bug fixes and interface

healthcareio/__main__.py

@@ -10,8 +10,104 @@ 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 xreader.py --parse claims|remits --config <path>
+    python x12parser <action>
+
+    action:
+        - parser
+        - create.plugin
+        - register.plugin
+        - 
     Embedded    :
 
 """
 # import healthcareio
+import typer
+from typing import Optional
+from typing_extensions import Annotated
+import uuid
+import os
+import version
+import json
+import time
+from healthcareio import x12
+from healthcareio.x12.parser import X12Parser
+
+# import healthcareio
+# import healthcareio.x12.util
+# from healthcareio.x12.parser import X12Parser
+app = typer.Typer()
+CONFIG_FOLDER = os.sep.join([os.environ['HOME'],'.healthcareio'])
+@app.command(name='init')
+def config(email:str,provider:str='sqlite') :
+    """
+    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)
+    """
+    _db = "healthcareio"
+    # _PATH = os.sep.join([os.environ['HOME'],'.healthcareio'])
+    
+    if not os.path.exists(CONFIG_FOLDER) :
+        os.mkdir(CONFIG_FOLDER)
+
+    if provider in ['sqlite','sqlite3'] :        
+        _db = os.sep.join([CONFIG_FOLDER,_db+'.db3'])
+
+    _config = {
+        "store":{
+            "provider":provider,"database":_db,"context":"write"
+        },
+        "plugins":None,
+        "system":{
+            "uid":str(uuid.uuid4()),
+            "email":email,
+            "version":version.__version__,
+            "copyright":version.__author__
+
+        }
+    }
+    #
+    # store this on disk
+    f = open(os.sep.join([CONFIG_FOLDER,'config.json']),'w')
+    f.write(json.dumps(_config))
+    f.close()
+@app.command(name='about')
+def copyright():
+
+    for note in [version.__name__,version.__author__,version.__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
+    """
+    
+    _plugins,_parents   = x12.plugins.instance(path=plugin_folder)
+    _files              = x12.util.file.Location.get(path=claim_folder,chunks=10)
+    _path = config_path if config_path else os.sep.join([CONFIG_FOLDER,'config.json'])
+    
+    if os.path.exists(_path) :
+        f = open(_path)
+        _config  = json.loads(f.read())
+        f.close()
+        _store = _config['store']
+        # print (len(_files))
+        jobs = []
+        for _chunks in _files:
+            pthread = X12Parser(plugins=_plugins,parents=_parents,files=_chunks, store=_store)
+            pthread.start()
+            jobs.append(pthread)
+        while jobs :
+            jobs = [pthread for pthread in jobs if pthread.is_alive()]
+            time.sleep(1)
+        pass
+    else:
+        pass
+    #
+    #
+if __name__ == '__main__' :
+    
+    app()

healthcareio/healthcare-io.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+                                                                                                                                                        #!/usr/bin/env python3
 """
 (c) 2019 Claims Toolkit, 
 Health Information Privacy Lab, Vanderbilt University Medical Center

healthcareio/version.py

@@ -1,5 +1,5 @@
 __author__ = 'The Phi Technology LLC'
-__version__ = '1.0'
+__version__ = '2.0-RC'
 __license__ = """
 (c) 2019 EDI Parser Toolkit, 
 Health Information Privacy Lab, Vanderbilt University Medical Center & The Phi Technology
@@ -8,10 +8,18 @@ Steve L. Nyemba <steve.l.nyemba@vumc.org>
 Khanhly Nguyen <khanhly.t.nguyen@gmail.com>
 
 
-This code is intended to process and parse healthcare x12 837 (claims) and x12 835 (remittances) into human readable JSON format.
-The claims/outpout can be forwarded to a NoSQL Data store like couchdb and mongodb
+This framework is intended to parse and structure healthcare x12 837 (claims) and x12 835 (remittances) into human readable formats
+- ( parse {x12} ) --> ( store as JSON ) --> ( export to database)
+
+The supported databases are mysql, postgresql, sqlite3, mongodb, couchdb ... 
+More information on supported databases is available at https://hiplab.mc.vanderbilt.edu/git/hiplab/data-transport.git
+
+Sample 835 and 837 claims (zipped) are available for download at https://x12.org/examples/
+
 Usage :
     Commandline :
     python xreader.py --parse claims|remits --config <path>
+    
     Embedded    :
-"""
+"""
+__name__ = "Healthcare/IO::Parser "+__version__

healthcareio/x12/__init__.py

@@ -21,6 +21,11 @@ import hashlib
 import json
 import os
 import sys
+# version 2.0
+# import util
+# from parser import X12Parser
+#-- end
+
 from itertools import islice
 from multiprocessing import Process
 import transport

