bug fix

healthcareio/__main__.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 """
 (c) 2019 EDI Parser Toolkit, 
 Health Information Privacy Lab, Vanderbilt University Medical Center
@@ -10,12 +11,12 @@ This code is intended to process and parse healthcare x12 837 (claims) and x12 8
 The claims/outpout can be forwarded to a NoSQL Data store like couchdb and mongodb
 Usage :
     Commandline :
-    python x12parser <action>
+    # parse {x12}
+    healthcare-io parse <x12_folder>
+
+    # export {x12}
+    healthcare-io export 
 
-    action:
-        - parser
-        - create.plugin
-        - register.plugin
         - 
     Embedded    :
 
@@ -26,11 +27,12 @@ from typing import Optional
 from typing_extensions import Annotated
 import uuid
 import os
-import version
+import meta
 import json
 import time
 from healthcareio import x12
 from healthcareio.x12.parser import X12Parser
+import requests
 
 # import healthcareio
 # import healthcareio.x12.util
@@ -39,11 +41,12 @@ app = typer.Typer()
 CONFIG_FOLDER = os.sep.join([os.environ['HOME'],'.healthcareio'])
 @app.command(name='init')
 def config(email:str,provider:str='sqlite') :
-    """
+    """\b
     Generate configuration file needed with default data store. For supported data-store providers visit https://hiplab.mc.vanderbilt.edu/git/hiplab/data-transport.git
     
     :email      your email    
-    \r:provider   data store provider (visit https://hiplab.mc.vanderbilt.edu/git/hiplab/data-transport.git)
+    
+    :provider   data store provider (visit https://hiplab.mc.vanderbilt.edu/git/hiplab/data-transport.git)
     """
     _db = "healthcareio"
     # _PATH = os.sep.join([os.environ['HOME'],'.healthcareio'])
@@ -62,27 +65,55 @@ def config(email:str,provider:str='sqlite') :
         "system":{
             "uid":str(uuid.uuid4()),
             "email":email,
-            "version":version.__version__,
-            "copyright":version.__author__
+            "version":meta.__version__,
+            "copyright":meta.__author__
 
         }
     }
     #
+    # Let create or retrieve a user's key/token to make sure he/she has access to features they need
+    # This would also allow us to allow the users to be informed of new versions
+    #
+    try:
+        host = "https://healthcareio.the-phi.com" if 'PARSER_HOST_URL' not in os.environ else os.environ['PARSER_HOST']
+        url = f"{host}/api/users/signup"
+        _body = {"email":email,"version":meta.__version__}
+        _headers = {"content-type":"application/json"}
+        resp  = requests.post(url,headers=_headers,data=json.dumps(_body))
+        if resp.ok :
+            _config['system'] = dict(_config['system'],**resp.json())
+    except Exception as e:
+        print (e)
+        pass
     # store this on disk
     f = open(os.sep.join([CONFIG_FOLDER,'config.json']),'w')
     f.write(json.dumps(_config))
     f.close()
+    _msg = f"""
+        Thank you for considering using our {{x12}} parser verion {meta.__version__}
+        The generatted configuration file found at {CONFIG_FOLDER}
+        The database provider is {provider}
+
+        visit {host} to learn more about the features,
+    
+    """
+
+    print (_msg)
 @app.command(name='about')
 def copyright():
 
-    for note in [version.__name__,version.__author__,version.__license__]:
+    for note in [meta.__name__,meta.__author__,meta.__license__]:
         print (note)
 
     pass
 @app.command()
 def parse (claim_folder:str,plugin_folder:str = None,config_path:str = None):
     """
-    This function will parse 837 and or 835 claims given a location of  parsing given claim folder and/or plugin folder
+    This function will parse 837 and or 835 claims given a location of  parsing given claim folder and/or plugin folder.
+    
+    plugin_folder   folder containing user defined plugins (default are loaded)
+    
+    config_path     default configuration path
     """
     
