| 1 | ################################################################################
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| 2 | #
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| 3 | # Process the PROCEDURES section of an intermediate CCR Level 3 XML file using
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| 4 | # a set of rules.
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| 5 | #
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| 6 | # Usage: ProcFix codelistcsvfile inputxmlfile outputxmlfile
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| 7 | #
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| 8 | # Where:
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| 9 | # codelistcsvfile: defines valid medical vocabulary codes for PROCEDURES
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| 10 | # inputxmlfile: input file
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| 11 | # outputxmlfile: output file (can be same name as input file)
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| 12 | #
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| 13 | # The process of producing quality measures XML for submission to CMS (as part
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| 14 | # of Meaningful Use certification) is quite complex. Briefly, the steps are:
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| 15 | #
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| 16 | # 1. The VistA EHR outputs a CCR record (XML).
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| 17 | #
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| 18 | # 2. The CCR is transformed to CCD Level 3 format (XML) using XSLT.
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| 19 | #
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| 20 | # 3. Due to data vagaries (desire to limit patient-identifying information and
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| 21 | # new Schematron validation directives introduced for 2011), additional
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| 22 | # processing is necessary to output a final XML file for submission to CMS.
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| 23 | #
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| 24 | # A series of sed, awk, and other (such as this program) commands are
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| 25 | # applied to slowly move the baseline CCD into a final format that will
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| 26 | # successfully validate with CMS. Some of the intermediate "XML" files
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| 27 | # produced during this multi-step transformation may not be well-formed,
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| 28 | # which makes it difficult to use tools such as XSLT.
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| 29 | #
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| 30 | # This program only assumes that the XML for the PROCEDURES section will be
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| 31 | # well-formed. Other sections of the input file may not be valid XML, but that
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| 32 | # will not adversely affect program operation.
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| 33 | #
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| 34 | ################################################################################
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| 35 |
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| 36 | import sys
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| 37 | import csv
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| 38 |
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| 39 | ################################################################################
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| 40 | # This function extracts the code value and OID from the supplied line and
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| 41 | # builds a code dictionary key of the form "OID:value"
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| 42 | ################################################################################
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| 43 | def build_code_key(line):
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| 44 | # Extract code value and OID
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| 45 | blankless_line = line.replace(' ', '')
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| 46 | i1 = blankless_line.find('code="')
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| 47 | i1 = i1 + len('code="');
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| 48 | i2 = blankless_line.find('"', i1)
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| 49 | code_value = blankless_line[i1 : i2];
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| 50 | i1 = blankless_line.find('codeSystem="')
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| 51 | i1 = i1 + len('codeSystem="')
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| 52 | i2 = blankless_line.find('"', i1)
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| 53 | code_system = blankless_line[i1 : i2]
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| 54 |
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| 55 | return code_system + ':' + code_value
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| 56 |
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| 57 | ################################################################################
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| 58 | # Read the CSV file, which is exported from Appendix G of the 2011 Downloadable
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| 59 | # Resources table. This file defines the medical vocabulary codes that may be
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| 60 | # used by the PROCEDURES section. File format:
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| 61 | #
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| 62 | # - Column 1 is the symbolic code set name
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| 63 | # - Column 2 is the HL7 OID (object identifier number) for the code set
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| 64 | # - Column 3 is the actual code value
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| 65 | #
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| 66 | # The symbolic code set name is defined by Appendix G using terminology such as
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| 67 | # C4 to mean CPT-4, SNM to mean SNOMED-CT, LN to mean LOINC, and so on. The
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| 68 | # VistA CCD output uses different symbolic names (for example, CPT-4 instead of
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| 69 | # C4). The CMS validation rules do not validate symbolic code set names.
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| 70 | #
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| 71 | # Since there is no code set naming contract between VistA CCD output and this
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| 72 | # program, it would be unwise to use observed values - so we will not check the
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| 73 | # symbolic code name attributes.
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| 74 | #
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| 75 | # Per CMS 2011 rules, we must check the code set OID and the associated code
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| 76 | # value. A dictionary is an easy way to manage the OID/value information.