healthcareio/x12/parser.py

@@ -11,8 +11,8 @@ import numpy as np
 import transport
 import copy
 # from healthcareio.x12.util import file as File, document as Document
-
-
+from datetime import datetime
+from healthcareio.logger import X12Logger
 import time
 class BasicParser (Process) :
     def __init__(self,**_args):
@@ -21,8 +21,26 @@ class BasicParser (Process) :
         self._parents   = _args['parents']
         self._files     = _args['files'] 
         self._store     = _args['store']
-    
+        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}
+            self._logger.log(module='BasicParser',action='init',data=_data)
+            
+    def log (self,**_args):
+        """
+        This function logs data into a specified location in JSON format
+            datetime,module,action,data
+        """
+        pass
     def apply(self,**_args):
+        """
+        :content    raw claim i.e CLP/CLM Loops and related content
+        :x12        file type 837|835
+        :document   document template with attributes pre-populated
+        """
         _content    = _args['content']
         _filetype   = _args['x12']
         _doc        = _args['document'] #{}
@@ -51,20 +69,27 @@ class BasicParser (Process) :
     def run(self):
         _handleContent = x12.util.file.Content()
         _handleDocument = x12.util.document.Builder(plugins = self._plugins,parents=self._parents)
-        _template = _plugins,_parents = x12.util.template(plugins=self._plugins)
+        _template = self._template #x12.util.template(plugins=self._plugins)
+        #
+        # @TODO: starting initializing parsing jobs :
+        #   - number of files, plugins meta data
+
+        _log = {}
         for _absolute_path in self._files :
             try:
                 
                 _content = _handleContent.read(filename=_absolute_path)                
                 _content,_filetype = _handleContent.split(_content)
                 
+                #
+                # LOG: filename with claims found in it
+                
                 #
                 # The first row is the header (it will be common to all claims)
                 _header = copy.deepcopy(_template[_filetype])
                 _header = self.apply(content=_content[0],x12=_filetype, document=_header)
                 _docs = []
                 
-                
                 for _rawclaim in _content[1:] :
                     
                     _document = copy.deepcopy(_header) #copy.deepcopy(_template[_filetype])
@@ -72,26 +97,30 @@ class BasicParser (Process) :
                     if  type(_absolute_path) == str:
                         _document['filename'] = _absolute_path
                     _doc = self.apply(content=_rawclaim,x12=_filetype, document=_document)
-                    if _doc :
-                        #
-                        # @TODO: Make sure the test here is the existence of the primary key
-                        # _doc = _handleDocument.merge(_doc,_header)
-                        
-                        
+                    if _doc :                                               
                         _docs.append(_doc)
                     else:
                         # print (['wtf ...',_rawclaim])
                         pass
                 #
+                # LOG: information abou the file that has just been processed.
+                _location = _absolute_path if type(_absolute_path) == str else 'In-Memory'
+                _data = {'filename':_location, 'available':len(_content[1:]),'x12':_filetype}
+                _args = {'module':'parse','action':'parse','data':_data}
+                _data['parsed'] = len(_docs)
+                self._logger.log(**_args)
+                #
                 # Let us submit the batch we have thus far
                 #
                 
-                self.post(documents=_docs,type=_filetype)
+                self.post(documents=_docs,x12=_filetype,filename=_location)
 
 
 
             except Exception as e:
-                
+                #
+                # LOG: We have filename and segment of the claim within filename
+                #
                 print (e)
     def post(self,**_args):
         pass
@@ -107,14 +136,17 @@ class X12Parser(BasicParser):
         _documents = _args['documents']
         if _documents :
             _store = copy.copy(self._store,**{})
-            TABLE = 'claims' if _args['type'] in ['837','claims'] else 'remits'
+            TABLE = 'claims' if _args['x12'] in ['837','claims'] else 'remits'
             _store['table'] = TABLE
             
             _writer = transport.factory.instance(**_store)                        
             _writer.write(_documents)
             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):
 #     """

healthcareio/x12/plugins/__init__.py

@@ -138,7 +138,7 @@ def instance(**_args):
     _map['835'] = _handler.merge(_map['*'],_map['835'])
     _map['837'] = _handler.merge(_map['*'],_map['837'])
     
-    if 'path' in _args:
+    if 'path' in _args and _args['path']:
         #
         # We can/will override the default modules given the user has provided a location
         # _module = imp.load_source('udf',_args['path'])
@@ -249,331 +249,331 @@ def filter (**_args) :
             
