Merge pull request #374 from ncihtan/add-htapp-2.1

add htapp 2.1 updates and relocate synapse json to surge
ncihtan · Apr 1, 2022 · cef05dc · cef05dc · vercel · Apr 1, 2022
2 parents b932d9c + cfd4bca
commit cef05dc
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Showing 7 changed files with 457,829 additions and 84,984 deletions.
diff --git a/data/get_syn_data.py b/data/get_syn_data.py
@@ -218,7 +218,10 @@ def generate_json(include_at_risk_populations, include_released_only):
             # only include released data
             if include_released_only and "entityId" in manifest_df.columns:
                 if center in release2_centers:
-                    manifest_df = manifest_df[manifest_df["entityId"].isin(include_release_ids)].copy()
+                    if center == "HTAN HTAPP" and ("Biospecimen" in component or "Diagnosis" in component or "Demographics" in component):
+                        pass
+                    else:
+                        manifest_df = manifest_df[manifest_df["entityId"].isin(include_release_ids)].copy()
                 elif center == "HTAN OHSU":
                     # only include one published case HTA9_1 for now
                     if "HTAN Parent Biospecimen ID" in manifest_df.columns and ("WES" in component or "ATAC" in component or "RNA" in component):

diff --git a/data/syn_metadata.json b/data/syn_metadata.json
@@ -1,20 +1,32 @@
 {
     "HTA1": {
         "Demographics": {
-            "synapseId": "syn25885192",
-            "numItems": 18
+            "synapseId": "syn28271984",
+            "numItems": 2
         },
         "Diagnosis": {
-            "synapseId": "syn25884447",
-            "numItems": 63
+            "synapseId": "syn28272861",
+            "numItems": 2
+        },
+        "Exposure": {
+            "synapseId": "syn25885213",
+            "numItems": 18
+        },
+        "FollowUp": {
+            "synapseId": "syn28260748",
+            "numItems": 13
+        },
+        "MolecularTest": {
+            "synapseId": "syn25885930",
+            "numItems": 108
         },
         "ScRNA-seqLevel1": {
-            "synapseId": "syn27222678",
-            "numItems": 272
+            "synapseId": "syn27223815",
+            "numItems": 242
         },
         "ScRNA-seqLevel2": {
-            "synapseId": "syn27222731",
-            "numItems": 122
+            "synapseId": "syn27224327",
+            "numItems": 87
         },
         "ScRNA-seqLevel3": {
             "synapseId": "syn25113381",
@@ -24,21 +36,21 @@
             "synapseId": "syn27236524",
             "numItems": 801
         },
-        "Exposure": {
-            "synapseId": "syn25884579",
-            "numItems": 63
+        "Therapy": {
+            "synapseId": "syn25885320",
+            "numItems": 58
         },
-        "FamilyHistory": {
-            "synapseId": "syn25884645",
-            "numItems": 63
+        "LungCancerTier3": {
+            "synapseId": "syn25882513",
+            "numItems": 52
         },
-        "FollowUp": {
-            "synapseId": "syn25884716",
-            "numItems": 63
+        "ClinicalDataTier2": {
+            "synapseId": "syn25882773",
+            "numItems": 15
         },
-        "Therapy": {
-            "synapseId": "syn25885086",
-            "numItems": 369
+        "FamilyHistory": {
+            "synapseId": "syn25885235",
+            "numItems": 18
         }
     },
     "HTA11": {
@@ -272,7 +284,7 @@
         },
         "ImagingLevel2": {
             "synapseId": "syn25200520",
-            "numItems": 41
+            "numItems": 78
         },
         "Biospecimen": {
             "synapseId": "syn25110812",