RubyGems - conceptql - Versions diffs - 0.6.0 → 0.7.0 - Mend

conceptql 0.6.0 → 0.7.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (126) hide show

checksums.yaml +4 -4
data/CHANGELOG.md +176 -0
data/README.md +4 -2
data/assets/diagram/diagram.css +331 -0
data/assets/diagram/fonts/OFL.txt +93 -0
data/assets/diagram/fonts/Roboto-400.ttf +0 -0
data/assets/diagram/fonts/Roboto-700.ttf +0 -0
data/assets/diagram/fonts/Roboto-Italic-400.ttf +0 -0
data/assets/diagram/fonts/Roboto-Italic-Latin.woff2 +0 -0
data/assets/diagram/fonts/Roboto-Normal-Latin.woff2 +0 -0
data/assets/diagram/operators.svg +224 -0
data/config/vocabularies.csv +85 -85
data/docs/spec/README.md +2624 -0
data/docs/spec/examples/after-operator.json +562 -0
data/docs/spec/examples/any-overlap-operator.json +106 -0
data/docs/spec/examples/before-operator.json +437 -0
data/docs/spec/examples/co-reported-operator.json +168 -0
data/docs/spec/examples/contains-operator.json +97 -0
data/docs/spec/examples/date-range-operator.json +275 -0
data/docs/spec/examples/death-operator.json +103 -0
data/docs/spec/examples/during-operator.json +178 -0
data/docs/spec/examples/episode-operator.json +80 -0
data/docs/spec/examples/equal-operator.json +79 -0
data/docs/spec/examples/ethnicity-operator.json +86 -0
data/docs/spec/examples/except-operator.json +536 -0
data/docs/spec/examples/filter-operator.json +218 -0
data/docs/spec/examples/first-operator.json +148 -0
data/docs/spec/examples/gender-operator.json +257 -0
data/docs/spec/examples/hospice-operator.json +40 -0
data/docs/spec/examples/hospitalization-operator.json +131 -0
data/docs/spec/examples/information-periods-operator.json +131 -0
data/docs/spec/examples/last-operator.json +148 -0
data/docs/spec/examples/match-operator.json +186 -0
data/docs/spec/examples/nth-occurrence-operator.json +300 -0
data/docs/spec/examples/numeric-filter-operator.json +77 -0
data/docs/spec/examples/one-in-two-out-operator.json +158 -0
data/docs/spec/examples/person-filter-operator.json +919 -0
data/docs/spec/examples/person-operator.json +274 -0
data/docs/spec/examples/place-of-service-filter-operator.json +57 -0
data/docs/spec/examples/provenance-operator.json +148 -0
data/docs/spec/examples/provider-filter-operator.json +77 -0
data/docs/spec/examples/race-operator.json +131 -0
data/docs/spec/examples/recall-operator.json +289 -0
data/docs/spec/examples/snf-operator.json +40 -0
data/docs/spec/examples/time-window-operator.json +736 -0
data/docs/spec/examples/trim-date-end-operator.json +201 -0
data/docs/spec/examples/trim-date-start-operator.json +201 -0
data/docs/spec/examples/union-operator.json +547 -0
data/docs/spec/examples/vocabulary-operator.json +232 -0
data/lib/conceptql/behaviors/metadatable.rb +68 -2
data/lib/conceptql/behaviors/provenanceable.rb +4 -1
data/lib/conceptql/behaviors/utilizable.rb +3 -0
data/lib/conceptql/code_case_mismatch_error.rb +50 -0
data/lib/conceptql/data_model/gdm.rb +23 -2
data/lib/conceptql/diagram_renderer/app.rb +59 -0
data/lib/conceptql/diagram_renderer/configuration.rb +87 -0
data/lib/conceptql/diagram_renderer/diagram_data.rb +80 -0
data/lib/conceptql/diagram_renderer/drawing.rb +255 -0
data/lib/conceptql/diagram_renderer/geometry.rb +380 -0
data/lib/conceptql/diagram_renderer/input_error.rb +11 -0
data/lib/conceptql/diagram_renderer/js_format.rb +112 -0
data/lib/conceptql/diagram_renderer/resvg.rb +120 -0
data/lib/conceptql/diagram_renderer/sprite.rb +73 -0
data/lib/conceptql/diagram_renderer/static.rb +70 -0
data/lib/conceptql/diagram_renderer/svg.rb +73 -0
data/lib/conceptql/diagram_renderer/tree_layout.rb +287 -0
data/lib/conceptql/diagram_renderer.rb +82 -0
data/lib/conceptql/lexicon/lexicon_strategy.rb +16 -0
data/lib/conceptql/lexicon.rb +63 -11
data/lib/conceptql/nodifier.rb +5 -3
data/lib/conceptql/operators/after.rb +15 -1
data/lib/conceptql/operators/any_overlap.rb +6 -1
data/lib/conceptql/operators/before.rb +11 -1
data/lib/conceptql/operators/binary_operator_operator.rb +12 -2
data/lib/conceptql/operators/co_reported.rb +9 -4
data/lib/conceptql/operators/contains.rb +6 -1
data/lib/conceptql/operators/count.rb +2 -0
data/lib/conceptql/operators/date_range.rb +15 -3
data/lib/conceptql/operators/death.rb +5 -1
data/lib/conceptql/operators/dedup.rb +2 -0
data/lib/conceptql/operators/during.rb +6 -1
data/lib/conceptql/operators/episode.rb +13 -2
data/lib/conceptql/operators/equal.rb +11 -1
data/lib/conceptql/operators/ethnicity.rb +19 -7
data/lib/conceptql/operators/except.rb +10 -1
data/lib/conceptql/operators/filter.rb +6 -1
data/lib/conceptql/operators/first.rb +19 -9
data/lib/conceptql/operators/from.rb +3 -0
data/lib/conceptql/operators/gender.rb +10 -2