             _map[x12] = {key:_item[key] for key in _found }
     return _map
-def getTableName(**_args) :
-    _plugins = _args['plugins']
-    _meta = _args['meta']
-    _x12 = _meta['x12']
-    _foreignkeys = _args['tableKeys']
-    _attributes = list(_meta['map'].values()) if 'map' in _meta else _meta['columns']
-    if 'field' in _meta or 'container' in _meta:
-        _tableName = _meta['field'] if 'field' in _meta else _meta['container']
+# def getTableName(**_args) :
+#     _plugins = _args['plugins']
+#     _meta = _args['meta']
+#     _x12 = _meta['x12']
+#     _foreignkeys = _args['tableKeys']
+#     _attributes = list(_meta['map'].values()) if 'map' in _meta else _meta['columns']
+#     if 'field' in _meta or 'container' in _meta:
+#         _tableName = _meta['field'] if 'field' in _meta else _meta['container']
         
-        # _table = {_id:_attributes}
+#         # _table = {_id:_attributes}
     
-    elif 'anchor' in _meta :
-        _tableName = _meta['anchor'].values()
-        # for _name in _meta['anchor'].values() :
-        #     _table[_name] = _attributes
-    elif 'parent' in _meta and _meta['parent']:
-        #
-        # We can have a parent with no field/container/anchor
-        # We expect either a map or columns ...
-        #
-        _parentElement = _meta['parent']
-        _parentMeta = _plugins[_x12][_parentElement].meta
-        _parentTable = getTableName(plugins=_plugins,meta = _parentMeta,tableKeys=_foreignkeys)
-        _tableName = list(_parentTable.keys())[0]
-        # _table[_id] = _parentTable[_id] + _attributes
-        _attributes = _parentTable[_tableName] + _attributes
-        # print (_meta)
-    else:
-        #
-        # baseline tables have no parent, we need to determine the name
-        #
-        _tableName = 'claims' if _x12 == '837' else 'remits'
-        # print (_id,_attributes)
+#     elif 'anchor' in _meta :
+#         _tableName = _meta['anchor'].values()
+#         # for _name in _meta['anchor'].values() :
+#         #     _table[_name] = _attributes
+#     elif 'parent' in _meta and _meta['parent']:
+#         #
+#         # We can have a parent with no field/container/anchor
+#         # We expect either a map or columns ...
+#         #
+#         _parentElement = _meta['parent']
+#         _parentMeta = _plugins[_x12][_parentElement].meta
+#         _parentTable = getTableName(plugins=_plugins,meta = _parentMeta,tableKeys=_foreignkeys)
+#         _tableName = list(_parentTable.keys())[0]
+#         # _table[_id] = _parentTable[_id] + _attributes
+#         _attributes = _parentTable[_tableName] + _attributes
+#         # print (_meta)
+#     else:
+#         #
+#         # baseline tables have no parent, we need to determine the name
+#         #
+#         _tableName = 'claims' if _x12 == '837' else 'remits'
+#         # print (_id,_attributes)
         
