girder-sample-tracker 2.0.1__tar.gz → 2.0.2__tar.gz

{girder_sample_tracker-2.0.1/girder_sample_tracker.egg-info → girder_sample_tracker-2.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: girder-sample-tracker
-Version: 2.0.1
+Version: 2.0.2
 Summary: Girder Plugin adding a simple tracker for material samples
 License: BSD
 Classifier: Development Status :: 4 - Beta
@@ -19,6 +19,7 @@ Dynamic: classifier
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: license
+Dynamic: license-file
 Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary

{girder_sample_tracker-2.0.1 → girder_sample_tracker-2.0.2}/girder_sample_tracker/models/sample.py

@@ -64,6 +64,15 @@ class Sample(AccessControlledModel):
 
         return sample
 
+    def remove_event(self, sample, event, user=None):
+        self.collection.update_one(
+            {
+                "_id": sample["_id"],
+            },
+            {"$pull": {"events": {**event}}},
+        )
+        return self.load(sample["_id"], user=user)
+
     def qr_code(self, sample, url):
         buf = io.BytesIO()
         qr = qrcode.QRCode(

{girder_sample_tracker-2.0.1 → girder_sample_tracker-2.0.2}/girder_sample_tracker/rest/sample.py

@@ -3,6 +3,7 @@ import math
 from urllib.parse import urlparse
 
 import cherrypy
+import dateutil.parser
 from girder.api import access
 from girder.api.describe import Description, autoDescribeRoute
 from girder.api.rest import (
@@ -13,23 +14,13 @@ from girder.api.rest import (
 )
 from girder.constants import AccessType, SortDir, TokenScope
 from girder.exceptions import RestException, ValidationException
+from girder.models.user import User
 from girder.utility import ziputil
 from girder.utility.progress import ProgressContext
 
 from ..models.sample import Sample as SampleModel
 
 
-def bytesio_iterator(bio, chunk_size=4096):
-    """
-    Iterates over the content of a BytesIO object in chunks.
-    """
-    while True:
-        chunk = bio.read(chunk_size)
-        if not chunk:
-            break
-        yield chunk
-
-
 class Sample(Resource):
     def __init__(self):
         super(Sample, self).__init__()
@@ -46,17 +37,25 @@ class Sample(Resource):
         self.route("GET", (":id", "access"), self.get_access)
         self.route("PUT", (":id", "access"), self.update_access)
         self.route("POST", (":id", "event"), self.create_event)
+        self.route("DELETE", (":id", "event"), self.delete_event)
 
     @access.public
     @autoDescribeRoute(
-        Description("List samples").pagingParams(
+        Description("List samples")
+        .param("query", "A regular expression to filter sample names", required=False)
+        .pagingParams(
             defaultSort="name", defaultSortDir=SortDir.DESCENDING
         )
     )
     @filtermodel(model="sample", plugin="sample_tracker")
-    def list_samples(self, limit, offset, sort):
+    def list_samples(self, query, limit, offset, sort):
+        if query:
+            query = {"name": {"$regex": query, "$options": "i"}}
+        else:
+            query = {}
+
         return SampleModel().findWithPermissions(
-            query={},
+            query=query,
             offset=offset,
             limit=limit,
             sort=sort,
@@ -130,15 +129,25 @@ class Sample(Resource):
             raise ValidationException(
                 "Batch size must be at least 1, but no more than 64."
             )
+
         if not eventTypes:
             eventTypes = []
         user = self.getCurrentUser()
         samples = []
         if batchSize > 1:
-            format_str = "{name}{i:0" + str(math.ceil(math.log10(batchSize))) + "d}"
+            if "{number" not in name:
+                name = name + "{number:0" + str(math.ceil(math.log10(batchSize))) + "d}"
+
+            try:
+                name.format(number=1)
+            except KeyError:
+                raise ValidationException(
+                    "Name must contain a '{number}' placeholder for batch creation."
+                )
+
             for i in range(batchSize):
                 sample = SampleModel().create(
-                    format_str.format(name=name, i=i + 1),
+                    name.format(number=i + 1),
                     user,
                     description=description,
                     eventTypes=eventTypes,
@@ -300,6 +309,26 @@ class Sample(Resource):
         }
         return SampleModel().add_event(sample, event)
 
+    @access.user
+    @autoDescribeRoute(
+        Description("Delete an event for a sample")
+        .modelParam(
+            "id", "The ID of the sample", model=SampleModel, level=AccessType.ADMIN
+        )
+        .jsonParam("event", "Event to remove", required=True, requireObject=True)
+    )
+    @filtermodel(model="sample", plugin="sample_tracker")
+    def delete_event(self, sample, event):
+        creator = User().load(event["creator"], force=True)
+        processed_event = {
+            "created": dateutil.parser.parse(event.get("created")),
+            "creator": creator["_id"],
+            "eventType": event.get("eventType"),
+        }
+        return SampleModel().remove_event(
+            sample, processed_event, user=self.getCurrentUser()
+        )
+
     @access.public(scope=TokenScope.DATA_READ, cookie=True)
     @autoDescribeRoute(
         Description("Download a sample").modelParam(
@@ -312,7 +341,11 @@ class Sample(Resource):
         qr_img = SampleModel().qr_code(sample, girder_base)
         setResponseHeader("Content-Type", "image/png")
         setContentDisposition(f"{sample['name']}.png")
-        return bytesio_iterator(qr_img)
+
+        def stream():
+            yield from qr_img
+
+        return stream
 
     @access.public(scope=TokenScope.DATA_READ, cookie=True)
     @autoDescribeRoute(