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| 77 | # The key will be OID + ':' + CodeValue, and the value will be CodeValue.
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| 78 | ################################################################################
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| 79 | def create_code_dictionary(csvfilename):
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| 80 | csvfile = open(csvfilename, 'r')
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| 81 | codedict = {}
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| 82 | try:
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| 83 | reader = csv.reader(csvfile)
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| 84 | for row in reader:
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| 85 | key = row[1] + ":" + row[2]
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| 86 | codedict[key] = row[2]
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| 87 | finally:
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| 88 | csvfile.close()
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| 89 |
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| 90 | return codedict
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| 91 |
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| 92 | ################################################################################
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| 93 | # Do a pattern match on the supplied line using the supplied patterns. Both
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| 94 | # the line and patterns are processed (local copies) to remove all blanks. This
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| 95 | # is necessary because XML attributes inside an element have arbitrary spacing
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| 96 | # rules. For example,
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| 97 | #
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| 98 | # <element attr = "value"...
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| 99 | # <element attr = "value"...
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| 100 | # <element attr="value"
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| 101 | #
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| 102 | # Are all valid XML. Removing all whitespace makes sane pattern matching
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| 103 | # possible.
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| 104 | ################################################################################
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| 105 | def match(line, pat1, pat2="", pat3="", pat4=""):
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| 106 | blankless_line = line.replace(' ', '')
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| 107 | match_list = [pat1.replace(' ', '')]
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| 108 | if len(pat2) > 0:
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| 109 | match_list.append(pat2.replace(' ', ''))
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| 110 | if len(pat3) > 0:
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| 111 | match_list.append(pat3.replace(' ', ''))
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| 112 | if len(pat4) > 0:
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| 113 | match_list.append(pat4.replace(' ', ''))
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| 114 |
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| 115 | for pattern in match_list:
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| 116 | if blankless_line.find(pattern) < 0:
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| 117 | return 0
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| 118 |
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| 119 | return 1
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| 120 |
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| 121 | ################################################################################
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| 122 | # Find the start and end of the PROCEDURES section. According to the CMS 2011
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| 123 | # specs, the structure for PROCEDURES is:
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| 124 | #
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| 125 | # <component>
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| 126 | # <section>
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| 127 | # <templateId root="2.16.840.1.113883.10.20.1.12"/>
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| 128 | # <code code="47519-4" codeSystem="2.16.840.1.113883.6.1"/>
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| 129 | # ...various PROCEDURES elements
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| 130 | # </section>
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| 131 | # </component>
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| 132 | #
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| 133 | # Note that there can be multiple templateId elements. However, the one given
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| 134 | # above (2.16.840.1.113883.10.20.1.12) is mandatory and serves (in conjuction
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| 135 | # with the code element) to identify the PROCEDURES section.
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| 136 | #
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| 137 | ################################################################################
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| 138 | def find_procedures_section(source):
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| 139 | start_index = 0
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| 140 | searching = 1
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| 141 | end_index = len(source) - 1
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| 142 | min_procedures_len = 6
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| 143 |
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| 144 | while searching:
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| 145 | # If within minimum target size at the end, give up
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| 146 | if start_index + min_procedures_len >= end_index:
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| 147 | break
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| 148 |
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| 149 | # No <component> element means no PROCEDURES. Quit searching.
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| 150 | patterns = ["<component>"]
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| 151 | component_start = find_line(start_index, end_index, patterns)
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| 152 | if component_start < 0:
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| 153 | break
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| 154 |
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| 155 | # Missing <component> end means no PROCEDURES (really malformed XML).
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| 156 | # However, if have <component></component> on same line, then it's
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| 157 | # an empty component, so keep searching.
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| 158 | patterns = ["</component>"]
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| 159 | component_end = find_line(component_start, end_index, patterns)
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| 160 | if component_end < 0:
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| 161 | break
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| 162 | if component_start == component_end:
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| 163 | start_index = component_start + 1
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| 164 | continue
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| 165 |
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| 166 | # Search for <section> element bounded by component. If not found,
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| 167 | # continue search after component end.
