Merge branch 'release/1.12.0'

.gitmodules

@@ -0,0 +1,3 @@
+[submodule ".vscode"]
+	path = .vscode
+	url = https://github.com/ctsit/.vscode

AUTHORS

@@ -32,6 +32,9 @@ Contributors at the University of Florida
  * Ajantha Ramineni
  * Taeber Rapczak
  * Andrei Sura
+ * Rishabh Tatiraju
+ * Kshitij Sinha
+ * Emily Olsen
 
 
 Other Contributors

CHANGELOG

@@ -1,5 +1,23 @@
 Changelog
 =========
+## [1.12.0] - 2023-10-23
+### Summary
+This release adds processing for Telephone Initial Packets and Neuropath version 11 to NACCulator. 
+
+### Added
+ * Add Neuropath 11 option to processing with complete form and builder files (Samantha Emerson)
+ * Split neuropath into versions 10 and 11 (Samantha Emerson)
+ * Add TIP to NACCulator options (Samantha Emerson)
+ * Add unit tests for tip (Samantha Emerson)
+ * Add visitnum to error and warning printouts (Samantha Emerson)
+ * Add vscode config submodule (Michael Bentz)
+ * Add 'CLS' to CLS warnings for clarity of which form is being talked about (Samantha Emerson)
+
+### Updated
+ * Add logic to milestone event detection to skip forms marked as Incomplete (0) (Samantha Emerson)
+ * Add skip to warning for incomplete CLS (Samantha Emerson)
+ * Update and add unit tests (Samantha Emerson)
+
 ## [1.11.0] - 2022-08-31
 ### Summary
 This release updates documentation on the developer end for the functions within NACCulator's code.

README.md

@@ -32,11 +32,11 @@ NACCulator will automatically skip PTIDs with errors, so the output `data.txt`
 file will be ready to submit to NACC.
 In order to properly filter the data in the csv, NACCulator is expecting that
 REDCap visits (denoted by `redcap_event_name`) contain certain keywords:
-    "initial" for initial visit packets,
-    "follow" for all followups,
+    "initial" for all initial visit packets (including telephone and optional modules such as lbd),
+    "follow" for all followups (including version 3.1 telephone and optional modules),
     "milestone" for milestone packets,
     "neuropath" for neuropathology packets,
-    "telephone" for telephone followup packets,
+    "tele" for old (version 3.0) telephone followups,
     "covid" for covid-related survey packets
 
 NACCulator collects data from the Z1X form first and uses that to determine the
@@ -54,8 +54,8 @@ the `-file` flag._
 
     $ redcap2nacc -h
     usage: redcap2nacc [-h]
-                       [-fvp | -ivp | -tfp | -np | -m | -cv | -csf | -f {cleanPtid,replaceDrugId,fixHeaders,fillDefault,updateField,removePtid,removeDateRecord,getPtid}]
-                       [-lbd | -ftld] [-file FILE] [-meta FILTER_META] [-ptid PTID]
+                       [-fvp | -ivp | -tip | -tfp | -tfp3 | -np | -np10 | -m | -cv | -csf | -f {cleanPtid,replaceDrugId,fixHeaders,fillDefault,updateField,removePtid,removeDateRecord,getPtid}]
+                       [-lbd | lbdsv | -ftld] [-file FILE] [-meta FILTER_META] [-ptid PTID]
                        [-vnum VNUM] [-vtype VTYPE]
 
     Process redcap export data through nacculator.
@@ -65,23 +65,25 @@ the `-file` flag._
       -fvp                  Set this flag to process as FVP data
       -ivp                  Set this flag to process as IVP data
       -tfp                  Set this flag to process as Telephone Followup Packet v3.2 data
+      -tip                  Set this flag to process as Telephone Initial Packet data
       -tfp3                 Set this flag to process as TFP v3.0 (pre-2020) data
-      -np                   Set this flag to process as Neuropathology data
+      -np                   Set this flag to process as Neuropathology version 11 data
+      -np10                 Set this flag to process as Neuropathology version 10 data
       -m                    Set this flag to process as Milestone data
       -cv                   Set this flag to process as COVID data
       -csf                  Set this flag to process as NACC BIDSS CSF data
 
       -f {cleanPtid,replaceDrugId,fixHeaders,fillDefault,updateField,removePtid,removeDateRecord,getPtid}, --filter {cleanPtid,replaceDrugId,fixHeaders,fillDefault,updateField,removePtid,removeDateRecord,getPtid}
-                              Set this flag to process the filter
+                              Set this flag to run the data through the chosen filter
       -lbd                  Set this flag to process as Lewy Body Dementia data (FORMVER = 3)
       -lbdsv                Set this flag to process as Lewy Body Dementia short version data (FORMVER = 3.1)
       -ftld                 Set this flag to process as Frontotemporal Lobar Degeneration data
 
-      -file FILE            Path of the csv file to be processed.
+      -file FILE            Path of the csv file to be processed
       -meta FILTER_META     Input file for the filter metadata (in case -filter is used)
       -ptid PTID            Ptid for which you need the records
-      -vnum VNUM            Ptid for which you need the records
-      -vtype VTYPE          Ptid for which you need the records
+      -vnum VNUM            Visit number for which you need the records
+      -vtype VTYPE          Visit type for which you need the records
 
 
 **Example** - Process a Neuropathology form:
@@ -359,9 +361,9 @@ To run all the tests:
     $ python3 -m unittest
 
 
-To run only the tests in a file:
+To run only the tests in a specific file:
 
-    $ python3 tests/WHICHEVER_test.py
+    $ python3 tests/test_$SPECIFIC_FILE.py
 
 
 ### Generating Forms

nacc/csf/blanks.py

@@ -10,7 +10,7 @@
 import sys
 
 
-def convert_rule_to_python(name: str, rule: str) -> bool:
+def convert_rule_to_python(name: str, rule: str, options) -> bool:
     """
     Converts the text `rule` into a python function.
 

nacc/cv/blanks.py

@@ -10,7 +10,7 @@
 import sys
 
 
-def convert_rule_to_python(name: str, rule: str) -> bool:
+def convert_rule_to_python(name: str, rule: str, options) -> bool:
     """
     Converts the text `rule` into a python function.
 

nacc/ftld/blanks.py

@@ -10,7 +10,7 @@
 import sys
 
 
-def convert_rule_to_python(name: str, rule: str) -> bool:
+def convert_rule_to_python(name: str, rule: str, options) -> bool:
     """
     Converts the "rule" string into a python function using "blanks" from the
     associated forms.py file. The fieldname being checked here is "name".

nacc/lbd/blanks.py

@@ -10,7 +10,7 @@
 import sys
 
 
-def convert_rule_to_python(name: str, rule: str) -> bool:
+def convert_rule_to_python(name: str, rule: str, options) -> bool:
     """
     Converts the "rule" string into a python function using "blanks" from the
     associated forms.py file. The fieldname being checked here is "name".