Replace all instances of mysql clients with mariadb clients, fix build

README.md

@@ -26,11 +26,11 @@ Alternatively, do it manually:
 Run this on the command-line to create a database and import the schema stored in the SQL files:
 
 ```bash
-mysql -e "CREATE DATABASE ispyb"
-mysql ispyb < schemas/ispyb/tables.sql
-mysql ispyb < schemas/ispyb/lookups.sql
-mysql ispyb < schemas/ispyb/data.sql
-mysql ispyb < schemas/ispyb/routines.sql
+mariadb -e "CREATE DATABASE ispyb"
+mariadb ispyb < schemas/ispyb/tables.sql
+mariadb ispyb < schemas/ispyb/lookups.sql
+mariadb ispyb < schemas/ispyb/data.sql
+mariadb ispyb < schemas/ispyb/routines.sql
 ```
 
 Note that the `data.sql` file contains test data, so is only useful in a development environment.
@@ -40,15 +40,15 @@ Note that the `data.sql` file contains test data, so is only useful in a develop
 Then apply the grants:
 
 ```bash
-mysql ispyb < grants/ispyb_acquisition.sql
-mysql ispyb < grants/ispyb_import.sql
-mysql ispyb < grants/ispyb_processing.sql
-mysql ispyb < grants/ispyb_ro_nopii.sql
-mysql ispyb < grants/ispyb_scripts_processing.sql
-mysql ispyb < grants/ispyb_ssx_writer.sql
-mysql ispyb < grants/ispyb_touchscreen.sql
-mysql ispyb < grants/ispyb_web.sql
-mysql ispyb < grants/ispyb_web_verify_tests.sql
+mariadb ispyb < grants/ispyb_acquisition.sql
+mariadb ispyb < grants/ispyb_import.sql
+mariadb ispyb < grants/ispyb_processing.sql
+mariadb ispyb < grants/ispyb_ro_nopii.sql
+mariadb ispyb < grants/ispyb_scripts_processing.sql
+mariadb ispyb < grants/ispyb_ssx_writer.sql
+mariadb ispyb < grants/ispyb_touchscreen.sql
+mariadb ispyb < grants/ispyb_web.sql
+mariadb ispyb < grants/ispyb_web_verify_tests.sql
 ```
 
 Note that the grants files are based on roles, so to actually use these grants, you also need to create database users and grant the roles to them. This is described in the header section of the grant files.
@@ -78,17 +78,17 @@ In order to update a production database, please follow this procedure:
 
 1. For all *.sql files in `schemas/ispyb/updates` that have not already been run, read any comments inside the files to decide if/when you should run them. Run a file e.g. like this:
 ```bash
-mysql ispyb < schemas/ispyb/updates/2019_03_29_BLSession_archived.sql
+mariadb ispyb < schemas/ispyb/updates/2019_03_29_BLSession_archived.sql
 ```
 2. If `schemas/ispyb/routines.sql` has been updated since you installed it, you can simply re-run it. E.g.:
 ```bash
-mysql ispyb < schemas/ispyb/routines.sql
+mariadb ispyb < schemas/ispyb/routines.sql
 ```
 3. If you ran the `routines.sql`, then re-apply the grants for the routines. E.g.:
 ```bash
-mysql ispyb < grants/ispyb_acquisition.sql
-mysql ispyb < grants/ispyb_processing.sql
-mysql ispyb < grants/ispyb_web.sql
+mariadb ispyb < grants/ispyb_acquisition.sql
+mariadb ispyb < grants/ispyb_processing.sql
+mariadb ispyb < grants/ispyb_web.sql
 ```
 
 ## Useful scripts

bin/backup.sh

@@ -13,7 +13,7 @@ then
 fi
 
 # Note: --defaults-file must be given as first option
-DUMP_W_OPTS="mysqldump --defaults-file=../.my.cnf --add-drop-table --create-options --disable-keys --extended-insert --skip-add-locks --quick --set-charset --single-transaction --max_allowed_packet=1G --default-character-set=utf8 --skip-comments --skip-dump-date"
+DUMP_W_OPTS="mariadb-dump --defaults-file=../.my.cnf --add-drop-table --create-options --disable-keys --extended-insert --skip-add-locks --quick --set-charset --single-transaction --max_allowed_packet=1G --default-character-set=utf8 --skip-comments --skip-dump-date"
 
