From 02da4766255463ad68a0e0ad5f5908cbde68d99c Mon Sep 17 00:00:00 2001
From: Olivier Korach <olivier.korach@gmail.com>
Date: Sun, 6 Oct 2024 11:06:19 +0200
Subject: [PATCH 01/14] Move all config in conf

---
 .sonarcloud.properties                        |  9 ----
 .flake8 => conf/.flake8                       |  0
 deploy.bat => conf/deploy.bat                 |  0
 deploy.sh => conf/deploy.sh                   |  0
 pylintrc => conf/pylintrc                     |  0
 release.Dockerfile => conf/release.Dockerfile |  0
 run_linters.sh => conf/run_linters.sh         |  8 +++-
 run_tests.sh => conf/run_tests.sh             |  0
 scan.sh => conf/scan.sh                       |  0
 .../shellcheck2sonar.py                       |  0
 .../snapshot.Dockerfile                       |  0
 .../sonar-project.properties                  |  0
 migration.Dockerfile                          | 42 -------------------
 13 files changed, 6 insertions(+), 53 deletions(-)
 delete mode 100644 .sonarcloud.properties
 rename .flake8 => conf/.flake8 (100%)
 rename deploy.bat => conf/deploy.bat (100%)
 rename deploy.sh => conf/deploy.sh (100%)
 rename pylintrc => conf/pylintrc (100%)
 rename release.Dockerfile => conf/release.Dockerfile (100%)
 rename run_linters.sh => conf/run_linters.sh (83%)
 rename run_tests.sh => conf/run_tests.sh (100%)
 rename scan.sh => conf/scan.sh (100%)
 rename shellcheck2sonar.py => conf/shellcheck2sonar.py (100%)
 rename snapshot.Dockerfile => conf/snapshot.Dockerfile (100%)
 rename sonar-project.properties => conf/sonar-project.properties (100%)
 delete mode 100644 migration.Dockerfile

diff --git a/.sonarcloud.properties b/.sonarcloud.properties
deleted file mode 100644
index 248db4465..000000000
--- a/.sonarcloud.properties
+++ /dev/null
@@ -1,9 +0,0 @@
-# Required metadata
-# sonar.projectVersion=1.0
-
-# Comma-separated paths to directories with sources (required)
-sonar.sources=.
-# Encoding of the source files
-sonar.sourceEncoding=UTF-8
-sonar.exclusions=**/*.csv,**/*.xls*
-sonar.python.version=3.6
\ No newline at end of file
diff --git a/.flake8 b/conf/.flake8
similarity index 100%
rename from .flake8
rename to conf/.flake8
diff --git a/deploy.bat b/conf/deploy.bat
similarity index 100%
rename from deploy.bat
rename to conf/deploy.bat
diff --git a/deploy.sh b/conf/deploy.sh
similarity index 100%
rename from deploy.sh
rename to conf/deploy.sh
diff --git a/pylintrc b/conf/pylintrc
similarity index 100%
rename from pylintrc
rename to conf/pylintrc
diff --git a/release.Dockerfile b/conf/release.Dockerfile
similarity index 100%
rename from release.Dockerfile
rename to conf/release.Dockerfile
diff --git a/run_linters.sh b/conf/run_linters.sh
similarity index 83%
rename from run_linters.sh
rename to conf/run_linters.sh
index 306ab1009..d4949bc4d 100755
--- a/run_linters.sh
+++ b/conf/run_linters.sh
@@ -19,7 +19,11 @@
 # Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 #
 
-buildDir="build"
+ME="$( basename "${BASH_SOURCE[0]}" )"
+ROOTDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && cd .. && pwd )"
+CONFDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+buildDir="$ROOTDIR/build"
 pylintReport="$buildDir/pylint-report.out"
 # banditReport="$buildDir/bandit-report.json"
 flake8Report="$buildDir/flake8-report.out"
@@ -29,7 +33,7 @@ externalIssueReport="$buildDir/external-issue-report.json"
 
