#############################################################################################
#
# Sequence of commands executed to test LIMS client and Web Services.
# Each line has the following form
# 
# <unique command name>:<command>
#
# Lines starting with '#' are ignored.
# For each command a corresponding file named <unique command name> should exists in 
# the folder 'expected-out'
#
# - common ----------------------------
pre-login: login -u test -p <password>
pre-register-group: register-group /CISD
pre-assign-home-group: assign-home-group test /CISD
pre-register-group-with-wrong-leader: register-group /another-test-group -d willFail -l unknown_user
pre-register-group-with-leader: register-group /testgroup -d myDescription --leader test
register-role-assignments-strict: register-role-assignments testdata/register-role-assignments/role-assignments-strict.txt
pre-logout: logout
common-login: login -u test -p <password>
common-register-basic-viruses: register-materials VIRUS testdata/register-viruses/basic-viruses.txt
common-register-basic-controls: register-materials CONTROL testdata/register-controls/basic-controls.txt
3V-list-empty-projects: list-projects -P
common-register-project-default: register-project DEFAULT
common-list-initial-contacts: list-contacts
common-fail-unassign-control-layout-property-type: unassign-control-layout-property-type PLATE_GEOMETRY
common-fail-reassign-control-layout-property-type: assign-control-layout-property-type PLATE_GEOMETRY --mandatory=false
common-fail-register-oligos-with-unknown-column: register-materials oligo testdata/register-oligos/oligos1.txt
common-list-plate-types: list-plate-types
# - group -------------------------------
common-list-database-instances: list-database-instances -P
common-list-groups: list-groups -P
common-list-groups-from-db: list-groups -db cisd
common-register-project-unknown-group-fails: register-project /unknown/Proj
common-register-project-in-group: register-project /testgroup/testproj
common-list-projects-testgroup: list-projects cisd:/testgroup
common-list-projects-cisd: list-projects /cisd
common-fail-list-projects-nonexistent-group: list-projects /nonexistent
# -- simple properties
common-register-property-type-with-internally-managed-vocabulary-fails: register-property-types testdata/vocabulary-properties/propertyTypeInternalVocabulary.txt
common-fail-duplicated-assign-oligo-desc: assign-material-property-type OLIGO USER.DESCRIPTION
common-fail-assign-unknown-material-desc: assign-material-property-type YYY USER.DESCRIPTION
common-fail-assign-oligo-unknown-property: assign-material-property-type OLIGO PPP
common-assign-change-internally-managed-fail: assign-material-property-type OLIGO USER.NUCLEOTIDE_SEQUENCE --mandatory=false
common-assign-oligo-refseq: assign-material-property-type OLIGO USER.REFSEQ -m=true
common-register-property-types: register-property-types testdata/register-propertytypes/examplePropertyTypes.txt
common-register-property-types-twice: register-property-types testdata/register-propertytypes/examplePropertyTypesTwice.txt
common-assign-control-boolean-prop: assign-material-property-type CONTROL USER.IS_VALID
common-assign-control-date-prop: assign-material-property-type CONTROL USER.PURCHASE_DATE
common-list-property-types: list-property-types
common-list-material-property-types: list-material-property-types
common-list-property-types-pretty-print: list-property-types --pretty-print
common-assign-property-master-plate: assign-plate-property-type MASTER_PLATE USER.DESCRIPTION
# ---
common-register-experiments-failed: register-experiments SIRNA_HCS testdata/register-experiments/example3VExperiments.txt
common-list-empty-control-layouts-tsv: list-control-layouts
common-list-empty-control-layouts: list-control-layouts -P
common-assign-control-layout-property-type: assign-control-layout-property-type USER.DESCRIPTION
common-register-control-layout: register-control-layout -f testdata/register-controllayouts/properties.txt testdata/register-controllayouts/CL1.txt
common-list-contacts: list-contacts
common-list-contacts-pretty-print: list-contacts -P
common-assign-home-group: assign-home-group test /CISD
common-fail-assign-home-group-nonexistent-user: assign-home-group nonexistent /CISD
common-fail-assign-home-group-nonexistent-group: assign-home-group test /NONEXISTENT
common-list-contacts2: list-contacts
common-list-control-layouts: list-control-layouts
common-get-control-layout-type-info: get-control-layout-type-info
