Merge pull request #22 from NIB-SI/develop

fixes before webinar

Author: ablejec

.gitignore

@@ -64,3 +64,5 @@ $RECYCLE.BIN/
 Network Trash Folder
 Temporary Items
 .apdisk
+Metadata.md
+xCheckMetadata.md

INSTRUCTIONS-v-5-0-0.docx

@@ -1,4 +1,4 @@
-# pISA-tree: Standard project directory tree (ISA compliant)
+# pISA-tree: Standard project directory tree (ISA-tab compliant)
 
 This set of batch files is used to create standard directory tree for research projects.
 Batch files are provided to make standardized nested directories in accordance with the ISA-tab framework (**I**nvestigation/**S**tudy/**A**ssay).
@@ -7,7 +7,7 @@ Installation:
 
 1. Download (zip file) or clone the repository from [NIB GitHub](https://github.com/NIB-SI/pISA/archive/projects.zip).
 2. Extract files into your local pISA projects directory (ignore or delete .git-related files).
-3. User instructions are in INSTRUCTIONS.\* files.
+3. User instructions are in INSTRUCTIONS\* file.
 
 Additional info:
 * files in `doc` folder

INSTRUCTIONS-v-6.pdf

@@ -0,0 +1 @@
+Creation date	%today%

INSTRUCTIONS.MD

@@ -0,0 +1 @@
+Creation date	%today%

README.MD

@@ -1,3 +1,4 @@
+Creation date	%today%
 Dnase ID	DNase_$
 Date DNAse_treatment	%today%
 Storage_DNAse_treated	CU0370

Templates/DRY/R/AssayType.ini

@@ -1,3 +1,4 @@
+Creation date	%today%
 RNA ID	$_RNA
 ng/ul	Blank
 260/280	Blank
@@ -15,4 +16,3 @@ Operator	Katja Stare/Anna Coll/Rebecca Vollmeier/Barbara Dusak/Maru
 cDNA ID	$_cDNA
 DateRT	%today%
 Notes	
-

Templates/DRY/Stat/AssayType.ini

@@ -1,3 +1,4 @@
+Creation date	%today%
 RT ID	RT_$
 Add column 1	Blank
 Add column 2	Blank

Templates/WET/DNAse/AssayType.ini

@@ -12,6 +12,7 @@ rem Backup copy if assay folder exists
 rem robocopy %1 X-%1 /MIR
 rem ------------------------------------------------------
 rem
+TITLE pISA-tree
 setlocal EnableDelayedExpansion
 set LF=^
 