 ${DUMP_W_OPTS} --skip-triggers --no-data "${DB}" | sed -e 's/DEFINER=[^*]*\*/SQL SECURITY INVOKER \*/' | sed 's/ AUTO_INCREMENT=[0-9]*\b//g' > ${OUT_DIR}/tables.sql
 

bin/db_procs_to_rst.sh

@@ -5,7 +5,7 @@ db=$1
 file=$(mktemp /tmp/tsv.XXXXXX)
 
 # Execute the sql to generate the csv outfile
-mysql --defaults-file=../.my.cnf --skip-column-names --batch --raw -D $db < sql/db_procs_to_tsv.sql  > ${file}
+mariadb --defaults-file=../.my.cnf --skip-column-names --batch --raw -D $db < sql/db_procs_to_tsv.sql  > ${file}
 
 # Construct rst file with csv table
 echo ".. csv-table:: Procedure signatures with comments"

bin/db_tables_to_rst.sh

@@ -4,7 +4,7 @@ db=$1
 
 file=$(mktemp /tmp/tsv.XXXXXX)
 
-mysql --defaults-file=../.my.cnf -D $db --skip-column-names --batch --raw < sql/db_tables_to_tsv.sql > ${file}
+mariadb --defaults-file=../.my.cnf -D $db --skip-column-names --batch --raw < sql/db_tables_to_tsv.sql > ${file}
 sed -i 's/\t/,/g' ${file}
 
 echo ".. csv-table:: Tables, columns and comments"

bin/forget_all_labs.sh

@@ -18,12 +18,12 @@ DB=$2
 PROPOSAL=$3
 SESSNUM=$4
 
-PID=`mysql --defaults-file=${MYCNF} -s -D ${DB} -e "SELECT proposalId FROM Proposal WHERE concat(proposalCode, proposalNumber)='${PROPOSAL}';"`
-SID=`mysql --defaults-file=${MYCNF} -s -D ${DB} -e "SELECT sessionId FROM BLSession WHERE proposalId='${PID}' AND visit_number=${SESSNUM};"`
-PERSID=`mysql --defaults-file=${MYCNF} -s -D ${DB} -e "SELECT personId FROM Proposal WHERE proposalId=${PID};"`
-LABID=`mysql --defaults-extra-file=${MYCNF} -s -D ${DB} -e "SELECT laboratoryId FROM Person WHERE personId=${PERSID};"`
+PID=`mariadb --defaults-file=${MYCNF} -s -D ${DB} -e "SELECT proposalId FROM Proposal WHERE concat(proposalCode, proposalNumber)='${PROPOSAL}';"`
+SID=`mariadb --defaults-file=${MYCNF} -s -D ${DB} -e "SELECT sessionId FROM BLSession WHERE proposalId='${PID}' AND visit_number=${SESSNUM};"`
+PERSID=`mariadb --defaults-file=${MYCNF} -s -D ${DB} -e "SELECT personId FROM Proposal WHERE proposalId=${PID};"`
+LABID=`mariadb --defaults-extra-file=${MYCNF} -s -D ${DB} -e "SELECT laboratoryId FROM Person WHERE personId=${PERSID};"`
 
