microsoft / r-server-hospital-length-of-stay Goto Github PK

Error when deploying - I was advised to update the dsvm_arm.json template with the latest SKU version (Windows 2016) to use either 19.08.09 or 20.01.10.

Steps taken:

1. Updated the SKU to use 20.01.10:

2. When deploying, I ran into another issue, which is as follows:

The 'conflict' status message is as follows:

{
"status": "Failed",
"error": {
"code": "VMExtensionProvisioningError",
"message": "VM has reported a failure when processing extension 'HospitalSetup'. Error message: "Finished executing command"\r\n\r\nMore information on troubleshooting is available at https://aka.ms/VMExtensionCSEWindowsTroubleshoot "
}
}

3. Attached the deployment files:

Deployment-configureTemplate.zip

Please advise if these GitHub files (Arm templates) will be updated?

The template dsvm_arm is using "version": "18.02.00" which is not available anymore or my subscription type doesn't support it.My Subscription is Visual Studio Enterprise.

Running Get-AzVMImage -Location "West US" -PublisherName "microsoft-ads" -Offer "windows-data-science-vm" -Skus "windows2016" I get all available images versions and 18.02.00 is not listed.

I was able to deploy successfully using version 03.25.19

Please check it so the documentation can be updated.

There are important files that Microsoft projects should all have that are not present in this repository. A pull request has been opened to add the missing file(s). When the pr is merged this issue will be closed automatically.

Microsoft teams can learn more about this effort and share feedback within the open source guidance available internally.

Merge this pull request

This repository is currently missing a LICENSE file.

A license helps users understand how to use your project in a compliant manner. You can find the standard MIT license Microsoft uses at: https://github.com/microsoft/repo-templates/blob/main/shared/LICENSE.

If you would like to learn more about open source licenses, please visit the document at https://aka.ms/license (Microsoft-internal guidance).

I have this error while running first step.

`Rows Read: 100000, Total Rows Processed: 100000, Total Chunk Time: 0.729 seconds

Elapsed time to compute low/high values and/or factor levels: 0.994 secs.

[unixODBC][Driver Manager]Can't open lib 'SQL Server' : file not found

Caught exception in file: /builddir/ExaRoot/ExaCore/CxAnalysis.cpp, line: 6660. ThreadID: 1493723264 Rethrowing.

[unixODBC][Driver Manager]Connnection does not exist

ODBC Error in SQLDisconnect
Caught exception in file: /builddir/ExaRoot/ExaCore/CxAnalysis.cpp, line: 5830. ThreadID: 1493723264 Rethrowing.
Caught exception in file: /builddir/ExaRoot/ExaCore/CxAnalysis.cpp, line: 5378. ThreadID: 1493723264 Rethrowing.
DataStep error: [unixODBC][Driver Manager]Can't open lib 'SQL Server' : file not found

DataStep function failed. Please see the console output for more information.
Traceback (most recent call last):
File "step1_data_preprocessing.py", line 43, in
rx_data_step(input_data=LoS_text, output_file=LengthOfStay_sql, overwrite=True)
File "/opt/mssql/mlservices/libraries/PythonServer/revoscalepy/utils/RxFunctionUtils.py", line 8, in wrapper
return func(*args,**kwds)
File "/opt/mssql/mlservices/libraries/PythonServer/revoscalepy/etl/RxDataStep.py", line 319, in rx_data_step
functionname=function_name, params=call_parameters)
File "/opt/mssql/mlservices/libraries/PythonServer/revoscalepy/RxSerializable.py", line 375, in rx_native_call
ret = px_call(functionname, params)
RuntimeError: revoscalepy function failed.
`

Hello, is there a publication related to the dataset used in this project?

Hi, I wanted to know what is the data source and general pointer to how the data was collected and sampled. Can you please share them here.

Thanks

Hi

From the log file I see a run of errors. Is there anything that can be fixed given my desktop environment?

