Merge branch 'dev' of lab/parse-edi into master
This commit is contained in:
steve
Gogs
commit
03a8ac82df
12
README.md
12
README.md
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@ -27,7 +27,7 @@ We wrote this frame to be used in both command line or as a library within in yo
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1. signup to get parsing configuration
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The parser is driven by a configuration, file you need by signing up.
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The parser is driven by a configuration file that specifies fields to parse and how to parse them. You need by signing up, to get a copy of the configuration file.
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healthcare-io.py --signup <email> [--store <mongo|sqlite>]
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@ -49,7 +49,17 @@ We wrote this frame to be used in both command line or as a library within in yo
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--batch number of processes to spawn to parse the files
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--resume tells the parser to resume parsing
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if all files weren't processed or new files were added into the folder
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4. export data to a relational data-store
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The parser will export data into other data-stores as a relational tables allowing users to construct views to support a variety of studies.
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healthcare-io.py --export <835|837> --config <path-export.json>
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with:
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--config configuration to support data-store
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**Embedded in Code :**
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The Healthcare/IO **parser** can be used within your code base as a library and handle storing data in a data store of choice
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@ -0,0 +1,314 @@
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|
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
|
|
@ -0,0 +1,331 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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||||
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||||
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||||
<UML:EntityAttribute xmi.id="u1rGJT5BzOnTc" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="date" isSpecification="false" namespace="uYFy5I3jZovwB" values="125" isRoot="false"/>
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|
||||
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|
||||
</UML:Entity>
|
||||
<UML:Entity xmi.id="uQLb3AjtJtg1u" isLeaf="false" isAbstract="false" visibility="public" name="procedures" isSpecification="false" namespace="Entity_Relationship_Model" isRoot="false">
|
||||
<UML:EntityAttribute xmi.id="uAjDOjucMMjVA" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="claim_id" isSpecification="false" namespace="uQLb3AjtJtg1u" values="125" isRoot="false"/>
|
||||
<UML:EntityAttribute xmi.id="uvwYZ2ZXVtktZ" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="code" isSpecification="false" namespace="uQLb3AjtJtg1u" values="125" isRoot="false"/>
|
||||