-LABIDS=`mysql --defaults-file=${MYCNF} -D ${DB} --skip-column-names --silent --raw -e "SELECT laboratoryId FROM Laboratory WHERE laboratoryId=${LABID}   OR   laboratoryId IN (SELECT p.laboratoryId FROM Person p INNER JOIN LabContact lc USING(personId) WHERE lc.proposalId=${PID})   OR   laboratoryId IN (SELECT laboratoryId FROM Person p INNER JOIN Session_has_Person shp USING(personId) WHERE shp.sessionId=${SID})   OR   laboratoryId IN (SELECT laboratoryId FROM Person p INNER JOIN ProposalHasPerson php USING(personId) WHERE php.proposalId=${PID})   OR   laboratoryId IN (SELECT p.laboratoryId FROM Person p INNER JOIN Container c ON c.ownerId=p.personId WHERE c.sessionId=${SID})   OR   laboratoryId IN (SELECT p.laboratoryId FROM Person p INNER JOIN Container c ON c.ownerId=p.personId INNER JOIN Dewar d USING(dewarId) INNER JOIN Shipping s USING(shippingId) WHERE s.proposalId=${PID})   OR   laboratoryId IN (SELECT pe.laboratoryId FROM Person pe INNER JOIN Container c ON c.ownerId=pe.personId INNER JOIN BLSample bls USING(containerId) INNER JOIN Crystal USING(crystalId) INNER JOIN Protein p USING(proteinId) WHERE p.proposalId=${PID})   OR  laboratoryId IN (SELECT pe.laboratoryId FROM Person pe INNER JOIN Shipping s ON pe.personId=s.deliveryAgent_flightCodePersonId WHERE s.proposalId=${PID})"`
+LABIDS=`mariadb --defaults-file=${MYCNF} -D ${DB} --skip-column-names --silent --raw -e "SELECT laboratoryId FROM Laboratory WHERE laboratoryId=${LABID}   OR   laboratoryId IN (SELECT p.laboratoryId FROM Person p INNER JOIN LabContact lc USING(personId) WHERE lc.proposalId=${PID})   OR   laboratoryId IN (SELECT laboratoryId FROM Person p INNER JOIN Session_has_Person shp USING(personId) WHERE shp.sessionId=${SID})   OR   laboratoryId IN (SELECT laboratoryId FROM Person p INNER JOIN ProposalHasPerson php USING(personId) WHERE php.proposalId=${PID})   OR   laboratoryId IN (SELECT p.laboratoryId FROM Person p INNER JOIN Container c ON c.ownerId=p.personId WHERE c.sessionId=${SID})   OR   laboratoryId IN (SELECT p.laboratoryId FROM Person p INNER JOIN Container c ON c.ownerId=p.personId INNER JOIN Dewar d USING(dewarId) INNER JOIN Shipping s USING(shippingId) WHERE s.proposalId=${PID})   OR   laboratoryId IN (SELECT pe.laboratoryId FROM Person pe INNER JOIN Container c ON c.ownerId=pe.personId INNER JOIN BLSample bls USING(containerId) INNER JOIN Crystal USING(crystalId) INNER JOIN Protein p USING(proteinId) WHERE p.proposalId=${PID})   OR  laboratoryId IN (SELECT pe.laboratoryId FROM Person pe INNER JOIN Shipping s ON pe.personId=s.deliveryAgent_flightCodePersonId WHERE s.proposalId=${PID})"`
 
 while read -r LABID; do
   `./forget_lab.sh ${MYCNF} ${DB} ${LABID}`

bin/forget_all_persons.sh

@@ -21,11 +21,11 @@ SESSNUM=$4
 
 # Get the proposal PID and the session SID:
 
-PID=`mysql --defaults-file=${MYCNF} -s -D ${DB} -e "SELECT proposalId FROM Proposal WHERE concat(proposalCode, proposalNumber)='${PROPOSAL}';"`
-SID=`mysql --defaults-file=${MYCNF} -s -D ${DB} -e "SELECT sessionId FROM BLSession WHERE proposalId='${PID}' AND visit_number=${SESSNUM};"`
+PID=`mariadb --defaults-file=${MYCNF} -s -D ${DB} -e "SELECT proposalId FROM Proposal WHERE concat(proposalCode, proposalNumber)='${PROPOSAL}';"`
+SID=`mariadb --defaults-file=${MYCNF} -s -D ${DB} -e "SELECT sessionId FROM BLSession WHERE proposalId='${PID}' AND visit_number=${SESSNUM};"`
 
