diff --git a/Dockerfile b/Dockerfile index 121539001..54c2f28b3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -10,7 +10,7 @@ RUN apt-get update && apt-get upgrade -y RUN apt-get install -y \ git wget lsb-core lsb-release -RUN git clone https://github.com/BU-ISCIII/iskylims.git /srv/iskylims +RUN git clone https://github.com/saramonzon/iskylims.git /srv/iskylims WORKDIR /srv/iskylims RUN git checkout develop @@ -23,4 +23,4 @@ ENV PYTHONPATH="/opt/iskylims/virtualenv/lib/python3.10/site-packages:${PYTHONPA # Expose EXPOSE 8001 # Start the application -CMD ["python3", "/opt/iskylims/manage.py", "runserver", "0:8001"] +CMD ["python3", "/opt/iskylims/manage.py", "runserver", "0:8001"] \ No newline at end of file diff --git a/conf/first_install_tables.json b/conf/first_install_tables.json index 00d55deb9..6e8319d60 100644 --- a/conf/first_install_tables.json +++ b/conf/first_install_tables.json @@ -1333,48 +1333,6 @@ "generated_at": "2023-01-23T17:15:24.556" } }, -{ - "model": "drylab.resolutionstates", - "pk": 1, - "fields": { - "state_value": "Recorded" - } -}, -{ - "model": "drylab.resolutionstates", - "pk": 2, - "fields": { - "state_value": "In Progress" - } -}, -{ - "model": "drylab.resolutionstates", - "pk": 3, - "fields": { - "state_value": "Delivery" - } -}, -{ - "model": "drylab.resolutionstates", - "pk": 4, - "fields": { - "state_value": "Cancelled" - } -}, -{ - "model": "drylab.resolutionstates", - "pk": 5, - "fields": { - "state_value": "Rejected" - } -}, -{ - "model": "drylab.resolutionstates", - "pk": 6, - "fields": { - "state_value": "Queued" - } -}, { "model": "wetlab.poolstates", "pk": 1, @@ -1803,12 +1761,20 @@ }, { "model": "wetlab.runconfigurationtest", - "pk": 4, + "pk": 2, "fields": { - "run_test_name": "NextSeq_Test", + "run_test_name": "NextSeq_Test_001", "run_test_folder": "NextSeq_Test" } }, +{ + "model": "wetlab.runconfigurationtest", + "pk": 3, + "fields": { + "run_test_name": "NovaSeq_Test_001", + "run_test_folder": "NovaSeq_Test" + } +}, { "model": "wetlab.configsetting", "pk": 1, @@ -20050,10 +20016,82 @@ "model": "drylab.servicestate", "pk": 8, "fields": { - "state_value": "waiting_information", - "state_display": "Waiting Information", + "state_value": "on_hold", + "state_display": "On hold", "description": "Service is on hold, waiting for user provides more information", "show_in_stats": true } +}, +{ + "model": "drylab.resolutionstates", + "pk": 1, + "fields": { + "state_value": "recorded", + "state_display": "Recorded", + "description": "Resolution has been successful recorded in iSkyLIMS" + } +}, +{ + "model": "drylab.resolutionstates", + "pk": 2, + "fields": { + "state_value": "approved", + "state_display": "Approved", + "description": "Resolution request has been accepted" + } +}, +{ + "model": "drylab.resolutionstates", + "pk": 3, + "fields": { + "state_value": "rejected", + "state_display": "Rejected", + "description": "Resolution can not be handle because is not in porfoloio or for any other reason" + } +}, +{ + "model": "drylab.resolutionstates", + "pk": 4, + "fields": { + "state_value": "queued", + "state_display": "Queued", + "description": "Resolution is the the list, waiting for a bioinformatic to be handled" + } +}, +{ + "model": "drylab.resolutionstates", + "pk": 5, + "fields": { + "state_value": "in_progress", + "state_display": "In Progress", + "description": "Bioinformatic is working on the Resolution" + } +}, +{ + "model": "drylab.resolutionstates", + "pk": 6, + "fields": { + "state_value": "delivered", + "state_display": "Delivered", + "description": "Resolution wascompleted and results were sent to the user" + } +}, +{ + "model": "drylab.resolutionstates", + "pk": 7, + "fields": { + "state_value": "archived", + "state_display": "Archived", + "description": null + } +}, +{ + "model": "drylab.resolutionstates", + "pk": 8, + "fields": { + "state_value": "on_hold", + "state_display": "On hold", + "description": "Resolution is on hold, waiting for user provides more information" + } } ] diff --git a/conf/logging_test_config.ini b/conf/logging_test_config.ini deleted file mode 100644 index dd73e3038..000000000 --- a/conf/logging_test_config.ini +++ /dev/null @@ -1,20 +0,0 @@ -[loggers] -keys=root - -[handlers] -keys=logfile - -[formatters] -keys=logfileformatter - -[logger_root] -level=DEBUG -handlers=logfile - -[formatter_logfileformatter] -format=%(asctime)s %(funcName)-12s %(levelname)-8s %(lineno)s %(message)s - -[handler_logfile] -class=handlers.RotatingFileHandler -args=('/srv/iSkyLIMS/logs/test_wetlab.log','a',500000,5) -formatter=logfileformatter diff --git a/docker-compose.yml b/docker-compose.yml index a623293e3..293fa54f3 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -35,7 +35,7 @@ services: - /etc/localtime:/etc/localtime:ro - /usr/share/zoneinfo:/usr/share/zoneinfo - ngs_data_vol:/mnt - command: '-S -s "ngs_data;/mnt;yes;yes;no;samba_user;none;none;ngs data samba share" -u "samba_user;sambapasswd" -p' + command: '-S -s "ngs_data;/mnt/test_ngs_data;yes;yes;no;samba_user;none;none;ngs data samba share" -u "samba_user;sambapasswd" -p' app: build: . diff --git a/docker_install.sh b/docker_install.sh index 60f308a4c..c0b1eb5ee 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -1,5 +1,81 @@ #!