-        pass
-    #
-    # Are there any anchors
-    if _x12 == '837':
-        _keys  = [_foreignkeys['claims']]
-    elif _x12 == '835' :
-        _keys = [_foreignkeys['remits']]
-    else:
-        _keys = list(set(_foreignkeys.values()))
-    _attr = []
-    for _item in _attributes :
-        if type(_item) == list :
-            _attr += _item
-        else:
-            _attr.append(_item)
-    _keys = list(set(_keys) - set(_attr))
-    _attr = _keys + _attr
-    # if 'container' in _meta and _meta['container'] == 'procedures' :
-    #     print (_attributes)
-    _tableName = [_tableName] if type(_tableName) == str else _tableName
-    return dict.fromkeys(_tableName,_attr)
-def _getTableName (**_args):
-    """
-    This function provides a list of attributes associated with an entity
-    The function infers a relational structure from the JSON representation of a claim and plugin specifications
-    """
-    _meta = _args['meta']
-    _xattr = list(_meta['map'].values()) if 'map' in _meta else _meta['columns']
-    _plugins = _args['plugins']
-    _foreignkeys = _args['tableKeys']
-    #
-    # Fix attributes, in case we have an index associated with multiple fields
-    #
-    _attr = []
-    if 'anchor' not in _meta and not _meta['parent']:
-        for _item in _xattr :
-            _attr += _item if type(_item) == list else [_item]
-    _name = None
-    _info = {}
-    _infoparent = {}
-    if 'field' in _meta :
-        _name = _meta['field']
-    elif 'container' in _meta :
-        _name = _meta['container']
-    elif 'anchor' in _meta :
+#         pass
+#     #
+#     # Are there any anchors
+#     if _x12 == '837':
+#         _keys  = [_foreignkeys['claims']]
+#     elif _x12 == '835' :
+#         _keys = [_foreignkeys['remits']]
+#     else:
+#         _keys = list(set(_foreignkeys.values()))
+#     _attr = []
+#     for _item in _attributes :
+#         if type(_item) == list :
+#             _attr += _item
+#         else:
+#             _attr.append(_item)
+#     _keys = list(set(_keys) - set(_attr))
+#     _attr = _keys + _attr
+#     # if 'container' in _meta and _meta['container'] == 'procedures' :
+#     #     print (_attributes)
+#     _tableName = [_tableName] if type(_tableName) == str else _tableName
+#     return dict.fromkeys(_tableName,_attr)
+# def _getTableName (**_args):
+#     """
+#     This function provides a list of attributes associated with an entity
+#     The function infers a relational structure from the JSON representation of a claim and plugin specifications
+#     """
+#     _meta = _args['meta']
+#     _xattr = list(_meta['map'].values()) if 'map' in _meta else _meta['columns']
+#     _plugins = _args['plugins']
+#     _foreignkeys = _args['tableKeys']
+#     #
+#     # Fix attributes, in case we have an index associated with multiple fields
+#     #
+#     _attr = []
+#     if 'anchor' not in _meta and not _meta['parent']:
+#         for _item in _xattr :
+#             _attr += _item if type(_item) == list else [_item]
+#     _name = None
+#     _info = {}
+#     _infoparent = {}
+#     if 'field' in _meta :
+#         _name = _meta['field']
+#     elif 'container' in _meta :
+#         _name = _meta['container']
+#     elif 'anchor' in _meta :
         
-        _name = list(_meta['anchor'].values())
-    # if _name :
-    #     _name = _name if type(_name) == list else [_name]
-    #     _info = dict.fromkeys(_name,_attr)
-    if _meta['parent'] :
-        _parentElement = filter(elements=[_meta['parent']],plugins=_plugins)
-        _x12 = list(_parentElement.keys())[0]
-        _id = list(_parentElement[_x12].keys())[0]
-        _infoparent = getTableName(meta = _parentElement[_x12][_id].meta,plugins=_plugins,tableKeys=_foreignkeys)
+#         _name = list(_meta['anchor'].values())
+#     # if _name :
+#     #     _name = _name if type(_name) == list else [_name]
+#     #     _info = dict.fromkeys(_name,_attr)
+#     if _meta['parent'] :
+#         _parentElement = filter(elements=[_meta['parent']],plugins=_plugins)
+#         _x12 = list(_parentElement.keys())[0]
+#         _id = list(_parentElement[_x12].keys())[0]
+#         _infoparent = getTableName(meta = _parentElement[_x12][_id].meta,plugins=_plugins,tableKeys=_foreignkeys)
         
-    if _meta['x12'] == '*' :
-        _name = ['claims','remits'] if not _name else _name
-        _attr =  list(set(_foreignkeys.values())) + _attr
-    else:
-        _name = 'claims' if _meta['x12'] == '837' and not _name else ('remits' if not _name and _meta['x12'] == '835' else _name)
-        _id = 'claims' if _meta['x12'] == '837' else 'remits'
-        if _id in _foreignkeys:
-            _attr = [_foreignkeys[_id]] + _attr
+#     if _meta['x12'] == '*' :
+#         _name = ['claims','remits'] if not _name else _name
+#         _attr =  list(set(_foreignkeys.values())) + _attr
+#     else:
+#         _name = 'claims' if _meta['x12'] == '837' and not _name else ('remits' if not _name and _meta['x12'] == '835' else _name)
+#         _id = 'claims' if _meta['x12'] == '837' else 'remits'
+#         if _id in _foreignkeys:
+#             _attr = [_foreignkeys[_id]] + _attr
         
         
-    # if not _name :
-    #     if _meta['x12'] == '*' :
-    #         _name = ['claims','remits']
-    #     else:
-    #         _name = 'claims' if _meta['x12'] == '837' else 'remits'
-    #
-    # Let us make sure we can get the keys associated here ...
-    #
-    # filter (elements = [])
-    _name = _name if type(_name) == list else [_name]
-    _info = dict.fromkeys(_name,_attr)
-    if _infoparent:
-        _info = dict(_info,**_infoparent)    
+#     # if not _name :
+#     #     if _meta['x12'] == '*' :
+#     #         _name = ['claims','remits']
+#     #     else:
+#     #         _name = 'claims' if _meta['x12'] == '837' else 'remits'
+#     #
+#     # Let us make sure we can get the keys associated here ...
+#     #
+#     # filter (elements = [])
+#     _name = _name if type(_name) == list else [_name]
+#     _info = dict.fromkeys(_name,_attr)
+#     if _infoparent:
+#         _info = dict(_info,**_infoparent)    
     
