Waters connect implementation #3386

rita-gwen · 2025-03-05T20:53:58Z

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…ike: https://devconnect.waters.com:48444/?sampleSetId=<sample set id>&injectionId=<injection id> - added support for connecting to and browsing waters_connect servers in Skyline - added folder hierarchy for remote accounts in the "Look in" dropdown for OpenDataSourceDialog (previously only worked for disk drives) * redirected UNIFI to use ABI's protobuf-net.dll (I don't think it was ever actually using the unifi-protobuf-net.dll) * refactored ParallelDownloadQueue into a separate class shared by UnifiData::Impl and WatersConnectImpl (a new implementation derived from UnifiData::Impl, but WatersConnect uses a separate queue for each channel) * added optional performance timers in VendorReaderTestHarness * disabled lockmass prompt for UNIFI in Skyline as it does not support it * improved error handling in Skyline UNIFI browsing * refactored and renamed existing UNIFI tests to work for both APIs * added SRM SIC prefix to UNIFI SRM chromatograms * added extraction of precursor and product m/z for SIM/SRM chromatograms from metadata if parsing from id fails * added scan polarity to GetChromatogramMetadata

User can select a template on Waters Connect and selected entry is stored in ExportMethodDlg. Select Template code STILL NEEDED: Allow users to ONLY selected from Remote Connection and ONLY from Waters Connect connection Next: Select output folder ONLY in Waters Connect Generate JSON to send to Waters Connect webservice to export the method to Waters Connect.

…tMethod

…ike: https://devconnect.waters.com:48444/?sampleSetId=<sample set id>&injectionId=<injection id> - added support for connecting to and browsing waters_connect servers in Skyline - added folder hierarchy for remote accounts in the "Look in" dropdown for OpenDataSourceDialog (previously only worked for disk drives) * redirected UNIFI to use ABI's protobuf-net.dll (I don't think it was ever actually using the unifi-protobuf-net.dll) * refactored ParallelDownloadQueue into a separate class shared by UnifiData::Impl and WatersConnectImpl (a new implementation derived from UnifiData::Impl, but WatersConnect uses a separate queue for each channel) * added optional performance timers in VendorReaderTestHarness * disabled lockmass prompt for UNIFI in Skyline as it does not support it * improved error handling in Skyline UNIFI browsing * refactored and renamed existing UNIFI tests to work for both APIs * added SRM SIC prefix to UNIFI SRM chromatograms * added extraction of precursor and product m/z for SIM/SRM chromatograms from metadata if parsing from id fails * added scan polarity to GetChromatogramMetadata

…onnect

…he same sample set don't need to repeatedly get that metadata - fixed "Look In" browsing for waters_connect; "Up One Level" and selecting a folder higher up the hierarchy were not working

…new CommonMsData project * moved Util dependencies of above classes to CommonUtil (e.g. TryTwice, NameValueParameters, Assume, FileEx) * fixed TestRunner exception handler to recurse through all InnerExceptions, not just the first one * added CommonMsData to Product-template.wxs and fixed its assembly name

…waters_connect connections (to avoid socket exhaustion when importing hundreds of small replicates) * added dependencies of Microsoft.Extensions.Http to Shared/Lib (since they are also required by C++, can't just use NuGet) * added Microsoft.Extensions.Http NuGet package to CommonMsData so dependencies are handled properly with the .NET executables * set AutoGenerateBindingRedirects to true for Skyline, TestRunner, SeeMS, and MSConvertGUI (bindings redirects seem to be mandatory now because different dependencies depend on different versions of System.Runtime.CompilerServices.Unsafe) * added BindingRedirectGenerator project to generate .exe.config files with binding redirects for C++ executables, as well as the msvc.jam machinery to call it and install the .exe.config files alongside the .exe

* added new .exe.config files to Product-template.wxs and Skyline.csproj * fixed Skyline Jamfile to use install rule for msconvert and BiblioSpec so .exe.config files are copied with .exe

Refactor to follow the common pattern for the exporters Make sure this is run in a separate thread and progress bar is shown. Implement multiple method file upload Multiple minor fixes.

…tMethod

…ttps://github.com/ProteoWizard/pwiz into Skyline/work/20240918_Waters_Connect_ExportMethod

- read/write indicators for the folders - template text box tooltip - method name refactoring - leftovers from the merge.