data/lib/conceptql/operators/hospice.rb +7 -1
data/lib/conceptql/operators/hospitalization.rb +6 -1
data/lib/conceptql/operators/information_periods.rb +26 -7
data/lib/conceptql/operators/invalid.rb +4 -0
data/lib/conceptql/operators/last.rb +19 -9
data/lib/conceptql/operators/match.rb +6 -1
data/lib/conceptql/operators/multiple_vocabularies.rb +17 -3
data/lib/conceptql/operators/numeric.rb +4 -0
data/lib/conceptql/operators/numeric_filter.rb +13 -3
data/lib/conceptql/operators/occurrence.rb +33 -12
data/lib/conceptql/operators/one_in_two_out.rb +22 -5
data/lib/conceptql/operators/operator.rb +8 -4
data/lib/conceptql/operators/person.rb +5 -1
data/lib/conceptql/operators/person_filter.rb +14 -1
data/lib/conceptql/operators/place_of_service_filter.rb +14 -3
data/lib/conceptql/operators/provenance.rb +17 -8
data/lib/conceptql/operators/provider_filter.rb +18 -6
data/lib/conceptql/operators/race.rb +14 -9
data/lib/conceptql/operators/read.rb +11 -1
data/lib/conceptql/operators/recall.rb +34 -2
data/lib/conceptql/operators/snf.rb +7 -1
data/lib/conceptql/operators/sum.rb +4 -0
data/lib/conceptql/operators/temporal_operator.rb +4 -2
data/lib/conceptql/operators/time_window.rb +27 -4
data/lib/conceptql/operators/trim_date.rb +6 -14
data/lib/conceptql/operators/trim_date_end.rb +9 -3
data/lib/conceptql/operators/trim_date_start.rb +9 -3
data/lib/conceptql/operators/union.rb +13 -1
data/lib/conceptql/operators/vocabulary.rb +80 -6
data/lib/conceptql/paths.rb +9 -1
data/lib/conceptql/version.rb +1 -1
data/lib/conceptql/vocabularies/drg_systems.rb +3 -2
data/lib/conceptql/vocabularies/entry.rb +14 -11
data/lib/conceptql/vocabularies/vocabulary_class_factory.rb +2 -1
data/lib/conceptql.rb +3 -0
metadata +75 -2
data/doc/spec.md +0 -2091

data/docs/spec/examples/after-operator.json ADDED Viewed

@@ -0,0 +1,562 @@
+{
+  "spec_id": "after-operator",
+  "examples": [
+    {
+      "title": "All MIs that occurred after a patient's first case of diabetes (250.01)",
+      "statement": [
+        "after",
+        {
+          "left": ["icd9", "412"],
+          "right": ["icd9", "250.01"]
+        }
+      ],
+      "help": true,
+      "columns": [
+        "person_id",
+        "criterion_id",
+        "criterion_table",
+        "criterion_domain",
+        "start_date",
+        "end_date",
+        "source_value"
+      ],
+      "rows": [
+        [
+          77,
+          58165,
+          "observations",
+          "condition_occurrence",
+          "2010-10-06",
+          "2010-10-06",
+          "412"
+        ],
+        [
+          96,
+          20748,
+          "observations",
+          "condition_occurrence",
+          "2008-09-21",
+          "2008-09-24",
+          "412"
+        ],
+        [
+          110,
+          62592,
+          "observations",
+          "condition_occurrence",
+          "2010-06-27",
+          "2010-06-27",
+          "412"
+        ],
+        [
+          152,
+          84298,
+          "observations",
+          "condition_occurrence",
+          "2010-11-22",
+          "2010-11-22",
+          "412"
+        ],
+        [
+          187,
+          87583,
+          "observations",
+          "condition_occurrence",
+          "2010-12-26",
+          "2010-12-26",
+          "412"
+        ],
+        [
+          190,
+          61423,
+          "observations",
+          "condition_occurrence",
+          "2009-04-09",
+          "2009-04-09",
+          "412"
+        ],
+        [
+          214,
+          83257,
+          "observations",
+          "condition_occurrence",
+          "2009-11-12",
+          "2009-11-12",
+          "412"
+        ],
+        [
+          223,
+          38682,
+          "observations",
+          "condition_occurrence",
+          "2008-07-28",
+          "2008-07-28",
+          "412"
+        ],
+        [
+          223,
+          39893,
+          "observations",
+          "condition_occurrence",
+          "2008-10-31",
+          "2008-10-31",
+          "412"
+        ]
+      ],
+      "tree": {
+        "format": "conceptql-diagram/v1",
+        "statements": [
+          {
+            "name": "after",
+            "base": "filter",
+            "humanName": "After",
+            "outputTypes": ["condition_occurrence"],
+            "parameters": {},
+            "values": [],
+            "children": [
+              {
+                "name": "icd9",
+                "base": "selection",
+                "humanName": "ICD-9 CM",
+                "vocabularyId": "ICD9CM",
+                "outputTypes": ["condition_occurrence"],
+                "parameters": {},