<UML:EntityAttribute xmi.id="uK1hOh0gYH7UR" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="amount" isSpecification="false" namespace="uQLb3AjtJtg1u" values="125" isRoot="false"/>
|
||||
<UML:EntityAttribute xmi.id="uzXoWRaQEBR4N" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="line_charge_amount" isSpecification="false" namespace="uQLb3AjtJtg1u" values="125" isRoot="false"/>
|
||||
<UML:EntityAttribute xmi.id="uTu2N31LFQjZs" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="submitted_units_of_service" isSpecification="false" namespace="uQLb3AjtJtg1u" values="125" isRoot="false"/>
|
||||
<UML:EntityAttribute xmi.id="uX3uZJhBt3XbF" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="revenue_code" isSpecification="false" namespace="uQLb3AjtJtg1u" values="125" isRoot="false"/>
|
||||
<UML:EntityAttribute xmi.id="u1iY5DjVfwxct" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="paid_units_of_service" isSpecification="false" namespace="uQLb3AjtJtg1u" values="125" isRoot="false"/>
|
||||
<UML:EntityAttribute xmi.id="udHyId5EQgnxd" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="line_paid_amount" isSpecification="false" namespace="uQLb3AjtJtg1u" values="125" isRoot="false"/>
|
||||
<UML:EntityAttribute xmi.id="ucBf8PfYusdLF" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="_index" isSpecification="false" namespace="uQLb3AjtJtg1u" values="125" isRoot="false"/>
|
||||
</UML:Entity>
|
||||
<UML:Entity xmi.id="uxCXzVM24yYaX" isLeaf="false" isAbstract="false" visibility="public" name="provider" isSpecification="false" namespace="Entity_Relationship_Model" isRoot="false">
|
||||
<UML:EntityAttribute xmi.id="ucbfGJzClrgx7" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="claim_id" isSpecification="false" namespace="uxCXzVM24yYaX" values="125" isRoot="false"/>
|
||||
<UML:EntityAttribute xmi.id="ui5GIXpde552t" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="provider_id" isSpecification="false" namespace="uxCXzVM24yYaX" values="125" isRoot="false"/>
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||||
<UML:EntityAttribute xmi.id="uqpcLcCfQxPc1" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="adjustment_fiscal_year" isSpecification="false" namespace="uxCXzVM24yYaX" values="125" isRoot="false"/>
|
||||
<UML:EntityAttribute xmi.id="u8EKwCD4KJD35" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="adjustment_amount" isSpecification="false" namespace="uxCXzVM24yYaX" values="125" isRoot="false"/>
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<UML:EntityAttribute xmi.id="ugSzBbS45Appb" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="_index" isSpecification="false" namespace="uxCXzVM24yYaX" values="125" isRoot="false"/>
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||||
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|
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<UML:Entity xmi.id="uFhe3BvJ5GFMv" isLeaf="false" isAbstract="false" visibility="public" name="remits" isSpecification="false" namespace="Entity_Relationship_Model" isRoot="false">
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<UML:EntityAttribute xmi.id="uaPrhdtHj174f" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="claim_id" isSpecification="false" namespace="uFhe3BvJ5GFMv" values="125" isRoot="false"/>
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|
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<UML:EntityAttribute xmi.id="u2TjnY4FpRX7E" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="payment_amount" isSpecification="false" namespace="uFhe3BvJ5GFMv" values="125" isRoot="false"/>
|
