add custom_id example in CSV import example

Author: NicolasCARPi

examples/09-import-csv.py

@@ -59,7 +59,8 @@ def getMetadataFromRow(row):
     for keyval in row.items():
         field_type = 'text'
         # we don't import these columns as metadata
-        if keyval[0] == 'Name' or keyval[0] == 'Comment':
+        # Name is the tile, Comment is in the body, and ID is the custom_id.
+        if keyval[0] == 'Name' or keyval[0] == 'Comment' or keyval[0] == 'ID':
             continue
         # special case for url/URL column, we make it a type: url
         if keyval[0].lower() == 'url':
@@ -84,19 +85,33 @@ def getMetadataFromRow(row):
 
 # The column "Comment" will get added to the body of the resource
 def getBodyFromRow(row) -> str:
-    metadata = { 'extra_fields': {} }
     for keyval in row.items():
         if keyval[0] == 'Comment':
             return f'<p>{keyval[1]}</p>'
     return ''
 
+###########################################
+######## WHERE THE MAGIC HAPPENS ##########
+###########################################
+
 # Note: use encoding='utf-8-sig' in the open() call if your file has BOM (Byte Order Mark)
 # Also make sure that the CSV file was saved as UTF-8 to avoid issues with special characters
 with open(CSV_PATH, newline='') as csvfile:
+    # let's read the CSV using the standard "csv" library from python. No need for anything fancier.
     csvreader = csv.DictReader(csvfile, delimiter=',', quotechar='"')
+    # now we loop over each row in our CSV
     for row in csvreader:
         # here we add the tag "-20°C freezer" to every row
+        # the API allows setting tags during creation (POST) of a resource or experiment, so we use it here
         response = itemsApi.post_item_with_http_info(body={'category_id': RESOURCE_CATEGORY_ID, 'tags': ['-20°C freezer']})
         locationHeaderInResponse = response[2].get('Location')
+        # that's our ID of the newly created resource
         itemId = int(locationHeaderInResponse.split('/').pop())
-        itemsApi.patch_item(itemId, body={'title': row['Name'], 'body': getBodyFromRow(row), 'metadata': getMetadataFromRow(row)})
+
+        # Patch the item to change its content:
+        # the "Name" column becomes our title
+        # the "Body" is generated from the "Comment" column content with the "getBodyFromRow()" function
+        # for the "ID" column we match it to the "custom_id" property in elab
+        # and the extra fields (metadata) is built with a function
+        # the single line below will make all those changes at once
+        itemsApi.patch_item(itemId, body={'title': row['Name'], 'body': getBodyFromRow(row), 'custom_id': row['ID'], 'metadata': getMetadataFromRow(row)})

examples/data/antibodies.csv

@@ -1,7 +1,7 @@
-Name,Vendor,Vendor Reference,URL,Concentration,Price,Raised in,Recognizes,Comment
-DDX3 (D19B4) Rabbit mAb,Cell Signaling,8192,https://www.cellsignal.com/products/primary-antibodies/ddx3-d19b4-rabbit-mab/8192,100 μg/mL,110,Rabbit,"Human, Mouse, Rat, Monkey",Use at 1:000 for WB
-CAPZB (E4H6C) Rabbit mAb,Cell Signaling,10333,https://www.cellsignal.com/products/primary-antibodies/capzb-e4h6c-rabbit-mab/10333,1 mg/mL,80,Rabbit,"Human, Mouse, Rat",Works very well in WB at 1:10000
-RBAP46/RBAP48 (D4F8) Rabbit mAb,Cell Signaling,9067,https://www.cellsignal.com/products/primary-antibodies/rbap46-rbap48-d4f8-rabbit-mab/9067,5 mg/mL,30,Rabbit,"Human, Mouse, Rat, Monkey","Use at 1:500 for IF, not tested in WB yet. Aliquots done by Éric on July 9th, 2023"
-Phospho-GIT2 (Tyr392) (D8N9A) Rabbit mAb,Cell Signaling,11873,https://www.cellsignal.com/products/primary-antibodies/phospho-git2-tyr392-d8n9a-rabbit-mab/11873,50 μg/mL,300,Rabbit,Human,Got it from Chloé.
-Recombinant Anti-Lamin A + Lamin C antibody [EPR4100] - Nuclear Envelope Marker,Abcam,ab108595,https://www.abcam.com/products/primary-antibodies/lamin-a--lamin-c-antibody-epr4100-nuclear-envelope-marker-ab108595.html,12 μg/mL,250,Rabbit,Human,"The antibody recognizes full length Lamin A/C and the cleaved large unit. We have data to indicate that this antibody gives non-specific staining in IHC with mouse tissues. Based on this we believe the antibody is not suitable for use with mouse samples, as there will be non-specific staining."
-Recombinant Anti-Calcineurin A antibody,Abcam,ab282104,https://www.abcam.com/products/primary-antibodies/calcineurin-a-antibody-epr24997-22-ab282104.html,30 mg/mL,132,Rabbit,"Human, Mouse, Rat",
+Name,ID,Vendor,Vendor Reference,URL,Concentration,Price,Raised in,Recognizes,Comment
+DDX3 (D19B4) Rabbit mAb,3,Cell Signaling,8192,https://www.cellsignal.com/products/primary-antibodies/ddx3-d19b4-rabbit-mab/8192,100 μg/mL,110,Rabbit,"Human, Mouse, Rat, Monkey",Use at 1:000 for WB
+CAPZB (E4H6C) Rabbit mAb,4,Cell Signaling,10333,https://www.cellsignal.com/products/primary-antibodies/capzb-e4h6c-rabbit-mab/10333,1 mg/mL,80,Rabbit,"Human, Mouse, Rat",Works very well in WB at 1:10000
+RBAP46/RBAP48 (D4F8) Rabbit mAb,5,Cell Signaling,9067,https://www.cellsignal.com/products/primary-antibodies/rbap46-rbap48-d4f8-rabbit-mab/9067,5 mg/mL,30,Rabbit,"Human, Mouse, Rat, Monkey","Use at 1:500 for IF, not tested in WB yet. Aliquots done by Éric on July 9th, 2023"
+Phospho-GIT2 (Tyr392) (D8N9A) Rabbit mAb,8,Cell Signaling,11873,https://www.cellsignal.com/products/primary-antibodies/phospho-git2-tyr392-d8n9a-rabbit-mab/11873,50 μg/mL,300,Rabbit,Human,Got it from Chloé.
+Recombinant Anti-Lamin A + Lamin C antibody [EPR4100] - Nuclear Envelope Marker,10,Abcam,ab108595,https://www.abcam.com/products/primary-antibodies/lamin-a--lamin-c-antibody-epr4100-nuclear-envelope-marker-ab108595.html,12 μg/mL,250,Rabbit,Human,"The antibody recognizes full length Lamin A/C and the cleaved large unit. We have data to indicate that this antibody gives non-specific staining in IHC with mouse tissues. Based on this we believe the antibody is not suitable for use with mouse samples, as there will be non-specific staining."
+Recombinant Anti-Calcineurin A antibody,14,Abcam,ab282104,https://www.abcam.com/products/primary-antibodies/calcineurin-a-antibody-epr24997-22-ab282104.html,30 mg/mL,132,Rabbit,"Human, Mouse, Rat","This antibody, a unique guardian in the arsenal of immunity, stands alone in its precision, tailored to target and defend against threats with unparalleled specificity."