     _plugins,_parents   = x12.plugins.instance(path=plugin_folder)
@@ -94,7 +125,7 @@ def parse (claim_folder:str,plugin_folder:str = None,config_path:str = None):
         _config  = json.loads(f.read())
         f.close()
         _store = _config['store']
-        # print (len(_files))
+    #     # print (len(_files))
         jobs = []
         for _chunks in _files:
             pthread = X12Parser(plugins=_plugins,parents=_parents,files=_chunks, store=_store)
@@ -103,11 +134,29 @@ def parse (claim_folder:str,plugin_folder:str = None,config_path:str = None):
         while jobs :
             jobs = [pthread for pthread in jobs if pthread.is_alive()]
             time.sleep(1)
-        pass
-    else:
-        pass
+    #     pass
+    # else:
+    #     pass
+    print ("...................... FINISHED .........................")
     #
     #
+
+@app.command(name="export")    
+def publish (file_type:str,path:str):
+    """
+    This function will export to a different database
+    file_type       values are either claims or remits 
+    
+    path            path to export configuration (data transport file)
+
+    file_type       claims or remits
+    """
+    if file_type in ['837','claims'] :
+        _type = 'claims'
+    elif file_type in ['835','remits']:
+        _type = 'remits'
+    
+        
 if __name__ == '__main__' :
     
     app()

healthcareio/x12/parser.py

@@ -7,6 +7,7 @@ import os
 import json
 # from  healthcareio.x12.util
 from healthcareio import x12
+from healthcareio.x12.util import file, document
 import numpy as np
 import transport
 import copy
@@ -14,19 +15,21 @@ import copy
 from datetime import datetime
 from healthcareio.logger import X12Logger
 import time
+import pandas as pd
+
+
 class BasicParser (Process) :
     def __init__(self,**_args):
         super().__init__()
         self._plugins   = _args['plugins']
         self._parents   = _args['parents']
         self._files     = _args['files'] 
-        self._store     = _args['store']
+        self._store     = dict(_args['store'],**{'lock':True})
         self._template = x12.util.template(plugins=self._plugins)
-        # self._logger    = _args['logger'] if 'logger' in _args else None
         self._logger = X12Logger(store = self._store)
         if self._logger :
             _info = { key:len(self._plugins[key].keys())for key in self._plugins}
-            _data = {'plugins':_info,'files': len(self._files),'model':self._template}
+            _data = {'plugins':_info,'files': len(self._files),'model': self._template}
             self._logger.log(module='BasicParser',action='init',data=_data)
             
     def log (self,**_args):
@@ -34,6 +37,8 @@ class BasicParser (Process) :
         This function logs data into a specified location in JSON format
             datetime,module,action,data
         """
+        if self._logger :
+            self._logger.log(**_args)
         pass
     def apply(self,**_args):
         """
@@ -44,15 +49,17 @@ class BasicParser (Process) :
         _content    = _args['content']
         _filetype   = _args['x12']
         _doc        = _args['document'] #{}
-        _documentHandler = x12.util.document.Builder(plugins = self._plugins,parents=self._parents)
-        try:
         
+        _documentHandler = x12.util.document.Builder(plugins = self._plugins,parents=self._parents, logger=self._logger)
+        try:
+            _tmp = {}
             for _row in _content :
                 # _data = None
                 
                 _data,_meta = _documentHandler.bind(row=_row,x12=_filetype)
                 
                 if _data and _meta :
+                    
                     _doc = _documentHandler.build(data=_data,document=_doc,meta=_meta,row=_row)
                     # print (['*** ',_doc])
                     pass
@@ -61,15 +68,18 @@ class BasicParser (Process) :
         except Exception as e:
             #
             # Log something here ....
-            print (_row)
+            # print (_row)
+            
             print (e)
             # print (_row,_doc.keys())
             pass
         return _doc
     def run(self):
-        _handleContent = x12.util.file.Content()
-        _handleDocument = x12.util.document.Builder(plugins = self._plugins,parents=self._parents)
+        _handleContent = file.Content() #x12.util.file.Content()
+        _handleDocument = document.Builder(plugins = self._plugins,parents=self._parents,logger=self._logger) 
+        
         _template = self._template #x12.util.template(plugins=self._plugins)
+        
         #
         # @TODO: starting initializing parsing jobs :
         #   - number of files, plugins meta data
@@ -89,10 +99,14 @@ class BasicParser (Process) :
                 _header = copy.deepcopy(_template[_filetype])
                 _header = self.apply(content=_content[0],x12=_filetype, document=_header)
                 _docs = []
-                
+                _ids = []
                 for _rawclaim in _content[1:] :
                     