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<UML:EntityAttribute xmi.id="uO0RFshYIUxyV" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="patient_amount" isSpecification="false" namespace="uFhe3BvJ5GFMv" values="125" isRoot="false"/>
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<UML:EntityAttribute xmi.id="u26a7mGlibP31" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="patient_status" isSpecification="false" namespace="uFhe3BvJ5GFMv" values="125" isRoot="false"/>
|
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<UML:EntityAttribute xmi.id="uqT7KYiudzE2a" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="status" isSpecification="false" namespace="uFhe3BvJ5GFMv" values="125" isRoot="false"/>
|
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<UML:EntityAttribute xmi.id="utDLqzoqgcm98" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="total_paid_amt" isSpecification="false" namespace="uFhe3BvJ5GFMv" values="125" isRoot="false"/>
|
||||
<UML:EntityAttribute xmi.id="u4760sev0qJdC" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="total_claim_charge_amount" isSpecification="false" namespace="uFhe3BvJ5GFMv" values="125" isRoot="false"/>
|
||||
<UML:EntityAttribute xmi.id="uYOWi0TRwwQ9C" allow_null="1" dbindex_type="1100" isLeaf="false" isAbstract="false" visibility="public" initialValue="" attributes="" type="uy27kWMqeaG0m" auto_increment="0" name="patient_responsibility_amount" isSpecification="false" namespace="uFhe3BvJ5GFMv" values="125" isRoot="false"/>
|
||||
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|
||||
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|
||||
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|
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|
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|
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|
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|
||||
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|
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|
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
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|
||||
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|
||||
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|
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|
||||
<listitem type="833" id="utB3YD4uBHDFe" open="0"/>
|
||||
<listitem type="833" id="uCGGZqIN2sQH3" open="0"/>
|
||||
<listitem type="833" id="uPRzkRJCCJabo" open="0"/>
|
||||
<listitem type="833" id="uJB8h1NGbex2g" open="0"/>
|
||||
</listitem>
|
||||
<listitem type="832" id="uYFy5I3jZovwB" open="0">
|
||||
<listitem type="833" id="udhZrX8aJ7mx2" open="0"/>
|
||||
<listitem type="833" id="u19O44eIBLpSx" open="0"/>
|
||||
<listitem type="833" id="uh1XMXOFqqkLH" open="0"/>
|
||||
<listitem type="833" id="u1rGJT5BzOnTc" open="0"/>
|
||||
<listitem type="833" id="u24TxypfX1ehF" open="0"/>
|
||||
</listitem>
|
||||
<listitem type="832" id="uQLb3AjtJtg1u" open="0">
|
||||
<listitem type="833" id="ucBf8PfYusdLF" open="0"/>
|
||||
<listitem type="833" id="uK1hOh0gYH7UR" open="0"/>
|
||||
<listitem type="833" id="uAjDOjucMMjVA" open="0"/>
|
||||
<listitem type="833" id="uvwYZ2ZXVtktZ" open="0"/>
|
||||
<listitem type="833" id="uzXoWRaQEBR4N" open="0"/>
|
||||
<listitem type="833" id="udHyId5EQgnxd" open="0"/>
|
||||
<listitem type="833" id="u1iY5DjVfwxct" open="0"/>
|
||||
<listitem type="833" id="uX3uZJhBt3XbF" open="0"/>
|
||||
<listitem type="833" id="uTu2N31LFQjZs" open="0"/>
|
||||
</listitem>
|
||||
<listitem type="832" id="uxCXzVM24yYaX" open="0">