 echo "Running pylint"
 rm -f $pylintReport
-pylint ./*.py ./*/*.py -r n --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" | tee $pylintReport
+pylint --rcfile $CONFDIR/pylintrc ./*.py ./*/*.py -r n --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" | tee $pylintReport
 re=$?
 if [ "$re" == "32" ]; then
     >&2 echo "ERROR: pylint execution failed, errcode $re, aborting..."
diff --git a/run_tests.sh b/conf/run_tests.sh
similarity index 100%
rename from run_tests.sh
rename to conf/run_tests.sh
diff --git a/scan.sh b/conf/scan.sh
similarity index 100%
rename from scan.sh
rename to conf/scan.sh
diff --git a/shellcheck2sonar.py b/conf/shellcheck2sonar.py
similarity index 100%
rename from shellcheck2sonar.py
rename to conf/shellcheck2sonar.py
diff --git a/snapshot.Dockerfile b/conf/snapshot.Dockerfile
similarity index 100%
rename from snapshot.Dockerfile
rename to conf/snapshot.Dockerfile
diff --git a/sonar-project.properties b/conf/sonar-project.properties
similarity index 100%
rename from sonar-project.properties
rename to conf/sonar-project.properties
diff --git a/migration.Dockerfile b/migration.Dockerfile
deleted file mode 100644
index 35cb679c8..000000000
--- a/migration.Dockerfile
+++ /dev/null
@@ -1,42 +0,0 @@
-FROM alpine:3.20.3
-LABEL maintainer="olivier.korach@gmail.com" 
-ENV IN_DOCKER="Yes"
-
-ARG USERNAME=sonar
-ARG USER_UID=1000
-ARG GROUPNAME=sonar
-
-# Create the user
-RUN addgroup -S ${GROUPNAME} && adduser -u ${USER_UID} -S ${USERNAME} -G ${GROUPNAME}
-
-# Install python/pip
-ENV PYTHONUNBUFFERED=1
-RUN apk add --update --no-cache python3 && ln -sf python3 /usr/bin/python
-
-# create a virtual environment and add it to PATH so that it is 
-# applied for all future RUN and CMD calls
-ENV VIRTUAL_ENV=/opt/venv
-RUN python3 -m venv ${VIRTUAL_ENV}
-ENV PATH="${VIRTUAL_ENV}/bin:${PATH}"
-
-WORKDIR /opt/sonar-migration
-
-COPY ./sonar sonar
-COPY ./requirements.txt .
-COPY ./cli cli
-COPY ./setup_migration.py .
-COPY ./sonar_migration .
-COPY ./README.md .
-COPY ./LICENSE .
-COPY ./sonar/audit sonar/audit
-
-RUN pip install --upgrade pip \
-&& pip install --no-cache-dir -r requirements.txt \
-&& pip install --no-cache-dir --upgrade pip setuptools wheel \
-&& python setup_migration.py bdist_wheel \
-&& pip install dist/sonar_migration-py3-*.whl --force-reinstall
-
-USER ${USERNAME}
-WORKDIR /home/${USERNAME}
-
-ENTRYPOINT ["sonar-migration"]

From 176fcde18a8b30ad86ca2a151945cfdbc4df8e2c Mon Sep 17 00:00:00 2001
From: Olivier Korach <olivier.korach@gmail.com>
Date: Sun, 6 Oct 2024 11:07:07 +0200
Subject: [PATCH 02/14] Move api-doc in doc

