diff --git a/scripts/Synapse/analyzeLinkageAlgorithms.ipynb b/scripts/Synapse/analyzeLinkageAlgorithms.ipynb index 18ac9f76..d3b287a8 100644 --- a/scripts/Synapse/analyzeLinkageAlgorithms.ipynb +++ b/scripts/Synapse/analyzeLinkageAlgorithms.ipynb @@ -17,6 +17,15 @@ "Part 4 generates the final result statistics of the performance of each algorithm on the testing set." ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%pip install --upgrade pip" + ] + }, { "cell_type": "code", "execution_count": null, diff --git a/scripts/Synapse/convertParquetMPI.ipynb b/scripts/Synapse/convertParquetMPI.ipynb index 9cb0ea3d..34bbe786 100644 --- a/scripts/Synapse/convertParquetMPI.ipynb +++ b/scripts/Synapse/convertParquetMPI.ipynb @@ -10,6 +10,15 @@ "This notebook reads in patient data from an uploaded parquet file (`mpi_incoming_filename`), converts to FHIR, and writes the data to blob storage." ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%pip install --upgrade pip" + ] + }, { "cell_type": "code", "execution_count": null, diff --git a/scripts/Synapse/generateIRISCaseFiles.ipynb b/scripts/Synapse/generateIRISCaseFiles.ipynb index 8423846a..78df51ef 100644 --- a/scripts/Synapse/generateIRISCaseFiles.ipynb +++ b/scripts/Synapse/generateIRISCaseFiles.ipynb @@ -17,6 +17,15 @@ "Both .txt files conform to the LAC UDF upload spec with two rows per ECR and 2 recent COVID tests from the 20 tests stored in the ECR datastore." ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%pip install --upgrade pip" + ] + }, { "cell_type": "code", "execution_count": null, diff --git a/scripts/Synapse/updateECRDataStore.ipynb b/scripts/Synapse/updateECRDataStore.ipynb index 253800e7..9f99ac1a 100644 --- a/scripts/Synapse/updateECRDataStore.ipynb +++ b/scripts/Synapse/updateECRDataStore.ipynb @@ -10,6 +10,15 @@ "This notebook updates the ECR datastore delta table with new ECR records (`PARSED_ECR_PATH`); a new ECR datastore delta table is created if one does not already exist." ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%pip install --upgrade pip" + ] + }, { "cell_type": "code", "execution_count": null, diff --git a/scripts/Synapse/updateECRDataStoreIncidentID.ipynb b/scripts/Synapse/updateECRDataStoreIncidentID.ipynb index 270a16fe..3abeec0b 100644 --- a/scripts/Synapse/updateECRDataStoreIncidentID.ipynb +++ b/scripts/Synapse/updateECRDataStoreIncidentID.ipynb @@ -19,6 +19,15 @@ "Set up and prep data. Load ECR datastore (`ecr`) and MII delta tables (`mii`). Load the data necessary for identifying positive COVID tests (`covid_test_type_codes`, `covid_positive_results`)" ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%pip install --upgrade pip" + ] + }, { "cell_type": "code", "execution_count": null, diff --git a/scripts/Synapse/updateECRDataStoreIrisID.ipynb b/scripts/Synapse/updateECRDataStoreIrisID.ipynb index 24360d1a..5e9c19ac 100644 --- a/scripts/Synapse/updateECRDataStoreIrisID.ipynb +++ b/scripts/Synapse/updateECRDataStoreIrisID.ipynb @@ -11,6 +11,15 @@ "This notebook joins the ECR datastore (`ecr`) and Person table from the Master Patient Index (`person`) on `person_id` to update the ECR datastore's `iris_id` with the most up-to-date `external_person_id` in the `person` table." ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%pip install --upgrade pip" + ] + }, { "cell_type": "code", "execution_count": null, diff --git a/scripts/Synapse/updateECRDataStorePersonID.ipynb b/scripts/Synapse/updateECRDataStorePersonID.ipynb index fc8785a4..cb7d73fd 100644 --- a/scripts/Synapse/updateECRDataStorePersonID.ipynb +++ b/scripts/Synapse/updateECRDataStorePersonID.ipynb @@ -11,6 +11,15 @@ "This notebook joins the ECR datastore (`ecr`) and Patient table from the Master Patient Index (`patient`) on `patient_id` to update the ECR datastore's `person_id` with the most up-to-date `person_id` in the `patient` table. " ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%pip install --upgrade pip" + ] + }, { "cell_type": "code", "execution_count": null, diff --git a/scripts/Synapse/updateMII.ipynb b/scripts/Synapse/updateMII.ipynb index d527e788..68264772 100644 --- a/scripts/Synapse/updateMII.ipynb +++ b/scripts/Synapse/updateMII.ipynb @@ -10,6 +10,15 @@ "This notebook inserts and updates data from an uploaded parquet file (`mii_incoming_file_path`) into a Master Incident Index (MII) delta table (`mii_delta_table_path`). " ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%pip install --upgrade pip" + ] + }, { "cell_type": "code", "execution_count": null, diff --git a/terraform/modules/shared/main.tf b/terraform/modules/shared/main.tf index 45c87d18..725794e2 100644 --- a/terraform/modules/shared/main.tf +++ b/terraform/modules/shared/main.tf @@ -279,7 +279,7 @@ locals { "record-linkage", ]) - phdi_version = "v1.1.1" + phdi_version = "v1.1.2" } data "docker_registry_image" "ghcr_data" {