|
||||
<listitem type="833" id="ugSzBbS45Appb" open="0"/>
|
||||
<listitem type="833" id="u8EKwCD4KJD35" open="0"/>
|
||||
<listitem type="833" id="uqpcLcCfQxPc1" open="0"/>
|
||||
<listitem type="833" id="ucbfGJzClrgx7" open="0"/>
|
||||
<listitem type="833" id="ui5GIXpde552t" open="0"/>
|
||||
</listitem>
|
||||
<listitem type="832" id="uFhe3BvJ5GFMv" open="0">
|
||||
<listitem type="833" id="ueFTa93wS5vpr" open="0"/>
|
||||
<listitem type="833" id="uTI9AfIOT6Vgi" open="0"/>
|
||||
<listitem type="833" id="uh7Mo4vNDxjEP" open="0"/>
|
||||
<listitem type="833" id="uM8YUylmQOOZz" open="0"/>
|
||||
<listitem type="833" id="uIOoyY9AcSXqj" open="0"/>
|
||||
<listitem type="833" id="umBq8tNVoHLwQ" open="0"/>
|
||||
<listitem type="833" id="ussv42OpwEC3o" open="0"/>
|
||||
<listitem type="833" id="uaPrhdtHj174f" open="0"/>
|
||||
<listitem type="833" id="uMxluIdcl530X" open="0"/>
|
||||
<listitem type="833" id="uRKSgcFBa5IZo" open="0"/>
|
||||
<listitem type="833" id="uTmKxBb1U6HHd" open="0"/>
|
||||
<listitem type="833" id="uO0RFshYIUxyV" open="0"/>
|
||||
<listitem type="833" id="uYOWi0TRwwQ9C" open="0"/>
|
||||
<listitem type="833" id="u26a7mGlibP31" open="0"/>
|
||||
<listitem type="833" id="u2TjnY4FpRX7E" open="0"/>
|
||||
<listitem type="833" id="uVwZLtkVRxhLS" open="0"/>
|
||||
<listitem type="833" id="uqT7KYiudzE2a" open="0"/>
|
||||
<listitem type="833" id="u4760sev0qJdC" open="0"/>
|
||||
<listitem type="833" id="utDLqzoqgcm98" open="0"/>
|
||||
<listitem type="833" id="uGKSxco6bkhJK" open="0"/>
|
||||
<listitem type="833" id="uFR0HPZWCHTOd" open="0"/>
|
||||
<listitem type="833" id="u35C8cp4M74EZ" open="0"/>
|
||||
<listitem type="833" id="u8b87l43udLdm" open="0"/>
|
||||
<listitem type="833" id="uutC8Ww5MIEDw" open="0"/>
|
||||
</listitem>
|
||||
<listitem label="remits" type="834" id="uKioLvROZP9sj" open="0"/>
|
||||
<listitem type="832" id="uDyfldNoIv0VN" open="0">
|
||||
<listitem type="833" id="uiSnbXbl5xZgj" open="0"/>
|
||||
<listitem type="833" id="uHlzHdGAzTLje" open="0"/>
|
||||
<listitem type="833" id="uXzmRTjxt5urK" open="0"/>
|
||||
<listitem type="833" id="uZaNNwlpF8G8D" open="0"/>
|
||||
<listitem type="833" id="uTVrpMWQGZv9k" open="0"/>
|
||||
<listitem type="833" id="uDVH1N8QTr4Hh" open="0"/>
|
||||
<listitem type="833" id="uTdAUNse734xO" open="0"/>
|
||||
<listitem type="833" id="usy1XBeLxeUGA" open="0"/>
|
||||
</listitem>
|
||||
</listitem>
|
||||
<listitem type="801" id="Logical_View" open="1">
|
||||
<listitem label="class diagram" type="807" id="ucgtgQRSMYlOp" open="0"/>
|
||||
<listitem type="830" id="Datatypes" open="0">
|
||||
<listitem type="829" id="udJEUGSmFsMc7" open="1"/>
|
||||
<listitem type="829" id="uKoxqBVMuFAFv" open="1"/>
|
||||
<listitem type="829" id="usYHH6veFLtOr" open="0"/>
|
||||
<listitem type="829" id="u4xIFQFMKzJrw" open="0"/>
|
||||
<listitem type="829" id="uy27kWMqeaG0m" open="0"/>
|
||||
<listitem type="829" id="u0C5GYVgNAN71" open="1"/>
|
||||
<listitem type="829" id="u9FKE3RWhiqcG" open="1"/>
|
||||
<listitem type="829" id="uhDxBNpwOBqQw" open="1"/>
|
||||
<listitem type="829" id="u2wysBNkFNdqp" open="0"/>
|
||||
<listitem type="829" id="uHqbfHWPho1Ur" open="1"/>
|
||||
<listitem type="829" id="u2CL1gZXtSnOS" open="0"/>
|
||||
<listitem type="829" id="uUrqcj6xGhwaC" open="0"/>
|
||||
<listitem type="829" id="uuismMojqbmsx" open="0"/>
|
||||
<listitem type="829" id="uO1NrEETU4UC8" open="0"/>
|
||||
<listitem type="829" id="uya6iY5Q7DGeZ" open="1"/>
|
||||
<listitem type="829" id="uaeIOuN6e4FU1" open="1"/>