---
 {api-doc => doc/api}/Makefile                              | 0
 {api-doc => doc/api}/make.bat                              | 0
 {api-doc => doc/api}/source/aggregation_permissions.rst    | 0
 {api-doc => doc/api}/source/aggregations.rst               | 0
 {api-doc => doc/api}/source/application_permissions.rst    | 0
 {api-doc => doc/api}/source/applications.rst               | 0
 {api-doc => doc/api}/source/branches.rst                   | 0
 {api-doc => doc/api}/source/components.rst                 | 0
 {api-doc => doc/api}/source/conf.py                        | 0
 {api-doc => doc/api}/source/devops.rst                     | 0
 {api-doc => doc/api}/source/findings.rst                   | 0
 {api-doc => doc/api}/source/global_permissions.rst         | 0
 {api-doc => doc/api}/source/groups.rst                     | 0
 {api-doc => doc/api}/source/hotspots.rst                   | 0
 {api-doc => doc/api}/source/index.rst                      | 0
 {api-doc => doc/api}/source/issues.rst                     | 0
 {api-doc => doc/api}/source/languages.rst                  | 0
 {api-doc => doc/api}/source/measures.rst                   | 0
 {api-doc => doc/api}/source/metrics.rst                    | 0
 {api-doc => doc/api}/source/organizations.rst              | 0
 {api-doc => doc/api}/source/permission_templates.rst       | 0
 {api-doc => doc/api}/source/permissions.rst                | 0
 {api-doc => doc/api}/source/platform.rst                   | 0
 {api-doc => doc/api}/source/portfolio_permissions.rst      | 0
 {api-doc => doc/api}/source/portfolios.rst                 | 0
 {api-doc => doc/api}/source/project_permissions.rst        | 0
 {api-doc => doc/api}/source/projects.rst                   | 0
 {api-doc => doc/api}/source/pullrequests.rst               | 0
 {api-doc => doc/api}/source/quality_permissions.rst        | 0
 {api-doc => doc/api}/source/qualitygate_permissions.rst    | 0
 {api-doc => doc/api}/source/qualitygates.rst               | 0
 {api-doc => doc/api}/source/qualityprofile_permissions.rst | 0
 {api-doc => doc/api}/source/qualityprofiles.rst            | 0
 {api-doc => doc/api}/source/rules.rst                      | 0
 {api-doc => doc/api}/source/sq_object.rst                  | 0
 {api-doc => doc/api}/source/tasks.rst                      | 0
 {api-doc => doc/api}/source/tokens.rst                     | 0
 {api-doc => doc/api}/source/users.rst                      | 0
 {api-doc => doc/api}/source/webhooks.rst                   | 0
 39 files changed, 0 insertions(+), 0 deletions(-)
 rename {api-doc => doc/api}/Makefile (100%)
 rename {api-doc => doc/api}/make.bat (100%)
 rename {api-doc => doc/api}/source/aggregation_permissions.rst (100%)
 rename {api-doc => doc/api}/source/aggregations.rst (100%)
 rename {api-doc => doc/api}/source/application_permissions.rst (100%)
 rename {api-doc => doc/api}/source/applications.rst (100%)
 rename {api-doc => doc/api}/source/branches.rst (100%)
 rename {api-doc => doc/api}/source/components.rst (100%)
 rename {api-doc => doc/api}/source/conf.py (100%)
 rename {api-doc => doc/api}/source/devops.rst (100%)
 rename {api-doc => doc/api}/source/findings.rst (100%)
 rename {api-doc => doc/api}/source/global_permissions.rst (100%)
 rename {api-doc => doc/api}/source/groups.rst (100%)
 rename {api-doc => doc/api}/source/hotspots.rst (100%)
 rename {api-doc => doc/api}/source/index.rst (100%)
 rename {api-doc => doc/api}/source/issues.rst (100%)
 rename {api-doc => doc/api}/source/languages.rst (100%)
 rename {api-doc => doc/api}/source/measures.rst (100%)
 rename {api-doc => doc/api}/source/metrics.rst (100%)
 rename {api-doc => doc/api}/source/organizations.rst (100%)
 rename {api-doc => doc/api}/source/permission_templates.rst (100%)
 rename {api-doc => doc/api}/source/permissions.rst (100%)
 rename {api-doc => doc/api}/source/platform.rst (100%)
 rename {api-doc => doc/api}/source/portfolio_permissions.rst (100%)
 rename {api-doc => doc/api}/source/portfolios.rst (100%)
 rename {api-doc => doc/api}/source/project_permissions.rst (100%)
 rename {api-doc => doc/api}/source/projects.rst (100%)
 rename {api-doc => doc/api}/source/pullrequests.rst (100%)
 rename {api-doc => doc/api}/source/quality_permissions.rst (100%)
 rename {api-doc => doc/api}/source/qualitygate_permissions.rst (100%)
 rename {api-doc => doc/api}/source/qualitygates.rst (100%)
 rename {api-doc => doc/api}/source/qualityprofile_permissions.rst (100%)
 rename {api-doc => doc/api}/source/qualityprofiles.rst (100%)
 rename {api-doc => doc/api}/source/rules.rst (100%)
 rename {api-doc => doc/api}/source/sq_object.rst (100%)
 rename {api-doc => doc/api}/source/tasks.rst (100%)
 rename {api-doc => doc/api}/source/tokens.rst (100%)
 rename {api-doc => doc/api}/source/users.rst (100%)
 rename {api-doc => doc/api}/source/webhooks.rst (100%)