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| 168 | patterns = ["<section>"]
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| 169 | section_start = find_line(component_start+1, component_end, patterns)
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| 170 | if section_start < 0:
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| 171 | start_index = component_end + 1
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| 172 | continue
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| 173 |
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| 174 | # Mission <section> end means malformed XML inside this <component>.
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| 175 | # Recover by continuing search after <component> end. Also continue
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| 176 | # search if <section></section> on same line.
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| 177 | patterns = ["</section>"]
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| 178 | section_end = find_line(section_start, component_end, patterns)
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| 179 | if section_end < 0 or section_start == section_end:
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| 180 | start_index = component_end + 1
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| 181 | continue
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| 182 |
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| 183 | patterns = ["<templateId", 'root="2.16.840.1.113883.10.20.1.12"']
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| 184 | template_index = find_line(section_start+1, section_end, patterns)
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| 185 | if template_index < 0:
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| 186 | start_index = component_end + 1
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| 187 | continue
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| 188 |
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| 189 | patterns = ["<code", \
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| 190 | 'code="47519-4"', \
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| 191 | 'codeSystem="2.16.840.1.113883.6.1"']
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| 192 | code_index = find_line(template_index+1, section_end, patterns)
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| 193 | if code_index > 0:
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| 194 | return (component_start, component_end)
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| 195 |
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| 196 | return (-1, -1)
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| 197 |
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| 198 | ################################################################################
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| 199 | # Entry point: check command arguments and do the work
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| 200 | ################################################################################
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| 201 | # Check for proper usage
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| 202 | if len(sys.argv) != 3:
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| 203 | print('Usage: ' + sys.argv[0] + \
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| 204 | ' codelistcsvfile xmlfile')
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| 205 | sys.exit(1)
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| 206 |
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| 207 | # Create the medical code dictionary using supplied Appendix G data
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| 208 | code_dictionary = create_code_dictionary(sys.argv[1])
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| 209 |
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| 210 | # Now read in the quasi-XML source file into a list.
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| 211 |
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| 212 | infile = open(sys.argv[2], 'r')
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| 213 | source_lines = infile.readlines()
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| 214 | infile.close()
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| 215 | print("Processing ", sys.argv[2])
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| 216 |
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| 217 | # Open the output file and start processing the input. First, we're looking
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| 218 | # for the start of the PROCEDURES section. According to the CMS 2011 specs,
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| 219 | # the structure for PROCEDURES is:
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| 220 | #
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| 221 | # <component>
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| 222 | # <section>
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| 223 | # <templateId root="2.16.840.1.113883.10.20.1.12"/>
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| 224 | # <code code="47519-4" codeSystem="2.16.840.1.113883.6.1"/>
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| 225 | # ...various PROCEDURES elements
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| 226 | # </section>
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| 227 | # </component>
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| 228 | #
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| 229 | # Note that there can be multiple templateId elements. However, the one given
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| 230 | # above (2.16.840.1.113883.10.20.1.12) is mandatory and serves (in conjuction
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| 231 | # with the code element) to identify the PROCEDURES section.
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| 232 |
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| 233 | found_procedures = 0
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| 234 | kill_procedures_text = 0
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| 235 | finding_entry = 0
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| 236 | found_entry = 0
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| 237 | finding_procedures = 0
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| 238 |
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| 239 | # Process lines.
