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progenetix · Oct 21, 2024 · 12e29a0 · 12e29a0
1 parent 5c085ed
commit 12e29a0
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Showing 31 changed files with 479 additions and 355 deletions.
diff --git a/bycon/byconServiceLibs/export_file_generation.py b/bycon/byconServiceLibs/export_file_generation.py
@@ -61,12 +61,10 @@ def pgxseg_biosample_meta_line(biosample, group_id_key="histological_diagnosis_i
     g_lab_k = re.sub("_id", "_label", g_id_k)
     line = [ f'#sample=>id={biosample.get("id", "¡¡¡NONE!!!")}' ]
     for par, par_defs in io_params.items():
-        if (in_pgxseg := par_defs.get("compact", False)) is False:
-            continue
-
         parameter_type = par_defs.get("type", "string")
-        db_key = par_defs.get("db_key", "___undefined___")
-        p_type =par_defs.get("type", "string")
+        if not (db_key := par_defs.get("db_key")):
+            continue
+        p_type = par_defs.get("type", "string")
         v = get_nested_value(biosample, db_key, p_type)
         h_v = ""
         if isinstance(v, list):

diff --git a/bycon/byconServiceLibs/service_helpers.py b/bycon/byconServiceLibs/service_helpers.py
@@ -18,7 +18,7 @@ def __init__(self, sleep=0.01):
     #----------------------------- public -------------------------------------#
     #--------------------------------------------------------------------------#
 
-    def makeID(prefix=""):
+    def makeID(self, prefix=""):
         time.sleep(self.sleep)
         linker = "-" if len(str(prefix)) > 0 else ""
         return f'{prefix}{linker}{base36.dumps(int(time.time() * 1000))}'