diff --git a/api-doc/Makefile b/doc/api/Makefile
similarity index 100%
rename from api-doc/Makefile
rename to doc/api/Makefile
diff --git a/api-doc/make.bat b/doc/api/make.bat
similarity index 100%
rename from api-doc/make.bat
rename to doc/api/make.bat
diff --git a/api-doc/source/aggregation_permissions.rst b/doc/api/source/aggregation_permissions.rst
similarity index 100%
rename from api-doc/source/aggregation_permissions.rst
rename to doc/api/source/aggregation_permissions.rst
diff --git a/api-doc/source/aggregations.rst b/doc/api/source/aggregations.rst
similarity index 100%
rename from api-doc/source/aggregations.rst
rename to doc/api/source/aggregations.rst
diff --git a/api-doc/source/application_permissions.rst b/doc/api/source/application_permissions.rst
similarity index 100%
rename from api-doc/source/application_permissions.rst
rename to doc/api/source/application_permissions.rst
diff --git a/api-doc/source/applications.rst b/doc/api/source/applications.rst
similarity index 100%
rename from api-doc/source/applications.rst
rename to doc/api/source/applications.rst
diff --git a/api-doc/source/branches.rst b/doc/api/source/branches.rst
similarity index 100%
rename from api-doc/source/branches.rst
rename to doc/api/source/branches.rst
diff --git a/api-doc/source/components.rst b/doc/api/source/components.rst
similarity index 100%
rename from api-doc/source/components.rst
rename to doc/api/source/components.rst
diff --git a/api-doc/source/conf.py b/doc/api/source/conf.py
similarity index 100%
rename from api-doc/source/conf.py
rename to doc/api/source/conf.py
diff --git a/api-doc/source/devops.rst b/doc/api/source/devops.rst
similarity index 100%
rename from api-doc/source/devops.rst
rename to doc/api/source/devops.rst
diff --git a/api-doc/source/findings.rst b/doc/api/source/findings.rst
similarity index 100%
rename from api-doc/source/findings.rst
rename to doc/api/source/findings.rst
diff --git a/api-doc/source/global_permissions.rst b/doc/api/source/global_permissions.rst
similarity index 100%
rename from api-doc/source/global_permissions.rst
rename to doc/api/source/global_permissions.rst
diff --git a/api-doc/source/groups.rst b/doc/api/source/groups.rst
similarity index 100%
rename from api-doc/source/groups.rst
rename to doc/api/source/groups.rst
diff --git a/api-doc/source/hotspots.rst b/doc/api/source/hotspots.rst
similarity index 100%
rename from api-doc/source/hotspots.rst
rename to doc/api/source/hotspots.rst
diff --git a/api-doc/source/index.rst b/doc/api/source/index.rst
similarity index 100%
rename from api-doc/source/index.rst
rename to doc/api/source/index.rst
diff --git a/api-doc/source/issues.rst b/doc/api/source/issues.rst
similarity index 100%
rename from api-doc/source/issues.rst
rename to doc/api/source/issues.rst
diff --git a/api-doc/source/languages.rst b/doc/api/source/languages.rst
similarity index 100%
rename from api-doc/source/languages.rst
rename to doc/api/source/languages.rst
diff --git a/api-doc/source/measures.rst b/doc/api/source/measures.rst
similarity index 100%
rename from api-doc/source/measures.rst
rename to doc/api/source/measures.rst
diff --git a/api-doc/source/metrics.rst b/doc/api/source/metrics.rst
similarity index 100%
rename from api-doc/source/metrics.rst
rename to doc/api/source/metrics.rst
diff --git a/api-doc/source/organizations.rst b/doc/api/source/organizations.rst
similarity index 100%
rename from api-doc/source/organizations.rst
rename to doc/api/source/organizations.rst
diff --git a/api-doc/source/permission_templates.rst b/doc/api/source/permission_templates.rst
similarity index 100%
rename from api-doc/source/permission_templates.rst
rename to doc/api/source/permission_templates.rst
diff --git a/api-doc/source/permissions.rst b/doc/api/source/permissions.rst
similarity index 100%
rename from api-doc/source/permissions.rst
rename to doc/api/source/permissions.rst
diff --git a/api-doc/source/platform.rst b/doc/api/source/platform.rst
similarity index 100%
rename from api-doc/source/platform.rst
rename to doc/api/source/platform.rst
diff --git a/api-doc/source/portfolio_permissions.rst b/doc/api/source/portfolio_permissions.rst
similarity index 100%
rename from api-doc/source/portfolio_permissions.rst
rename to doc/api/source/portfolio_permissions.rst
diff --git a/api-doc/source/portfolios.rst b/doc/api/source/portfolios.rst
similarity index 100%
rename from api-doc/source/portfolios.rst
rename to doc/api/source/portfolios.rst
diff --git a/api-doc/source/project_permissions.rst b/doc/api/source/project_permissions.rst
similarity index 100%
rename from api-doc/source/project_permissions.rst
rename to doc/api/source/project_permissions.rst
diff --git a/api-doc/source/projects.rst b/doc/api/source/projects.rst
similarity index 100%
rename from api-doc/source/projects.rst
rename to doc/api/source/projects.rst
diff --git a/api-doc/source/pullrequests.rst b/doc/api/source/pullrequests.rst
similarity index 100%
rename from api-doc/source/pullrequests.rst
rename to doc/api/source/pullrequests.rst
diff --git a/api-doc/source/quality_permissions.rst b/doc/api/source/quality_permissions.rst
similarity index 100%
rename from api-doc/source/quality_permissions.rst
rename to doc/api/source/quality_permissions.rst
diff --git a/api-doc/source/qualitygate_permissions.rst b/doc/api/source/qualitygate_permissions.rst
similarity index 100%
rename from api-doc/source/qualitygate_permissions.rst
rename to doc/api/source/qualitygate_permissions.rst
diff --git a/api-doc/source/qualitygates.rst b/doc/api/source/qualitygates.rst
similarity index 100%
rename from api-doc/source/qualitygates.rst
rename to doc/api/source/qualitygates.rst
diff --git a/api-doc/source/qualityprofile_permissions.rst b/doc/api/source/qualityprofile_permissions.rst
similarity index 100%
rename from api-doc/source/qualityprofile_permissions.rst
rename to doc/api/source/qualityprofile_permissions.rst
diff --git a/api-doc/source/qualityprofiles.rst b/doc/api/source/qualityprofiles.rst
similarity index 100%
rename from api-doc/source/qualityprofiles.rst
rename to doc/api/source/qualityprofiles.rst
diff --git a/api-doc/source/rules.rst b/doc/api/source/rules.rst
similarity index 100%
rename from api-doc/source/rules.rst
rename to doc/api/source/rules.rst
diff --git a/api-doc/source/sq_object.rst b/doc/api/source/sq_object.rst
similarity index 100%
rename from api-doc/source/sq_object.rst
rename to doc/api/source/sq_object.rst
diff --git a/api-doc/source/tasks.rst b/doc/api/source/tasks.rst
similarity index 100%
rename from api-doc/source/tasks.rst
rename to doc/api/source/tasks.rst
diff --git a/api-doc/source/tokens.rst b/doc/api/source/tokens.rst
similarity index 100%
rename from api-doc/source/tokens.rst
rename to doc/api/source/tokens.rst
diff --git a/api-doc/source/users.rst b/doc/api/source/users.rst
similarity index 100%
rename from api-doc/source/users.rst
rename to doc/api/source/users.rst
diff --git a/api-doc/source/webhooks.rst b/doc/api/source/webhooks.rst
similarity index 100%
rename from api-doc/source/webhooks.rst
rename to doc/api/source/webhooks.rst