/usr/bin/bash +ISKYLIMS_VERSION="3.0.0" + +usage() { +cat << EOF +This script install and upgrade the iskylims app. + +usage : $0 --demo_data + Optional input data: + --demo_data | provide already dowloaded demo data from zenodo + + +Examples: + Install demo docker system + bash $0 + + Provide already downloaded data from zenodo (compressed) + bash $0 --demo_data /path/to/iskylims_demo_data.tar.gz +EOF +} + +# translate long options to short +reset=true + +for arg in "$@" +do + if [ -n "$reset" ]; then + unset reset + set -- # this resets the "$@" array so we can rebuild it + fi + case "$arg" in + # OPTIONAL + --demo_data) set -- "$@" -d ;; + + # ADITIONAL + --help) set -- "$@" -h ;; + --version) set -- "$@" -v ;; + # PASSING VALUE IN PARAMETER + *) set -- "$@" "$arg" ;; + esac +done + +# SETTING DEFAULT VALUES +demo_data=false + +# PARSE VARIABLE ARGUMENTS WITH getops +options=":d:vh" +while getopts $options opt; do + case $opt in + d) + demo_data=$OPTARG + ;; + h ) + usage + exit 1 + ;; + v ) + echo $ISKYLIMS_VERSION + exit 1 + ;; + \?) + echo "Invalid Option: -$OPTARG" 1>&2 + usage + exit 1 + ;; + : ) + echo "Option -$OPTARG requires an argument." >&2 + exit 1 + ;; + * ) + echo "Unimplemented option: -$OPTARG" >&2; + exit 1 + ;; + esac +done +shift $((OPTIND-1)) + echo "Deploying test containers..." docker compose build --no-cache docker compose up -d @@ -12,22 +88,30 @@ docker exec -it iskylims_app python3 manage.py migrate docker exec -it iskylims_app python3 manage.py makemigrations django_utils core wetlab drylab docker exec -it iskylims_app python3 manage.py migrate -echo "Loading in database initial data" -docker exec -it iskylims_app python3 manage.py loaddata conf/first_install_tables.json - echo "Creating super user " docker exec -it iskylims_app python3 manage.py createsuperuser +echo "Loading in database initial data" +docker exec -it iskylims_app python3 manage.py loaddata conf/first_install_tables.json +docker exec -it iskylims_app python3 manage.py loaddata test/test_data.json + echo "Download testing files and copy it to samba container" -wget https://zenodo.org/record/8091169/files/iskylims_demo_data.tar.gz -docker cp iskylims_demo_data.tar.gz samba:/mnt +if [ "$demo_data" == "false" ];then + wget https://zenodo.org/record/8091169/files/iskylims_demo_data.tar.gz + demo_data="./iskylims_demo_data.tar.gz" +fi +docker cp $demo_data samba:/mnt docker exec -it samba tar -xf /mnt/iskylims_demo_data.tar.gz -C /mnt echo "deleting compress testing file" docker exec -it samba rm /mnt/iskylims_demo_data.tar.gz -rm iskylims_demo_data.tar.gz +if [ "$demo_data" == "false" ];then + rm -f $demo_data +fi echo "Running crontab" docker exec -it iskylims_app python3 manage.py crontab add +docker exec -it iskylims_app cron + echo "You can now access iskylims via: http://localhost:8001" \ No newline at end of file diff --git a/drylab/api/serializers.py b/drylab/api/serializers.py index 1b868a60f..5ff930337 100644 --- a/drylab/api/serializers.py +++ b/drylab/api/serializers.py @@ -65,7 +65,10 @@ class ProfileUserSerializer(serializers.ModelSerializer): profile_center = serializers.StringRelatedField() def to_representation(self, instance): - output_label = self.context["output_label"] + try: + output_label = self.context["output_label"] + except KeyError: + output_label = False data = super(ProfileUserSerializer, self).to_representation(instance) data_update = OrderedDict() for key in self.fields: @@ -89,7 +92,10 @@ class UserIDSerializer(serializers.ModelSerializer): profile = ProfileUserSerializer(many=False) def to_representation(self, instance): - output_label = self.context["output_label"] + try: + output_label = self.context["output_label"] + except KeyError: + output_label = False data = super(UserIDSerializer, self).to_representation(instance) data_update = OrderedDict() for key in self.fields: @@ -121,7 +127,10 @@ def to_representation(self, service): class PipelinesSerializer(serializers.ModelSerializer): def to_representation(self, instance): - output_label = self.context["output_label"] + try: + output_label = self.context["output_label"] + except KeyError: + output_label = False data = super(PipelinesSerializer, self).to_representation(instance) data_update = OrderedDict() for key in self.fields: @@ -146,7 +155,10 @@ class DeliverySerializer(serializers.ModelSerializer): pipelines_in_delivery = PipelinesSerializer(many=True) def to_representation(self, instance): - output_label = self.context["output_label"] + try: + output_label = self.context["output_label"] + except KeyError: + output_label = False data = super(DeliverySerializer, self).to_representation(instance) data_update = OrderedDict() for key in self.fields: @@ -183,7 +195,10 @@ class ResolutionSerializer(serializers.ModelSerializer): resolution_assigned_user = serializers.StringRelatedField(many=False) def to_representation(self, instance): - output_label = self.context["output_label"] + try: + output_label = self.context["output_label"] + except KeyError: + output_label = False data = super(ResolutionSerializer, self).to_representation(instance) data_update = OrderedDict() for key in self.fields: @@ -220,7 +235,10 @@ class Meta: class RequestedSamplesInServicesSerializer(serializers.ModelSerializer): def to_representation(self, instance): - output_label = self.context["output_label"] + try: + output_label = self.context["output_label"] + except KeyError: + output_label = False data = super(RequestedSamplesInServicesSerializer, self).to_representation( instance ) @@ -268,7 +286,10 @@ class ServiceSerializer(serializers.ModelSerializer): samples = RequestedSamplesInServicesSerializer(many=True) def to_representation(self, instance): - output_label = self.context["output_label"] + try: + output_label = self.context["output_label"] + except KeyError: + output_label = False data = super(ServiceSerializer, self).to_representation(instance) data_update = OrderedDict() for key in self.fields: diff --git a/drylab/config.py b/drylab/config.py index c1ab8aa37..3050784f9 100644 --- a/drylab/config.py +++ b/drylab/config.py @@ -7,7 +7,7 @@ INTERNAL_SEQUENCING_UNIT = "UCCT" # DIRECTORIES # -USER_REQUESTED_SERVICE_FILE_DIRECTORY = "drylab/servicesRequestFiles" +USER_REQUESTED_SERVICE_FILE_DIRECTORY = "drylab/service_files" PIPELINE_FILE_DIRECTORY = "drylab/pipelinesFiles" # CSS file to be used for creating the PDF files diff --git a/install.sh b/install.sh index 52bec505d..bc84e90d1 100644 --- a/install.sh +++ b/install.sh @@ -1,6 +1,6 @@ #!