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ASI_Convert.bat
How one double-click (Task Scheduler) turns the slide and order files SCC already writes into GenASIs case files. Presenter: Aryn Perez-White, Laboratory Integration Specialist
SCC already writes what ASI needs
The data already exists
SCC already writes everything ASI needs: slide files and order files for every case.
Written for MetaSystems
Those files are written in the MetaSystems layout. The .bat reads them, matches each slide to its order, and rewrites the information in the layout GenASIs imports.
No new SCC interface
Orders going into ASI need no new SCC interface. We reuse output SCC already produces.
Three read-only sources become one GenASIs case
Read-only sources
.sif in Metafer; cases.txt in Ikaros\Orders; order .xml in Orders
ASI_Convert.bat
Matches each slide to its order by HL accession, builds one case file
ASI\Import
One .xml per case, e.g. HL-26-0001234_CHRBM_....xml
GenASIs Import Service
Picks up the file, creates or updates the case
The .bat also keeps its own records in ASI\_Bridge: a tracker CSV and a copy of every file sent.
Where the files live on the SCC share
METASYSTEMS (read only)
Ikaros > Orders > cases.txt (chromosome orders) Metafer > *.sif (one per slide; Include, Archive ignored) Orders > *.xml (FISH orders; Orders\Archive ignored) Result, Results, Examples (not used)
Combined by ASI_Convert.bat
cases.txt, .sif files and Orders .xml converge here ASI_Convert.bat sits in the ASI folder BIODOT sits alongside, untouched
ASI (written by the .bat)
Import: the .bat writes one .xml per case _Bridge: tracker CSV, Sent copies, staging Export: ASI results back to SCC, later
The same tree exists under SITE1\LIVE\CYTOGENETICS for go-live.
Each file supplies part of the case
One double-click runs six steps
Finds folders
Looks up from the .bat until it finds METASYSTEMS
Picks slides
.sif files from the last 30 days
Loads orders
cases.txt and Orders .xml from the last 120 days
Matches, groups
Slide to order by HL accession; one file per case
Writes case
Built in staging, moved whole into ASI\Import; copy kept
Records it
Tracker marks Converted, so reruns never resend
How a slide file is read
Chromosome slide name
SlideName HL-26-0001234_CHRBM.H-2 gives case HL-26-0001234_CHRBM, culture H and slide H-2.
FISH slide name
SlideName HL-26-123.AML_ADULT_3 gives case HL-26-123, panel AML_ADULT and slide 3.
Probes from PS_ lines
FISH probes come from the IncludeSIF lines that start with PS_. The PS_ prefix is removed and the probes are joined with "; ".
Barcode and folder
The slide barcode is the .sif file name. Only .sif files in the top Metafer folder are read; Include holds scan templates, not cases.
Field mapping: SCC to GenASIs
Open question: SCC calls it Sex; GenASIs maps one tag only. We send <Gender> because a test file with <Gender> imported successfully; ASI to confirm.
Slide fields sent to GenASIs
Matching rules and edge cases
Accessions normalized
Short and padded accession formats are normalized so they match the same case.
Ikaros column shifts
Ikaros moved the DOB and patient-number columns between versions, so the date-formatted column is used as DOB (Investigating more if signed off).
Excel-mangled IDs skipped
Old IDs mangled by Excel, such as HL-2.3E8, are skipped rather than guessed.
No order yet
A slide with no order is flagged. Orders are searched back 120 days.
New slide, existing case
A new slide for a case already sent re-sends the whole case with all its slides, and GenASIs updates that case. Will confirm with ASI
Records and audit trail
Tracker CSV
ASI\_Bridge\ASI_Tracker.csv has one row per slide (slide time, slide ID, slide name, case, status, output file, run time) and opens in Excel.
Sent copies
A copy of every file sent is kept in ASI\_Bridge\Sent, one folder per month.
Staging
Each file is built in ASI\_Bridge\staging and moved whole into ASI\Import, so GenASIs never reads a half-written file.
Import warning
A yellow warning appears if a file waits in ASI\Import over 30 minutes.
A CHRBM slide becomes a karyotyping case
Example numbers are made up (TEST data). cases.txt row: "HL-26-0001234_CHRBM","BLUE","STEAK","10/15/1980",,"F","BMASP"
FISH slides on one accession share a case
In (TEST data)
HL260000123A0303.sif SlideName=HL-26-123.AML_ADULT_3 Probes PS_CBFB_MYH11 and PS_D20S108-8 Order file HL-26-123_FISH_AML_ADULT.xml
Out (GenASIs case)
Name and PatientID: HL-26-123 Gender 1 (male); Technology 2 (FISH) 3 slides in one case; slide 3 barcode HL260000123A0303 ProbeID "CBFB_MYH11; D20S108-8" File: HL-26-0000123_FISH_<run time>.xml (leading zeros in the file name)
Example numbers are made up (TEST data). IT recommended leading zeros, so the file name now carries them (HL-26-0000123_FISH_<run time>.xml). The case Name stays as SCC writes it (HL-26-123); adding zeros to the case Name is a decision for the lead supervisor or director.