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| 240 | line_index = -1
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| 241 | procedures_start_index = -1
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| 242 | procedures_end_index = -1
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| 243 | entry_start_index = 0
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| 244 | valid_entry_count = 0
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| 245 |
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| 246 | # Iterate over the source file lines
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| 247 | for line in source_lines[:]:
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| 248 | line_index = line_index + 1
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| 249 |
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| 250 | # Look for the start of the PROCEDURES section
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| 251 | if match(line, "<component>"):
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| 252 | finding_procedures = 1
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| 253 | procedures_start_index = line_index
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| 254 | elif finding_procedures and match(line, "<section>"):
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| 255 | finding_procedures = 1
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| 256 | elif finding_procedures and match(line, \
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| 257 | "<templateId", \
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| 258 | 'root="2.16.840.1.113883.10.20.1.12"'):
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| 259 | finding_procedures = 1
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| 260 | elif finding_procedures and match(line, \
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| 261 | "<code", \
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| 262 | 'code="47519-4"', \
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| 263 | 'codeSystem="2.16.840.1.113883.6.1"'):
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| 264 | finding_procedures = 0
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| 265 | found_procedures = 1
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| 266 | kill_procedures_text = 1
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| 267 | finding_entry = 0
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| 268 | found_entry = 0
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| 269 | else:
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| 270 | finding_procedures = 0
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| 271 |
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| 272 | if not found_procedures:
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| 273 | continue
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| 274 |
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| 275 | # Look for end of the PROCEDURES section, which stops all special processing
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| 276 | if match(line, "</component>") and found_procedures:
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| 277 | if valid_entry_count == 0:
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| 278 | for n in range(procedures_start_index, line_index+1):
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| 279 | source_lines[n] = ""
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| 280 | break
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| 281 |
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| 282 | # Replace a real <text> element with one that is empty. Only do this once
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| 283 | # and in the PROCEDURES header.
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| 284 | if kill_procedures_text and match(line, "<text>"):
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| 285 | text_start_index = line_index + 1
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| 286 | continue
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| 287 |
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| 288 | if kill_procedures_text and match(line, "</text>"):
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| 289 | for n in range(text_start_index, line_index):
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| 290 | source_lines[n] = ""
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| 291 | kill_procedures_text = 0
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| 292 | continue
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| 293 |
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| 294 | # Look for an entry element inside the PROCEDURES section. Looking for:
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| 295 | # <entry typeCode="DRIV">
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| 296 | # <procedure classCode="PROC" moodCode="EVN">
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| 297 | # <templateId root="2.16.840.1.113883.10.20.1.29" ... />
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| 298 | # ... (multiple templateId elements are permitted) ...
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| 299 | # <id root="PROCEDURE_4141_10" extension="CCRObjectID"/>
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| 300 | # <code displayName="..." code="99242"
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| 301 | # codeSystemName="CPT-4" codeSystem="2.16.840.1.113883.6.12"/>
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| 302 |
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| 303 | if match(line, '<entry typeCode="DRIV">'):
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| 304 | finding_entry = 1
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| 305 | entry_start_index = line_index
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| 306 | elif finding_entry and \
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| 307 | match(line, '<procedure classCode="PROC"', 'moodCode="EVN">'):
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| 308 | finding_entry = 1
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| 309 | elif finding_entry and \
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| 310 | match(line, '<templateId root="2.16.840.1.113883.10.20.1.29"'):
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| 311 | finding_entry = 1
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| 312 | elif finding_entry and match(line, '<code'):
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| 313 | code_key = build_code_key(line)
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| 314 | finding_entry = 0
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| 315 | found_entry = 1
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| 316 |
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| 317 | # If at end of the procedure entry, validate against the codes. Output if
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| 318 | # valid using the set-aside entry list. Otherwise output an empty line.
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| 319 | if found_entry and match(line, "</entry>"):
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| 320 | if code_key in code_dictionary:
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| 321 | valid_entry_count = valid_entry_count + 1
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| 322 | else:
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| 323 | for n in range(entry_start_index, line_index+1):
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| 324 | source_lines[n] = ""
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| 325 | print(" Deleting procedure entry with invalid code ", code_key)
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| 326 | finding_entry = 0
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| 327 | found_entry = 0
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| 328 |
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| 329 | # Output the modified source line array
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| 330 | outfile = open(sys.argv[2], 'wt')
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| 331 | for line in source_lines:
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| 332 | if len(line) > 0:
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| 333 | outfile.write(line)
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| 334 | print(" Processing complete, valid entry count: ", valid_entry_count)
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| 335 | if valid_entry_count == 0:
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| 336 | print(" Entire procedure section has been deleted")
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| 337 | outfile.close()
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| 338 | sys.exit(0)
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| 339 |
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| 340 |
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| 341 |
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| 342 |
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| 343 |
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| 344 |
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| 345 |
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| 346 |
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| 347 |
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| 348 |
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| 349 |
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| 350 |
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| 351 |
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