 # Get all personIds related to the PID and SID
-PERSIDS=`mysql --defaults-file=${MYCNF} -D ${DB} --skip-column-names --silent --raw -e "SELECT personId FROM Proposal WHERE proposalId=${PID} UNION SELECT personId FROM Person WHERE personId IN (SELECT personId FROM LabContact WHERE proposalId=${PID})   OR   personId IN (SELECT personId FROM Session_has_Person WHERE sessionId=${SID})   OR   personId IN (SELECT personId FROM ProposalHasPerson WHERE proposalId=${PID})   OR   personId IN (SELECT ownerId FROM Container WHERE sessionId=${SID})   OR   personId IN (SELECT c.ownerId FROM Container c INNER JOIN Dewar d USING(dewarId) INNER JOIN Shipping s USING(shippingId) WHERE s.proposalId=${PID})   OR   personId IN (SELECT c.ownerId FROM Container c INNER JOIN BLSample bls USING(containerId) INNER JOIN Crystal USING(crystalId) INNER JOIN Protein p USING(proteinId) WHERE p.proposalId=${PID})   OR   personId IN (SELECT s.deliveryAgent_flightCodePersonId FROM Shipping s WHERE s.proposalId=${PID});"`
+PERSIDS=`mariadb --defaults-file=${MYCNF} -D ${DB} --skip-column-names --silent --raw -e "SELECT personId FROM Proposal WHERE proposalId=${PID} UNION SELECT personId FROM Person WHERE personId IN (SELECT personId FROM LabContact WHERE proposalId=${PID})   OR   personId IN (SELECT personId FROM Session_has_Person WHERE sessionId=${SID})   OR   personId IN (SELECT personId FROM ProposalHasPerson WHERE proposalId=${PID})   OR   personId IN (SELECT ownerId FROM Container WHERE sessionId=${SID})   OR   personId IN (SELECT c.ownerId FROM Container c INNER JOIN Dewar d USING(dewarId) INNER JOIN Shipping s USING(shippingId) WHERE s.proposalId=${PID})   OR   personId IN (SELECT c.ownerId FROM Container c INNER JOIN BLSample bls USING(containerId) INNER JOIN Crystal USING(crystalId) INNER JOIN Protein p USING(proteinId) WHERE p.proposalId=${PID})   OR   personId IN (SELECT s.deliveryAgent_flightCodePersonId FROM Shipping s WHERE s.proposalId=${PID});"`
 
 # iterate over and forget:
 

bin/forget_lab.sh

@@ -16,4 +16,4 @@ MYCNF=$1
 DB=$2
 LABID=$3
 
-mysql --defaults-file=${MYCNF} -s -D ${DB} -e "UPDATE Laboratory SET name='lab-${LABID}', laboratoryUUID=NULL, city=NULL, address=NULL, country=NULL, url=NULL, organization=NULL, laboratoryPk=NULL, postcode=NULL WHERE laboratoryId=${LABID};"
+mariadb --defaults-file=${MYCNF} -s -D ${DB} -e "UPDATE Laboratory SET name='lab-${LABID}', laboratoryUUID=NULL, city=NULL, address=NULL, country=NULL, url=NULL, organization=NULL, laboratoryPk=NULL, postcode=NULL WHERE laboratoryId=${LABID};"

bin/forget_pdb.sh

@@ -16,4 +16,4 @@ MYCNF=$1
 DB=$2
 PDBID=$3
 
-mysql --defaults-file=${MYCNF} -s -D ${DB} -e "UPDATE PDB SET name=pdbId, contents=NULL, code=NULL WHERE pdbId=${PDBID};"
+mariadb --defaults-file=${MYCNF} -s -D ${DB} -e "UPDATE PDB SET name=pdbId, contents=NULL, code=NULL WHERE pdbId=${PDBID};"

bin/forget_person.sh

@@ -16,5 +16,5 @@ MYCNF=$1
 DB=$2
 PERSONID=$3
 
-mysql --defaults-file=${MYCNF} -s -D ${DB} -e "UPDATE Person SET familyName='Doe', givenName='John', title=NULL, emailAddress='hello@example.com', phoneNumber=NULL, login='john-${PERSONID}', faxNumber=NULL, cache=NULL, externalId=NULL WHERE personId='${PERSONID}';"
-mysql --defaults-file=${MYCNF} -s -D ${DB} -e "UPDATE LabContact SET cardName=concat('Doe', labContactId), defaultCourrierCompany='Doe', courierAccount='12345', billingReference=NULL, dewarAvgCustomsValue=0, dewarAvgTransportValue=0 WHERE personId='${PERSONID}';"
+mariadb --defaults-file=${MYCNF} -s -D ${DB} -e "UPDATE Person SET familyName='Doe', givenName='John', title=NULL, emailAddress='hello@example.com', phoneNumber=NULL, login='john-${PERSONID}', faxNumber=NULL, cache=NULL, externalId=NULL WHERE personId='${PERSONID}';"
+mariadb --defaults-file=${MYCNF} -s -D ${DB} -e "UPDATE LabContact SET cardName=concat('Doe', labContactId), defaultCourrierCompany='Doe', courierAccount='12345', billingReference=NULL, dewarAvgCustomsValue=0, dewarAvgTransportValue=0 WHERE personId='${PERSONID}';"