/bin/bash -ISKYLIMS_VERSION="2.x.x" +ISKYLIMS_VERSION="3.x.x" usage() { cat << EOF @@ -417,7 +417,7 @@ if [ $upgrade == true ]; then rsync -rlv conf/ $INSTALL_PATH/conf/ rsync -rlv --fuzzy --delay-updates --delete-delay \ --exclude "logs" --exclude "documents" --exclude "migrations" --exclude "__pycache__" \ - README.md LICENSE conf core drylab clinic wetlab django_utils $INSTALL_PATH + README.md LICENSE test conf core drylab clinic wetlab django_utils $INSTALL_PATH # update the settings.py and the main urls echo "Update settings and url file." @@ -531,10 +531,6 @@ if [ $upgrade == true ]; then echo "Running collect statics..." python manage.py collectstatic echo "Done collect statics" - - echo "Running crontab add..." - python manage.py crontab add - echo "Done crontab add" if [ $tables == true ] ; then echo "Loading pre-filled tables..." @@ -556,16 +552,16 @@ if [ $upgrade == true ]; then echo "" echo "Restart apache server to update changes" if [[ $linux_distribution == "Ubuntu" ]]; then - apache_user="apache2" + apache_daemon="apache2" else - apache_user="httpd" + apache_daemon="httpd" fi # systemctl restart $apache_user if ! [ $? -eq 0 ]; then echo -e "${ORANGE}Apache server restart failed. trying with sudo{NC}" - sudo systemctl restart $apache_user + sudo systemctl restart $apache_daemon fi fi printf "\n\n%s" @@ -599,10 +595,16 @@ if [ $install == true ]; then user=$SUDO_USER group=$(groups | cut -d" " -f1) - + # Find out server Linux distribution linux_distribution=$(lsb_release -i | cut -f 2-) + if [[ $linux_distribution == "Ubuntu" ]]; then + apache_group="www-data" + else + apache_group="apache" + fi + echo "Starting iSkyLIMS installation" if [ -d $INSTALL_PATH ]; then echo "There already is an installation of iskylims in $INSTALL_PATH." @@ -655,6 +657,8 @@ if [ $install == true ]; then ## Create the installation folder mkdir -p $INSTALL_PATH/conf + chown -R $user:$apache_group $INSTALL_PATH + chmod 775 $INSTALL_PATH # Copy requirements before moving to install path rsync -rlv conf/requirements.txt $INSTALL_PATH/conf/requirements.txt @@ -684,12 +688,6 @@ if [ $install == true ]; then python -m pip install wheel python -m pip install -r conf/requirements.txt - ## Create apache group if it does not exist. - if ! grep -q apache /etc/group - then - groupadd apache - fi - cd - if [ "$install_type" == "full" ] || [ "$install_type" == "app" ]; then @@ -732,41 +730,35 @@ if [ $install == true ]; then fi else mkdir -p $INSTALL_PATH/logs - chown $user:apache $INSTALL_PATH/logs + chown $user:$apache_group $INSTALL_PATH/logs chmod 775 $INSTALL_PATH/logs fi - rsync -rlv README.md LICENSE conf core drylab \ + rsync -rlv README.md LICENSE test conf core drylab \ wetlab clinic django_utils $INSTALL_PATH cd $INSTALL_PATH # Create necessary folders echo "Created documents structure" + mkdir -p $INSTALL_PATH/documents/wetlab mkdir -p $INSTALL_PATH/documents/wetlab/tmp - mkdir -p $INSTALL_PATH/documents/wetlab/SampleSheets + mkdir -p $INSTALL_PATH/documents/wetlab/sample_sheet mkdir -p $INSTALL_PATH/documents/wetlab/images_plot mkdir -p $INSTALL_PATH/documents/wetlab/templates - chown $user:apache $INSTALL_PATH/documents - chmod 775 $INSTALL_PATH/documents - chown $user:apache $INSTALL_PATH/documents/wetlab/tmp - chmod 775 $INSTALL_PATH/documents/wetlab/tmp - chown $user:apache $INSTALL_PATH/documents/wetlab/SampleSheets - chmod 775 $INSTALL_PATH/documents/wetlab/SampleSheets - chown $user:apache $INSTALL_PATH/documents/wetlab/images_plot - chmod 775 $INSTALL_PATH/documents/wetlab/images_plot - chown $user:apache $INSTALL_PATH/documents/wetlab/templates - chmod 775 $INSTALL_PATH/documents/wetlab/templates + mkdir -p $INSTALL_PATH/documents/wetlab/sample_sheets_lib_prep mkdir -p $INSTALL_PATH/documents/drylab - chown $user:apache $INSTALL_PATH/documents/drylab - chmod 775 $INSTALL_PATH/documents/drylab - + mkdir -p $INSTALL_PATH/documents/drylab/service_files + + chown -R $user:$apache_group $INSTALL_PATH/documents + chmod 775 $INSTALL_PATH/documents + # Copy illumina sample sheet templates cp $INSTALL_PATH/conf/*_template.csv $INSTALL_PATH/documents/wetlab/templates/ # update logging configuration file cp $INSTALL_PATH/conf/template_logging_config.ini $INSTALL_PATH/wetlab/logging_config.ini - sed -i "/INSTALL_PATH/${INSTALL_PATH}/g" $INSTALL_PATH/wetlab/logging_config.ini + sed -i "s|INSTALL_PATH|${INSTALL_PATH}|g" $INSTALL_PATH/wetlab/logging_config.ini # Starting iSkyLIMS echo "activate the virtualenv" @@ -792,9 +784,6 @@ if [ $install == true ]; then # copy static files echo "Run collectstatic" python manage.py collectstatic - - echo "Running crontab" - python manage.py crontab add cd - diff --git a/samplesheet_NextSeq_GEN_436.csv b/samplesheet_NextSeq_GEN_436.csv new file mode 100644 index 000000000..523204efa --- /dev/null +++ b/samplesheet_NextSeq_GEN_436.csv @@ -0,0 +1,109 @@ +[Header] +IEMFileVersion,5 +Experiment Name,NextSeq_GEN_436 +Date,15/06/2023 +Workflow,GenerateFASTQ +Application,NextSeq FASTQ Only +Instrument Type,NextSeq/MiniSeq +Assay,Illumina DNA Prep +"Index Adapters,""IDT-Ilmn DNA-RNA UD Indexes SetA Tagmentation""" +Chemistry,Amplicon + +[Reads] +149 +149 + +[Settings] +Adapter,CTGTCTCTTATACACATCT + +[Data] +Sample_ID,Sample_Name,Sample_Plate,Sample_Well,Index_Plate_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description +22K0483,22K0483,bhi1506,A01,A01,UDP0001,GAACTGAGCG,UDP0001,CGCTCCACGA,NextSeq_GEN_436_20230615,test_user1 +23Eco0173,23Eco0173,bhi1506,A02,B01,UDP0002,AGGTCAGATA,UDP0002,TATCTTGTAG,NextSeq_GEN_436_20230615,test_user1 +23Eco0175,23Eco0175,bhi1506,A03,C01,UDP0003,CGTCTCATAT,UDP0003,AGCTACTATA,NextSeq_GEN_436_20230615,test_user1 +23Eco0176,23Eco0176,bhi1506,A04,D01,UDP0004,ATTCCATAAG,UDP0004,CCACCAGGCA,NextSeq_GEN_436_20230615,test_user1 +23Eco0177,23Eco0177,bhi1506,A05,E01,UDP0005,GACGAGATTA,UDP0005,AGGATAATGT,NextSeq_GEN_436_20230615,test_user1 +23Eco0178,23Eco0178,bhi1506,A06,F01,UDP0006,AACATCGCGC,UDP0006,ACAAGTGGAC,NextSeq_GEN_436_20230615,test_user1 +23Eco0184,23Eco0184,bhi1506,A07,G01,UDP0007,CTAGTGCTCT,UDP0007,TACTGTTCCA,NextSeq_GEN_436_20230615,test_user1 +23Eco0185,23Eco0185,bhi1506,A08,H01,UDP0008,GATCAAGGCA,UDP0008,ATTAACAAGG,NextSeq_GEN_436_20230615,test_user1 +23Eco0186,23Eco0186,bhi1506,A09,A02,UDP0009,GACTGAGTAG,UDP0009,CACTATCAAC,NextSeq_GEN_436_20230615,test_user1 +23Eco0187,23Eco0187,bhi1506,A10,B02,UDP0010,AGTCAGACGA,UDP0010,TGTCGCTGGT,NextSeq_GEN_436_20230615,test_user1 +23Eco0188,23Eco0188,bhi1506,A11,C02,UDP0011,CCGTATGTTC,UDP0011,ACAGTGTATG,NextSeq_GEN_436_20230615,test_user1 +23Eco0189,23Eco0189,bhi1506,A12,D02,UDP0012,GAGTCATAGG,UDP0012,AGCGCCACAC,NextSeq_GEN_436_20230615,test_user1 +23Eco0192,23Eco0192,bhi1506,B01,E02,UDP0013,CTTGCCATTA,UDP0013,CCTTCGTGAT,NextSeq_GEN_436_20230615,test_user1 +23Eco0193,23Eco0193,bhi1506,B02,F02,UDP0014,GAAGCGGCAC,UDP0014,AGTAGAGCCG,NextSeq_GEN_436_20230615,test_user1 +23Eco0194,23Eco0194,bhi1506,B03,G02,UDP0015,TCCATTGCCG,UDP0015,TCGTGCATTC,NextSeq_GEN_436_20230615,test_user1 +23Eco0195,23Eco0195,bhi1506,B04,H02,UDP0016,CGGTTACGGC,UDP0016,CTATAGTCTT,NextSeq_GEN_436_20230615,test_user1 +23Eco0196,23Eco0196,bhi1506,B05,A03,UDP0017,GAGAATGGTT,UDP0017,TTGCTGCCGA,NextSeq_GEN_436_20230615,test_user1 +23Entb0011,23Entb0011,bhi1506,B06,B03,UDP0018,AGAGGCAACC,UDP0018,CCATCATTAG,NextSeq_GEN_436_20230615,test_user1 +23Entb0088,23Entb0088,bhi1506,B07,C03,UDP0019,CCATCATTAG,UDP0019,AGAGGCAACC,NextSeq_GEN_436_20230615,test_user1 +23Entb0089,23Entb0089,bhi1506,B08,D03,UDP0020,GATAGGCCGA,UDP0020,GCCATGTGCG,NextSeq_GEN_436_20230615,test_user1 +23Entb0090,23Entb0090,bhi1506,B09,E03,UDP0021,ATGGTTGACT,UDP0021,AGGACAGGCC,NextSeq_GEN_436_20230615,test_user1 +23K0523,23K0523,bhi1506,B10,F03,UDP0022,TATTGCGCTC,UDP0022,CCTAACACAG,NextSeq_GEN_436_20230615,test_user1 +23K0524,23K0524,bhi1506,B11,G03,UDP0023,ACGCCTTGTT,UDP0023,ACGTTCCTTA,NextSeq_GEN_436_20230615,test_user1 +23K0525,23K0525,bhi1506,B12,H03,UDP0024,TTCTACATAC,UDP0024,TTACAGTTAG,NextSeq_GEN_436_20230615,test_user1 +23K0526,23K0526,bhi1506,C01,A04,UDP0025,AACCATAGAA,UDP0025,CCATCTCGCC,NextSeq_GEN_436_20230615,test_user1 +23K0527,23K0527,bhi1506,C02,B04,UDP0026,GGTTGCGAGG,UDP0026,TTGCTCTATT,NextSeq_GEN_436_20230615,test_user1 +23K0528,23K0528,bhi1506,C03,C04,UDP0027,TAAGCATCCA,UDP0027,AATGGATTGA,NextSeq_GEN_436_20230615,test_user1 +23K0529,23K0529,bhi1506,C04,D04,UDP0028,ACCACGACAT,UDP0028,CCGCATACGA,NextSeq_GEN_436_20230615,test_user1 +23K0530,23K0530,bhi1506,C05,E04,UDP0029,GCCGCACTCT,UDP0029,CGAGGTCGGA,NextSeq_GEN_436_20230615,test_user1 +23K0531,23K0531,bhi1506,C06,F04,UDP0030,CCACCAGGCA,UDP0030,ATTCCATAAG,NextSeq_GEN_436_20230615,test_user1 +23K0532,23K0532,bhi1506,C07,G04,UDP0031,GTGACACGCA,UDP0031,GTCCGTAAGC,NextSeq_GEN_436_20230615,test_user1 +23K0533,23K0533,bhi1506,C08,H04,UDP0032,ACAGTGTATG,UDP0032,CCGTATGTTC,NextSeq_GEN_436_20230615,test_user1 +23K0534,23K0534,bhi1506,C09,A05,UDP0033,TGATTATACG,UDP0033,TGTAATCGAC,NextSeq_GEN_436_20230615,test_user1 +23K0535,23K0535,bhi1506,C10,B05,UDP0034,CAGCCGCGTA,UDP0034,CACGGCTAGT,NextSeq_GEN_436_20230615,test_user1 +23K0536,23K0536,bhi1506,C11,C05,UDP0035,GGTAACTCGC,UDP0035,TCACCAACTT,NextSeq_GEN_436_20230615,test_user1 +23K0537,23K0537,bhi1506,C12,D05,UDP0036,ACCGGCCGTA,UDP0036,AATATTGCCA,NextSeq_GEN_436_20230615,test_user1 +23K0538,23K0538,bhi1506,D01,E05,UDP0037,TGTAATCGAC,UDP0037,CGCGGTGATC,NextSeq_GEN_436_20230615,test_user1 +23K0539,23K0539,bhi1506,D02,F05,UDP0038,GTGCAGACAG,UDP0038,ACGGATGGTA,NextSeq_GEN_436_20230615,test_user1 +23K0540,23K0540,bhi1506,D03,G05,UDP0039,CAATCGGCTG,UDP0039,TTCCTACAGC,NextSeq_GEN_436_20230615,test_user1 +23K0541,23K0541,bhi1506,D04,H05,UDP0040,TATGTAGTCA,UDP0040,CATTAGTGCG,NextSeq_GEN_436_20230615,test_user1 +23K0542,23K0542,bhi1506,D05,A06,UDP0041,ACTCGGCAAT,UDP0041,TTCAGTTGTC,NextSeq_GEN_436_20230615,test_user1 +23K0543,23K0543,bhi1506,D06,B06,UDP0042,GTCTAATGGC,UDP0042,CCTGACCACT,NextSeq_GEN_436_20230615,test_user1 +23K0544,23K0544,bhi1506,D07,C06,UDP0043,CCATCTCGCC,UDP0043,AACCATAGAA,NextSeq_GEN_436_20230615,test_user1 +23K0545,23K0545,bhi1506,D08,D06,UDP0044,CTGCGAGCCA,UDP0044,TGGCCGGATT,NextSeq_GEN_436_20230615,test_user1 +23K0546,23K0546,bhi1506,D09,E06,UDP0045,CGTTATTCTA,UDP0045,AACCTTATGG,NextSeq_GEN_436_20230615,test_user1 +23K0547,23K0547,bhi1506,D10,F06,UDP0046,AGATCCATTA,UDP0046,TGGTAGAGAT,NextSeq_GEN_436_20230615,test_user1 +23K0548,23K0548,bhi1506,D11,G06,UDP0047,GTCCTGGATA,UDP0047,TTCGCCACCG,NextSeq_GEN_436_20230615,test_user1 +23K0550,23K0550,bhi1506,D12,H06,UDP0048,CAGTGGCACT,UDP0048,CCTATTGTTA,NextSeq_GEN_436_20230615,test_user1 +23K0551,23K0551,bhi1506,E01,A07,UDP0049,AGTGTTGCAC,UDP0049,CGTGTACCAG,NextSeq_GEN_436_20230615,test_user1 +23K0552,23K0552,bhi1506,E02,B07,UDP0050,GACACCATGT,UDP0050,TACACGTTGA,NextSeq_GEN_436_20230615,test_user1 +23K0553,23K0553,bhi1506,E03,C07,UDP0051,CCTGTCTGTC,UDP0051,TCACAACAGT,NextSeq_GEN_436_20230615,test_user1 +23K0554,23K0554,bhi1506,E04,D07,UDP0052,TGATGTAAGA,UDP0052,AAGGACGCAC,NextSeq_GEN_436_20230615,test_user1 +23K0572,23K0572,bhi1506,E05,E07,UDP0053,GGAATTGTAA,UDP0053,AGGATGTGCT,NextSeq_GEN_436_20230615,test_user1 +23K0573,23K0573,bhi1506,E06,F07,UDP0054,GCATAAGCTT,UDP0054,TGCGACGGAA,NextSeq_GEN_436_20230615,test_user1 +23K0574,23K0574,bhi1506,E07,G07,UDP0055,CTGAGGAATA,UDP0055,AGTGGTTAAG,NextSeq_GEN_436_20230615,test_user1 +23K0575,23K0575,bhi1506,E08,H07,UDP0056,AACGCACGAG,UDP0056,TATCCGAGGC,NextSeq_GEN_436_20230615,test_user1 +23K0576,23K0576,bhi1506,E09,A08,UDP0057,TCTATCCTAA,UDP0057,CCAGTCGACG,NextSeq_GEN_436_20230615,test_user1 +23K0577,23K0577,bhi1506,E10,B08,UDP0058,CTCGCTTCGG,UDP0058,TTGACTAGTA,NextSeq_GEN_436_20230615,test_user1 +23K0578,23K0578,bhi1506,E11,C08,UDP0059,CTGTTGGTCC,UDP0059,AACGGTCTAT,NextSeq_GEN_436_20230615,test_user1 +23K0579,23K0579,bhi1506,E12,D08,UDP0060,TTACCTGGAA,UDP0060,CTGGAACTGT,NextSeq_GEN_436_20230615,test_user1 +23K0580,23K0580,bhi1506,F01,E08,UDP0061,TGGCTAATCA,UDP0061,CTACATGCCT,NextSeq_GEN_436_20230615,test_user1 +23K0581,23K0581,bhi1506,F02,F08,UDP0062,AACACTGTTA,UDP0062,TGAGACTTGC,NextSeq_GEN_436_20230615,test_user1 +23K0582,23K0582,bhi1506,F03,G08,UDP0063,ATTGCGCGGT,UDP0063,GCGGAGCCAA,NextSeq_GEN_436_20230615,test_user1 +23K0583,23K0583,bhi1506,F04,H08,UDP0064,TGGCGCGAAC,UDP0064,AGTATCAGTT,NextSeq_GEN_436_20230615,test_user1 +23K0584,23K0584,bhi1506,F05,A09,UDP0065,TAATGTGTCT,UDP0065,TATGCCTTAC,NextSeq_GEN_436_20230615,test_user1 +23K0585,23K0585,bhi1506,F06,B09,UDP0066,ATACCAACGC,UDP0066,CGCAGCAATT,NextSeq_GEN_436_20230615,test_user1 +23K0586,23K0586,bhi1506,F07,C09,UDP0067,AGGATGTGCT,UDP0067,GGAATTGTAA,NextSeq_GEN_436_20230615,test_user1 +23K0587,23K0587,bhi1506,F08,D09,UDP0068,CACGGAACAA,UDP0068,GTGCTAGGTT,NextSeq_GEN_436_20230615,test_user1 +23K0588,23K0588,bhi1506,F09,E09,UDP0069,TGGAGTACTT,UDP0069,TCCACACAGA,NextSeq_GEN_436_20230615,test_user1 +23K0589,23K0589,bhi1506,F10,F09,UDP0070,GTATTGACGT,UDP0070,TTGGAATTCC,NextSeq_GEN_436_20230615,test_user1 +23K0590,23K0590,bhi1506,F11,G09,UDP0071,CTTGTACACC,UDP0071,AAGCGCGCTT,NextSeq_GEN_436_20230615,test_user1 +23K0591,23K0591,bhi1506,F12,H09,UDP0072,ACACAGGTGG,UDP0072,ACAACGCTCA,NextSeq_GEN_436_20230615,test_user1 +23K0592,23K0592,bhi1506,G01,A10,UDP0073,CCTGCGGAAC,UDP0073,AGCCTATGAT,NextSeq_GEN_436_20230615,test_user1 +23K0593,23K0593,bhi1506,G02,B10,UDP0074,TTCATAAGGT,UDP0074,CCTTCTAACA,NextSeq_GEN_436_20230615,test_user1 +23K0594,23K0594,bhi1506,G03,C10,UDP0075,CTCTGCAGCG,UDP0075,TACATCCATC,NextSeq_GEN_436_20230615,test_user1 +23K0595,23K0595,bhi1506,G04,D10,UDP0076,CTGACTCTAC,UDP0076,TGACGGCCGT,NextSeq_GEN_436_20230615,test_user1 +23K0597,23K0597,bhi1506,G05,E10,UDP0077,TCTGGTATCC,UDP0077,GTAAGCAACG,NextSeq_GEN_436_20230615,test_user1 +23K0598,23K0598,bhi1506,G06,F10,UDP0078,CATTAGTGCG,UDP0078,TATGTAGTCA,NextSeq_GEN_436_20230615,test_user1 +23K0599,23K0599,bhi1506,G07,G10,UDP0079,ACGGTCAGGA,UDP0079,AACGAGGCCG,NextSeq_GEN_436_20230615,test_user1 +23K0600,23K0600,bhi1506,G08,H10,UDP0080,GGCAAGCCAG,UDP0080,CGGATGCTTG,NextSeq_GEN_436_20230615,test_user1 +23K0601,23K0601,bhi1506,G09,A11,UDP0081,TGTCGCTGGT,UDP0081,AGTCAGACGA,NextSeq_GEN_436_20230615,test_user1 +23Sm0003,23Sm0003,bhi1506,G10,B11,UDP0082,ACCGTTACAA,UDP0082,TCGCTATGAG,NextSeq_GEN_436_20230615,test_user1 +23Sm0005,23Sm0005,bhi1506,G11,C11,UDP0083,TATGCCTTAC,UDP0083,TAATGTGTCT,NextSeq_GEN_436_20230615,test_user1 +23Sm0006,23Sm0006,bhi1506,G12,D11,UDP0084,ACAAGTGGAC,UDP0084,AACATCGCGC,NextSeq_GEN_436_20230615,test_user1 +23Sm0007,23Sm0007,bhi1506,H01,E11,UDP0085,TGGTACCTAA,UDP0085,AGTACTCATG,NextSeq_GEN_436_20230615,test_user1 +23Sm0008,23Sm0008,bhi1506,H02,F11,UDP0086,TTGGAATTCC,UDP0086,GTATTGACGT,NextSeq_GEN_436_20230615,test_user1 +23Sm0004,23Sm0004,bhi1506,H03,G11,UDP0087,CCTCTACATG,UDP0087,AGGAGGTATC,NextSeq_GEN_436_20230615,test_user1 +23Ent0085,23Ent0085,bhi1506,H04,H11,UDP0088,GGAGCGTGTA,UDP0088,ACTTACGGAT,NextSeq_GEN_436_20230615,test_user1 +23Entb0091,23Entb0091,bhi1506,H05,A12,UDP0089,GTCCGTAAGC,UDP0089,AAGATACACG,NextSeq_GEN_436_20230615,test_user1 diff --git a/test/test_data.json b/test/test_data.json new file mode 100644 index 000000000..dd1dfc3fa --- /dev/null +++ b/test/test_data.json @@ -0,0 +1,16307 @@ +[ + { + "model": "core.stateincountry", + "pk": 1, + "fields": { + "state_name": "Spain", + "apps_name": "wetlab" + } + }, + { + "model": "core.city", + "pk": 1, + "fields": { + "belongs_to_state": 1, + "city_name": "Madrid", + "geo_loc_latitude": "1111", + "geo_loc_longitude": "1111", + "apps_name": "wetlab" + } + }, + { + "model": "core.labrequest", + "pk": 1, + "fields": { + "lab_city": 1, + "lab_name": "Institute of Health Carlos III", + "lab_name_coding": "ISCIII", + "lab_unit": "Bioinformatics Unit (BU-ISCIII)", + "lab_contact_name": "Sara Monzon", + "lab_phone": "1111111", + "lab_email": "sara@gmail.com", + "address": "", + "apps_name": "wetlab" + } + }, + { + "model": "core.protocols", + "pk": 1, + "fields": { + "type": 4, + "name": "Blood sample dna extraction", + "description": "" + } + }, + { + "model": "core.protocols", + "pk": 2, + "fields": { + "type": 3, + "name": "illumina nextera lib prep", + "description": "" + } + }, + { + "model": "core.protocols", + "pk": 3, + "fields": { + "type": 8, + "name": "sequencing protocol", + "description": "" + } + }, + { + "model": "core.protocolparameters", + "pk": 1, + "fields": { + "protocol_id": 1, + "parameter_name": "Concentration", + "parameter_description": "DNA concentration measure, pe absorbance", + "parameter_order": 1, + "parameter_used": true, + "parameter_type": "string", + "parameter_option_values": "", + "parameter_max_value": "9999", + "parameter_min_value": "0" + } + }, + { + "model": "core.protocolparameters", + "pk": 2, + "fields": { + "protocol_id": 1, + "parameter_name": "Purity", + "parameter_description": "DNA purity measure , pe absorbance", + "parameter_order": 2, + "parameter_used": true, + "parameter_type": "string", + "parameter_option_values": "", + "parameter_max_value": "9999", + "parameter_min_value": "0" + } + }, + { + "model": "core.protocolparameters", + "pk": 3, + "fields": { + "protocol_id": 2, + "parameter_name": "Concentration", + "parameter_description": "library