = []
+        if not len(names):
+            msg = 'The template string must contain at least one reference in brases'
+            raise ValidationException(msg)
+
+    if not doc['value']:
+        doc['value'] = None
+
+
 @setting_utilities.validator({
     PluginSettings.WSI_DEID_BASE + 'hide_metadata_keys',
     PluginSettings.WSI_DEID_BASE + 'hide_metadata_keys_format_aperio',

wsi_deid/config.py

@@ -22,6 +22,7 @@
     'show_next_item': True,
     'show_metadata_in_lists': True,
     'show_next_folder': True,
+    'name_template': '{tokenid}',
     'no_redact_control_keys': {
         r'^internal;aperio_version$': '',
         r'^internal;openslide;openslide\.(?!comment$)': '',

wsi_deid/jobs.py

@@ -9,7 +9,7 @@
 
 from . import config, matching_api
 from .constants import TokenOnlyPrefix
-from .process import get_image_barcode, get_image_text, refile_image
+from .process import get_image_barcode, get_image_name, get_image_text, refile_image
 
 
 def start_ocr_item_job(job):
@@ -163,8 +163,9 @@ def match_images_via_api(imageIds, userId, job, reportInfo):
         tokenId = result[0]['token_id']
         info = {'fields': result[0].get('tumors')[0]}
         oldName = item['name']
-        item = refile_image(item, user, tokenId, TokenOnlyPrefix + tokenId,
-                            {TokenOnlyPrefix + tokenId: info})
+        newNameRoot = get_image_name(tokenId, info)
+        item = refile_image(item, user, tokenId, TokenOnlyPrefix + newNameRoot,
+                            {TokenOnlyPrefix + newNameRoot: info})
         Job().updateJob(
             job,
             log=f'Moved item {oldName} to folder {tokenId} as {item["name"]} based on api lookup\n',

wsi_deid/process.py

@@ -1724,6 +1724,18 @@ def get_image_barcode(item):
     return results
 
 
+def get_image_name(prefix, info):
+    template = config.getConfig('name_template') or '{tokenId}'
+    try:
+        name = template.format(tokenId=prefix, **info['fields'])
+        if name != template and name:
+            return name
+    except Exception:
+        logger.exception(
+            'Could not fill name template (%r) with tokenId=%s, %r', template, prefix, info)
+    return prefix
+
+
 def refile_image(item, user, tokenId, imageId, uploadInfo=None):
     """
     Refile an item to a new name and folder.

wsi_deid/web_client/templates/ConfigView.pug

@@ -192,6 +192,14 @@ form#g-wsi_deid-form(role="form")
       p.g-hui-description
         | All of the settings in this section can be specified through the Girder configuration file.  If changed via these settings, these values override the values in the configuration file.
 
+    .form-group
+      label(for="g-wsi-deid-base_name_template") Image Name Template
+      p.g-hui-description
+        | By default, items imported and matched to a database are given a name of the returned tokenId and a unique image number.  Additional data from the database record can be added as part of the name.  The template is in the python format string style.
+      input#g-wsi-deid-base_name_template.form-control.input-sm(
+          type="text", value=settings['wsi_deid.base_name_template'] || '',
+          title='A python template string style, such as "{tokenId}"',
+          spellcheck="false")
     .form-group
       input#g-wsi-deid-base_add_title_to_label.input-sm(type="checkbox", checked=(settings['wsi_deid.base_add_title_to_label'] ? "checked" : undefined))
       label(for="g-wsi-deid-base_add_title_to_label") Add File Name To Label

wsi_deid/web_client/views/HierarchyWidget.js

@@ -196,19 +196,19 @@ function addControls(key, settings) {
             {
                 key: 'redactlist',
                 text: 'Redact Checked',
-                class: 'btn-info disabled',
+                class: 'btn-primary disabled',
                 action: 'list/process',
                 check: () => settings.show_metadata_in_lists
             }, {
                 key: 'import',
                 text: 'Import',
-                class: 'btn-info',
+                class: 'btn-primary',
                 action: 'ingest',
                 check: () => settings.show_import_button !== false
             }, {
                 key: 'ocr',
                 text: 'Find label text',
-                class: 'btn-info',
+                class: 'btn-primary',
                 action: 'ocrall',
                 check: _.constant(true)
             }
@@ -217,13 +217,13 @@ function addControls(key, settings) {
             {
                 key: 'export',
                 text: 'Export Recent',
-                class: 'btn-info',
+                class: 'btn-primary',
                 action: 'export',
                 check: () => settings.show_export_button !== false
             }, {
                 key: 'exportall',
                 text: 'Export All',
-                class: 'btn-info',
+                class: 'btn-primary',
                 action: 'exportall',
                 check: () => settings.show_export_button !== false
             }
@@ -232,7 +232,7 @@ function addControls(key, settings) {
             {
                 key: 'finishlist',
                 text: 'Approve Checked',
-                class: 'btn-info disabled',
+                class: 'btn-primary disabled',
                 action: 'list/finish',
                 check: () => settings.show_metadata_in_lists
             }
@@ -241,7 +241,7 @@ function addControls(key, settings) {
             {
                 key: 'redactlist',
                 text: 'Redact Checked',
-                class: 'btn-info disabled',
+                class: 'btn-primary disabled',
                 action: 'list/process',
                 check: () => settings.show_metadata_in_lists
             }
@@ -250,7 +250,7 @@ function addControls(key, settings) {
             {
                 key: 'import',
                 text: 'Import',
-                class: 'btn-info',
+                class: 'btn-primary',
                 action: 'ingest',
                 check: () => settings.show_import_button !== false
             }