-    return _info
+#     return _info
         
         
 
-def getTableKeys(**_args):
-    _plugins=_args['plugins']
-    _pointer = filter(elements=['CLM'],plugins=_plugins)
-    _keys = {}
-    for _element in ['CLM','CLP'] :
-        _pointer = filter(elements=[_element],plugins=_plugins)
-        if not _pointer  :
-            continue
-        _pointer = list(_pointer.values())[0]
-        _meta = _pointer[_element].meta
-        _name = _meta['map'][1] if 'map' in _meta else _meta['columns'][0]
-        _id = 'claims' if _element == 'CLM' else 'remits'
-        _keys[_id] = _name
-    return _keys
-    # print (list(_pointer.values())[0]['CLM'].meta)
-    # print (_pointer.values()[0].meta)
-def sql (**_args):
-    _plugins = _args['plugins']
-    # _info = {'foreign':{},'keys':{'claims':None,'remits':None}}
-    _documentHandler = x12.util.document.Builder(plugins=_plugins,parents=_args['parents'])
-    _tableKeys = getTableKeys(plugins=_plugins)
-    _schemas = {}
-    for key in _plugins :
-        _mpointers = _plugins[key]
-        for _element in _mpointers :
-            _pointer = _mpointers[_element]
-            _meta = _pointer.meta
-            _info = getTableName(meta=_meta,plugins=_plugins,tableKeys=_tableKeys)
-            # _schemas = dict(_schemas,**_info)
-            if _info :
-                _schemas = _documentHandler.merge(_schemas,_info)
-            # print (_info)
-    return _schemas
-            # if not _info :
-            #     print (_meta)
-            #     continue
-            # if _meta['x12'] in ['837','837'] :
-            #     _schema_id = 'claims' if _meta['x12'] == '837' else 'remits'
-            #     _schema_id = [_schema_id]
-            # else:
-            #     _schema_id = ['claims','remits']
+# def getTableKeys(**_args):
+#     _plugins=_args['plugins']
+#     _pointer = filter(elements=['CLM'],plugins=_plugins)
+#     _keys = {}
+#     for _element in ['CLM','CLP'] :
+#         _pointer = filter(elements=[_element],plugins=_plugins)
+#         if not _pointer  :
+#             continue
+#         _pointer = list(_pointer.values())[0]
+#         _meta = _pointer[_element].meta
+#         _name = _meta['map'][1] if 'map' in _meta else _meta['columns'][0]
+#         _id = 'claims' if _element == 'CLM' else 'remits'
+#         _keys[_id] = _name
+#     return _keys
+#     # print (list(_pointer.values())[0]['CLM'].meta)
+#     # print (_pointer.values()[0].meta)
+# def sql (**_args):
+#     _plugins = _args['plugins']
+#     # _info = {'foreign':{},'keys':{'claims':None,'remits':None}}
+#     _documentHandler = x12.util.document.Builder(plugins=_plugins,parents=_args['parents'])
+#     _tableKeys = getTableKeys(plugins=_plugins)
+#     _schemas = {}
+#     for key in _plugins :
+#         _mpointers = _plugins[key]
+#         for _element in _mpointers :
+#             _pointer = _mpointers[_element]
+#             _meta = _pointer.meta
+#             _info = getTableName(meta=_meta,plugins=_plugins,tableKeys=_tableKeys)
+#             # _schemas = dict(_schemas,**_info)
+#             if _info :
+#                 _schemas = _documentHandler.merge(_schemas,_info)
+#             # print (_info)
+#     return _schemas
+#             # if not _info :
+#             #     print (_meta)
+#             #     continue
+#             # if _meta['x12'] in ['837','837'] :
+#             #     _schema_id = 'claims' if _meta['x12'] == '837' else 'remits'
+#             #     _schema_id = [_schema_id]
+#             # else:
+#             #     _schema_id = ['claims','remits']
 
-            # if _info :
-            #     #
-            #     # foreign tables need to be placed here
+#             # if _info :
+#             #     #
+#             #     # foreign tables need to be placed here
                