Built to stay out of the way
It never
Moves, edits or deletes METASYSTEMS files Installs anything or runs as a service Uses the internet Sends a slide twice or guesses a missing order
It always
Reads only the last 30 days of slides Writes only to ASI\Import and ASI\_Bridge Keeps a copy of every file sent; lists slides with no order Warns if ASI hasn't picked up a file within 30 minutes
One .bat file, no separate .ps1
Double-click works
Windows runs a .bat when it's double-clicked. A .ps1 opens in Notepad by design.
The script is inside
The top lines start PowerShell and hand it the code stored at the bottom of the same file.
No server setting changes
"-ExecutionPolicy Bypass" applies to that one run only, unless Group Policy blocks it.
One file, any folder
There's nothing to keep in sync. The same file works in TEST now and in LIVE later.
Three ways to run it, one place to check
Double-click
Converts slides from the last 30 days.
ASI_Convert.bat dry
Preview only. It shows what would happen and writes nothing.
ASI_Convert.bat 45
Looks back 45 days instead of 30. Can build one for any date range but will most likely make it search for any date to match .xml to .sif - only to show we can have dates flagged
Where results appear
A summary in the window, new case files in ASI\Import, and every slide's status in ASI\_Bridge\ASI_Tracker.csv.
The summary tells you what to do
A phased path to full integration
Phase 1: Orders into ASI (now)
ASI_Convert.bat sends demographics and slides when ready to scan Matches the functionality we have today with MetaSystems Built and in TEST; no SCC cost
Phase 2: Reports and images to SCC (next)
Only if wanted ASI exports finalized case report and images to ASI\Export Files are attached to the case in SCC Needs SCC (DMI) to pick up the files
Phase 3: Scores into SCC fields (later)
Cell counts, FISH signal scoring, karyotype strings into defined SCC fields Technologists stop entering results twice GenASIs already exports case and karyotyping statistics This is where SCC development is needed
Phase 1 gets us current functionality. SCC only becomes necessary when we want results and scores flowing back into SCC.
Not included in my solution
ASI_Convert.bat only sends orders into ASI. It does not bring anything back into SCC. If FISH is scored in ASI, the scores do not reach SCC on their own. Until Phase 2 or 3 is built, a technologist or director must copy and paste or manually enter the scores into SCC. Getting results back into SCC means either requesting an SCC quote for just that piece, or planning it as the Phase 2 solution.
Options and follow-up
Keep Phase 1 in-house
Run ASI_Convert.bat for orders into ASI. Engage SCC only for Phases 2 and 3, quoted separately.
If we choose otherwise
I can turn this deck into a clear SCC roadmap: folders, file types, triggers, field mapping and example files. SCC could also quote only the results-back-to-SCC piece.
Explore DMI first
Request access to SCC's DMI (I have none today) to see what it already does, like generic XML import and attaching files, before paying for custom work.
Set expectations if paying SCC
Itemize the quote by phase: orders at agreed triggers, multi-slide grouping, reports and images, scores into fields, error handling, validation, documentation, go-live, maintenance, timelines.
Request a discount
HematoLogics now has a Laboratory Integration Specialist in house. Share this deck, the working Phase 1 and the field mapping, and request a reduced quote since the specification is complete.
Each team has a short checklist
IT
Allow PowerShell from the TEST share Read METASYSTEMS; write ASI\Import and ASI\_Bridge Point GenASIs Import Service at ASI\Import - in process Later: a Task Scheduler entry
ASI (Kareem, Jose)
Open: Sex or Gender tag (one only). Sending <Gender> (1 male, 2 female); confirm Confirm tag names; date format M/d/yyyy AutomationCode names (TBD; placeholder in use) Probe name mapping for FISH What happens to files after import
Us
Run in TEST alongside normal work Compare each case with SCC Write up the validation Copy the .bat to LIVE Lead supervisor / director: zeros in the FISH case Name?
Out of scope: results and images coming back from ASI into SCC are a separate piece that still needs SCC.
Next step: IT confirms access, ASI confirms the field mapping, and we start parallel validation in TEST. Contact: Aryn Perez-White, Laboratory Integration Specialist