From 1e8c99817ec18bd15c49531b07715d6a5986c8dc Mon Sep 17 00:00:00 2001
From: Olivier Korach <olivier.korach@gmail.com>
Date: Sun, 6 Oct 2024 11:11:13 +0200
Subject: [PATCH 03/14] Set conf config file for linters

---
 conf/run_linters.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/conf/run_linters.sh b/conf/run_linters.sh
index d4949bc4d..e7300d911 100755
--- a/conf/run_linters.sh
+++ b/conf/run_linters.sh
@@ -33,7 +33,7 @@ externalIssueReport="$buildDir/external-issue-report.json"
 
 echo "Running pylint"
 rm -f $pylintReport
-pylint --rcfile $CONFDIR/pylintrc ./*.py ./*/*.py -r n --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" | tee $pylintReport
+pylint --rcfile $CONFDIR/pylintrc $ROOTDIR/*.py $ROOTDIR/*/*.py -r n --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" | tee $pylintReport
 re=$?
 if [ "$re" == "32" ]; then
     >&2 echo "ERROR: pylint execution failed, errcode $re, aborting..."
@@ -43,11 +43,11 @@ fi
 echo "Running flake8"
 rm -f $flake8Report
 # See .flake8 file for settings
-flake8 . >$flake8Report
+flake8 --config "$CONFIG/.flake8" "$ROOTDIR" >$flake8Report
 
 # echo "Running bandit"
 # rm -f $banditReport
 # bandit --exit-zero -f json --skip B311,B303,B101 -r . -x .vscode,./tests >$banditReport
 
 echo "Running shellcheck"
-shellcheck ./*.sh ./*/*.sh -s bash -f json | ./shellcheck2sonar.py >$externalIssueReport
+shellcheck $ROOTDIR/*.sh $ROOTDIR/*/*.sh -s bash -f json | $CONFDIR/shellcheck2sonar.py >$externalIssueReport

From 96d35ca138f6b909fa7a33f51f9d50a9bffa1929 Mon Sep 17 00:00:00 2001
From: Olivier Korach <olivier.korach@gmail.com>
Date: Sun, 6 Oct 2024 11:13:34 +0200
Subject: [PATCH 04/14] Make all runs relative to repo root

---
 conf/run_tests.sh | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/conf/run_tests.sh b/conf/run_tests.sh
index 2efe1bec9..ce7931e65 100755
--- a/conf/run_tests.sh
+++ b/conf/run_tests.sh
@@ -19,14 +19,18 @@
 # Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 #
 
-buildDir="build"
+ME="$( basename "${BASH_SOURCE[0]}" )"
+ROOTDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && cd .. && pwd )"
+CONFDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+buildDir="$ROOTDIR/build"
 coverageReport="$buildDir/coverage.xml"
 
 [ ! -d $buildDir ] && mkdir $buildDir
 
 echo "Running tests"
-chmod u-rw test/sif_not_readable.json
+unreadableSif=$ROOTDIR/test/sif_not_readable.json
+chmod u-rw $unreadableSif
 export SONAR_HOST_URL=${1:-${SONAR_HOST_URL_TEST}}
-coverage run --source=. -m pytest test/
+coverage run --source=$ROOTDIR -m pytest $ROOTDIR/test/
 coverage xml -o $coverageReport
-chmod u+rw test/sif_not_readable.json
+chmod u+rw $unreadableSif

From 21d06b9bc3aba90dc8bd1265b7b69a038db268b5 Mon Sep 17 00:00:00 2001
From: Olivier Korach <olivier.korach@gmail.com>
Date: Sun, 6 Oct 2024 11:15:50 +0200
Subject: [PATCH 05/14] Make scan relative to repo root

---
 conf/scan.sh | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/conf/scan.sh b/conf/scan.sh
index 0ac37e681..c68e58ac4 100755
--- a/conf/scan.sh
+++ b/conf/scan.sh
@@ -19,6 +19,10 @@
 # Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 #
 
+ME="$( basename "${BASH_SOURCE[0]}" )"
+ROOTDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && cd .. && pwd )"
+CONFDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
 dolint=true
 dotest=false
 