-            #     for _id in _schema_id :
-            #         if type(_info) == list :
-            #             _schemas[_id]['attributes'] += _info
-            #         else:
-            #             _schemas[_id]['foreign'] = dict(_schemas[_id]['foreign'],**_info)
-            # else:
-            #     #
-            #     # This one goes to the main tables
-            #     for _id in _schema_id :
-            #         print (_info)
-            #         _schemas[_id]['attributes'] += list(_info.values())
+#             #     for _id in _schema_id :
+#             #         if type(_info) == list :
+#             #             _schemas[_id]['attributes'] += _info
+#             #         else:
+#             #             _schemas[_id]['foreign'] = dict(_schemas[_id]['foreign'],**_info)
+#             # else:
+#             #     #
+#             #     # This one goes to the main tables
+#             #     for _id in _schema_id :
+#             #         print (_info)
+#             #         _schemas[_id]['attributes'] += list(_info.values())
                     
                 
                 
 
 
 
-# DEFAULT_PLUGINS='healthcareio.x12.plugins.default'
-# class MODE :
-#     TRUST,CHECK,TEST,TEST_AND_CHECK= [0,1,2,3]
-# def instance(**_args) :
-#     pass    
-# def has(**_args) :
-#     """
-#     This function will inspect if a function is valid as a plugin or not    
-#     name : function name for a given file
-#     path    : python file to examine
-#     """
-#     _pyfile = _args['path'] if 'path' in _args else ''
-#     _name = _args['name']
-#     # p = os.path.exists(_pyfile)
-#     _module = {}
-#     if os.path.exists(_pyfile):
-#         _info  = IL.utils.spec_from_file_location(_name,_pyfile)
-#         if _info :
-#             _module = IL.utils.module_from_spec(_info)
-#             _info.load.exec(_module)
+# # DEFAULT_PLUGINS='healthcareio.x12.plugins.default'
+# # class MODE :
+# #     TRUST,CHECK,TEST,TEST_AND_CHECK= [0,1,2,3]
+# # def instance(**_args) :
+# #     pass    
+# # def has(**_args) :
+# #     """
+# #     This function will inspect if a function is valid as a plugin or not    
+# #     name : function name for a given file
+# #     path    : python file to examine
+# #     """
+# #     _pyfile = _args['path'] if 'path' in _args else ''
+# #     _name = _args['name']
+# #     # p = os.path.exists(_pyfile)
+# #     _module = {}
+# #     if os.path.exists(_pyfile):
+# #         _info  = IL.utils.spec_from_file_location(_name,_pyfile)
+# #         if _info :
+# #             _module = IL.utils.module_from_spec(_info)
+# #             _info.load.exec(_module)
             
         
-#     else:
-#         _module = sys.modules[DEFAULT_PLUGINS]
-#     return hasattr(_module,_name)
-# def get(**_args) :
-#     """
-#     This function will inspect if a function is valid as a plugin or not    
-#     name : function name for a given file
-#     path    : python file to examine
-#     """
-#     _pyfile = _args['path'] if 'path' in _args else ''
-#     _name = _args['name']
-#     # p = os.path.exists(_pyfile)
-#     _module = {}
-#     if os.path.exists(_pyfile):
-#         _info  = IL.utils.spec_from_file_location(_name,_pyfile)
-#         if _info :
-#             _module = IL.utils.module_from_spec(_info)
-#             _info.load.exec(_module)
+# #     else:
+# #         _module = sys.modules[DEFAULT_PLUGINS]
+# #     return hasattr(_module,_name)
+# # def get(**_args) :
+# #     """
+# #     This function will inspect if a function is valid as a plugin or not    
+# #     name : function name for a given file
+# #     path    : python file to examine
+# #     """
+# #     _pyfile = _args['path'] if 'path' in _args else ''
+# #     _name = _args['name']
+# #     # p = os.path.exists(_pyfile)
+# #     _module = {}
+# #     if os.path.exists(_pyfile):
+# #         _info  = IL.utils.spec_from_file_location(_name,_pyfile)
+# #         if _info :
+# #             _module = IL.utils.module_from_spec(_info)
+# #             _info.load.exec(_module)
             
         
-#     else:
-#         _module = sys.modules[DEFAULT_PLUGINS]
-#     return getattr(_module,_name) if hasattr(_module,_name) else None
+# #     else:
+# #         _module = sys.modules[DEFAULT_PLUGINS]
+# #     return getattr(_module,_name) if hasattr(_module,_name) else None
 