                     _document = copy.deepcopy(_header) #copy.deepcopy(_template[_filetype])
+                    if 'claim_id' in _document :
+                        #
+                        # @TODO: Have a way to get the attribute for CLP or CLM
+                        _ids.append(_document['claim_id'])
                     # _document = dict(_document,**_header)
                     if  type(_absolute_path) == str:
                         _document['filename'] = _absolute_path
@@ -108,7 +122,9 @@ class BasicParser (Process) :
                 _data = {'filename':_location, 'available':len(_content[1:]),'x12':_filetype}
                 _args = {'module':'parse','action':'parse','data':_data}
                 _data['parsed'] = len(_docs)
-                self._logger.log(**_args)
+
+                self.log(**_args)
+                self.log(module='parse',action='file-count', data={'file_name':_absolute_path,'file_type':_filetype,'claims':_ids, 'claim_count':len(_ids)})
                 #
                 # Let us submit the batch we have thus far
                 #
@@ -135,78 +151,17 @@ class X12Parser(BasicParser):
         
         _documents = _args['documents']
         if _documents :
-            _store = copy.copy(self._store,**{})
+            _store = copy.deepcopy(self._store)
             TABLE = 'claims' if _args['x12'] in ['837','claims'] else 'remits'
             _store['table'] = TABLE
+            _store['cotnext'] = 'write'
             
             _writer = transport.factory.instance(**_store)                        
-            _writer.write(_documents)
+            _writer.write(_documents,table=TABLE)
             if getattr(_writer,'close') :
                 _writer.close()
         #
         # LOG: report what was written
         _data = {'x12':_args['x12'], 'documents':len(_documents),'filename':_args['filename']}
-        self._logger.log(module='write',action='write',data=_data)
-
-# def instance (**_args):
-#     """
-#     :path
-#     """
-#     # _files = x12.util.Files.get(_args['file'])
-    
-#     # #
-#     # # We can split these files (multi-processing)
-#     # #
-#     # _jobCount = 1 if 'jobs' not in _args else int (_args['jobs'])
-#     # _files = np.array_split(_files,_jobCount)
-#     # PATH = os.sep.join([os.environ['HOME'],'.healthcareio','config.json'])
-#     # if 'config' in _args :
-#     #     PATH = _args['config']
-#     # f = open(PATH)
-#     # _config = json.loads(f.read())
-#     # f.close()
-#     # jobs = []
-#     # for _batch in _files :
-#     #     pthread = Parser(files=_batch,config=_config)
-#     #     pthread.start()
-#     #     jobs.append(pthread)
-#     #     time.sleep(1)
-#     pass
-
-
-# class parser (Process) :
-#     _CONFIGURATION = {}
-#     def __init__(self,path=None) :
-#         if not parser._CONFIGURATION :
-#             _path = path if path else os.sep.join([os.environ['HOME'],'.healthcareio/config.json'])
-#             #
-#             # @TODO: Load custom configuration just in case we need to do further processing
-#             config = json.loads(open(path).read())
-#             parser._CONFIGURATION = config['parser']
-#             #
-#             # do we have a custom configuration in this location
-#             #
-#             _custompath = _path.replace('config.json','')
-#             _custompath = _custompath if not _custompath.endswith(os.sep) else _custompath[:-1]
-#             _custompath = os.sep.join([_custompath,'custom'])
-#             if os.exists(_custompath) :
-#                 files = os.listdir(_custompath)
-#                 if files :
-#                     _filename = os.sep.join([_custompath,files[0]])
-#                     _customconf = json.loads(open(_filename).read())
-#                     #
-#                     # merge with existing configuration
-
-            
-#         else:
-#             pass
-
-#         #
-#         #
-#     class getter :
-#         def value(self,) :
-#             pass
-#     class setter :
-#         def files(self,files):
-#             pass
-        
+        # self._logger.log(module='write',action='write',data=_data)
+        self.log(module='parse',action='write',data=_data)

healthcareio/x12/plugins/default/claims.py

@@ -1,7 +1,7 @@
 import numpy as np
 from .. import parser
 from datetime import datetime
-@parser(element='NM1',x12='*', anchor={'41':'submitter','40':'receiver','82':'rendering_provider','85':'billing_provider','87':'pay_to_provider','IL':'patient','PR':'payer','QC':'patient','DN':'referring_provider','77':'provider','2':'billing_provider'}, map={1:'type',3:'name',-1:'id'})    
+@parser(element='NM1',x12='*', anchor={'41':'submitter','40':'receiver','82':'rendering_provider','85':'billing_provider','87':'pay_to_provider','IL':'patient','PR':'payer','QC':'patient','DN':'referring_provider','77':'provider','2':'billing_provider'}, map={1:'type',3:'name_1',4:'name_2',-1:'id'})    
 def NM1 (**_args):
     """
     Expected Element NM1

