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new import tool #3182

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merged 9 commits into from
Apr 21, 2023
Merged

new import tool #3182

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77776c7
new import tool
v-mserdar Mar 17, 2023
c46774d
revised app.config
v-mserdar Mar 17, 2023
ab6f61a
Revised based on code review
v-mserdar Mar 21, 2023
b952211
revisions to handle oss; code cleanup
v-mserdar Mar 29, 2023
495031b
updated readme to assist oss usage; added config setting for delay wh…
v-mserdar Mar 31, 2023
a91df5c
revisions from code review
v-mserdar Mar 31, 2023
a4bc7ea
final code review revisions
v-mserdar Mar 31, 2023
22a7dbc
changes from code review
v-mserdar Apr 11, 2023
d346461
Adding one additional comment for clarify
v-mserdar Apr 18, 2023
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7 changes: 7 additions & 0 deletions Microsoft.Health.Fhir.sln
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Original file line number Diff line number Diff line change
Expand Up @@ -146,6 +146,8 @@ Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Microsoft.Health.TaskManage
EndProject
Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Microsoft.Health.Fhir.Store.Utils", "src\Microsoft.Health.Fhir.Store.Utils\Microsoft.Health.Fhir.Store.Utils.csproj", "{7A736E5F-DA6E-483F-AD5B-EE8F66828E36}"
EndProject
Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "RegisterAndMonitorImport", "tools\RegisterAndMonitorImport\RegisterAndMonitorImport.csproj", "{E85BCB9A-5D6E-45AD-BE67-AEFA060FEBF1}"
EndProject
Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Importer", "tools\Importer\Importer.csproj", "{F6B94905-B496-46AD-B2A7-2ABCB0B2A6B4}"
EndProject
Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Exporter", "tools\Exporter\Exporter.csproj", "{E468B6C6-9098-4293-AFD6-3B1675D67063}"
Expand Down Expand Up @@ -344,6 +346,10 @@ Global
{7A736E5F-DA6E-483F-AD5B-EE8F66828E36}.Debug|Any CPU.Build.0 = Debug|Any CPU
{7A736E5F-DA6E-483F-AD5B-EE8F66828E36}.Release|Any CPU.ActiveCfg = Release|Any CPU
{7A736E5F-DA6E-483F-AD5B-EE8F66828E36}.Release|Any CPU.Build.0 = Release|Any CPU
{E85BCB9A-5D6E-45AD-BE67-AEFA060FEBF1}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
{E85BCB9A-5D6E-45AD-BE67-AEFA060FEBF1}.Debug|Any CPU.Build.0 = Debug|Any CPU
{E85BCB9A-5D6E-45AD-BE67-AEFA060FEBF1}.Release|Any CPU.ActiveCfg = Release|Any CPU
{E85BCB9A-5D6E-45AD-BE67-AEFA060FEBF1}.Release|Any CPU.Build.0 = Release|Any CPU
{F6B94905-B496-46AD-B2A7-2ABCB0B2A6B4}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
{F6B94905-B496-46AD-B2A7-2ABCB0B2A6B4}.Debug|Any CPU.Build.0 = Debug|Any CPU
{F6B94905-B496-46AD-B2A7-2ABCB0B2A6B4}.Release|Any CPU.ActiveCfg = Release|Any CPU
Expand Down Expand Up @@ -474,6 +480,7 @@ Global
{03AD4FC4-A56F-4E94-B295-B02A9E3E3CCD} = {7457B218-2651-49B5-BED8-22233889516A}
{BB7512E7-E148-4AF8-9D34-AA47A6AE692D} = {7457B218-2651-49B5-BED8-22233889516A}
{7A736E5F-DA6E-483F-AD5B-EE8F66828E36} = {B70945F4-01A6-4351-955B-C4A2943B5E3B}
{E85BCB9A-5D6E-45AD-BE67-AEFA060FEBF1} = {B70945F4-01A6-4351-955B-C4A2943B5E3B}
{F6B94905-B496-46AD-B2A7-2ABCB0B2A6B4} = {B70945F4-01A6-4351-955B-C4A2943B5E3B}
{E468B6C6-9098-4293-AFD6-3B1675D67063} = {B70945F4-01A6-4351-955B-C4A2943B5E3B}
{A0320AE9-3F87-44A3-8263-5AF7E00085D4} = {38B3BA4A-3510-4615-BCC4-4C9B96A486C4}
Expand Down
56 changes: 56 additions & 0 deletions tools/RegisterAndMonitorImport/App.config
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@@ -0,0 +1,56 @@
<?xml version="1.0" encoding="utf-8" ?>
<configuration>
<!--
This code allows to import resources from a storage container to a FHIR service.
Input data must be provided in ndjson format in one container in Azure blobs storage.
-->
<appSettings>
<!--
If you just want to monitor an import then provide a url for this key/value
Note that if this is provided then it only performs this operation and will not do any import.
https://{your fhir endpoint}/_operations/import/{import id}
The expected endpoint would be similar to this:
-->
<add key="MonitorImportStatusEndpoint" value="" />