@@ -40,7 +44,7 @@ do
   shift
 done
 
-buildDir="build"
+buildDir="$ROOTDIR/build"
 pylintReport="$buildDir/pylint-report.out"
 banditReport="$buildDir/bandit-report.json"
 flake8Report="$buildDir/flake8-report.out"
@@ -58,7 +62,7 @@ if [ "$dolint" != "false" ]; then
   ./run_linters.sh
 fi
 
-version=$(grep PACKAGE_VERSION sonar/version.py | cut -d "=" -f 2 | sed -e "s/[\'\" ]//g" -e "s/^ +//" -e "s/ +$//")
+version=$(grep PACKAGE_VERSION $ROOTDIR/sonar/version.py | cut -d "=" -f 2 | sed -e "s/[\'\" ]//g" -e "s/^ +//" -e "s/ +$//")
 
 cmd="sonar-scanner -Dsonar.projectVersion=$version \
   -Dsonar.python.flake8.reportPaths=$flake8Report \

From 60f8079293b5620630dbbb1c21f10cd4b8c17baf Mon Sep 17 00:00:00 2001
From: Olivier Korach <olivier.korach@gmail.com>
Date: Sun, 6 Oct 2024 11:19:46 +0200
Subject: [PATCH 06/14] Specify properties file location in conf

---
 conf/scan.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conf/scan.sh b/conf/scan.sh
index c68e58ac4..b18ed2951 100755
--- a/conf/scan.sh
+++ b/conf/scan.sh
@@ -65,6 +65,7 @@ fi
 version=$(grep PACKAGE_VERSION $ROOTDIR/sonar/version.py | cut -d "=" -f 2 | sed -e "s/[\'\" ]//g" -e "s/^ +//" -e "s/ +$//")
 
 cmd="sonar-scanner -Dsonar.projectVersion=$version \
+  -Dproject.settings=$CONFDIR/sonar-project.properties \
   -Dsonar.python.flake8.reportPaths=$flake8Report \
   -Dsonar.python.pylint.reportPaths=$pylintReport \
   -Dsonar.python.bandit.reportPaths=$banditReport \

From b23e5ce54172ef96af5d9e5ae6ff94766b076781 Mon Sep 17 00:00:00 2001
From: Olivier Korach <olivier.korach@gmail.com>
Date: Sun, 6 Oct 2024 11:20:23 +0200
Subject: [PATCH 07/14] Run everything all relative to repo root

---
 conf/deploy.sh | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/conf/deploy.sh b/conf/deploy.sh
index 1e23abe1c..3d4ea21f8 100755
--- a/conf/deploy.sh
+++ b/conf/deploy.sh
@@ -19,6 +19,10 @@
 # Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 #
 
+ME="$( basename "${BASH_SOURCE[0]}" )"
+ROOTDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && cd .. && pwd )"
+CONFDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
 build_docs=1
 build_image=1
 release=0
@@ -44,19 +48,19 @@ while [ $# -ne 0 ]; do
 done
 
 black --line-length=150 .
-rm -rf build dist
-python3 setup.py bdist_wheel
+rm -rf $ROOTDIR/build $ROOTDIR/dist
+python3 $ROOTDIR/setup.py bdist_wheel
 
 # Deploy locally for tests
-pip install --upgrade --force-reinstall dist/sonar_tools-*-py3-*.whl
+pip install --upgrade --force-reinstall $ROOTDIR/dist/sonar_tools-*-py3-*.whl
 
 if [ "$build_image" == "1" ]; then
-    docker build -t olivierkorach/sonar-tools:3.5 -t olivierkorach/sonar-tools:latest -f snapshot.Dockerfile . --load
+    docker build -t olivierkorach/sonar-tools:3.5 -t olivierkorach/sonar-tools:latest -f $CONFDIR/snapshot.Dockerfile $ROOTDIR --load
 fi
 
 if [ "$build_docs" == "1" ]; then
-    rm -rf api-doc/build
-    sphinx-build -b html api-doc/source api-doc/build
+    rm -rf doc/api/build
+    sphinx-build -b html doc/api/source doc/api/build
 fi
 
 # Deploy on pypi.org once released
@@ -64,10 +68,10 @@ if [ "$release" = "1" ]; then
     echo "Confirm release [y/n] ?"
     read -r confirm
     if [ "$confirm" = "y" ]; then
-        python3 -m twine upload dist/sonar_tools-*-py3-*.whl
+        python3 -m twine upload $ROOTDIR/dist/sonar_tools-*-py3-*.whl
     fi
 fi
 
 if [ "$release_docker" = "1" ]; then
-    docker buildx build --push --platform linux/amd64,linux/arm64 -t olivierkorach/sonar-tools:3.5  -t olivierkorach/sonar-tools:latest -f release.Dockerfile .
+    docker buildx build --push --platform linux/amd64,linux/arm64 -t olivierkorach/sonar-tools:3.5  -t olivierkorach/sonar-tools:latest -f $ROOTDIR/release.Dockerfile .
 fi
\ No newline at end of file

