Merge pull request #85 from samply/release-v1.0.1

Release v1.0.1

.travis.yml

@@ -3,14 +3,13 @@ jdk: openjdk11
 rvm: 2.5
 before_install: gem install jekyll
 before_script:
-- wget -q https://fhir.github.io/latest-ig-publisher/org.hl7.fhir.validator.jar -O validator.jar
-- wget -q http://hl7.org/fhir/uv/ips/2019Sep/validator.pack -O ips.pack
+- wget -q https://storage.googleapis.com/ig-build/org.hl7.fhir.validator.jar -O validator.jar
 script:
 - mkdir input-cache
-- wget -q https://fhir.github.io/latest-ig-publisher/org.hl7.fhir.publisher.jar -O input-cache/org.hl7.fhir.publisher.jar
+- wget -q https://storage.googleapis.com/ig-build/org.hl7.fhir.publisher.jar -O input-cache/org.hl7.fhir.publisher.jar
 - JAVA_TOOL_OPTIONS=-Dfile.encoding=UTF-8
 - java -jar input-cache/org.hl7.fhir.publisher.jar -ig ig.ini
-- java -jar validator.jar -version 4.0.1 -ig ips.pack -ig output/validator-de.bbmri.fhir.pack input/examples
+- java -jar validator.jar -ig output/validator-de.bbmri.fhir.pack -version 4.0.1 input/examples
 deploy:
   provider: pages
   skip_cleanup: true

README.md

@@ -2,14 +2,4 @@
 
 # BBMRI FHIR® Implementation Guide
 
-[Profile Overview](https://github.com/samply/bbmri-fhir-ig/blob/master/bbmri-ig/input/pagecontent/overview.md)
-
-![Overview profiles](https://github.com/samply/bbmri-fhir-ig/blob/master/bbmri-ig/input/images/GBA-DatamodellFHIR_V05.png)
-
-[Validator Instructions](https://github.com/samply/bbmri-fhir-ig/blob/master/bbmri-ig/input/pagecontent/Validation.md)
-
-[Using References in Bundles](https://github.com/samply/bbmri-fhir-ig/blob/master/bbmri-ig/input/pagecontent/BundleReferences.md)
-
-[Mappings to other projects](https://github.com/samply/bbmri-fhir-ig/blob/master/bbmri-ig/input/pagecontent/mappings.md)
-
-[Referenced Implementation Guides](https://github.com/samply/bbmri-fhir-ig/blob/master/bbmri-ig/input/pagecontent/referencedIGs.md)
+This is the repository for the BBMRI.de/GBA sources. The latest release build can be found here: https://samply.github.io/bbmri-fhir-ig/

_genonce.sh

@@ -1,9 +1,8 @@
 #!/bin/bash
 publisher_jar=org.hl7.fhir.publisher.jar
 input_cache_path=./input-cache/
-set -e
 echo Checking internet connection...
-wget -q --spider tx.fhir.org
+curl -sSf tx.fhir.org > /dev/null
 
 if [ $? -eq 0 ]; then
 	echo "Online"
@@ -17,12 +16,12 @@ echo "$txoption"
 
 publisher=$input_cache_path/$publisher_jar
 if test -f "$publisher"; then
-	JAVA -jar $publisher -ig ig.ini $txoption $*
+	java -jar $publisher -ig ig.ini $txoption $*
 
 else
 	publisher=../$publisher_jar
 	if test -f "$publisher"; then
-		JAVA -jar $publisher -ig ig.ini $txoption $*
+		java -jar $publisher -ig ig.ini $txoption $*
 	else
 		echo IG Publisher NOT FOUND in input-cache or parent folder.  Please run _updatePublisher.  Aborting...
 	fi

_updatePublisher.bat

@@ -1,10 +1,44 @@
 @ECHO OFF
-SET dlurl=https://fhir.github.io/latest-ig-publisher/org.hl7.fhir.publisher.jar
+
+SETLOCAL
+
+SET dlurl=https://storage.googleapis.com/ig-build/org.hl7.fhir.publisher.jar
 SET publisher_jar=org.hl7.fhir.publisher.jar
 SET input_cache_path=%CD%\input-cache\
+SET skipPrompts=false
+
+set update_bat_url=https://raw.githubusercontent.com/FHIR/sample-ig/master/_updatePublisher.bat
+set gen_bat_url=https://raw.githubusercontent.com/FHIR/sample-ig/master/_genonce.bat
+set gencont_bat_url=https://raw.githubusercontent.com/FHIR/sample-ig/master/_gencontinuous.bat
+set gencont_sh_url=https://raw.githubusercontent.com/FHIR/sample-ig/master/_gencontinuous.sh
+set gen_sh_url=https://raw.githubusercontent.com/FHIR/sample-ig/master/_genonce.sh
+set update_sh_url=https://raw.githubusercontent.com/FHIR/sample-ig/master/_updatePublisher.sh
+
+IF "%~1"=="/f" SET skipPrompts=true
+
+
+ECHO.
+ECHO Checking internet connection...
+PING tx.fhir.org -n 1 -w 1000 | FINDSTR TTL && GOTO isonline
+ECHO We're offline, nothing to do...
+GOTO end
+
+:isonline
+ECHO We're online
+
+
+:processflags
+SET ARG=%1
+IF DEFINED ARG (
+	IF "%ARG%"=="-f" SET FORCE=true
+	IF "%ARG%"=="--force" SET FORCE=true
+	SHIFT
+	GOTO processflags
+)
 
 FOR %%x IN ("%CD%") DO SET upper_path=%%~dpx
 
+ECHO.
 IF NOT EXIST "%input_cache_path%%publisher_jar%" (
 	IF NOT EXIST "%upper_path%%publisher_jar%" (
 		SET jarlocation="%input_cache_path%%publisher_jar%"
@@ -16,30 +50,44 @@ IF NOT EXIST "%input_cache_path%%publisher_jar%" (
 		ECHO IG Publisher FOUND in parent folder
 		SET jarlocation="%upper_path%%publisher_jar%"
 		SET jarlocationname=Parent folder
-		GOTO:upgrade
+		GOTO upgrade
 	)
 ) ELSE (
 	ECHO IG Publisher FOUND in input-cache
 	SET jarlocation="%input_cache_path%%publisher_jar%"
 	SET jarlocationname=Input Cache
-	GOTO:upgrade
+	GOTO upgrade
 )
 
 :create
-ECHO Will place publisher jar here: %input_cache_path%%publisher_jar%
-SET /p create="Ok? (Y/N)"
+IF DEFINED FORCE (
+	MKDIR "%input_cache_path%" 2> NUL
+	GOTO download
+)
+
+IF "%skipPrompts%"=="true" (
+	SET create="Y"
+) ELSE (
+	SET /p create="Ok? (Y/N) "
+)
 IF /I "%create%"=="Y" (
+    ECHO Will place publisher jar here: %input_cache_path%%publisher_jar%
 	MKDIR "%input_cache_path%" 2> NUL
-	GOTO:download
+	GOTO download
 )
-GOTO:done
+GOTO done
 
 :upgrade
-SET /p overwrite="Overwrite %jarlocation%? (Y/N)"
+IF "%skipPrompts%"=="true" (
+	SET overwrite="Y"
+) ELSE (
+	SET /p overwrite="Overwrite %jarlocation%? (Y/N) "
+)
+
 IF /I "%overwrite%"=="Y" (
-	GOTO:download
+	GOTO download
 )
-GOTO:done
+GOTO done
 
 :download
 ECHO Downloading most recent publisher to %jarlocationname% - it's ~100 MB, so this may take a bit
@@ -60,14 +108,111 @@ CALL POWERSHELL -command if ('System.Net.WebClient' -as [type]) {(new-object Sys
 GOTO done
 
 :win7
-CALL bitsadmin /transfer GetPublisher /download /priority normal "%dlurl%" "%jarlocation%"
+rem this may be triggering the antivirus - bitsadmin.exe is a known threat
+rem CALL bitsadmin /transfer GetPublisher /download /priority normal "%dlurl%" "%jarlocation%"
+
+rem this didn't work in win 10
+rem CALL Start-BitsTransfer /priority normal "%dlurl%" "%jarlocation%"
+
+rem this should work - untested
+call (New-Object Net.WebClient).DownloadFile('%dlurl%', '%jarlocation%')
 GOTO done
 
 :win8.1
 :win8
 :vista
-ECHO This script does not yet support Windows %winver%.  Please ask for help on http://chat.fhir.org
 GOTO done
 
+
+
 :done
-PAUSE
+
+
+
+
+ECHO.
+ECHO Updating scripts
+IF "%skipPrompts%"=="true" (
+	SET updateScripts="Y"
+) ELSE (
+	SET /p updateScripts="Update scripts? (Y/N) "
+)
+IF /I "%updateScripts%"=="Y" (
+	GOTO scripts
+)
+GOTO end
+
+
+:scripts
+
+REM Download all batch files (and this one with a new name)
+
+SETLOCAL DisableDelayedExpansion
+
+
+
+:dl_script_1
+ECHO Updating _updatePublisher.sh
+call POWERSHELL -command if ('System.Net.WebClient' -as [type]) {(new-object System.Net.WebClient).DownloadFile(\"%update_sh_url%\",\"_updatePublisher.new.sh\") } else { Invoke-WebRequest -Uri "%update_sh_url%" -Outfile "_updatePublisher.new.sh" }
+if %ERRORLEVEL% == 0 goto upd_script_1
+echo "Errors encountered during download: %errorlevel%"
+goto dl_script_2
+:upd_script_1
+start copy /y "_updatePublisher.new.sh" "_updatePublisher.sh" ^&^& del "_updatePublisher.new.sh" ^&^& exit
+
+
+:dl_script_2
+ECHO Updating _genonce.bat
+call POWERSHELL -command if ('System.Net.WebClient' -as [type]) {(new-object System.Net.WebClient).DownloadFile(\"%gen_bat_url%\",\"_genonce.new.bat\") } else { Invoke-WebRequest -Uri "%gen_bat_url%" -Outfile "_genonce.bat" }
+if %ERRORLEVEL% == 0 goto upd_script_2
+echo "Errors encountered during download: %errorlevel%"
+goto dl_script_3
+:upd_script_2
+start copy /y "_genonce.new.bat" "_genonce.bat" ^&^& del "_genonce.new.bat" ^&^& exit
+
+:dl_script_3
+ECHO Updating _gencontinuous.bat
+call POWERSHELL -command if ('System.Net.WebClient' -as [type]) {(new-object System.Net.WebClient).DownloadFile(\"%gencont_bat_url%\",\"_gencontinuous.new.bat\") } else { Invoke-WebRequest -Uri "%gencont_bat_url%" -Outfile "_gencontinuous.bat" }
+if %ERRORLEVEL% == 0 goto upd_script_3
+echo "Errors encountered during download: %errorlevel%"
+goto dl_script_4
+:upd_script_3
+start copy /y "_gencontinuous.new.bat" "_gencontinuous.bat" ^&^& del "_gencontinuous.new.bat" ^&^& exit
+
+
+:dl_script_4
+ECHO Updating _genonce.sh
+call POWERSHELL -command if ('System.Net.WebClient' -as [type]) {(new-object System.Net.WebClient).DownloadFile(\"%gen_sh_url%\",\"_genonce.new.sh\") } else { Invoke-WebRequest -Uri "%gen_sh_url%" -Outfile "_genonce.sh" }
+if %ERRORLEVEL% == 0 goto upd_script_4
+echo "Errors encountered during download: %errorlevel%"
+goto dl_script_5
+:upd_script_4
+start copy /y "_genonce.new.sh" "_genonce.sh" ^&^& del "_genonce.new.sh" ^&^& exit
+
+:dl_script_5
+ECHO Updating _gencontinuous.sh
+call POWERSHELL -command if ('System.Net.WebClient' -as [type]) {(new-object System.Net.WebClient).DownloadFile(\"%gencont_sh_url%\",\"_gencontinuous.new.sh\") } else { Invoke-WebRequest -Uri "%gencont_sh_url%" -Outfile "_gencontinuous.sh" }
+if %ERRORLEVEL% == 0 goto upd_script_5
+echo "Errors encountered during download: %errorlevel%"
+goto dl_script_6
+:upd_script_5
+start copy /y "_gencontinuous.new.sh" "_gencontinuous.sh" ^&^& del "_gencontinuous.new.sh" ^&^& exit
+
+
+
+:dl_script_6
+ECHO Updating _updatePublisher.bat
+call POWERSHELL -command if ('System.Net.WebClient' -as [type]) {(new-object System.Net.WebClient).DownloadFile(\"%update_bat_url%\",\"_updatePublisher.new.bat\") } else { Invoke-WebRequest -Uri "%update_bat_url%" -Outfile "_updatePublisher.new.bat" }
+if %ERRORLEVEL% == 0 goto upd_script_6
+echo "Errors encountered during download: %errorlevel%"
+goto end
+:upd_script_6
+start copy /y "_updatePublisher.new.bat" "_updatePublisher.bat" ^&^& del "_updatePublisher.new.bat" ^&^& exit
+
+
+:end
+
+
+IF "%skipPrompts%"=="true" (
+  PAUSE
+}

_updatePublisher.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-dlurl=https://fhir.github.io/latest-ig-publisher/org.hl7.fhir.publisher.jar
+dlurl=https://storage.googleapis.com/ig-build/org.hl7.fhir.publisher.jar
 publisher_jar=org.hl7.fhir.publisher.jar
 input_cache_path=./input-cache/
 
@@ -9,6 +9,20 @@ if ! type "curl" > /dev/null; then
 	exit 1
 fi
 
+FORCE=false
+
+while :; do
+    case $1 in
+        -f|--force) FORCE=true ;;
+        --)
+            shift
+            break
+            ;;
+        *) break
+    esac
+    shift
+done
+
 publisher="$input_cache_path$publisher_jar"
 if test -f "$publisher"; then
 	echo "IG Publisher FOUND in input-cache"
@@ -31,15 +45,17 @@ else
 	fi
 fi
 
-if "$upgrade"; then
-	message="Overwrite $jarlocation?"
-else
-	echo Will place publisher jar here: "$jarlocation"
-	message="Ok?"
+if [[ "$FORCE" != true ]]; then
+  if "$upgrade"; then
+    message="Overwrite $jarlocation? (Y/N) "
+  else
+    echo Will place publisher jar here: "$jarlocation"
+    message="Ok (enter 'y' or 'Y' to continue, any other key to cancel)?"
+  fi
+  read -r -p "$message" response
 fi
 
-read -r -p "$message" response
-if [[ "$response" =~ ^([yY])$ ]]; then
+if [[ "$FORCE" == true ]] || [[ "$response" =~ ^([yY])$ ]]; then
 	echo "Downloading most recent publisher to $jarlocationname - it's ~100 MB, so this may take a bit"
 #	wget "https://fhir.github.io/latest-ig-publisher/org.hl7.fhir.publisher.jar" -O "$jarlocation" 
 	curl $dlurl -o "$jarlocation" --create-dirs