|
||||
<listitem type="829" id="u8zuwCW44JB95" open="1"/>
|
||||
<listitem type="829" id="uGdQJaRR6gTOr" open="1"/>
|
||||
<listitem type="829" id="uYevwcNN1qRSX" open="1"/>
|
||||
<listitem type="829" id="uApLJztW3N1vU" open="1"/>
|
||||
<listitem type="829" id="uHcFFwtOW2QoG" open="0"/>
|
||||
<listitem type="829" id="unwvIxd81D8F6" open="0"/>
|
||||
<listitem type="829" id="u8U3EclXHUBqf" open="0"/>
|
||||
<listitem type="829" id="umes0MFf2bAXI" open="0"/>
|
||||
<listitem type="829" id="uc2wrhdQQFdKR" open="0"/>
|
||||
<listitem type="829" id="uCMJShOyEcx65" open="1"/>
|
||||
<listitem type="829" id="uN90WSzxg70L5" open="0"/>
|
||||
<listitem type="829" id="uMXT4n4yeeGxP" open="1"/>
|
||||
<listitem type="829" id="uZPyITrjct7nt" open="1"/>
|
||||
<listitem type="829" id="uJlnCmWCjiZyb" open="1"/>
|
||||
<listitem type="829" id="uJ6eIdSRnQ1mC" open="1"/>
|
||||
<listitem type="829" id="uFa0n9CbZAGQz" open="1"/>
|
||||
<listitem type="829" id="uUmpoisGYNixK" open="1"/>
|
||||
<listitem type="829" id="uks0OAl3npzAp" open="0"/>
|
||||
<listitem type="829" id="uegsqNCOwThlg" open="0"/>
|
||||
<listitem type="829" id="uIzLslKdzkNSu" open="0"/>
|
||||
<listitem type="829" id="u3gksr7QwMjSv" open="0"/>
|
||||
<listitem type="829" id="uCYvllFCLICqv" open="1"/>
|
||||
<listitem type="829" id="uaxm6xi0OF7H9" open="0"/>
|
||||
<listitem type="829" id="uJPiqYCPjwNHv" open="1"/>
|
||||
</listitem>
|
||||
</listitem>
|
||||
<listitem type="802" id="Use_Case_View" open="1"/>
|
||||
</listitem>
|
||||
</listview>
|
||||
<codegeneration>
|
||||
<codegenerator language="SQL"/>
|
||||
</codegeneration>
|
||||
</XMI.extensions>
|
||||
</XMI>
|
||||
|
|
@ -44,6 +44,7 @@ import numpy as np
|
|||
from multiprocessing import Process
|
||||
import time
|
||||
from healthcareio import x12
|
||||
from healthcareio.export import export
|
||||
import smart
|
||||
from healthcareio.server import proxy
|
||||
import pandas as pd
|
||||
|
|
@ -57,6 +58,24 @@ if not os.path.exists(PATH) :
|
|||
import platform
|
||||
import sqlite3 as lite
|
||||
# PATH = os.sep.join([os.environ['HOME'],'.edi-parser'])
|
||||
HELP_MESSAGE = """
|
||||
cli:
|
||||
|
||||
healthcare-io.py --<[signup|init]> <email> --store <sqlite|mongo> [--batch <value>]
|
||||
healthcare-io.py --parse --folder <path> [--batch <value>] [--resume]
|
||||
healthcare-io.py --check-update
|
||||
healthcare-io.py --export <835|837> --config <config-path>
|
||||
action :
|
||||
--signup|init signup user and get configuration file
|
||||
--parse starts parsing
|
||||
--check checks for updates
|
||||
--export export data of a 835 or 837 into another database
|
||||
parameters :
|
||||
--<[signup|init]> signup or get a configuration file from a parsing server
|
||||
--folder location of the files (the program will recursively traverse it)
|
||||
--store data store mongo or sqlite or mongodb
|
||||
--resume will attempt to resume if there was an interruption
|
||||
"""
|
||||
def signup (**args) :
|
||||
"""
|
||||
:email user's email address
|
||||
|
|
@ -125,77 +144,77 @@ def init():
|
|||
#
|
||||
# Global variables that load the configuration files
|
||||
|
||||
def parse(**args):
|
||||
"""
|
||||
This function will parse the content of a claim or remittance (x12 format) give the following parameters
|
||||
:filename absolute path of the file to be parsed
|
||||
:type claims|remits in x12 format
|
||||
"""
|
||||
global INFO
|
||||
if not INFO :
|
||||
INFO = init()
|
||||
if args['type'] == 'claims' :
|
||||
CONFIG = INFO['parser']['837']
|
||||