@@ -118,7 +119,7 @@ if exist %tmpldir%\DRY\%NewType% (
   goto Ask4)
 rem type ok
 md %tmpldir%\%IDClass%\%NewType%
-copy NUL %tmpldir%\%IDClass%\%NewType%\AssayType.ini /Y > NUL
+echo Creation date	%today%> %tmpldir%\%IDClass%\%NewType%\AssayType.ini
 echo New %IDClass% Assay Type was created: %NewType%
 set "IDType=%NewType%"
 )
@@ -235,11 +236,11 @@ call:getLayer _S_ sname
 call:getLayer _A_ aname
 rem -------------------------------------- make ASSAY_DESCRIPTION
 set descFile=".\_ASSAY_METADATA.TXT"
-echo project:	%pname%> %descFile%
-echo Investigation:	%iname%>> %descFile%
+echo Assay:	%Adir%> %descFile%
 echo Study:	%sname%>> %descFile%
-echo Assay:	%Adir%>> %descFile%
-echo ### ASSAY>> %descFile%
+echo Investigation:	%iname%>> %descFile%
+echo project:	%pname%>> %descFile%
+rem echo ### ASSAY>> %descFile%
 echo Short Name:	%ID%>> %descFile%
 echo Assay Class:	 %IDClass%>> %descFile%
 echo Assay Type:	 %IDType%>> %descFile%
@@ -248,7 +249,21 @@ rem ECHO ON
   rem if exist ../%analytesInput% ( copy ../%analytesInput% ./%analytesInput% )
   call:inputMeta "Title" aTitle *
   call:inputMeta "Description" aDesc *
+rem echo Assay Path:	%cd:\=/%>> %descFile%
+rem set phenodata file
+SETLOCAL ENABLEDELAYEDEXPANSION
+SET "pfns="
+FOR /f "delims=" %%i IN ('dir %iroot%\phenodata_20*.* /B') DO (
+    SET pfns=!pfns!%%i/
+)
+SETLOCAL DISABLEDELAYEDEXPANSION
+call:getMenu "Select phenodata file" "%pfns%None" pfn
+if "%pfn%" EQU "None" ( echo Phenodata:	%pfn%>> %descFile%
+) ELSE ( echo Phenodata:	%iroot:\=/%/%pfn%>> %descFile%)
 rem ---- Type specific fields
+set tasdir=%tmpldir%\%IDClass%\%IDType%
+    set "line1="
+    set "line2="
 if /I "%IDClass%"=="WET" goto wetclass
 if /I "%IDClass%"=="DRY" goto dryclass
 rem if /I "%IDType%" == "R" goto R
@@ -265,16 +280,13 @@ rem echo tst %tmpldir%\%IDClass%\%IDType%\AssayType.ini
 rem dir %tmpldir%
 rem dir ..\%tmpldir%
 rem Assay type directory
-set tasdir=%tmpldir%\%IDClass%\%IDType%
 rem dir %tasdir%
 rem dir %tmpldir%
 :: echo %cd%
 set "analytesInput=Analytes.txt"
-call:getSamples %IDName% %iroot%\phenodata.txt %aroot%\%analytesInput%
+call:getSamples %IDName% %iroot%\%pfn% %aroot%\%analytesInput%
 setlocal disabledelayedexpansion
 rem  if exist %sroot%\%analytesInput% ( copy %sroot%\%analytesInput% %aroot%\%analytesInput% )
-  set "line1="
-  set "line2="
   rem dir %tmpldir%\%IDClass%\%IDType%\
 if exist %tasdir%\AssayType.ini call:processAnalytes %tasdir%\AssayType.ini
 
@@ -292,8 +304,8 @@ REM ---------------------------------------- /dryclass
 :Finish
 echo Data:	>> %descFile%
 rem ------------------------------------  include common.ini from project level
-copy %descFile%+..\common.ini %descFile% >NUL
-echo ASSAY:	%ID%>> ..\_STUDY_METADATA.TXT
+copy %descFile%+..\common.ini %descFile% \b >NUL
+rem echo ASSAY:	%ID%>> ..\_STUDY_METADATA.TXT
 copy %sroot%\showTree.bat . >NUL
 copy %sroot%\showMetadata.bat . >NUL
 copy %sroot%\xcheckMetadata.bat . >NUL
@@ -302,8 +314,12 @@ rem
 rem  make main readme.md file
 rem type README.MD
 rem dir .
-rem cls
-rem type %descFile%
+cls
+echo ======================================
+echo Assay METADATA
+echo ======================================
+rem call:showDesc %descFile%
+type %descFile%
 cd ..
 rem copy existing files from nonversioned tree (if any)
 rem robocopy X-%ID% %ID% /E
@@ -369,7 +385,7 @@ rem call:getInput "%~1" xMeta "%~3"
 rem Type input or get menu?
 
 call:getMenu "%~1" %~3/getMenu xMeta "%~3"
-echo %~1:	%xMeta% >> %descFile%
+echo %~1:	%xMeta%>> %descFile%
 rem call:writeAnalytes %analytesInput% "%~1" %xMeta% 
 rem
 
@@ -397,7 +413,7 @@ rem call:getInput "%~1" xMeta "%~3"
 rem Type input or get menu?
 
 call:getInput "%~1" xMeta "%~3"
-echo %~1:	%xMeta% >> %descFile%
+echo %~1:	%xMeta%>> %descFile%
 rem call:writeAnalytes %analytesInput% "%~1" %xMeta% 
 rem
 