bin/forget_protein.sh

@@ -16,4 +16,4 @@ MYCNF=$1
 DB=$2
 PROTEINID=$3
 
-mysql --defaults-file=${MYCNF} -s -D ${DB} -e "UPDATE Protein SET name='prot-${PROTEINID}', acronym='prot-${PROTEINID}', safetyLevel='GREEN', molecularMass=NULL, proteinType=NULL, sequence=NULL, componentTypeId=NULL, concentrationTypeId=NULL, externalId=NULL, density=NULL, abundance=NULL WHERE proteinId=${PROTEINID};"
+mariadb --defaults-file=${MYCNF} -s -D ${DB} -e "UPDATE Protein SET name='prot-${PROTEINID}', acronym='prot-${PROTEINID}', safetyLevel='GREEN', molecularMass=NULL, proteinType=NULL, sequence=NULL, componentTypeId=NULL, concentrationTypeId=NULL, externalId=NULL, density=NULL, abundance=NULL WHERE proteinId=${PROTEINID};"

bin/forget_sample.sh

@@ -16,4 +16,4 @@ MYCNF=$1
 DB=$2
 BLSAMPLEID=$3
 
-mysql --defaults-file=${MYCNF} -s -D ${DB} -e "UPDATE BLSample SET name='s-${BLSAMPLEID}', code='c-${BLSAMPLEID}', comments=NULL WHERE blSampleId='${BLSAMPLEID}';"
+mariadb --defaults-file=${MYCNF} -s -D ${DB} -e "UPDATE BLSample SET name='s-${BLSAMPLEID}', code='c-${BLSAMPLEID}', comments=NULL WHERE blSampleId='${BLSAMPLEID}';"

bin/forget_shipping.sh

@@ -16,4 +16,4 @@ MYCNF=$1
 DB=$2
 SHIPPINGID=$3
 
-mysql --defaults-file=${MYCNF} -s -D ${DB} -e "UPDATE Shipping SET shippingName='s-${SHIPPINGID}', comments=NULL, SAFETYLEVEL=NULL, deliveryAgent_agentCode=NULL, deliveryAgent_flightCode=NULL, deliveryAgent_label=NULL, deliveryAgent_productcode=NULL WHERE shippingId='${SHIPPINGID}';"
+mariadb --defaults-file=${MYCNF} -s -D ${DB} -e "UPDATE Shipping SET shippingName='s-${SHIPPINGID}', comments=NULL, SAFETYLEVEL=NULL, deliveryAgent_agentCode=NULL, deliveryAgent_flightCode=NULL, deliveryAgent_label=NULL, deliveryAgent_productcode=NULL WHERE shippingId='${SHIPPINGID}';"

bin/forget_subsample.sh

@@ -16,4 +16,4 @@ MYCNF=$1
 DB=$2
 BLSUBSAMPLEID=$3
 
-mysql --defaults-file=${MYCNF} -s -D ${DB} -e "UPDATE BLSubSample SET comments=NULL WHERE blSubSampleId='${BLSUBSAMPLEID}';"
+mariadb --defaults-file=${MYCNF} -s -D ${DB} -e "UPDATE BLSubSample SET comments=NULL WHERE blSubSampleId='${BLSUBSAMPLEID}';"

bin/forget_unused_shipments.sh

@@ -22,9 +22,9 @@ SESSNUM=$4
 
 # Get the proposal PID:
 
-PID=`mysql --defaults-file=${MYCNF} -s -D ${DB} -e "SELECT proposalId FROM Proposal WHERE concat(proposalCode, proposalNumber)='${PROPOSAL}';"`
+PID=`mariadb --defaults-file=${MYCNF} -s -D ${DB} -e "SELECT proposalId FROM Proposal WHERE concat(proposalCode, proposalNumber)='${PROPOSAL}';"`
 
-SID=`mysql --defaults-extra-file=${MYCNF} -s -D ${DB} -e "SELECT sessionId FROM BLSession WHERE proposalId='${PID}' AND visit_number=${SESSNUM};"`
+SID=`mariadb --defaults-extra-file=${MYCNF} -s -D ${DB} -e "SELECT sessionId FROM BLSession WHERE proposalId='${PID}' AND visit_number=${SESSNUM};"`
 