concentration measure", + "parameter_order": 1, + "parameter_used": true, + "parameter_type": "string", + "parameter_option_values": "", + "parameter_max_value": "", + "parameter_min_value": "" + } + }, + { + "model": "core.protocolparameters", + "pk": 4, + "fields": { + "protocol_id": 2, + "parameter_name": "Fragment lenght", + "parameter_description": "mean fragment length with bioanalyzer", + "parameter_order": 2, + "parameter_used": true, + "parameter_type": "string", + "parameter_option_values": "", + "parameter_max_value": "", + "parameter_min_value": "" + } + }, + { + "model": "core.protocolparameters", + "pk": 5, + "fields": { + "protocol_id": 3, + "parameter_name": "Notes", + "parameter_description": "", + "parameter_order": 1, + "parameter_used": true, + "parameter_type": "", + "parameter_option_values": "", + "parameter_max_value": "", + "parameter_min_value": "" + } + }, + { + "model": "core.sampletype", + "pk": 1, + "fields": { + "sample_type": "blood", + "apps_name": "wetlab", + "optional_fields": "0,7,8,9", + "generated_at": "2023-07-25T16:16:59.630" + } + }, + { + "model": "core.species", + "pk": 3, + "fields": { + "species_name": "Escherichia coli", + "ref_genome_name": "Unknown", + "ref_genome_size": "Unknown", + "ref_genome_id": "Unknown", + "apps_name": "wetlab", + "generated_at": "2023-07-25T16:19:41.572" + } + }, + { + "model": "core.commercialkits", + "pk": 1, + "fields": { + "platform_kits": null, + "name": "dna extraction qiagen", + "provider": "qiagen", + "cat_number": "123123", + "description": "", + "generated_at": "2023-07-25T16:19:41.572", + "protocol_kits": [ + 1 + ] + } + }, + { + "model": "core.commercialkits", + "pk": 2, + "fields": { + "platform_kits": null, + "name": "illlumina kit 1", + "provider": "Illumina", + "cat_number": "11111111111", + "description": "", + "generated_at": "2023-07-25T16:19:53.240", + "protocol_kits": [ + 2 + ] + } + }, + { + "model": "core.commercialkits", + "pk": 3, + "fields": { + "platform_kits": 9, + "name": "miseq kit 1", + "provider": "Illumina", + "cat_number": "123123", + "description": "", + "generated_at": "2023-07-25T16:20:47.362", + "protocol_kits": [] + } + }, + { + "model": "core.userlotcommercialkits", + "pk": 1, + "fields": { + "user": 1, + "based_commercial": 1, + "uses_number": 89, + "chip_lot": "23123123123", + "latest_used_date": "2023-07-25T16:58:27.412", + "expiration_date": "2023-09-30", + "run_out": false, + "generated_at": "2023-07-25T16:21:00.298" + } + }, + { + "model": "core.userlotcommercialkits", + "pk": 2, + "fields": { + "user": 1, + "based_commercial": 2, + "uses_number": 0, + "chip_lot": "1341425345", + "latest_used_date": null, + "expiration_date": "2023-10-01", + "run_out": false, + "generated_at": "2023-07-25T16:21:09.903" + } + }, + { + "model": "core.sampleprojects", + "pk": 1, + "fields": { + "sample_project_name": "custom_project", + "sample_project_manager": "saramonzon", + "sample_project_contact": "", + "sample_project_description": "", + "apps_name": "wetlab", + "generated_at": "2023-07-25T16:17:15.970" + } + }, + { + "model": "core.sampleprojectsfields", + "pk": 1, + "fields": { + "sample_projects_id": 1, + "sample_project_field_classification_id": null, + "sample_project_field_name": "External lab", + "sample_project_field_description": "", + "sample_project_field_order": 1, + "sample_project_field_used": true, + "sample_project_field_type": "String", + "sample_project_option_list": "", + "sample_project_searchable": true, + "generated_at": "2023-07-25T16:19:01.096" + } + }, + { + "model": "core.sampleprojectsfields", + "pk": 2, + "fields": { + "sample_projects_id": 1, + "sample_project_field_classification_id": null, + "sample_project_field_name": 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"22K0483", + "sample_location": "False", + "sample_entry_date": "2023-07-25T00:00:00", + "collection_sample_date": null, + "unique_sample_id": "AAA-0001", + "sample_code_id": "admin_22K0483", + "reused_number": 0, + "sequencing_date": "2023-07-25T17:13:31.420", + "completed_date": null, + "generated_at": "2023-07-25T16:55:48.746", + "only_recorded": false + } + }, + { + "model": "core.samples", + "pk": 93, + "fields": { + "sample_state": 5, + "patient_core": null, + "lab_request": 1, + "sample_type": 1, + "sample_user": 1, + "species": 3, + "sample_project": 1, + "sample_name": "23Eco0173", + "sample_location": "False", + "sample_entry_date": "2023-07-25T00:00:00", + "collection_sample_date": null, + "unique_sample_id": "AAA-0002", + "sample_code_id": "admin_23Eco0173", + "reused_number": 0, + "sequencing_date": "2023-07-25T17:13:31.360", + "completed_date": null, + "generated_at": "2023-07-25T16:55:48.767", + "only_recorded": false + } + }, + { + "model": "core.samples", + "pk": 94, + "fields": { + "sample_state": 5, + "patient_core": null, + "lab_request": 1, + "sample_type": 1, + "sample_user": 1, + "species": 3, + "sample_project": 1, + "sample_name": "23Eco0175", + "sample_location": "False", + "sample_entry_date": "2023-07-25T00:00:00", + "collection_sample_date": null, + "unique_sample_id": "AAA-0003", + "sample_code_id": "admin_23Eco0175", + "reused_number": 0, + "sequencing_date": "2023-07-25T17:13:31.357", + "completed_date": null, + "generated_at": "2023-07-25T16:55:48.781", + "only_recorded": false + } + }, + { + "model": "core.samples", + "pk": 95, + "fields": { + "sample_state": 5, + "patient_core": null, + "lab_request": 1, + "sample_type": 1, + "sample_user": 1, + "species": 3, + "sample_project": 1, + "sample_name": "23Eco0176", + "sample_location": "False", + "sample_entry_date": "2023-07-25T00:00:00", + "collection_sample_date": null, + "unique_sample_id": "AAA-0004", + "sample_code_id": "admin_23Eco0176", + "reused_number": 