…tMethod

…account.

…ttps://github.com/ProteoWizard/pwiz into Skyline/work/20240918_Waters_Connect_ExportMethod

- JSON schema update - test fixes

…le set commit.

- adduct removed from the compound/peptide name - single quant transition per adduct - RT, start time and end time made nullable - info dialog added after successful upload - audit reason JSON field removed - fix for authentication exception in the account edit dialog - fix for the exception handling in the mock HTTP handlers

rita-gwen · 2025-09-20T20:41:53Z

These are mostly the changes requested by Stephen earlier this week:
Rita A Chupalov Thanks for that, we done some testing. Some initial findings...

Remove adduct name from analyte name when passing on the API
Ensure a single transition per adduct has a quan ion set
Do not pass RT if it is unknown

we are changing this to be nullable on the API, the service will be updated asap

Do not pass start and end time if scheduleType = FullGradientTime

we are changing these to be nullable on the API, the service will be updated asap

Display a success dialog with method names and ID's - it may be useful for the user to be able to copy the ID's so they can search with them in w_c.
Display a error dialog with the w_c error model info - it may be useful if the user can copy this info.
Remove audit reason string - this is geting removed from the API.
Sample Set import fails if Sample Set selected (rather than injections inside Sample Set)

re. #5, standard Skyline message dialog allows user to copy the message using Ctrl-C. The error dialog already shows the server response string as part of the exception message. It can be copied using Show More button.
It looks like the start and end times are still not nullable on the API, I am getting an exception with the standard method upload.
I need some clarification regarding the internal standard field since there are multiple standards possible in Skyline. Is this quantification, RTi or QC standard.
This commit does not include the fix on the #8. It is probably result of merging the sample set logic into this branch. Matt's input on this might be helpful.

rita-gwen · 2025-09-20T20:45:53Z

This commit also includes a fix on the problem Eddie discovered earlier when incorrect credentials in the Account Edit dialog cause exception:

Failed authentication shows the "report / don't report" exception dialog.
Expected: an error message. Actual: a stack trace appears in exception reporting dialog
Repro: open Tools => Options => Remote Accounts. Enter invalid credentials. Click [Connect].

…tMethod

- run duration field is enabled for the standard method - missing multiple method check fixed - RT is added to the standard method if present - library rank is added to the quant ion logic - missing quant ion in the last adduct fixed

…ttps://github.com/ProteoWizard/pwiz into Skyline/work/20240918_Waters_Connect_ExportMethod

Code inspection violation fix.

- show results from all methods in multiple method upload - fix for comma in the compound name - fix for the space in the folder name - w_c => Waters Connect - Run Duration disappeared

…tMethod

…ttps://github.com/ProteoWizard/pwiz into Skyline/work/20240918_Waters_Connect_ExportMethod

…tMethod

…ttps://github.com/ProteoWizard/pwiz into Skyline/work/20240918_Waters_Connect_ExportMethod

rita-gwen · 2025-10-09T15:55:49Z

pwiz_tools/Shared/CommonMsData/RemoteApi/RemoteSession.cs

        }
    }
+
+    public class ProgressableStreamContents


Don't need this, remove

chambm and others added 30 commits December 12, 2024 11:41

Merge branch 'master' into Skyline/work/20240918_Waters_Connect

9894f5e

* restored OpenDataSourceDialog changes after merge

6fe5164

Add

38cf598

latest updates

4d98290

Merge branch 'master' into Skyline/work/20240918_Waters_Connect_Expor…

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…tMethod

Intermediate commit to merge from master. Save dialog is working.

ab142a0

Missed a file in the last commit

5daf3f9

Merge from master. ProteoWiz does not build.

34a4c63

Missed from the last commit

c844149

EditRemoteAccountDlg: set wizard pages tab when user selects Waters C…

6547203

…onnect

* added global cache for sample metadata so multiple injections for t…

a27eeea

…he same sample set don't need to repeatedly get that metadata - fixed "Look In" browsing for waters_connect; "Up One Level" and selecting a folder higher up the hierarchy were not working

* fixed CommonMsData RuntimeIdentifiers

ab3b9be

* added new .exe.config files to Product-template.wxs and Skyline.csproj * fixed Skyline Jamfile to use install rule for msconvert and BiblioSpec so .exe.config files are copied with .exe

* attempt to fix a couple build issues

9d8e3ad

Multiple TODO items:

2445ab8

Refactor to follow the common pattern for the exporters Make sure this is run in a separate thread and progress bar is shown. Implement multiple method file upload Multiple minor fixes.

