PXP-7894: change drs compact uri (#323)

* print current_app

* str current_app

* get object from flask

* :(

* print record contents

* stringify

* print index driver to find default prefix

* default pre

* config

* ToDo change selection to regex

* fix test

* Change how default prefix affects drs compact uri

* Move uri creation out to separate function

* remove prefix remnants from did

* Modified tests to use default prefix from settings

* Remove prints

* Test not quite right, need index driver used during test

* Change test to have no default prefix in index driver settings

* remove unused import

.secrets.baseline

@@ -3,7 +3,7 @@
     "files": null,
     "lines": null
   },
-  "generated_at": "2021-05-25T17:04:07Z",
+  "generated_at": "2021-09-30T18:17:02Z",
   "plugins_used": [
     {
       "name": "AWSKeyDetector"

indexd/drs/blueprint.py

@@ -84,6 +84,32 @@ def get_signed_url(object_id, access_id):
     return res, 200
 
 
+def create_drs_uri(did):
+    """
+    Return ga4gh-compilant drs format uri
+
+    Args:
+        did(str): did of drs object
+    """
+
+    default_prefix = blueprint.index_driver.config.get("DEFAULT_PREFIX")
+
+    if not default_prefix:
+        # For env without DEFAULT_PREFIX, uri will not be drs compliant
+        accession = did
+        self_uri = "drs://{}".format(accession)
+    else:
+        accession = (
+            did.replace(default_prefix, "", 1).replace("/", "", 1).replace(":", "", 1)
+        )
+
+        self_uri = "drs://{}:{}".format(
+            default_prefix.replace("/", "", 1).replace(":", "", 1), accession
+        )
+
+    return self_uri
+
+
 def indexd_to_drs(record, expand=False):
     """
     Convert record to ga4gh-compilant format
@@ -101,7 +127,7 @@ def indexd_to_drs(record, expand=False):
         else record["bundle_id"]
     )
 
-    self_uri = "drs://" + flask.current_app.hostname + "/" + did
+    self_uri = create_drs_uri(did)
 
     name = record["file_name"] if "file_name" in record else record["name"]
 
@@ -197,7 +223,7 @@ def bundle_to_drs(record, expand=False, is_content=False):
         else record["bundle_id"]
     )
 
-    drs_uri = "drs://" + flask.current_app.hostname + "/" + did
+    drs_uri = create_drs_uri(did)
 
     name = record["file_name"] if "file_name" in record else record["name"]
 

tests/test_drs.py

@@ -56,7 +56,26 @@ def test_drs_get(client, user):
         assert rec_2["checksums"][0]["checksum"] == data["hashes"][k]
         assert rec_2["checksums"][0]["type"] == k
     assert rec_2["version"]
-    assert rec_2["self_uri"] == "drs://fictitious-commons.io/" + rec_1["did"]
+    assert rec_2["self_uri"] == "drs://testprefix:" + rec_1["did"].split(":")[1]
+
+
+def test_drs_get_no_default(client, user):
+    # Change default index driver settings to use no prefix
+    settings["config"]["INDEX"]["driver"].config["DEFAULT_PREFIX"] = None
+    settings["config"]["INDEX"]["driver"].config["ADD_PREFIX_ALIAS"] = False
+
+    data = get_doc()
+    did = "ad8f4658-6acd-4f96-0dd8-3709890c959f"
+    data["did"] = did
+    res_1 = client.post("/index/", json=data, headers=user)
+    assert res_1.status_code == 200
+    res_2 = client.get("/ga4gh/drs/v1/objects/" + did)
+    assert res_2.status_code == 200
+    rec_2 = res_2.json
+    assert rec_2["self_uri"] == "drs://" + did
+
+    settings["config"]["INDEX"]["driver"].config["DEFAULT_PREFIX"] = "testprefix:"
+    settings["config"]["INDEX"]["driver"].config["ADD_PREFIX_ALIAS"] = True
 
 
 def test_drs_multiple_endpointurl(client, user):
@@ -187,11 +206,11 @@ def test_get_presigned_url_wrong_access_id(client, user):
 
 def test_get_drs_with_encoded_slash(client, user):
     data = get_doc()
-    data["did"] = "dg.TEST/ed8f4658-6acd-4f96-9dd8-3709890c959e"
+    data["did"] = "testprefix:ed8f4658-6acd-4f96-9dd8-3709890c959e"
     res_1 = client.post("/index/", json=data, headers=user)
     assert res_1.status_code == 200
     rec_1 = res_1.json
-    did = "dg.TEST%2Fed8f4658-6acd-4f96-9dd8-3709890c959e"
+    did = "testprefix%3aed8f4658-6acd-4f96-9dd8-3709890c959e"
     res_2 = client.get("/ga4gh/drs/v1/objects/" + did)
     assert res_2.status_code == 200
     rec_2 = res_2.json
@@ -201,7 +220,7 @@ def test_get_drs_with_encoded_slash(client, user):
         assert rec_2["checksums"][0]["checksum"] == data["hashes"][k]
         assert rec_2["checksums"][0]["type"] == k
     assert rec_2["version"]
-    assert rec_2["self_uri"] == "drs://fictitious-commons.io/" + rec_1["did"]
+    assert rec_2["self_uri"] == "drs://testprefix:" + rec_1["did"].split(":")[1]
 
 
 @responses.activate