Merge pull request #40 from Sage-Bionetworks/gh-28-add-bladder

add bladder class

geniesp/__main__.py

@@ -3,7 +3,7 @@
 
 import synapseclient
 
-from .bpc_config import Brca, Crc, Nsclc, Panc, Prostate
+from .bpc_config import Brca, Crc, Nsclc, Panc, Prostate, Bladder
 from .sp_config import Akt1, Erbb2, Fgfr4
 
 BPC_MAPPING = {
@@ -12,6 +12,7 @@
     "BrCa": Brca,
     "PANC": Panc,
     "Prostate": Prostate,
+    "BLADDER": Bladder,
     "AKT1": Akt1,
     "ERRB2": Erbb2,
     "FGFR4": Fgfr4,

geniesp/bpc_config.py

@@ -105,3 +105,23 @@ class Prostate(BpcProjectRunner):
         # "tree/a672a70ad5195e6e8359325f5cea10bef384b2ff/"
         # "geniesp/bpc_config.py"
     )
+
+class Bladder(BpcProjectRunner):
+    """NSCLC BPC sponsored project"""
+
+    # Sponsorted project name
+    _SPONSORED_PROJECT = "BLADDER"
+    # Redcap codes to cbioportal mapping synid and form key is in
+    _REDCAP_TO_CBIOMAPPING_SYNID = "syn25712693.14"
+    # Mapping from Synapse Table to form (derived files)
+    _DATA_TABLE_IDS = "syn22296821"
+    # Storage of not found samples
+    _SP_REDCAP_EXPORTS_SYNID = "syn21446571"
+    # Run `git rev-parse HEAD` in Genie_processing directory to
+    # obtain shadigest
+    _GITHUB_REPO = (
+        "https://github.com/Sage-Bionetworks/GENIE-Sponsored-Projects/"
+        # "tree/a672a70ad5195e6e8359325f5cea10bef384b2ff/"
+        # "geniesp/bpc_config.py"
+    )
+