Chemstation: How to specify data path for quant report?

[mordacious]

Hello,

I am using two different versions of Chemstation. Version B.01.00 allows me to specify the data path (and file name) when I generate a txt report. Version E.02.02.1431 does not allow me to specify the data path, the report is saved along with all of the files that are created automatically for each injection. We need to create txt files and save them together in one folder so we can import them to our LIMS.

Does anyone know how to change this?

Thank you

[tlahren]

The E.02 version, Is the MSChemstation? If so can your LIMS program import CSV files. It might be easier to import the CSV version using a macro. There is one already available called copycsv.mac. You may have to open it as a txt file and edit the destination locations but it should work. I know it is possible to do what you want. Just not sure off hand the best way to do it. We used to import all kinds of txt and csv files into a home grown LIMS system. The best part was that we wrote the LIMS program to search for the data files so we didn't have to manipulate multiple instrument softwares to do what we wanted. Let me know if you need more info... Here is the copycsv.mac. Paste it in notepad and save it with the .mac extention. Run it in the command line using "macro C:\MSDCHEM\MSEXE\copycsv.mac, go" without quotes. This is just the default file path.

Use the QT command to generate the quant.csv report.

name copycsv
fromfile$=_datapath$+_datafile$+"\quant.csv"
filelen=len(_datafile$)
newfile$=_datafile$[1:(filelen-2)]+".csv"
copy fromfile$,"i:\msdchem\rptdir\"+newfile$,DONTASK
rem fromfile$,filelen,newfile$,copycsv
return

Hope this helps a little. Let me know if you need more guidance.

Ty

[tlahren]

Here's a link to Agilent on how to use the copycsv.mac...

http://www.chem.agilent.com/Library/Sup ... a05272.pdf

Ty

[mordacious]

The E.02 version, Is the MSChemstation? If so can your LIMS program import CSV files. It might be easier to import the CSV version using a macro. There is one already available called copycsv.mac. You may have to open it as a txt file and edit the destination locations but it should work. I know it is possible to do what you want. Just not sure off hand the best way to do it. We used to import all kinds of txt and csv files into a home grown LIMS system. The best part was that we wrote the LIMS program to search for the data files so we didn't have to manipulate multiple instrument softwares to do what we wanted. Let me know if you need more info... Here is the copycsv.mac. Paste it in notepad and save it with the .mac extention. Run it in the command line using "macro C:\MSDCHEM\MSEXE\copycsv.mac, go" without quotes. This is just the default file path.

Use the QT command to generate the quant.csv report.

name copycsv
fromfile$=_datapath$+_datafile$+"\quant.csv"
filelen=len(_datafile$)
newfile$=_datafile$[1:(filelen-2)]+".csv"
copy fromfile$,"i:\msdchem\rptdir\"+newfile$,DONTASK
rem fromfile$,filelen,newfile$,copycsv
return

Hope this helps a little. Let me know if you need more guidance.

Ty

Yes, this is MSChemstation. So far it is working but I haven't processed any data yet. Thanks!

[mordacious]

tlahren - This works just how we would like but only if we don't have to do any manual integrations. The csv file does not update after manual integrations and saving. Do you know of a way to use this after doing any processing?

[tlahren]

If you do your manual integrations in QEDIT then "Save" as you exit QEDIT mode the changes are saved to the quant report. You will have to regenerate the CSV after the manual changes by using the following command which I usually program to one of the 5 custom tool buttons in the top right of the menu bar:

QT,,"C"

This will re-generate the quant.csv file from the most current quant report ("yourmethod".res file).

To edit the custom tool buttons either click on the button to open the file or if it has already been programed you will have to go to C:\MSDCHEM\1\MSEXE and open up file customtool1.mac. It will open as a text file initially and tell you to replace certain text with the code you want (above command). Now when you click the button (button 1 in this case) it will just run the single command QT,,"C".

NOTE: It is also possible to use this command for batch post-processing. Lets say you just finished manual integrations for a whole run. You can go to "Tools" "Do List" and configure this as a custom command. The Do List allows you to perform commands on selected samples all at once. Kind of like batch reprocessing. This may be the easiest way to regenerate new quant.csv files for an entire batch of samples. Then the last step would be to run your LIMS import.