 
-# def test (**_args):
-#     """
-#     This function will test a plugin to insure the plugin conforms to the norm we are setting here 
-#     :pointer  function to call
-#     """
-#     _params = {}
-#     try:
-#         if 'pointer' in _args :
-#             _caller = _args['pointer'] 
-#         else:
-#             _name = _args['name']
-#             _path = _args['path'] if 'path' in _args else None
-#             _caller = get(name=_name,path=_path)
-#         _params = _caller()
-#         #
-#         # the expected result is a list of field names [field_o,field_i] 
-#         # 
-#         return [_item for _item in _params if _item not in ['',None] and type(_item) == str]
-#     except Exception as e :
-#         return []
-#         pass
-# def inspect(**_args):
-#     _mode = _args['mode']
-#     _name= _args['name']
-#     _path= _args['path']
-#     if _mode == MODE.CHECK :
-#         _doapply = [has]
-#     elif _mode == MODE.TEST :
-#         _doapply = [test]
-#     elif _mode == MODE.TEST_AND_CHECK :
-#         _doapply = [has,test]  
-#     _status = True
-#     _plugin = {"name":_name}
-#     for _pointer in _doapply :
-#         _plugin[_pointer.__name__] = _pointer(name=_name,path=_path)
-#         if not _plugin[_pointer.__name__] :
-#             _status = False
-#             break    
-#     _plugin['loaded'] = _status
-#     return _plugin
-# def load(**_args):
-#     """
-#         This function will load all the plugins given an set of arguments :
-#         path    file
-#         name   list of functions to export
-#         mode     1- CHECK ONLY, 2 - TEST ONLY, 3- TEST_AND_CHECK
-#     """
-#     _path = _args ['path']
-#     _names= _args['names']
-#     _mode= _args ['mode'] if 'mode' in _args else MODE.TEST_AND_CHECK
-#     _doapply = []
-#     if _mode == MODE.CHECK :
-#         _doapply = [has]
-#     elif _mode == MODE.TEST :
-#         _doapply = [test]
-#     elif _mode == MODE.TEST_AND_CHECK :
-#         _doapply = [has,test] 
-#     # _plugins = []
-#     _plugins = {}
-#     for _name in _names :
-#         _plugin = {"name":_name}
-#         if 'inspect' in _args and _args['inspect'] :
-#             _plugin = inspect(name=_name,mode=_mode,path=_path)
-#         else:
-#             _plugin["method"] = ""
-#             _status = True
-#         _plugin['loaded'] = _status
-#         if _plugin['loaded'] :
-#             _plugin['pointer'] = get(name=_name,path=_path)
-#         else:
-#             _plugin['pointer'] = None
+# # def test (**_args):
+# #     """
+# #     This function will test a plugin to insure the plugin conforms to the norm we are setting here 
+# #     :pointer  function to call
+# #     """
+# #     _params = {}
+# #     try:
+# #         if 'pointer' in _args :
+# #             _caller = _args['pointer'] 
+# #         else:
+# #             _name = _args['name']
+# #             _path = _args['path'] if 'path' in _args else None
+# #             _caller = get(name=_name,path=_path)
+# #         _params = _caller()
+# #         #
+# #         # the expected result is a list of field names [field_o,field_i] 
+# #         # 
+# #         return [_item for _item in _params if _item not in ['',None] and type(_item) == str]
+# #     except Exception as e :
+# #         return []
+# #         pass
+# # def inspect(**_args):
+# #     _mode = _args['mode']
+# #     _name= _args['name']
+# #     _path= _args['path']
+# #     if _mode == MODE.CHECK :
+# #         _doapply = [has]
+# #     elif _mode == MODE.TEST :
+# #         _doapply = [test]
+# #     elif _mode == MODE.TEST_AND_CHECK :
+# #         _doapply = [has,test]  
+# #     _status = True
+# #     _plugin = {"name":_name}
+# #     for _pointer in _doapply :
+# #         _plugin[_pointer.__name__] = _pointer(name=_name,path=_path)
+# #         if not _plugin[_pointer.__name__] :
+# #             _status = False
+# #             break    
+# #     _plugin['loaded'] = _status
+# #     return _plugin
+# # def load(**_args):
+# #     """
+# #         This function will load all the plugins given an set of arguments :
+# #         path    file
+# #         name   list of functions to export
+# #         mode     1- CHECK ONLY, 2 - TEST ONLY, 3- TEST_AND_CHECK
+# #     """
+# #     _path = _args ['path']
+# #     _names= _args['names']
+# #     _mode= _args ['mode'] if 'mode' in _args else MODE.TEST_AND_CHECK
+# #     _doapply = []
+# #     if _mode == MODE.CHECK :
+# #         _doapply = [has]
+# #     elif _mode == MODE.TEST :
+# #         _doapply = [test]
+# #     elif _mode == MODE.TEST_AND_CHECK :
+# #         _doapply = [has,test] 
+# #     # _plugins = []
+# #     _plugins = {}
+# #     for _name in _names :
+# #         _plugin = {"name":_name}
+# #         if 'inspect' in _args and _args['inspect'] :
+# #             _plugin = inspect(name=_name,mode=_mode,path=_path)
+# #         else:
+# #             _plugin["method"] = ""
+# #             _status = True
+# #         _plugin['loaded'] = _status
+# #         if _plugin['loaded'] :
+# #             _plugin['pointer'] = get(name=_name,path=_path)
+# #         else:
+# #             _plugin['pointer'] = None
 