elif args['type'] == 'remits' :
|
||||
CONFIG = INFO['parser']['835']
|
||||
else:
|
||||
CONFIG = None
|
||||
if CONFIG :
|
||||
# CONFIG = CONFIG[-1] if 'version' not in args and (args['version'] < len(CONFIG)) else CONFIG[0]
|
||||
CONFIG = CONFIG[int(args['version'])-1] if 'version' in SYS_ARGS and int(SYS_ARGS['version']) < len(CONFIG) else CONFIG[-1]
|
||||
SECTION = CONFIG['SECTION']
|
||||
os.environ['HEALTHCAREIO_SALT'] = INFO['owner']
|
||||
# def parse(**args):
|
||||
# """
|
||||
# This function will parse the content of a claim or remittance (x12 format) give the following parameters
|
||||
# :filename absolute path of the file to be parsed
|
||||
# :type claims|remits in x12 format
|
||||
# """
|
||||
# global INFO
|
||||
# if not INFO :
|
||||
# INFO = init()
|
||||
# if args['type'] == 'claims' :
|
||||
# CONFIG = INFO['parser']['837']
|
||||
# elif args['type'] == 'remits' :
|
||||
# CONFIG = INFO['parser']['835']
|
||||
# else:
|
||||
# CONFIG = None
|
||||
# if CONFIG :
|
||||
# # CONFIG = CONFIG[-1] if 'version' not in args and (args['version'] < len(CONFIG)) else CONFIG[0]
|
||||
# CONFIG = CONFIG[int(args['version'])-1] if 'version' in SYS_ARGS and int(SYS_ARGS['version']) < len(CONFIG) else CONFIG[-1]
|
||||
# SECTION = CONFIG['SECTION']
|
||||
# os.environ['HEALTHCAREIO_SALT'] = INFO['owner']
|
||||
|
||||
|
||||
return get_content(args['filename'],CONFIG,SECTION)
|
||||
def resume (files,id,config):
|
||||
_args = config['store'].copy()
|
||||
if 'mongo' in config['store']['type'] :
|
||||
_args['type'] = 'mongo.MongoReader'
|
||||
reader = factory.instance(**_args)
|
||||
_files = []
|
||||
if 'resume' in config['analytics'] :
|
||||
_args = config['analytics']['resume'][id]
|
||||
_files = reader.read(**_args)
|
||||
_files = [item['name'] for item in _files if item['name'] != None]
|
||||
return list(set(files) - set(_files))
|
||||
# return get_content(args['filename'],CONFIG,SECTION)
|
||||
# def resume (files,id,config):
|
||||
# _args = config['store'].copy()
|
||||
# if 'mongo' in config['store']['type'] :
|
||||
# _args['type'] = 'mongo.MongoReader'
|
||||
# reader = factory.instance(**_args)
|
||||
# _files = []
|
||||
# if 'resume' in config['analytics'] :
|
||||
# _args = config['analytics']['resume'][id]
|
||||
# _files = reader.read(**_args)
|
||||
# _files = [item['name'] for item in _files if item['name'] != None]
|
||||
# return list(set(files) - set(_files))
|
||||
|
||||
return files
|
||||
pass
|
||||
def apply(files,store_info,logger_info=None):
|
||||
"""
|
||||
:files list of files to be processed in this given thread/process
|
||||
:store_info information about data-store, for now disk isn't thread safe
|
||||
:logger_info information about where to store the logs
|
||||
"""
|
||||
# return files
|
||||
# pass
|
||||
# def apply(files,store_info,logger_info=None):
|
||||
# """
|
||||
# :files list of files to be processed in this given thread/process
|
||||
# :store_info information about data-store, for now disk isn't thread safe
|
||||
# :logger_info information about where to store the logs
|
||||
# """
|
||||
|
||||
if not logger_info :
|
||||
logger = factory.instance(type='disk.DiskWriter',args={'path':os.sep.join([info['out-folder'],SYS_ARGS['parse']+'.log'])})
|
||||
else:
|
||||
logger = factory.instance(**logger_info)
|
||||
# if not logger_info :
|
||||
# logger = factory.instance(type='disk.DiskWriter',args={'path':os.sep.join([info['out-folder'],SYS_ARGS['parse']+'.log'])})
|
||||
# else:
|
||||
# logger = factory.instance(**logger_info)
|