+                "values": ["412"],
+                "children": [],
+                "counts": {
+                  "condition_occurrence": {
+                    "rows": 48,
+                    "n": 37
+                  }
+                }
+              },
+              {
+                "name": "icd9",
+                "base": "selection",
+                "humanName": "ICD-9 CM",
+                "vocabularyId": "ICD9CM",
+                "outputTypes": ["condition_occurrence"],
+                "parameters": {},
+                "values": ["250.01"],
+                "children": [],
+                "counts": {
+                  "condition_occurrence": {
+                    "rows": 82,
+                    "n": 45
+                  }
+                }
+              }
+            ],
+            "counts": {
+              "condition_occurrence": {
+                "rows": 9,
+                "n": 8
+              }
+            }
+          }
+        ]
+      }
+    },
+    {
+      "title": "Prescriptions of interest within three days after an office visit",
+      "statement": [
+        "after",
+        {
+          "left": [
+            "ndc",
+            "61392070054",
+            "65084025214",
+            "65726040125",
+            {
+              "label": "Prescriptions of Interest"
+            }
+          ],
+          "right": [
+            "cpt",
+            "99214",
+            {
+              "label": "Office Visit"
+            }
+          ],
+          "within": "3d"
+        }
+      ],
+      "help": true,
+      "columns": [
+        "person_id",
+        "criterion_id",
+        "criterion_table",
+        "criterion_domain",
+        "start_date",
+        "end_date",
+        "source_value"
+      ],
+      "rows": [
+        [
+          207,
+          11312,
+          "observations",
+          "drug_exposure",
+          "2010-08-13",
+          "2010-08-13",
+          "61392070054"
+        ]
+      ],
+      "tree": {
+        "format": "conceptql-diagram/v1",
+        "statements": [
+          {
+            "name": "after",
+            "base": "filter",
+            "humanName": "After",
+            "outputTypes": ["drug_exposure"],
+            "parameters": {
+              "within": "3d"
+            },
+            "values": [],
+            "children": [
+              {
+                "name": "ndc",
+                "base": "selection",
+                "humanName": "National Drug Code (FDA and manufacturers)",
+                "vocabularyId": "NDC",
+                "outputTypes": ["drug_exposure"],
+                "parameters": {
+                  "label": "Prescriptions of Interest"
+                },
+                "values": ["61392070054", "65084025214", "65726040125"],
+                "children": [],
+                "counts": {
+                  "drug_exposure": {
+                    "rows": 9,
+                    "n": 8
+                  }
+                }
+              },
+              {
+                "name": "cpt",
+                "base": "selection",
+                "humanName": "CPT",
+                "vocabularyId": "CPT4",
+                "outputTypes": ["procedure_occurrence"],
+                "parameters": {
+                  "label": "Office Visit"
+                },
+                "values": ["99214"],
+                "children": [],
+                "counts": {
+                  "procedure_occurrence": {
+                    "rows": 1073,
+                    "n": 175
+                  }
+                }
+              }
+            ],
+            "counts": {
+              "drug_exposure": {
+                "rows": 1,
+                "n": 1
+              }
+            }
+          }
+        ]
+      }
+    },
+    {
+      "title": "Heart attack diagnoses more than 1 week after a diagnosis of diabetes",
+      "statement": [
+        "after",
+        {
+          "left": [
+            "icd9",
+            "410.00",
+            "410.01",
+            "410.10",
+            "410.11",
+            {
+              "label": "Heart Attack Dx"
+            }
+          ],
+          "right": [
+            "icd9",
+            "250.01",
+            {
+              "label": "Diabetes Dx"
+            }
+          ],
+          "at_least": "1w"
+        }
+      ],
+      "help": true,
+      "columns": [
+        "person_id",
+        "criterion_id",
+        "criterion_table",
+        "criterion_domain",
+        "start_date",
+        "end_date",
+        "source_value"
+      ],
+      "rows": [
+        [
+          58,
+          79480,
+          "observations",