Cheers
Michael

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Windows PowerShell transcript start
Start time: 20200313112337
Username: XXXX
RunAs User: XXXX
Configuration Name:
Machine: XXXXXXX (Microsoft Windows NT 10.0.18362.0)
Host Application: C:\Windows\System32\WindowsPowerShell\v1.0\powershell.exe
Process ID: 3356
PSVersion: 5.1.18362.628
PSEdition: Desktop
PSCompatibleVersions: 1.0, 2.0, 3.0, 4.0, 5.0, 5.1.18362.628
BuildVersion: 10.0.18362.628
CLRVersion: 4.0.30319.42000
WSManStackVersion: 3.0
PSRemotingProtocolVersion: 2.3
SerializationVersion: 1.1.0.1

---

Transcript started, output file is c:\tmp\hospital_setup_log.txt
Start time: 3/13/2020 11:23:37 AM
This Solution was created on non DVSM Sku

Installing SQLServer Power Shell Module or Updating to latest
NuGet provider is required to continue
PowerShellGet requires NuGet provider version '2.8.5.201' or newer to interact with NuGet-based repositories. The NuGet provider must be available in 'C:\Program Files\PackageManagement\ProviderAssemblies' or 'C:\Users\XXXX\AppData\Local\PackageManagement\ProviderAssemblies'. You can also install the NuGet provider by running 'Install-PackageProvider -Name NuGet -MinimumVersion 2.8.5.201 -Force'. Do you want PowerShellGet to install and import the NuGet provider now?
&Yes &No &Suspend
Y
Cloning into 'C:\Solutions\Hospital'...
remote: Enumerating objects: 3, done.
remote: Counting objects: 100% (3/3), done.
remote: Compressing objects: 100% (2/2), done.
remote: Total 562 (delta 1), reused 1 (delta 1), pack-reused 559
Receiving objects: 100% (562/562), 88.44 MiB | 2.08 MiB/s, done.
Resolving deltas: 100% (320/320), done.

Servername set to XXXXX

Switching SQL Server to Mixed Mode

Configuring SQL to allow running of External Scripts

SQL Server Configured to allow running of External Scripts

Restarting SQL Services

SQL Services Restarted

Done with configuration changes to SQL Server

Installing latest Power BI.......
PS>TerminatingError(Start-BitsTransfer): "The operation being requested was not performed because the user has not logged on to the network. The specified service does not exist. (Exception from HRESULT: 0x800704DD)"
Start-BitsTransfer : The operation being requested was not performed because the user has not logged on to the network.
The specified service does not exist. (Exception from HRESULT: 0x800704DD)
At C:\users\XXXX\documents\projects\r-server-hospital-length-of-stay\resources\actionscripts\HospitalSetup.ps1:
179 char:1

• Start-BitsTransfer -Source "https://go.microsoft.com/fwlink/?LinkId=5 ...

•   + CategoryInfo          : NotSpecified: (:) [Start-BitsTransfer], COMException
    + FullyQualifiedErrorId : 
  

System.Runtime.InteropServices.COMException,Microsoft.BackgroundIntelligentTransfer.Management.NewBitsTransferCommand
Start-BitsTransfer : The operation being requested was not performed because the user has not logged on to the
network. The specified service does not exist. (Exception from HRESULT: 0x800704DD)
At C:\users\XXXX\documents\projects\r-server-hospital-length-of-stay\resources\actionscripts\HospitalSetup.ps1
:179 char:1

• Start-BitsTransfer -Source "https://go.microsoft.com/fwlink/?LinkId=5 ...

