bug fix: with references

README.md

@@ -60,6 +60,10 @@ We wrote this frame to be used in both command line or as a library within in yo
             --config    configuration to support data-store
         
     
+    **NOTE**
+
+    The output generates a set of tables that are the result of transforming unstructured data to relational structure. The tables can be bound with the attribute **_id**
+
     The configuration file needed to implement export is modelled after the following template:
 
 

healthcareio/export/export.py

@@ -83,23 +83,31 @@ def meta(config) :
         
         if type(config[prefix]) != dict :
             continue
-        if '@ref' in config[prefix] and set(['label','field','map']) & set(config[prefix]['@ref'].keys()):
+       
+        if '@ref' in config[prefix] : #and set(['label','field','map']) & set(config[prefix]['@ref'].keys()):
             for subprefix in config[prefix]['@ref'] :
                 _entry = config[prefix]['@ref'][subprefix]
-                _info += get_field(_entry)
+                if 'map' in _entry :
+                    _info += get_field(_entry)
+                else:
+                    _info += list(_entry.keys())
         elif set(['label','field','map']) & set(config[prefix].keys()):
             _entry = config[prefix]
             if 'map' in _entry :
                 _info += get_field(_entry)
             
 
+
     #
     # We need to organize the fields appropriately here
     #
+    
     fields = {"main":[],"rel":{}}
     for row in _info :
         if type(row) == str :
             fields['main'] += [row]
+            fields['main'] = list(set(fields['main']))
+            fields['main'].sort()
         else :
             
             fields['rel'] = jsonmerge.merge(fields['rel'],row)

healthcareio/export/workers.py

@@ -8,27 +8,58 @@
 """
 import transport
 import os
-from multiprocessing import Process
+from multiprocessing import Process, Lock
 import numpy as np
 import json
+import pandas as pd
+
 class Subject (Process):
+    cache = pd.DataFrame()
+    lock = Lock()
+    @staticmethod
+    def log(_args):
+        Subject.lock.acquire()
+        try:
+            Subject.cache = Subject.cache.append(pd.DataFrame([_args]))
+        except Exception as e :
+            print (e)
+        finally:
+            Subject.lock.release()
     def __init__(self,**_args):
         super().__init__()
         self.observers = _args['observers']
         self.index = 0
         self.name = _args['name']
         self.table = self.observers[1].table
+        self.m = {}
+        
+        
         pass
     def run(self):        
         self.notify()
     def notify(self):
         if self.index < len(self.observers) :
+            
             observer = self.observers[self.index]             
             _observer = None if self.index == 0 else self.observers[self.index -1]
             _invalues = None if not _observer else _observer.get()
+            if _observer is None :
+                self.m['table'] = self.name
+                
+
+
+
             observer.init(caller=self,invalues = _invalues)        
             self.index += 1            
             observer.execute()
+            print ({"table":self.table,"module":observer.name(),"status":observer.status})
+            # self.m[observer.name()] = observer.status
+            
+        else:
+            pass
+            
+            
+            
         
 class Worker :
     def __init__(self,**_args):
@@ -38,6 +69,7 @@ class Worker :
         self.logs = []
         self.schema = _args['schema']
         self.prefix = _args['prefix']
+        self.status = 0
         
     def name(self):
         return self.__class__.__name__ 
@@ -45,7 +77,7 @@ class Worker :
         """
         This function is designed to log to either the console or a data-store
         """
-        print (_args)
+        # print (_args)
         pass
     def init(self,**_args):
         """
@@ -60,9 +92,10 @@ class Worker :
         try:
             self._apply()
         except Exception as error:
-            print ()
+            pass
-            print (error)
+            # print ()
-            print ()
+            # print (error)
+            # print ()
         finally:
             
             self.caller.notify() 
@@ -101,10 +134,12 @@ class CreateSQL(Worker) :
             writer.apply(self._sql.replace(":table",sqltable))
             writer.close()
             log['status'] = 1
+            self.status = 1
         except Exception as e:
             log['status'] = 0
             log['info']  = {"error":e.args[0]}
-            print (e)
+            
+            # print (e)
         finally:
             self.log(**log)
 
@@ -141,25 +176,28 @@ class Reader(Worker):
         self.rows = []
   
     def _apply(self):
-        self.reader = transport.factory.instance(**self._info) ; 
+        try:
-        print()
+            self.reader = transport.factory.instance(**self._info) ; 
-        print (self.table)
+            self.rows = self.reader.read(mongo=self.pipeline)
-        print (json.dumps(self.pipeline))
-        print ()
-        self.rows = self.reader.read(mongo=self.pipeline)
 
-        N = len(self.rows) / self.MAX_ROWS  if len(self.rows) > self.MAX_ROWS else 1
+            N = len(self.rows) / self.MAX_ROWS  if len(self.rows) > self.MAX_ROWS else 1
-        N = int(N) 
+            N = int(N) 
-        # self.rows = rows
+            # self.rows = rows
-        _log = {"context":self.name(),"args":self._info['args']['db'], "status":1,"info":{"rows":len(self.rows),"table":self.table,"segments":N}}
+            _log = {"context":self.name(),"args":self._info['args']['db'], "status":1,"info":{"rows":len(self.rows),"table":self.table,"segments":N}}
-        self.rows  = np.array_split(self.rows,N)
+            self.rows  = np.array_split(self.rows,N)
 
             
-        # self.get = lambda : rows #np.array_split(rows,N)
+            # self.get = lambda : rows #np.array_split(rows,N)
-        self.reader.close()
+            self.reader.close()
+            self.status = 1
+            #
+        except Exception as e :
+            log['status'] = 0
+            log['info']  = {"error":e.args[0]}
+            
 
-        #
         self.log(**_log)
+        
         # @TODO: Call the caller and notify it that this here is done
     def get(self):       
         return self.rows
@@ -202,7 +240,7 @@ class Writer(Worker):
                     # writer.write(_e) 
 
         
-                
+            self.status  = 1            
         else:
             print ("No data was passed")
         

healthcareio/healthcare-io.py

@@ -391,14 +391,18 @@ if __name__ == '__main__' :
             
             pipes = export.Factory.instance(type=TYPE,write_store=_store) #"inspect":0,"cast":0}})  
             # pipes[0].run()
+            
             for thread in pipes:
                 if 'table' in SYS_ARGS and SYS_ARGS['table'] != thread.table :
                     continue 
                 thread.start()
                 time.sleep(1)                
-            while pipes :
+                thread.join()
-                pipes = [thread for thread in pipes if thread.is_alive()]     
+            
-                time.sleep(1)       
+            # print (Subject.cache)
+            # while pipes :
+            #     pipes = [thread for thread in pipes if thread.is_alive()]     
+            #     time.sleep(1)       
 
 
         

setup.py

@@ -8,7 +8,7 @@ import sys
 def read(fname):
     return open(os.path.join(os.path.dirname(__file__), fname)).read() 
 args = {
-    "name":"healthcareio","version":"1.5.9.1",
+    "name":"healthcareio","version":"1.5.6",
     "author":"Vanderbilt University Medical Center",
     "author_email":"steve.l.nyemba@vumc.org",
     "include_package_data":True,