||||
|
||||
writer = factory.instance(**store_info)
|
||||
for filename in files :
|
||||
# writer = factory.instance(**store_info)
|
||||
# for filename in files :
|
||||
|
||||
if filename.strip() == '':
|
||||
continue
|
||||
# content,logs = get_content(filename,CONFIG,CONFIG['SECTION'])
|
||||
#
|
||||
try:
|
||||
content,logs = parse(filename = filename,type=SYS_ARGS['parse'])
|
||||
# if filename.strip() == '':
|
||||
# continue
|
||||
# # content,logs = get_content(filename,CONFIG,CONFIG['SECTION'])
|
||||
# #
|
||||
# try:
|
||||
# content,logs = parse(filename = filename,type=SYS_ARGS['parse'])
|
||||
|
||||
if content :
|
||||
writer.write(content)
|
||||
if logs :
|
||||
[logger.write(dict(_row,**{"parse":SYS_ARGS['parse']})) for _row in logs]
|
||||
else:
|
||||
logger.write({"parse":SYS_ARGS['parse'],"name":filename,"completed":True,"rows":len(content)})
|
||||
except Exception as e:
|
||||
# if content :
|
||||
# writer.write(content)
|
||||
# if logs :
|
||||
# [logger.write(dict(_row,**{"parse":SYS_ARGS['parse']})) for _row in logs]
|
||||
# else:
|
||||
# logger.write({"parse":SYS_ARGS['parse'],"name":filename,"completed":True,"rows":len(content)})
|
||||
# except Exception as e:
|
||||
|
||||
logger.write({"parse":SYS_ARGS['parse'],"filename":filename,"completed":False,"rows":-1,"msg":e.args[0]})
|
||||
# print ([filename,len(content)])
|
||||
#
|
||||
# @TODO: forward this data to the writer and log engine
|
||||
# logger.write({"parse":SYS_ARGS['parse'],"filename":filename,"completed":False,"rows":-1,"msg":e.args[0]})
|
||||
# # print ([filename,len(content)])
|
||||
# #
|
||||
# # @TODO: forward this data to the writer and log engine
|
||||
#
|
||||
def upgrade(**args):
|
||||
"""
|
||||
|
|
@ -360,95 +379,27 @@ if __name__ == '__main__' :
|
|||
#
|
||||
# this function is designed to export the data to csv
|
||||
#
|
||||
format = SYS_ARGS['format'] if 'format' in SYS_ARGS else 'csv'
|
||||
format = format.lower()
|
||||
if set([format]) not in ['xls','csv'] :
|
||||
format = 'csv'
|
||||
path = SYS_ARGS['config']
|
||||
TYPE = SYS_ARGS['export'] if 'export' in SYS_ARGS else '835'
|
||||
if not os.path.exists(path) or TYPE not in ['835','837']:
|
||||
print (HELP_MESSAGE)
|
||||
else:
|
||||
#
|
||||
# Let's run the export function ..., This will push files into a data-store of choice Redshift, PostgreSQL, MySQL ...
|
||||
#
|
||||
_store = {"type":"sql.SQLWriter","args":json.loads( (open(path) ).read())}
|
||||
|
||||
pipes = export.Factory.instance(type=TYPE,write_store=_store) #"inspect":0,"cast":0}})
|
||||
# pipes[0].run()
|
||||
for thread in pipes:
|
||||
thread.start()
|
||||
time.sleep(1)
|
||||
while pipes :
|
||||
pipes = [thread for thread in pipes if thread.is_alive()]
|
||||
time.sleep(1)
|
||||
|
||||
|
||||
|
||||
else:
|
||||
msg = """
|
||||
cli:
|
||||
|
||||
healthcare-io.py --<[signup|init]> <email> --store <sqlite|mongo> [--batch <value>]
|
||||
healthcare-io.py --parse --folder <path> [--batch <value>] [--resume]
|
||||
healthcare-io.py --check-update
|
||||
action :
|
||||
--signup|init signup user and get configuration file
|
||||
--parse starts parsing
|
||||
--check checks for updates
|
||||
parameters :
|
||||
--<[signup|init]> signup or get a configuration file from a parsing server
|
||||
--folder location of the files (the program will recursively traverse it)
|
||||
--store data store mongo or sqlite or mongodb
|
||||
--resume will attempt to resume if there was an interruption
|
||||
"""
|
||||
print(msg)