+          "condition_occurrence",
+          "2009-02-24",
+          "2009-02-24",
+          "41011"
+        ]
+      ],
+      "tree": {
+        "format": "conceptql-diagram/v1",
+        "statements": [
+          {
+            "name": "after",
+            "base": "filter",
+            "humanName": "After",
+            "outputTypes": ["condition_occurrence"],
+            "parameters": {
+              "at_least": "1w"
+            },
+            "values": [],
+            "children": [
+              {
+                "name": "icd9",
+                "base": "selection",
+                "humanName": "ICD-9 CM",
+                "vocabularyId": "ICD9CM",
+                "outputTypes": ["condition_occurrence"],
+                "parameters": {
+                  "label": "Heart Attack Dx"
+                },
+                "values": ["410.00", "410.01", "410.10", "410.11"],
+                "children": [],
+                "counts": {
+                  "condition_occurrence": {
+                    "rows": 13,
+                    "n": 8
+                  }
+                }
+              },
+              {
+                "name": "icd9",
+                "base": "selection",
+                "humanName": "ICD-9 CM",
+                "vocabularyId": "ICD9CM",
+                "outputTypes": ["condition_occurrence"],
+                "parameters": {
+                  "label": "Diabetes Dx"
+                },
+                "values": ["250.01"],
+                "children": [],
+                "counts": {
+                  "condition_occurrence": {
+                    "rows": 82,
+                    "n": 45
+                  }
+                }
+              }
+            ],
+            "counts": {
+              "condition_occurrence": {
+                "rows": 1,
+                "n": 1
+              }
+            }
+          }
+        ]
+      }
+    },
+    {
+      "title": "All MIs that occurred after a male patient's 50th birthday",
+      "statement": [
+        "after",
+        {
+          "left": ["icd9", "412"],
+          "right": [
+            "time_window",
+            ["gender", "Male"],
+            {
+              "start": "50y",
+              "end": "50y"
+            }
+          ]
+        }
+      ],
+      "help": true,
+      "columns": [
+        "person_id",
+        "criterion_id",
+        "criterion_table",
+        "criterion_domain",
+        "start_date",
+        "end_date",
+        "source_value"
+      ],
+      "rows": [
+        [
+          54,
+          74606,
+          "observations",
+          "condition_occurrence",
+          "2008-06-05",
+          "2008-06-05",
+          "412"
+        ],
+        [
+          60,
+          986,
+          "observations",
+          "condition_occurrence",
+          "2009-07-19",
+          "2009-07-22",
+          "412"
+        ],
+        [
+          93,
+          82295,
+          "observations",
+          "condition_occurrence",
+          "2009-11-08",
+          "2009-11-08",
+          "412"
+        ],
+        [
+          96,
+          20748,
+          "observations",
+          "condition_occurrence",
+          "2008-09-21",
+          "2008-09-24",
+          "412"
+        ],
+        [
+          109,
+          89334,
+          "observations",
+          "condition_occurrence",
+          "2010-07-06",
+          "2010-07-06",
+          "412"
+        ],
+        [
+          110,
+          62592,
+          "observations",
+          "condition_occurrence",
+          "2010-06-27",
+          "2010-06-27",
+          "412"
+        ],
+        [
+          131,
+          172,
+          "observations",
+          "condition_occurrence",
+          "2008-03-22",
+          "2008-03-23",
+          "412"
+        ],
+        [
+          149,
+          28518,
+          "observations",
+          "condition_occurrence",
+          "2008-04-07",
+          "2008-04-07",
+          "412"
+        ],
+        [
+          152,
+          82988,
+          "observations",
+          "condition_occurrence",
+          "2008-08-16",
+          "2008-08-16",
+          "412"
+        ],
+        [
+          152,
+          84298,
+          "observations",
+          "condition_occurrence",
+          "2010-11-22",
+          "2010-11-22",
+          "412"
+        ]
+      ],
+      "tree": {
+        "format": "conceptql-diagram/v1",
+        "statements": [
+          {
+            "name": "after",
+            "base": "filter",
+            "humanName": "After",
+            "outputTypes": ["condition_occurrence"],