•   + CategoryInfo          : NotSpecified: (:) [Start-BitsTransfer], COMException
    + FullyQualifiedErrorId : System.Runtime.InteropServices.COMException,Microsoft.BackgroundIntelligentTransfer.Mana
   gement.NewBitsTransferCommand
  
  
  

Help Files Copied to Desktop

ServerName set to XXXXXXXX
This Version of SQL is not compatible with Py , Py Code and DB's will not be Created

Creating SQL Database for R
Calling Script to create the Hospital_R database

SQLServerDB Hospital_R Created

Calling Script to create the objects in the Hospital_R database
invoke-sqlcmd : Incorrect syntax near '='.
Incorrect syntax near the keyword 'with'. If this statement is a common table expression, an xmlnamespaces clause or a
change tracking context clause, the previous statement must be terminated with a semicolon.
At C:\Solutions\Hospital\Resources\ActionScripts\ConfigureSQL.ps1:129 char:1

• invoke-sqlcmd -inputfile $CreateSQLObjects -serverinstance $ServerNam ...

•   + CategoryInfo          : InvalidOperation: (:) [Invoke-Sqlcmd], SqlPowerShellSqlExecutionException
    + FullyQualifiedErrorId : SqlError,Microsoft.SqlServer.Management.PowerShell.GetScriptCommand
  

invoke-sqlcmd : Incorrect syntax near '='.
Incorrect syntax near the keyword 'with'. If this statement is a common table expression, an xmlnamespaces clause or a
change tracking context clause, the previous statement must be terminated with a semicolon.
At C:\Solutions\Hospital\Resources\ActionScripts\ConfigureSQL.ps1:129 char:1

• invoke-sqlcmd -inputfile $CreateSQLObjects -serverinstance $ServerNam ...

•   + CategoryInfo          : InvalidOperation: (:) [Invoke-Sqlcmd], SqlPowerShellSqlExecutionException
    + FullyQualifiedErrorId : SqlError,Microsoft.SqlServer.Management.PowerShell.GetScriptCommand
  
  
  

SQLServerObjects Created in Hospital_R Database

Configuring Hospital Solution for R

Name : Hospital
DsnType : System
Platform : 64-bit
DriverName : SQL Server Native Client 11.0
Attribute : {Database, Server, Trusted_Connection}

Import CSV File(s).

Loading LengthOfStay.csv into SQL Table....

Name : LengthOfStay

LengthOfStay table loaded from CSV File(s).

Loading LengthOfStay_Prod.csv into SQL Table....

Name : LengthOfStay_Prod

LengthOfStay_Prod table loaded from CSV File(s).

Finished loading .csv File(s).

Training Model and Scoring Data...
SqlServer\Invoke-Sqlcmd : A 'R' script error occurred during execution of 'sp_execute_external_script' with HRESULT
0x80004004.
An external script error occurred:
Error in library("MicrosoftML") :
there is no package called 'MicrosoftML'
Calls: source -> withVisible -> eval -> eval -> library

Error in ScaleR. Check the output for more information.
Error in eval(expr, envir, enclos) :
Error in ScaleR. Check the output for more information.
Calls: source -> withVisible -> eval -> eval -> .Call
Execution halted
Cannot insert the value NULL into column 'model', table 'Hospital_R.dbo.Models'; column does not allow nulls. INSERT
fails.
A 'R' script error occurred during execution of 'sp_execute_external_script' with HRESULT 0x80004004.
An external script error occurred:
Error in library("MicrosoftML") :
there is no package called 'MicrosoftML'
Calls: source -> withVisible -> eval -> eval -> library

Error in ScaleR. Check the output for more information.
Error in eval(expr, envir, enclos) :
Error in ScaleR. Check the output for more information.
Calls: source -> withVisible -> eval -> eval -> .Call
Execution halted
A 'R' script error occurred during execution of 'sp_execute_external_script' with HRESULT 0x80004004.
An external script error occurred:
Error in eval(expr, envir, enclos) :
could not find function "rxSerializeModel"
Calls: source -> withVisible -> eval -> eval

Error in ScaleR. Check the output for more information.
Error in eval(expr, envir, enclos) :
Error in ScaleR. Check the output for more information.
Calls: source -> withVisible -> eval -> eval -> .Call
Execution halted
Cannot insert the value NULL into column 'model', table 'Hospital_R.dbo.Models'; column does not allow nulls. INSERT
fails.
The statement has been terminated.
The statement has been terminated.
At C:\Solutions\Hospital\Resources\ActionScripts\ConfigureSQL.ps1:189 char:1

• SqlServer\Invoke-Sqlcmd -ServerInstance LocalHost -Database $dbName - ...