<!--
The amount of time to delay between calls to get the import status
The value should be a timespan value
-->
<add key="ImportStatusDelay" value="00:02:00" />

<!-- Azure blob storage parameters -->
<add key="ConnectionString" value="{Add your BlobServiceClient connection string here}" />
<add key="ContainerName" value="{Add your container}" />
<!--
the type of files it'll search for in the container
do not add a file extension as ndjson is assumed and added to the ResourceType automatically
if this is empty then it defaults to all
-->
<add key="ResourceType" value="Observation" />

<!--
a simple flag to indicate that when true we're going to use the token for our http POST/GET
this is useful when you have a Paas deployment
if you set to false then you could use it against an oss fhir service
-->
<add key="UseBearerToken" value="false" />

<!--
the number we want to import at a time
of course this can be a much larger value than 20 so adjust as needed
-->
<add key="NumberOfBlobsForImport" value="2" />

<!--
the following are for getting a token
note that the "resource" is required as that is the FHIR endpoint and is always used
even if the UseBearerToken is set to false
-->
<add key="TokenEndpoint" value="{add login url to your oauth2/token endpoint}" />
<add key="grant_type" value="Client_Credentials" />
<add key="client_id" value="{add your client id}" />
<add key="client_secret" value="{add your client secret}" />
<add key="resource" value="{add your FHIR endpoint}" />
</appSettings>
</configuration>
33 changes: 33 additions & 0 deletions tools/RegisterAndMonitorImport/ImportResponse.cs
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// -------------------------------------------------------------------------------------------------
// Copyright (c) Microsoft Corporation. All rights reserved.
// Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
// -------------------------------------------------------------------------------------------------

using System.Collections.Generic;
using System.Text.Json.Serialization;

namespace Microsoft.Health.Fhir.RegisterAndMonitorImport
{
#pragma warning disable CA1812 // Avoid uninstantiated internal classes
internal sealed class ImportResponse
{
[JsonPropertyName("error")]
public List<Json> Error { get; set; } = new();

[JsonPropertyName("output")]
public List<Json> Output { get; set; } = new();

public sealed class Json
{
[JsonPropertyName("type")]
public string Type { get; set; } = string.Empty;

[JsonPropertyName("count")]
public int Count { get; set; }

[JsonPropertyName("inputUrl")]
public string InputUrl { get; set; } = string.Empty;
}
}
#pragma warning disable CA1812 // Avoid uninstantiated internal classes
}
17 changes: 17 additions & 0 deletions tools/RegisterAndMonitorImport/Program.cs
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// -------------------------------------------------------------------------------------------------
// Copyright (c) Microsoft Corporation. All rights reserved.
// Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
// -------------------------------------------------------------------------------------------------

using System.Threading.Tasks;

namespace Microsoft.Health.Fhir.RegisterAndMonitorImport
{
public static class Program
{
public static async Task Main()
{
await RegisterAndMonitorImport.Run();
}
}
}
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