@@ -476,7 +492,7 @@ for /f "tokens=1 delims=/" %%a in ("%~3") do set first=%%a
 rem echo =%~3=%first%= REM test
 if "%xMeta%"=="Other" call:getInput "%~1" xMeta "%first%"
 :next
-echo %~1:	%xMeta%%prefix% >> %descFile%
+echo %~1:	%xMeta%%prefix%>> %descFile%
 rem call:writeAnalytes %analytesInput% "%~1" %xMeta% 
 rem
 REM (ENDLOCAL
@@ -529,7 +545,7 @@ rem IF EXIST %~1 (
       rem echo %searchtext% %modified%
       rem pause
       rem should replace special token with SampleId before writing
-       echo %%a	%%b!modified! >> tmp.txt 
+       echo %%a	%%b!modified!>> tmp.txt 
        rem echo Write: %%a	%%b!modified!
        endlocal
        rem echo off
@@ -737,16 +753,16 @@ setlocal enableextensions disabledelayedexpansion
      set "%~2=%my_file%")
 goto :eof
 rem ----------------------------------------------------------
-:getSamples --- get sample names from phenodata.txt
+:getSamples --- get sample names from %pfn%
 ::          --- %~1 column name
-::          --- %~2 phenodata file name (default is "%iroot%/phenodata.txt")
+::          --- %~2 phenodata file name (default is "%iroot%/%pfn%")
 ::          --- %~3 output file (default is "%sroot%/Analytes.txt")
 :: Return: writes the sample names (first two columns) to the output file
 :: Example: call:getSamples %Assay_ID%
 ::
 set "infile="
 set "outfile="
-if "%~2" NEQ "" (set "infile=%~2") else (set "infile=%iroot%/phenodata.txt")
+if "%~2" NEQ "" (set "infile=%~2") else (set "infile=%iroot%/%pfn%")
 if "%~3" NEQ "" (set "outfile=%~3") else (set "outfile=%sroot%/Analytes.txt")
 :: dir %infile%
 :: First line
@@ -780,7 +796,7 @@ for /f "EOL=: delims=" %%L in (%infile%) do (
     set "param2=!param2:~1!"
     set "param3=!param3:~1!"
     rem echo $1=!param1! $2=*!param2!* $3=*!param3!*
-    if "!param3!" NEQ "" echo !param1!	!param2!	!param3! >> %outfile%
+    if "!param3!" NEQ "" echo !param1!	!param2!	!param3!>> %outfile%
     endlocal
   )
 )
@@ -825,9 +841,9 @@ rem ------------------------------------------------------------
 ::             --- %~2 optional delimiter
 :: Return: current date in YYYYMMDD form
 :: Example: call:normalizeDate
-@echo on
-echo %~1
-echo +%~2+
+rem @echo on
+rem echo %~1
+rem echo +%~2+
 @Echo OFF
 rem get date format info from registry
 rem https://docs.microsoft.com/en-us/windows/desktop/intl/locale-idate
@@ -852,4 +868,14 @@ IF 1%3 LSS 100 (SET YYYYMMDD=0%3) ELSE (SET YYYYMMDD=%3)
 IF 1%2 LSS 100 (SET YYYYMMDD=0%2%sep%%YYYYMMDD%) ELSE (SET YYYYMMDD=%2%sep%%YYYYMMDD%)
 :: Similarly for the year - I've never seen a single-digit year
 IF 1%1 LSS 100 (SET YYYYMMDD=20%sep%%YYYYMMDD%) ELSE (SET YYYYMMDD=%1%sep%%YYYYMMDD%)
-GOTO :eof
+GOTO :eof
+rem -------------------------------------------------------------------
+:showDesc   --- show description file in columns 
+::          --- %~1 file name
+::
+:: Example: call:showDesc %descFile%
+::
+setlocal
+For /F "TOKENS=1,2" %%A In (%~1) echo %%A		%%B
+endlocal
+goto :EOF