|
||||
pass
|
||||
# """
|
||||
# The program was called from the command line thus we are expecting
|
||||
# parse in [claims,remits]
|
||||
# config os.sep.path.exists(path)
|
||||
# folder os.sep.path.exists(path)
|
||||
# store store ()
|
||||
# """
|
||||
# p = len( set(['store','config','folder']) & set(SYS_ARGS.keys())) == 3 and ('db' in SYS_ARGS or 'path' in SYS_ARGS)
|
||||
# TYPE = {
|
||||
# 'mongo':'mongo.MongoWriter',
|
||||
# 'couch':'couch.CouchWriter',
|
||||
# 'disk':'disk.DiskWriter'
|
||||
# }
|
||||
# INFO = {
|
||||
# '837':{'scope':'claims','section':'HL'},
|
||||
# '835':{'scope':'remits','section':'CLP'}
|
||||
# }
|
||||
# if p :
|
||||
# args = {}
|
||||
# scope = SYS_ARGS['config'][:-5].split(os.sep)[-1]
|
||||
# CONTEXT = INFO[scope]['scope']
|
||||
# #
|
||||
# # @NOTE:
|
||||
# # improve how database and data stores are handled.
|
||||
# if SYS_ARGS['store'] == 'couch' :
|
||||
# args = {'url': SYS_ARGS['url'] if 'url' in SYS_ARGS else 'http://localhost:5984'}
|
||||
# args['dbname'] = SYS_ARGS['db']
|
||||
|
||||
# elif SYS_ARGS ['store'] == 'mongo':
|
||||
# args = {'host':SYS_ARGS['host']if 'host' in SYS_ARGS else 'localhost:27017'}
|
||||
# if SYS_ARGS['store'] in ['mongo','couch']:
|
||||
# args['dbname'] = SYS_ARGS['db'] if 'db' in SYS_ARGS else 'claims_outcomes'
|
||||
# args['doc'] = CONTEXT
|
||||
|
||||
# TYPE = TYPE[SYS_ARGS['store']]
|
||||
# writer = factory.instance(type=TYPE,args=args)
|
||||
# if SYS_ARGS['store'] == 'disk':
|
||||
# writer.init(path = 'output-claims.json')
|
||||
# logger = factory.instance(type=TYPE,args= dict(args,**{"doc":"logs"}))
|
||||
# files = os.listdir(SYS_ARGS['folder'])
|
||||
# CONFIG = json.loads(open(SYS_ARGS['config']).read())
|
||||
# SECTION = INFO[scope]['section']
|
||||
|
||||
# for file in files :
|
||||
# if 'limit' in SYS_ARGS and files.index(file) == int(SYS_ARGS['limit']) :
|
||||
# break
|
||||
# else:
|
||||
# filename = os.sep.join([SYS_ARGS['folder'],file])
|
||||
|
||||
# try:
|
||||
# content,logs = get_content(filename,CONFIG,SECTION)
|
||||
# except Exception as e:
|
||||
# if sys.version_info[0] > 2 :
|
||||
# logs = [{"filename":filename,"msg":e.args[0]}]
|
||||
# else:
|
||||
# logs = [{"filename":filename,"msg":e.message}]
|
||||
# content = None
|
||||
# if content :
|
||||
|
||||
# writer.write(content)
|
||||
# if logs:
|
||||
|
||||
# logger.write(logs)
|
||||
|
||||
|
||||
# pass
|
||||
# else:
|
||||
# print (__doc__)
|
||||
print(HELP_MESSAGE)
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@ import transport
|
|||
import pandas as pd
|
||||
import numpy as np
|
||||
from healthcareio import x12
|
||||
|
||||
from healthcareio.export import export
|
||||
from multiprocessing import Process
|
||||
# from flask_socketio import SocketIO, emit, disconnect,send
|
||||
from healthcareio.server import proxy
|
||||
|
|
|
|||
|
|
@ -173,12 +173,14 @@ class Formatters :
|
|||
def pos(self,value):
|
||||
"""
|
||||
formatting place of service information within a segment (REF)
|
||||
@TODO: In order to accomodate the other elements they need to be specified in the configuration
|
||||
Otherwise it causes problems on export
|
||||
"""
|
||||
|
||||
xchar = '>' if '>' in value else ':'
|
||||
x = value.split(xchar)
|
||||
x = {"code":x[0],"indicator":x[1],"frequency":x[2]} if len(x) == 3 else {"code":x[0],"indicator":None,"frequency":None}
|
||||
return x
|
||||
return x['code']
|
||||
class Parser (Process):
|
||||
def __init__(self,path):
|
||||
"""
|
||||
|
|
|
|||
2
setup.py
2
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":"1.4.6",
|
||||
"name":"healthcareio","version":"1.4.8",
|
||||
"author":"Vanderbilt University Medical Center",
|
||||
"author_email":"steve.l.nyemba@vumc.org",
|
||||
"include_package_data":True,
|
||||
|
|
|
|||
Loading…
Reference in New Issue