documentation:software:atlas:achilles_v_1_5
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documentation:software:atlas:achilles_v_1_5 [2017/10/12 02:31] anthonysena |
documentation:software:atlas:achilles_v_1_5 [2018/03/12 14:36] (current) anthonysena [Concept Hierarchy] |
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| ===== TL;DR ===== | ===== TL;DR ===== | ||
| - | If you complete a full run of Achilles v.1.5.0 on your OMOP CDM v5 with the default settings, you will not need to complete any of the steps in this article. If you have an OMOP CDM v5 and you ran Achilles in the past (prior to v.1.5.0) then you will need to read and complete the steps below to work with WebAPI/Atlas V2.2.0. | + | If you complete a full run of Achilles v.1.5.0 on your OMOP CDM v5 with the default settings, you will not need to complete any of the steps in this article. If you have an OMOP CDM v5 and you ran Achilles in the past (prior to v.1.5.0) then you will need to read and complete the steps below to work with WebAPI/Atlas V2.2.0. If you'd like to run a command to apply all of the new changes, scroll to the bottom of the article. |
| Resources: | Resources: | ||
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| Achilles will now construct a new table in the results schema labeled ''concept_hierarchy'' using the OMOP vocabulary found in the CDM. This one-time operation is used to optimize query performance when by WebAPI against the ''ACHILLES_results'' table. | Achilles will now construct a new table in the results schema labeled ''concept_hierarchy'' using the OMOP vocabulary found in the CDM. This one-time operation is used to optimize query performance when by WebAPI against the ''ACHILLES_results'' table. | ||
| + | **Please Note**: If you update the vocabulary in your CDM, you should re-create (and re-index) the concept_hierarchy table. | ||
| ==== Creating the Concept Hierarchy ==== | ==== Creating the Concept Hierarchy ==== | ||
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| resultsDatabaseSchema <- "my_results_schema_goes_here" | resultsDatabaseSchema <- "my_results_schema_goes_here" | ||
| vocabDatabaseSchema <- "my_vocabulary_schema_goes_here" | vocabDatabaseSchema <- "my_vocabulary_schema_goes_here" | ||
| + | db <- "my_cdm_database_name" | ||
| achillesResults <- Achilles::achilles(connectionDetails, | achillesResults <- Achilles::achilles(connectionDetails, | ||
| cdmDatabaseSchema = cdmDatabaseSchema, | cdmDatabaseSchema = cdmDatabaseSchema, | ||
| Line 101: | Line 103: | ||
| resultsDatabaseSchema <- "my_results_schema_goes_here" | resultsDatabaseSchema <- "my_results_schema_goes_here" | ||
| vocabDatabaseSchema <- "my_vocabulary_schema_goes_here" | vocabDatabaseSchema <- "my_vocabulary_schema_goes_here" | ||
| + | db <- "my_cdm_database_name" | ||
| achillesResults <- Achilles::achilles(connectionDetails, | achillesResults <- Achilles::achilles(connectionDetails, | ||
| cdmDatabaseSchema = cdmDatabaseSchema, | cdmDatabaseSchema = cdmDatabaseSchema, | ||
documentation/software/atlas/achilles_v_1_5.1507775499.txt.gz · Last modified: 2017/10/12 02:31 by anthonysena
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