From 9ad9b085a4d49d4ed9fba7f8d11b0d6c47492b77 Mon Sep 17 00:00:00 2001
From: Olivier Korach <olivier.korach@gmail.com>
Date: Sun, 6 Oct 2024 11:22:29 +0200
Subject: [PATCH 08/14] Build everything from repo root

---
 migration/deploy.sh | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/migration/deploy.sh b/migration/deploy.sh
index 8f82a635c..a4a56f77e 100755
--- a/migration/deploy.sh
+++ b/migration/deploy.sh
@@ -19,6 +19,10 @@
 # Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 #
 
+ME="$( basename "${BASH_SOURCE[0]}" )"
+ROOTDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && cd .. && pwd )"
+CONFDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
 build_image=1
 release=0
 
@@ -40,14 +44,14 @@ while [ $# -ne 0 ]; do
 done
 
 black --line-length=150 .
-rm -rf build dist
-python3 setup_migration.py bdist_wheel
+rm -rf $ROOTDIR/build $ROOTDIR/dist
+python3 $ROOTDIR/setup_migration.py bdist_wheel
 
 # Deploy locally for tests
-pip install --upgrade --force-reinstall dist/sonar_migration-*-py3-*.whl
+pip install --upgrade --force-reinstall $ROOTDIR/dist/sonar_migration-*-py3-*.whl
 
 if [ "$build_image" == "1" ]; then
-    docker build -t olivierkorach/sonar-migration:latest -f migration/snapshot.Dockerfile . --load
+    docker build -t olivierkorach/sonar-migration:latest -f migration/snapshot.Dockerfile $ROOTDIR --load
 fi
 
 # Deploy on pypi.org once released
@@ -55,10 +59,10 @@ if [ "$release" = "1" ]; then
     echo "Confirm release [y/n] ?"
     read -r confirm
     if [ "$confirm" = "y" ]; then
-        python3 -m twine upload dist/sonar_migration-*-py3-*.whl
+        python3 -m twine upload $ROOTDIR/dist/sonar_migration-*-py3-*.whl
     fi
 fi
 
 if [ "$release_docker" = "1" ]; then
-    docker buildx build --push --platform linux/amd64,linux/arm64 -t olivierkorach/sonar-migration:0.3  -t olivierkorach/sonar-migration:latest -f migration/release.Dockerfile .
+    docker buildx build --push --platform linux/amd64,linux/arm64 -t olivierkorach/sonar-migration:0.3  -t olivierkorach/sonar-migration:latest -f migration/release.Dockerfile $ROOTDIR
 fi
\ No newline at end of file

From 7866d5e0bd1c31f275526d7f41c29d0a9be316c2 Mon Sep 17 00:00:00 2001
From: Olivier Korach <olivier.korach@gmail.com>
Date: Sun, 6 Oct 2024 11:31:33 +0200
Subject: [PATCH 09/14] Delete only what is needed before rebuilding

---
 conf/deploy.sh      | 2 +-
 migration/deploy.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/deploy.sh b/conf/deploy.sh
index 3d4ea21f8..c298bb01d 100755
--- a/conf/deploy.sh
+++ b/conf/deploy.sh
@@ -48,7 +48,7 @@ while [ $# -ne 0 ]; do
 done
 
 black --line-length=150 .
-rm -rf $ROOTDIR/build $ROOTDIR/dist
+rm -rf $ROOTDIR/build/lib/sonar $ROOTDIR/build/lib/cli $ROOTDIR/build/scripts*/sonar-tools $ROOTDIR/dist/sonar_tools*
 python3 $ROOTDIR/setup.py bdist_wheel
 
 # Deploy locally for tests
diff --git a/migration/deploy.sh b/migration/deploy.sh
index a4a56f77e..5f28c2bf0 100755
--- a/migration/deploy.sh
+++ b/migration/deploy.sh
@@ -44,7 +44,7 @@ while [ $# -ne 0 ]; do
 done
 
 black --line-length=150 .
-rm -rf $ROOTDIR/build $ROOTDIR/dist
+rm -rf $ROOTDIR/build/lib/migration $ROOTDIR/build/lib/cli $ROOTDIR/build/lib/sonar $ROOTDIR/build/scripts*/sonar_migration $ROOTDIR/dist/sonar_migration*
 python3 $ROOTDIR/setup_migration.py bdist_wheel
 
 # Deploy locally for tests

From 7864f76763704ebd6e80656bfceee55e8eccf41a Mon Sep 17 00:00:00 2001
From: Olivier Korach <olivier.korach@gmail.com>
Date: Sun, 6 Oct 2024 11:54:02 +0200
Subject: [PATCH 10/14] Fix problem with tests

---
 sonar/platform.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sonar/platform.py b/sonar/platform.py
index 3afe69399..280a31b38 100644
--- a/sonar/platform.py
+++ b/sonar/platform.py
@@ -222,6 +222,7 @@ def __run_request(
             headers["Authorization"] = f"Bearer {self.__token}"
             if kwargs.get("with_organization", True):
                 params["organization"] = self.organization
+        req_type, url = "", ""
         if log.get_level() >= logging.DEBUG:
             req_type = getattr(request, "__name__", repr(request)).upper()
             url = self.__urlstring(api, params)