healthcareio/x12/plugins/default/remits.py

@@ -57,9 +57,9 @@ def SVC (**_args):
     _data['paid_amount'] = np.float64(_data['paid_amount'])
     return _data
     pass
-@parser(element='N1',x12='835',anchor={'PR':'provider'},map={1:'name'})
-def N1(**_args):
-    pass
+# @parser(element='N1',x12='835',anchor={'PR':'provider'},map={1:'name'})
+# def N1(**_args):
+#     pass
 @parser(element='N3',x12='835',parent='N1',map={1:'address_line_1'})
 def N3(**_args):
     pass

healthcareio/x12/util/document.py

@@ -15,7 +15,7 @@ class Builder:
         self._plugins = copy.deepcopy(_args['plugins'])
         self._parents = copy.deepcopy(_args['parents'])
         self._loop = {}
-    
+        self._logger = None if 'logger' not in _args else _args['logger']
         
     def reset (self):
         self._last = {}
@@ -33,33 +33,6 @@ class Builder:
                 return  self._last[_id] if _id in self._last else None
         return None
    
-        # if _id in self._parents :
-        #     self._last[_id] = 
-
-        # if 'parent' in _meta : #hasattr(_meta,'parent'):
-        #     _hasField = 'field' in _meta 
-        #     _hasParent= _meta['element'] in self._parents
-        #     if _hasField and _hasParent: #_meta.element in self._parents  and hasattr(_meta,'field'):
-                
-        #         self._last = _item
-        #         pass
-        #     else:
-        #         for key in self._parents :
-        #             if _meta['element'] in self._parents[key] :
-                        
-        #                 _ikey       = list(self._last.keys())[0]
-        #                 _oldinfo    = self._last[_ikey]
-        #                 if type(_oldinfo) != dict :
-        #                     #
-        #                     # Only applicable against a dictionary not a list (sorry)
-        #                     pass
-        #                 else:
-        #                     _item  = {_ikey: self.merge(_oldinfo,_item)}
-                        
-        #                 break
-        #         pass
-        
-        # return _item   
     def count(self,_element):
         if _element not in self._loop :
             self._loop[_element] = 0
@@ -251,10 +224,12 @@ class Builder:
         if _field :
             if 'container' in _meta and type(_document[_field]) != list :
                 _document[_field] = []
-        if _field and _document:
+
+        if _field and _document :
             
             if _field not in _document :
                 _document[_field] =_data
+                pass
             else:
                 if 'container' in _meta :
                     _document[_field].append(_data)
@@ -263,9 +238,23 @@ class Builder:
         else:
             if not _field and 'anchor' in _meta :
                 #
-                # This is an unusual situation ...
+                # We should determine if the element is either a parent or has a parent
+                # This would allow us to avoid having runaway attributes and undermine structural integrity
+                #
+                
+                    
+                #
+                # The element has NOT been specified by the plugin (alas)
+                # For this case we would advise writing a user-defined plugin to handle this case
+                #
+                print (self._logger)
+                if self._logger :
+                    print (['....................'])
+                    self._logger.log(action='missing-plugin',module='build',data={'element':_row[0],'anchor':_row[1]})
+
+                return _document
                 pass
+            # print ([_row[0],set(_data) -  set(_document.keys())])
             _document = self.merge(_document,_data)
         return _document
 
-

setup.py

@@ -14,13 +14,13 @@ args = {
     "author":meta.__author__,
     "author_email":"steve.l.nyemba@vumc.org",
     "include_package_data":True,
-    "license":version.__license__,
+    "license":meta.__license__,
     "packages":find_packages(),
     "keywords":["healthcare","edi","x12","analytics","835","837","data","transport","protocol"]
 }
-args["install_requires"] = ['typer','flask-socketio','seaborn','jinja2','jsonmerge', 'weasyprint','data-transport@git+https://healthcareio.the-phi.com/git/code/transport.git','pymongo','numpy','cloudant','pika','boto','botocore','flask-session','smart_open','smart-top@git+https://healthcareio.the-phi.com/git/code/smart-top.git@data-collector']
+args["install_requires"] = ['typer','flask-socketio','seaborn','jinja2','jsonmerge', 'weasyprint','data-transport@git+https://healthcareio.the-phi.com/git/code/transport.git','pymongo','numpy','cloudant','pika','boto','botocore','flask-session','smart_open']
 args['url'] = 'https://hiplab.mc.vanderbilt.edu'
-args['scripts']= ['healthcareio/healthcare-io.py']
+args['scripts']= ['bin/healthcare-io']
 # args['entry_points'] = {
 #     'console_scripts'  : ['healthcareio=healthcareio:register']
 # }