•   + CategoryInfo          : InvalidOperation: (:) [Invoke-Sqlcmd], SqlPowerShellSqlExecutionException
    + FullyQualifiedErrorId : SqlError,Microsoft.SqlServer.Management.PowerShell.GetScriptCommand
  

SqlServer\Invoke-Sqlcmd : A 'R' script error occurred during execution of 'sp_execute_external_script' with HRESULT 0x80004004.
An external script error occurred:
Error in library("MicrosoftML") :
there is no package called 'MicrosoftML'
Calls: source -> withVisible -> eval -> eval -> library

Error in ScaleR. Check the output for more information.
Error in eval(expr, envir, enclos) :
Error in ScaleR. Check the output for more information.
Calls: source -> withVisible -> eval -> eval -> .Call
Execution halted
Cannot insert the value NULL into column 'model', table 'Hospital_R.dbo.Models'; column does not allow nulls. INSERT fails.
A 'R' script error occurred during execution of 'sp_execute_external_script' with HRESULT 0x80004004.
An external script error occurred:
Error in library("MicrosoftML") :
there is no package called 'MicrosoftML'
Calls: source -> withVisible -> eval -> eval -> library

Error in ScaleR. Check the output for more information.
Error in eval(expr, envir, enclos) :
Error in ScaleR. Check the output for more information.
Calls: source -> withVisible -> eval -> eval -> .Call
Execution halted
A 'R' script error occurred during execution of 'sp_execute_external_script' with HRESULT 0x80004004.
An external script error occurred:
Error in eval(expr, envir, enclos) :
could not find function "rxSerializeModel"
Calls: source -> withVisible -> eval -> eval

Error in ScaleR. Check the output for more information.
Error in eval(expr, envir, enclos) :
Error in ScaleR. Check the output for more information.
Calls: source -> withVisible -> eval -> eval -> .Call
Execution halted
Cannot insert the value NULL into column 'model', table 'Hospital_R.dbo.Models'; column does not allow nulls. INSERT fails.
The statement has been terminated.
The statement has been terminated.
At C:\Solutions\Hospital\Resources\ActionScripts\ConfigureSQL.ps1:189 char:1

• SqlServer\Invoke-Sqlcmd -ServerInstance LocalHost -Database $dbName - ...

•   + CategoryInfo          : InvalidOperation: (:) [Invoke-Sqlcmd], SqlPowerShellSqlExecutionException
    + FullyQualifiedErrorId : SqlError,Microsoft.SqlServer.Management.PowerShell.GetScriptCommand
  
  
  

R Server Configured in 00:05:05.5789036
npm WARN deprecated [email protected]: The sprintf package is deprecated in favor of sprintf-js.
npm WARN deprecated [email protected]: core-js@<3 is no longer maintained and not recommended for usage due to the number of issues. Please, upgra
de your dependencies to the actual version of core-js@3.

[email protected] postinstall C:\Solutions\Hospital\Website\node_modules\core-js
node -e "try{require('./postinstall')}catch(e){}"

Thank you for using core-js ( https://github.com/zloirock/core-js ) for polyfilling JavaScript standard library!

The project needs your help! Please consider supporting of core-js on Open Collective or Patreon:

https://opencollective.com/core-js
https://www.patreon.com/zloirock

Also, the author of core-js ( https://github.com/zloirock ) is looking for a good job -)

npm notice created a lockfile as package-lock.json. You should commit this file.
npm WARN [email protected] No repository field.

added 93 packages from 101 contributors and audited 220 packages in 5.745s

2 packages are looking for funding
run npm fund for details

found 0 vulnerabilities

Length of Stay Development Workflow Finished Successfully!

Total Deployment Time = 00:06:50.7079469

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Windows PowerShell transcript end
End time: 20200313113027

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