0, + "sequencing_date": 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"2023-07-25" + } + }, + { + "model": "drylab.requestedsamplesinservices", + "pk": 7, + "fields": { + "samples_in_service": 1, + "sample_key": "595", + "sample_name": "M4-22", + "sample_path": "230616_M03352_0408_000000000-DKW5N", + "run_name_key": "22", + "run_name": "MiSeq_GEN_381", + "project_key": "15", + "project_name": "MiSeq_GEN_381_20230616_REscudero", + "only_recorded_sample": false, + "generated_at": "2023-07-25" + } + }, + { + "model": "drylab.requestedsamplesinservices", + "pk": 8, + "fields": { + "samples_in_service": 1, + "sample_key": "594", + "sample_name": "M3-22", + "sample_path": "230616_M03352_0408_000000000-DKW5N", + "run_name_key": "22", + "run_name": "MiSeq_GEN_381", + "project_key": "15", + "project_name": "MiSeq_GEN_381_20230616_REscudero", + "only_recorded_sample": false, + "generated_at": "2023-07-25" + } + }, + { + "model": "drylab.requestedsamplesinservices", + "pk": 9, + "fields": { + "samples_in_service": 1, + "sample_key": "593", + "sample_name": "M2-22", + "sample_path": "230616_M03352_0408_000000000-DKW5N", + "run_name_key": "22", + "run_name": "MiSeq_GEN_381", + "project_key": "15", + "project_name": "MiSeq_GEN_381_20230616_REscudero", + "only_recorded_sample": false, + "generated_at": "2023-07-25" + } + }, + { + "model": "drylab.requestedsamplesinservices", + "pk": 10, + "fields": { + "samples_in_service": 1, + "sample_key": "592", + "sample_name": "M1-22", + "sample_path": "230616_M03352_0408_000000000-DKW5N", + "run_name_key": "22", + "run_name": "MiSeq_GEN_381", + "project_key": "15", + "project_name": "MiSeq_GEN_381_20230616_REscudero", + "only_recorded_sample": false, + "generated_at": "2023-07-25" + } + }, + { + "model": "drylab.requestedsamplesinservices", + "pk": 11, + "fields": { + "samples_in_service": 2, + "sample_key": "577", + "sample_name": "ARBMET1", + "sample_path": "230517_A01158_0104_BH7FKGDRX2", + "run_name_key": "21", + "run_name": "NovaSeq_GEN_083", + "project_key": "14", + "project_name": "NovaSeq_GEN_083_20230517_PSanchez", + "only_recorded_sample": false, + "generated_at": "2023-07-25" + } + }, + { + "model": "drylab.requestedsamplesinservices", + "pk": 12, + "fields": { + "samples_in_service": 2, + "sample_key": "588", + "sample_name": "ARBMET12", + "sample_path": "230517_A01158_0104_BH7FKGDRX2", + "run_name_key": "21", + "run_name": "NovaSeq_GEN_083", + "project_key": "14", + "project_name": "NovaSeq_GEN_083_20230517_PSanchez", + "only_recorded_sample": false, + "generated_at": "2023-07-25" + } + }, + { + "model": "drylab.requestedsamplesinservices", + "pk": 13, + "fields": { + "samples_in_service": 2, + "sample_key": "587", + "sample_name": "ARBMET11", + "sample_path": "230517_A01158_0104_BH7FKGDRX2", + "run_name_key": "21", + "run_name": "NovaSeq_GEN_083", + "project_key": "14", + "project_name": "NovaSeq_GEN_083_20230517_PSanchez", + "only_recorded_sample": false, + "generated_at": "2023-07-25" + } + }, + { + "model": "drylab.requestedsamplesinservices", + "pk": 14, + "fields": { + "samples_in_service": 2, + "sample_key": "586", + "sample_name": "ARBMET10", + "sample_path": "230517_A01158_0104_BH7FKGDRX2", + "run_name_key": "21", + "run_name": "NovaSeq_GEN_083", + "project_key": "14", + "project_name": "NovaSeq_GEN_083_20230517_PSanchez", + "only_recorded_sample": false, + "generated_at": "2023-07-25" + } + }, + { + "model": "drylab.requestedsamplesinservices", + "pk": 15, + "fields": { + "samples_in_service": 2, + "sample_key": "585", + "sample_name": "ARBMET9", + "sample_path": "230517_A01158_0104_BH7FKGDRX2", + "run_name_key": "21", + "run_name": "NovaSeq_GEN_083", + "project_key": "14", + "project_name": "NovaSeq_GEN_083_20230517_PSanchez", + "only_recorded_sample": false, + "generated_at": "2023-07-25" + } + }, + { + "model": "drylab.requestedsamplesinservices", + "pk": 16, + "fields": { + "samples_in_service": 2, + "sample_key": "584", + "sample_name": "ARBMET8", + "sample_path": "230517_A01158_0104_BH7FKGDRX2", + "run_name_key": "21", + "run_name": "NovaSeq_GEN_083", + "project_key": "14", + "project_name": "NovaSeq_GEN_083_20230517_PSanchez", + "only_recorded_sample": false, + "generated_at": "2023-07-25" + } + }, + { + "model": "drylab.requestedsamplesinservices", + "pk": 17, + "fields": { + "samples_in_service": 2, + "sample_key": "583", + "sample_name": "ARBMET7", + "sample_path": "230517_A01158_0104_BH7FKGDRX2", + "run_name_key": "21", + "run_name": "NovaSeq_GEN_083", + "project_key": "14", + "project_name": "NovaSeq_GEN_083_20230517_PSanchez", + "only_recorded_sample": false, + "generated_at": "2023-07-25" + } + }, + { + "model": "drylab.requestedsamplesinservices", + "pk": 18, + "fields": { + "samples_in_service": 3, + "sample_key": "582", + "sample_name": "ARBMET6", + "sample_path": "230517_A01158_0104_BH7FKGDRX2", + "run_name_key": "21", + "run_name": "NovaSeq_GEN_083", + "project_key": "14", + "project_name": "NovaSeq_GEN_083_20230517_PSanchez", + "only_recorded_sample": false, + "generated_at": "2023-07-25" + } + }, + { + "model": "drylab.requestedsamplesinservices", + "pk": 19, + "fields": { + "samples_in_service": 3, + "sample_key": "581", + "sample_name": "ARBMET5", + "sample_path": "230517_A01158_0104_BH7FKGDRX2", + "run_name_key": "21", + "run_name": "NovaSeq_GEN_083", + "project_key": "14", + "project_name": "NovaSeq_GEN_083_20230517_PSanchez", + "only_recorded_sample": false, + "generated_at": "2023-07-25" + } + }, + { + "model": "drylab.requestedsamplesinservices", + "pk": 20, + "fields": { + "samples_in_service": 