Hope this helps. Let me know if you need more assistance.

Ty

[mordacious]

If you do your manual integrations in QEDIT then "Save" as you exit QEDIT mode the changes are saved to the quant report. You will have to regenerate the CSV after the manual changes by using the following command which I usually program to one of the 5 custom tool buttons in the top right of the menu bar:

QT,,"C"

This will re-generate the quant.csv file from the most current quant report ("yourmethod".res file).

To edit the custom tool buttons either click on the button to open the file or if it has already been programed you will have to go to C:\MSDCHEM\1\MSEXE and open up file customtool1.mac. It will open as a text file initially and tell you to replace certain text with the code you want (above command). Now when you click the button (button 1 in this case) it will just run the single command QT,,"C".

NOTE: It is also possible to use this command for batch post-processing. Lets say you just finished manual integrations for a whole run. You can go to "Tools" "Do List" and configure this as a custom command. The Do List allows you to perform commands on selected samples all at once. Kind of like batch reprocessing. This may be the easiest way to regenerate new quant.csv files for an entire batch of samples. Then the last step would be to run your LIMS import.

Hope this helps. Let me know if you need more assistance.

Ty

Thanks so much, just one more thing! This works as well but instead of the new csv file going into the data path I specified in the copycsv.mac it is saving it in the path c:\MSDCHEM\1\data\103111 (or which ever date) and naming it as QUANT.csv. This is we were trying to avoid in the first place. Ultimately we need the csv to be saved on our specified data path and named as the data file name.

My next question would have been about the batch processing. That will come in so helpful

Ashley

[tlahren]

Ashley,

You can probably include the copycsv.mac in the batch reprocessing part. You would have to create new custom commands in Do List. One being the QT,,"C" command and the other would look exactly like this:

macro "copycsv.mac", go

This is assuming you have the copycsv.mac file under the default C:\MSDCHEM\1\MSEXE folder.

In Rev E you are allowed to run a sequence of commands in a specific order for each file in a batch. You can have it run the QT command first and then follow with the copycsv.mac command to create the copy in the LIMS directory.

The Agilent way of putting it in the deuser.mac only works for immediate, post-analysis automatic processing (way too many adjectives) as the deuser.mac is only processed after every time the method it is stored in is run. I realize this sounds a little confusing but it's hard to explain it all in text.

Another good source would be to call Agilent's tech support line 800-227-9770 and type options 3, 2, 2 then type the number 1701 for MSDChemstation support. You will get a chemstation expert on the phone or they will route you to a guy named Ron who is one of the "Good-ol-boys" of Chemstation. I learned a lot by doing this. I have never had to pay for this service or been asked for my customer number or anything like that.

Again, let me know if there's anything else you need clarification on.

Ty

[mordacious]

Ashley,

You can probably include the copycsv.mac in the batch reprocessing part. You would have to create new custom commands in Do List. One being the QT,,"C" command and the other would look exactly like this:

macro "copycsv.mac", go

This is assuming you have the copycsv.mac file under the default C:\MSDCHEM\1\MSEXE folder.

In Rev E you are allowed to run a sequence of commands in a specific order for each file in a batch. You can have it run the QT command first and then follow with the copycsv.mac command to create the copy in the LIMS directory.

The Agilent way of putting it in the deuser.mac only works for immediate, post-analysis automatic processing (way too many adjectives) as the deuser.mac is only processed after every time the method it is stored in is run. I realize this sounds a little confusing but it's hard to explain it all in text.

Another good source would be to call Agilent's tech support line 800-227-9770 and type options 3, 2, 2 then type the number 1701 for MSDChemstation support. You will get a chemstation expert on the phone or they will route you to a guy named Ron who is one of the "Good-ol-boys" of Chemstation. I learned a lot by doing this. I have never had to pay for this service or been asked for my customer number or anything like that.

Again, let me know if there's anything else you need clarification on.

Ty

We are all set, thanks for your help again! And can you believe a coworker was following along with this, didn't know it was me and figured it out herself So thanks for helping us both!

[tlahren]

That's actually pretty funny.

Good luck.

Ty