Save the template URL into settings

d41ca76

Mock HTTP testing framework added.

4ab75e8

Added DsvStreamReader class

d9ab192

Merge branch 'master' into Skyline/work/20240918_Waters_Connect_Expor…

ba363fc

…tMethod

Show tooltip for the WC template file textbox

0a3424c

Merge branch 'Skyline/work/20240918_Waters_Connect_ExportMethod' of h…

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…ttps://github.com/ProteoWizard/pwiz into Skyline/work/20240918_Waters_Connect_ExportMethod

Merge from initial WC branch

42a11a1

MockHttpHandler added.

2c6288f

Multiple changes:

d5edaa8

- read/write indicators for the folders - template text box tooltip - method name refactoring - leftovers from the merge.

Refactoring of the WatersConnect file dialogs.

8b14052

Caching the authentication token and method upload mock added.

3555d72

rita-gwen added 9 commits September 2, 2025 15:37

Merge branch 'master' into Skyline/work/20240918_Waters_Connect_Expor…

7f96e6a

…tMethod

Hiding local file system icons when the dialog is used with a remote …

f827598

…account.

Merge branch 'Skyline/work/20240918_Waters_Connect_ExportMethod' of h…

7340e57

…ttps://github.com/ProteoWizard/pwiz into Skyline/work/20240918_Waters_Connect_ExportMethod

Add/Edit account item added. Fixed upOneLevel button behavior.

e8e72f0

- missing multiple methods option fixed

af41473

- JSON schema update - test fixes

Manual merge from master. Some conflicts with the earlier waters samp…

dd5e940

…le set commit.

Test failure fix

ca71ad9

Fixes for the missing folder ID and multiple quant transitions

d9f1d82

rita-gwen added 18 commits September 22, 2025 14:56

Fix for JSON parsing error on empty folder

a22659b

Merge branch 'master' into Skyline/work/20240918_Waters_Connect_Expor…

a0cd139

…tMethod

Multiple changes

fd7c4f0

- run duration field is enabled for the standard method - missing multiple method check fixed - RT is added to the standard method if present - library rank is added to the quant ion logic - missing quant ion in the last adduct fixed

Merge branch 'Skyline/work/20240918_Waters_Connect_ExportMethod' of h…

06cc088

…ttps://github.com/ProteoWizard/pwiz into Skyline/work/20240918_Waters_Connect_ExportMethod

Fix for the spaces in the folder name

97e9b6b

Manual merge from master

44c2593

Merge fix

1cceac6

Fix null reference in the retention time parsing

2e23001

Code inspection violation fix.

Multiple changes:

f3dc595

- show results from all methods in multiple method upload - fix for comma in the compound name - fix for the space in the folder name - w_c => Waters Connect - Run Duration disappeared

Merge branch 'master' into Skyline/work/20240918_Waters_Connect_Expor…

5dcd678

…tMethod

Set defaults for the WC account in the account edit dialog

7ce1c79

Fix for the file name conflict with multiple methods upload

1d7d2de

Merge branch 'Skyline/work/20240918_Waters_Connect_ExportMethod' of h…

e8cf63a

…ttps://github.com/ProteoWizard/pwiz into Skyline/work/20240918_Waters_Connect_ExportMethod

waters_connect radio button wording and code inspection failures.

9eb1bce

Merge branch 'master' into Skyline/work/20240918_Waters_Connect_Expor…

8cbcb29

…tMethod

Merge branch 'master' into Skyline/work/20240918_Waters_Connect_Expor…

c0a2bc6

…tMethod

Account edit dialog formatting and default values fixes.

9ce4605

Merge branch 'Skyline/work/20240918_Waters_Connect_ExportMethod' of h…

8b5c599

…ttps://github.com/ProteoWizard/pwiz into Skyline/work/20240918_Waters_Connect_ExportMethod

rita-gwen commented Oct 9, 2025

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