3, + "sample_key": "580", + "sample_name": "ARBMET4", + "sample_path": "230517_A01158_0104_BH7FKGDRX2", + "run_name_key": "21", + "run_name": "NovaSeq_GEN_083", + "project_key": "14", + "project_name": "NovaSeq_GEN_083_20230517_PSanchez", + "only_recorded_sample": false, + "generated_at": "2023-07-25" + } + }, + { + "model": "drylab.requestedsamplesinservices", + "pk": 21, + "fields": { + "samples_in_service": 3, + "sample_key": "579", + "sample_name": "ARBMET3", + "sample_path": "230517_A01158_0104_BH7FKGDRX2", + "run_name_key": "21", + "run_name": "NovaSeq_GEN_083", + "project_key": "14", + "project_name": "NovaSeq_GEN_083_20230517_PSanchez", + "only_recorded_sample": false, + "generated_at": "2023-07-25" + } + }, + { + "model": "drylab.requestedsamplesinservices", + "pk": 22, + "fields": { + "samples_in_service": 3, + "sample_key": "578", + "sample_name": "ARBMET2", + "sample_path": "230517_A01158_0104_BH7FKGDRX2", + "run_name_key": "21", + "run_name": "NovaSeq_GEN_083", + "project_key": "14", + "project_name": "NovaSeq_GEN_083_20230517_PSanchez", + "only_recorded_sample": false, + "generated_at": "2023-07-25" + } + }, + { + "model": "drylab.resolution", + "pk": 1, + "fields": { + "resolution_service_id": 3, + "resolution_assigned_user": 1, + "resolution_state": 6, + "resolution_number": "SRVSGAFI003.1", + "resolution_estimated_date": "2023-07-29", + "resolution_date": "2023-07-25", + "resolution_queued_date": "2023-07-25", + "resolution_in_progress_date": null, + "resolution_delivery_date": null, + "resolution_notes": "", + "resolution_full_number": "SRVSGAFI003_20230725_WGMLST01_test_user1_S", + "resolution_pdf_file": "", + "resolution_pipelines": [], + "available_services": [ + 29 + ] + } + }, + { + "model": "auth.user", + "pk": 2, + "fields": { + "password": "pbkdf2_sha256$260000$WoFbBL6zQ3F4nCr3oAFzFd$kT3I+1KotzgT1zT8on4zXZte5vS07KnQr6RmDw2N+UU=", + "last_login": null, + "is_superuser": false, + "username": "test_user1", + "first_name": "", + "last_name": "", + "email": "", + "is_staff": false, + "is_active": true, + "date_joined": "2023-07-25T12:00:34", + "groups": [], + "user_permissions": [] + } + } +] \ No newline at end of file diff --git a/wetlab/admin.py b/wetlab/admin.py index 7c7ca8858..ae484d5bd 100644 --- a/wetlab/admin.py +++ b/wetlab/admin.py @@ -122,6 +122,17 @@ class CollectionIndexKitAdmin(admin.ModelAdmin): ) +class CollectionIndexValuesAdmin(admin.ModelAdmin): + list_display = ( + "collection_index_kit_id", + "default_well", + "index_7", + "i_7_seq", + "index_5", + "i_5_seq", + ) + + class SamplesInProjectAdmin(admin.ModelAdmin): list_display = [ "sample_name", @@ -275,6 +286,7 @@ class RunConfigurationTestAdmin(admin.ModelAdmin): admin.site.register(wetlab.models.RunningParameters, RunningParametersAdmin) admin.site.register(wetlab.models.RunProcess, RunProcessAdmin) admin.site.register(wetlab.models.CollectionIndexKit, CollectionIndexKitAdmin) +admin.site.register(wetlab.models.CollectionIndexValues, CollectionIndexValuesAdmin) admin.site.register(wetlab.models.Projects, ProjectsAdmin) admin.site.register(wetlab.models.RunErrors, RunErrorsAdmin) admin.site.register(wetlab.models.RunStates, RunStatesAdmin) diff --git a/wetlab/config.py b/wetlab/config.py index 38dc5beb1..dfedcd520 100644 --- a/wetlab/config.py +++ b/wetlab/config.py @@ -29,12 +29,11 @@ RUN_TEMP_DIRECTORY = "wetlab/tmp" RUN_TEMP_DIRECTORY_PROCESSING = "wetlab/tmp/processing" RUN_IMAGES_DIRECTORY = "wetlab/images_plot" -RUN_SAMPLE_SHEET_DIRECTORY = "wetlab/SampleSheets/" -# SAMPLE_SHEET_CREATED_ON_LAB = 'wetlab/SampleSheetsFromLab' +RUN_SAMPLE_SHEET_DIRECTORY = "wetlab/sample_sheet/" TEMPLATE_FILES_DIRECTORY = "wetlab/templates" -# Directory to store the imported user sampleSheets -LIBRARY_PREPARATION_SAMPLE_SHEET_DIRECTORY = "wetlab/SampleSheets4LibPrep/" +# Directory to store the imported user sample_sheet +LIBRARY_PREPARATION_SAMPLE_SHEET_DIRECTORY = "wetlab/sample_sheets_lib_prep/" ############################################################## diff --git a/wetlab/templates/wetlab/index.html b/wetlab/templates/wetlab/index.html index 9e49a3adc..be785dbf7 100644 --- a/wetlab/templates/wetlab/index.html +++ b/wetlab/templates/wetlab/index.html @@ -5,7 +5,6 @@
{% include 'registration/login_inline.html' %} -

{{organization_name}}

diff --git a/wetlab/utils/common.py b/wetlab/utils/common.py index 9d6aacde1..05d020029 100644 --- a/wetlab/utils/common.py +++ b/wetlab/utils/common.py @@ -3,7 +3,6 @@ import os import re import socket -import sys import traceback from datetime import datetime from logging.config import fileConfig @@ -124,15 +123,18 @@ def open_samba_connection(): logger = logging.getLogger(__name__) logger.debug("Starting function open_samba_connection") samba_data = get_samba_connection_data() - if not samba_data: + + try: + if samba_data["samba_folder_name"] != "": + samba_data["shared_folder_name"] = os.path.join( + samba_data["shared_folder_name"], + samba_data["samba_folder_name"], + ) + except KeyError: string_message = "Samba connection data on database is empty" logging_errors(string_message, True, False) - sys.exit(1) - if samba_data["samba_folder_name"] != "": - samba_data["shared_folder_name"] = os.path.join( - samba_data["shared_folder_name"], - samba_data["samba_folder_name"], - ) + raise + conn = SMBConnection( samba_data["user_id"], samba_data["user_password"], diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index 0db4b7cbf..c27d1833f 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -286,9 +286,9 @@ def search_update_new_runs(request_reason): if "ERROR" in users: string_message = ( experiment_name - + " : Description field does not contains userid." + + " : Description field does not contains userid or userid is not defined in iskylims." ) - wetlab.utils.common.logging_errors(string_message, True, False) + logger.info(string_message) wetlab.utils.crontab_process.handling_errors_in_run( experiment_name, "1" )