+            "parameters": {},
+            "values": [],
+            "children": [
+              {
+                "name": "icd9",
+                "base": "selection",
+                "humanName": "ICD-9 CM",
+                "vocabularyId": "ICD9CM",
+                "outputTypes": ["condition_occurrence"],
+                "parameters": {},
+                "values": ["412"],
+                "children": [],
+                "counts": {
+                  "condition_occurrence": {
+                    "rows": 48,
+                    "n": 37
+                  }
+                }
+              },
+              {
+                "name": "time_window",
+                "base": "temporal",
+                "humanName": "Time Window",
+                "outputTypes": ["person"],
+                "parameters": {
+                  "start": "50y",
+                  "end": "50y"
+                },
+                "values": [],
+                "children": [
+                  {
+                    "name": "gender",
+                    "base": "selection",
+                    "humanName": "Gender",
+                    "outputTypes": ["person"],
+                    "parameters": {},
+                    "values": ["Male"],
+                    "children": [],
+                    "counts": {
+                      "person": {
+                        "rows": 124,
+                        "n": 124
+                      }
+                    }
+                  }
+                ],
+                "counts": {
+                  "person": {
+                    "rows": 124,
+                    "n": 124
+                  }
+                }
+              }
+            ],
+            "counts": {
+              "condition_occurrence": {
+                "rows": 28,
+                "n": 20
+              }
+            }
+          }
+        ]
+      }
+    }
+  ]
+}

data/docs/spec/examples/any-overlap-operator.json ADDED Viewed

@@ -0,0 +1,106 @@
+{
+  "spec_id": "any-overlap-operator",
+  "examples": [
+    {
+      "title": "All MIs that overlap with the month of 2010-06",
+      "statement": [
+        "any_overlap",
+        {
+          "left": ["icd9", "412"],
+          "right": [
+            "date_range",
+            {
+              "start": "2010-06-01",
+              "end": "2010-06-30"
+            }
+          ]
+        }
+      ],
+      "help": true,
+      "columns": [
+        "person_id",
+        "criterion_id",
+        "criterion_table",
+        "criterion_domain",
+        "start_date",
+        "end_date",
+        "source_value"
+      ],
+      "rows": [
+        [
+          110,
+          62592,
+          "observations",
+          "condition_occurrence",
+          "2010-06-27",
+          "2010-06-27",
+          "412"
+        ],
+        [
+          217,
+          56467,
+          "observations",
+          "condition_occurrence",
+          "2010-06-22",
+          "2010-06-23",
+          "412"
+        ]
+      ],
+      "tree": {
+        "format": "conceptql-diagram/v1",
+        "statements": [
+          {
+            "name": "any_overlap",
+            "base": "filter",
+            "humanName": "Any Overlap",
+            "outputTypes": ["condition_occurrence"],
+            "parameters": {},
+            "values": [],
+            "children": [
+              {
+                "name": "icd9",
+                "base": "selection",
+                "humanName": "ICD-9 CM",
+                "vocabularyId": "ICD9CM",
+                "outputTypes": ["condition_occurrence"],
+                "parameters": {},
+                "values": ["412"],
+                "children": [],
+                "counts": {
+                  "condition_occurrence": {
+                    "rows": 48,
+                    "n": 37
+                  }
+                }
+              },
+              {
+                "name": "date_range",
+                "base": "selection",
+                "humanName": "Date Range",
+                "outputTypes": ["person"],
+                "parameters": {
+                  "start": "2010-06-01",
+                  "end": "2010-06-30"
+                },
+                "values": [],
+                "children": [],
+                "counts": {
+                  "person": {
+                    "rows": 249,
+                    "n": 249
+                  }
+                }
+              }
+            ],
+            "counts": {
+              "condition_occurrence": {
+                "rows": 2,
+                "n": 2
+              }
+            }
+          }
+        ]
+      }
+    }
+  ]
+}