 # Query to find all shippingIds of all used samples and sub-samples
 # on the session. Beware of NULLs!
@@ -69,7 +69,7 @@ WHERE s.proposalId=${PID}
     ${SHIPPINGID_USED_SELECT}
   )"
 
-SHIPPINGIDS=`mysql --defaults-file=${MYCNF} -D ${DB} --skip-column-names --silent --raw -e "${SHIPPINGID_UNUSED_SELECT};"`
+SHIPPINGIDS=`mariadb --defaults-file=${MYCNF} -D ${DB} --skip-column-names --silent --raw -e "${SHIPPINGID_UNUSED_SELECT};"`
 
 # Iterate over shippings and forget:
 
@@ -92,7 +92,7 @@ FROM (
   GROUP BY bls.blSampleId) q1
 WHERE q1.cnt1=0 AND q1.cnt2=0 AND q1.cnt3=0"
 
-BLSAMPLEIDS=`mysql --defaults-file=${MYCNF} -D ${DB} --skip-column-names --silent --raw -e "${BLSAMPLE_UNUSED_SELECT};"`
+BLSAMPLEIDS=`mariadb --defaults-file=${MYCNF} -D ${DB} --skip-column-names --silent --raw -e "${BLSAMPLE_UNUSED_SELECT};"`
 
 # Iterate over samples and forget:
 
@@ -117,7 +117,7 @@ FROM (
   GROUP BY blss.blSubSampleId) q2
 WHERE q2.cnt1=0 AND q2.cnt2=0 AND q2.cnt3=0"
 
-BLSUBSAMPLEIDS=`mysql --defaults-file=${MYCNF} -D ${DB} --skip-column-names --silent --raw -e "${BLSUBSAMPLE_UNUSED_SELECT};"`
+BLSUBSAMPLEIDS=`mariadb --defaults-file=${MYCNF} -D ${DB} --skip-column-names --silent --raw -e "${BLSUBSAMPLE_UNUSED_SELECT};"`
 
 # Iterate over sub-samples and forget:
 
@@ -127,7 +127,7 @@ done <<< "${BLSUBSAMPLEIDS}"
 
 # Query to find all unused proteins on the proposal
 
-PROTEINIDS=`mysql --defaults-file=${MYCNF} -D ${DB} --skip-column-names --silent --raw -e "SELECT p.proteinId
+PROTEINIDS=`mariadb --defaults-file=${MYCNF} -D ${DB} --skip-column-names --silent --raw -e "SELECT p.proteinId
 FROM Protein p
   LEFT JOIN Crystal c USING(proteinId)
   LEFT JOIN BLSample bls USING(crystalId)
@@ -147,7 +147,7 @@ done <<< "${PROTEINIDS}"
 
 # Query to find all unused PDBs on the proposal
 
-PDBIDS=`mysql --defaults-file=${MYCNF} -D ${DB} --skip-column-names --silent --raw -e "SELECT phpdb.pdbId
+PDBIDS=`mariadb --defaults-file=${MYCNF} -D ${DB} --skip-column-names --silent --raw -e "SELECT phpdb.pdbId
 FROM Protein_has_PDB phpdb
   JOIN Protein p USING(proteinId)
   WHERE p.proposalId=${PID}

bin/missed_updates.sh

@@ -19,7 +19,7 @@ source ${project_root}/bin/functions.sh
 all_sql_files=`cd ${project_root}/schemas/ispyb/updates && ls *.sql && cd ../..`
 
 # Get a list of all update files recorded in the SchemaStatus table
-done_sql_files=`mysql --defaults-file=${project_root}/.my.cnf -D $DB --skip-column-names --silent --raw -e "SELECT scriptName FROM SchemaStatus WHERE schemaStatus = 'DONE' ORDER BY recordTimeStamp;"`
+done_sql_files=`mariadb --defaults-file=${project_root}/.my.cnf -D $DB --skip-column-names --silent --raw -e "SELECT scriptName FROM SchemaStatus WHERE schemaStatus = 'DONE' ORDER BY recordTimeStamp;"`
 
 # Make a list of all update files not recorded in the SchemaStatus table
 arr=()