From 8c2d9c416d676502749308f16f4213c700669a3f Mon Sep 17 00:00:00 2001
From: Olivier Korach <olivier.korach@gmail.com>
Date: Sun, 6 Oct 2024 11:54:26 +0200
Subject: [PATCH 11/14] Move scanner properties file back in repo root

---
 conf/scan.sh                                              | 5 ++---
 conf/sonar-project.properties => sonar-project.properties | 0
 2 files changed, 2 insertions(+), 3 deletions(-)
 rename conf/sonar-project.properties => sonar-project.properties (100%)

diff --git a/conf/scan.sh b/conf/scan.sh
index b18ed2951..0d8448725 100755
--- a/conf/scan.sh
+++ b/conf/scan.sh
@@ -55,17 +55,16 @@ externalIssuesReport="$buildDir/external-issue-report.json"
 rm -rf -- ${buildDir:?"."}/* .coverage */__pycache__ */*.pyc # mediatools/__pycache__  testpytest/__pycache__ testunittest/__pycache__
 
 if [ "$dotest" == "true" ]; then
-  ./run_tests.sh
+  $CONFDIR/run_tests.sh
 fi
 
 if [ "$dolint" != "false" ]; then
-  ./run_linters.sh
+  $CONFDIR/run_linters.sh
 fi
 
 version=$(grep PACKAGE_VERSION $ROOTDIR/sonar/version.py | cut -d "=" -f 2 | sed -e "s/[\'\" ]//g" -e "s/^ +//" -e "s/ +$//")
 
 cmd="sonar-scanner -Dsonar.projectVersion=$version \
-  -Dproject.settings=$CONFDIR/sonar-project.properties \
   -Dsonar.python.flake8.reportPaths=$flake8Report \
   -Dsonar.python.pylint.reportPaths=$pylintReport \
   -Dsonar.python.bandit.reportPaths=$banditReport \
diff --git a/conf/sonar-project.properties b/sonar-project.properties
similarity index 100%
rename from conf/sonar-project.properties
rename to sonar-project.properties

From a309392d08dfd531f72f83bd02d486b8450b2f5d Mon Sep 17 00:00:00 2001
From: Olivier Korach <olivier.korach@gmail.com>
Date: Sun, 6 Oct 2024 11:55:55 +0200
Subject: [PATCH 12/14] Fix API docs path in exclusions

---
 sonar-project.properties | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sonar-project.properties b/sonar-project.properties
index 94f35155f..b1c9f88b6 100644
--- a/sonar-project.properties
+++ b/sonar-project.properties
@@ -12,7 +12,7 @@ sonar.python.flake8.reportPaths=build/flake8-report.out
 sonar.python.pylint.reportPaths=build/pylint-report.out
 # sonar.python.bandit.reportPaths=build/bandit-report.json
 
-sonar.exclusions=api-doc/**/*, build/**/*, test/**/*
-sonar.coverage.exclusions=setup*.py, migration/migration.py, test/**/*, shellcheck2sonar.py, cli/cust_measures.py, sonar/custom_measures.py, cli/support.py, cli/projects_export.py, , cli/projects_import.py
+sonar.exclusions=doc/api/**/*, build/**/*, test/**/*
+sonar.coverage.exclusions=setup*.py, migration/migration.py, test/**/*, conf/shellcheck2sonar.py, cli/cust_measures.py, sonar/custom_measures.py, cli/support.py, cli/projects_export.py, cli/projects_import.py
 sonar.cpd.exclusions=setup*.py, migration/migration.py
 sonar.tests=test

From 892324079fc79c96327e0ddeb7c7651414e3efad Mon Sep 17 00:00:00 2001
From: Olivier Korach <olivier.korach@gmail.com>
Date: Sun, 6 Oct 2024 11:59:43 +0200
Subject: [PATCH 13/14] Don't install bandit, not used anymore

---
 .github/workflows/build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 8aad1b3e7..dc668cdfb 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -28,7 +28,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install flake8 pylint bandit pytest coverage
+          pip install flake8 pylint pytest coverage
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
       #- name: Lint with flake8
       #  run: |

From 949a0b94cc1fd5027ca48e7b5834dd17f4cb0708 Mon Sep 17 00:00:00 2001
From: Olivier Korach <olivier.korach@gmail.com>
Date: Sun, 6 Oct 2024 12:00:46 +0200
Subject: [PATCH 14/14] Run linters in conf

---
 .github/workflows/build.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index dc668cdfb..d4fd0db35 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -49,8 +49,8 @@ jobs:
       - name: Run linters
         working-directory: .
         run: |
-          chmod +x ./run_linters.sh
-          ./run_linters.sh
+          chmod +x conf/run_linters.sh
+          conf/run_linters.sh
       #- name: Cache SonarQube packages
       #  uses: actions/cache@v4
       #  with: