nugenesis 8 file capture data adapters and print … 8 file capture data adapters and print capture...
TRANSCRIPT
©2013 Waters Corporation 1
NuGenesis 8 File Capture Data Adapters and Print Capture
©2013 Waters Corporation 2
Agenda
Overview of the SDMS capability of NuGenesis 8 capturing and cataloging both raw data (machine readable) and printed reports (human readable)
Hands-on demonstration of how to design a data adapter for capturing raw data
Illustrate the use of regular expressions to extract more challenging meta-data fields from printed reports
Q&A
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Typical Laboratory Workflow – Data Management
LIMS - ERP
Supervisor Assigns Test
Creation of CoAs and Reports
NuGenesis 8
Analyst Gets Specs and Method
Analyst Checks Instrumentation
Analyst Prepares Sample
Analyst Sets up Tests
Instrument Software (e.g. CDS, MS)
Analyst Transfers Results for Reuse
Review and Approval by Peers/Manager
Data is Archived and Managed
Calc Results and Compare to Specs
Analyst Runs Test
Analyst Processes and Transfers Data
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Data Processing and Capture – File Capture
File Project Agent
Metadata Catalogue - fully automated - rule based metadata extraction for ASCII files - metadata via format specific data adapter
- from content of PDF files - conversion possible
...
010010010010010 010010010010010 010010010101000 100100101110100 100101001001001 000100100100100
Source Process Capture
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Data Processing and Capture – Print Capture
Print Project Printer
Source Process Storage
Metadata Catalogue - like Windows printer - template based metadata extraction
- interaction possible - automated PDF generation (optional)
... ...
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Searching by Meta Data
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Data Management – Closing the Data Lifecycle
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Data Management – Data Lifecycle
Data Retention can be Enabled on a Project
Flexible Retention Policies
Complete Manual or Automatic Deletion After Expiration
Legal Holds will Prevent Any Change or Deletion
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Hands-on demonstration of how to design a data adapter for capturing raw data
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File Elements
File Name:
Dept_Study-date user.xls
1 2 3 4
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Folder Elements
Folder Elements: \\host\ShareName\ABC\123\EFG\filename.raw 1 2 3
Reverse Folder Elements: \\host\ShareName\ABC\123\EFG\filename.raw 5 4 3 2 1
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Data Adaptors
NuGenesis Generic
Application Specific
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File Capture PDFs
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Use of regular expressions to extract more challenging meta-data fields from printed
reports
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UNIFY vs. UNIFI
UNIFI (with an “I”) is a Scientific Information System used for instrument control, advanced data processing and mining, and comprehensive reporting.
UNIFY (with a “Y”) is a patented virtual print driver that appears to the operating system and to all applications as a standard Windows printer.
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Use a UNIFY Template
In this example, we are setting up the UNIFY printer to run in batch mode. The UNIFY Template concept is the same for Manual Mode.
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Create a UNIFY Template
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UNIFY Template Tools
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Relative to Marker
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Regular Expressions in Advanced Options
One useful utility when it comes to parsing information is the Regular Expressions.
A Regular Expression is used when you want the data extracted from the report to be parsed even further.
Type an example of the data value you plan to extract from the report and as you modify settings to specify the format for the extracted data value, you can preview what the value will look like.
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The format is :regexp= and then the options. For this data to be parsed, you will need to begin at the “-“ (b:”-“) and end at the “(“ (e:”(“).
As you can see, from the results in the template builder screen, this statement has parsed the data appropriately.
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Expressions are of the form x:”text” Uppercase letters in the expressions
denote case sensitivity. S: start (find first, truncate left) B: begin (find last, truncate left) E: end (find first, truncate right) F: finish (find last, truncate right) C: change (need two: first c: is find,
second c: is replace with) L: find from the left (find first); sets
current position – l:"X" Find first occurrence of "X"
and set cursor to that position – l:"" Set position to beginning of
string
R:find from the right (find last); sets current position – r:"X" Find last occurrence of “X”
and set cursor to that position – r:"" Set position to end of string
M: modify found text (L or R above) to new text – l:"abc" m:”xyz” Changes first
found occurrence of “abc” to “xyz” – l:”abc” l:”abc” m:”xyz” Changes second
found occurrence of “abc” to “xyz” – r:”abc” m:”bar” Changes last
found occurrence of “abc” to “xyz”
+: insert characters, e.g.: – +:"X" Inserts "X" into the string at
the current position – r:"" +:"*" Adds a * character to the end
of the string
P: set or change current position, e.g.: – p:”2” Set current position to 2 – p:”+2” Move current
position 2 to the right – p:”-2” Move current
position 2 to the left
T: terminate in specified direction, e.g.: – t:”l” Terminate from the left (keep
left of current position) – t:”r” Terminate from the right
(keep right of current position-1)
Expressions are of the form x:”text”
Uppercase letters in the expressions denote case sensitivity.
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Examples for text “c:\sub1\sub2\file1.txt”
Expression Result
s:”\” sub1\sub2\file1.txt
b:”\” file1.txt
e:”\” c:
f:”\” c:\sub1\sub2
s:”\” e:”\” sub1
s:”\” s:”\” e:”\” sub2
c:”sub” c:”dir” c:\dir1\dir2\file1.txt
s:”\” e:”\” sub1
S:”Sub” 2\file1.txt
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Questions?
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