-#         # _plugins.append(_plugin)
-#         _plugins[_name] = _plugin
-#     return _plugins
+# #         # _plugins.append(_plugin)
+# #         _plugins[_name] = _plugin
+# #     return _plugins
 
 
-# def parse(**_args):
-#     """
-#     This function will apply a function against a given function, and data
-#     :row   claim/remits pre-processed
-#     :plugins    list of plugins
-#     :conifg     configuration associated with
-#     """
-#     _row        = _args['row']
-#     _document   = _args['document']
-#     _config     = _args['config']
-#     """
-#     "apply":"@path:name"
-#     """
+# # def parse(**_args):
+# #     """
+# #     This function will apply a function against a given function, and data
+# #     :row   claim/remits pre-processed
+# #     :plugins    list of plugins
+# #     :conifg     configuration associated with
+# #     """
+# #     _row        = _args['row']
+# #     _document   = _args['document']
+# #     _config     = _args['config']
+# #     """
+# #     "apply":"@path:name"
+# #     """
     
-#     _info        = _args['config']['apply']
-#     _plug_conf  = _args['config']['plugin'] if 'plugin' in _args['config'] else {}
-#     if _info.startswith('@') :
-#         _path = '' #-- get this from general configuration
-#     elif _info.startswith('!'):
-#         _path = _info.split('!')[0][1:]
-#     _name = _info.split(':')[-1]
-#     _name = _args['config']['apply'].split(_path)
+# #     _info        = _args['config']['apply']
+# #     _plug_conf  = _args['config']['plugin'] if 'plugin' in _args['config'] else {}
+# #     if _info.startswith('@') :
+# #         _path = '' #-- get this from general configuration
+# #     elif _info.startswith('!'):
+# #         _path = _info.split('!')[0][1:]
+# #     _name = _info.split(':')[-1]
+# #     _name = _args['config']['apply'].split(_path)
 

healthcareio/x12/publish.py

@@ -106,11 +106,15 @@ def init(**_args):
     _indexes = np.array_split(np.arange(_df.shape[0]),SEGMENTS)
     jobs = []
     for _ii in _indexes :
-        
-       _data = format(rows= _df.iloc[_ii].to_dict(orient='records'),x12=_file_type,primary_key=_pkey)
-       
-       _thread = Process(target=post,args=({'store':_store['target'],'data':_data,'default':_default,'x12':_file_type},))
-       jobs.append(_thread)
+        try:
+            _data = format(rows= _df.iloc[_ii].to_dict(orient='records'),x12=_file_type,primary_key=_pkey)
+            
+            _thread = Process(target=post,args=({'store':_store['target'],'data':_data,'default':_default,'x12':_file_type},))
+            jobs.append(_thread)
+        except Exception as e:
+            #
+            # Log: sigment, 
+            pass
     if jobs :
         jobs[0].start()
         jobs[0].join()

healthcareio/x12/util/document.py

@@ -204,7 +204,6 @@ class Builder:
         
         _parent = None
         _data = {}
-        # _document = _args['document']
         if not _pointer :
             return None,None
         #

setup.py

@@ -2,21 +2,22 @@
 This is a build file for the 
 """
 from setuptools import setup, find_packages
+from healthcareio import version
 import os
 import sys
 
 def read(fname):
     return open(os.path.join(os.path.dirname(__file__), fname)).read() 
 args = {
-    "name":"healthcareio","version":"1.6.4.8",
-    "author":"Vanderbilt University Medical Center",
+    "name":"healthcareio","version":version.__version__,
+    "author":version.__author__,
     "author_email":"steve.l.nyemba@vumc.org",
     "include_package_data":True,
-    "license":"MIT",
+    "license":version.__license__,
     "packages":find_packages(),
     "keywords":["healthcare","edi","x12","analytics","835","837","data","transport","protocol"]
 }
-args["install_requires"] = ['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','smart-top@git+https://healthcareio.the-phi.com/git/code/smart-top.git@data-collector']
 args['url'] = 'https://hiplab.mc.vanderbilt.edu'
 args['scripts']= ['healthcareio/healthcare-io.py']
 # args['entry_points'] = {