common-fail-get-control-layout-info: get-control-layout-info NOT_EXISTING
common-get-control-layout-info: get-control-layout-info CL1
common-get-control-layout-info-pretty-print: get-control-layout-info --pretty-print CL1
common-fail-get-plate-info-of-control-layout: get-plate-info CL1
common-list-experiment-types: list-experiment-types
common-list-experiment-types-pretty-print: list-experiment-types --pretty-print
common-list-empty-experiments-tsv: list-experiments SIRNA_HCS
common-list-experiments: list-experiments SIRNA_HCS -P
common-list-material-types: list-material-types
common-list-material-types-pretty-print: list-material-types --pretty-print
common-get-material-type-info: get-material-type-info GENE
common-get-material-type-info-pretty-print: get-material-type-info --pretty-print GENE
common-assign-experiment-date-prop: assign-experiment-property-type SIRNA_HCS USER.PURCHASE_DATE
common-get-experiment-type-info: get-experiment-type-info --pretty-print SIRNA_HCS
common-list-invalid-material: list-materials BLABLA
common-list-viruses: list-materials VIRUS
common-register-viruses: register-materials VIRUS testdata/register-viruses/viruses.txt
common-list-new-viruses: list-materials VIRUS
common-register-viruses-twice: register-materials VIRUS testdata/register-viruses/viruses.txt
common-register-bacteria: register-materials BACTERIUM testdata/register-bacteria/bacteria.txt
common-list-bacteria: list-materials BACTERIUM
common-list-controls: list-materials CONTROL
common-list-controls-pretty-print: list-materials CONTROL --pretty-print
common-fail-assign-prop-control-wrong-value-types: assign-material-property-type -m CONTROL USER.SIZE \
-f testdata/assign-material-property-type/control-missing-props-real-type.txt
common-register-controls: register-materials CONTROL testdata/register-controls/controls.txt
# TODO 2008-03-27, Tomasz Pylak: it's a bug, new error message is not complete because we use lower-case codes. 
common-register-controls-twice: register-materials CONTROL testdata/register-controls/controls.txt
common-list-new-controls: list-materials CONTROL
# --- assign properties
common-fail-assign-control-mandatory-desc: assign-material-property-type -m CONTROL USER.EYE_COLOR
common-fail-assign-prop-change-to-mandatory-incomplete: assign-material-property-type CONTROL USER.EYE_COLOR -m \
-f testdata/assign-material-property-type/incomplete-missing-descriptions.txt
common-fail-assign-prop-change-to-mandatory-wrong-code: assign-material-property-type CONTROL USER.EYE_COLOR --mandatory \
-f testdata/assign-material-property-type/wrong-code-missing-descriptions.txt
common-assign-prop-change-to-mandatory: assign-material-property-type CONTROL USER.EYE_COLOR --mandatory \
-f testdata/assign-material-property-type/missing-descriptions.txt
common-assign-prop-change-to-mandatory-twice: assign-material-property-type CONTROL USER.EYE_COLOR --mandatory \
-f testdata/assign-material-property-type/missing-descriptions.txt
common-assign-prop-change-to-optional: assign-material-property-type CONTROL USER.EYE_COLOR
# assign new property type to a material, providing some missing values at the same time
common-assign-new-prop-with-value: assign-material-property-type CONTROL USER.VOLUME \
-f testdata/assign-material-property-type/control-missing-props-real-type.txt
# commands to register and check controls with real, integer and string properties, where some of them are null
common-assign-prop-control-size: assign-material-property-type CONTROL USER.SIZE
common-register-controls-with-properties: register-materials CONTROL testdata/assign-material-property-type/controls-with-properties.txt
common-list-controls-with-properties: list-materials CONTROL
# -- controlled vocabulary
common-register-vocabulary-organism: register-vocabulary USER.ORGANISM testdata/vocabulary-properties/vocabularyTermsOrganism.txt -d available-organism 
common-register-vocabulary-gender: register-vocabulary USER.GENDER testdata/vocabulary-properties/vocabularyTermsGender.txt
common-get-vocabulary-info: get-vocabulary-info USER.ORGANISM
common-get-vocabulary-info-empty-fail-tsv: get-vocabulary-info UNKNOWN
common-get-vocabulary-info-empty-fail: get-vocabulary-info UNKNOWN -P
common-list-vocabularies: list-vocabularies
common-register-vocabulary-human-add-terms-nonexisten-vocabulary-fail: register-vocabulary USER.HUMAN testdata/vocabulary-properties/vocabularyTermsHumanAdd.txt --add-terms
common-register-vocabulary-human: register-vocabulary USER.HUMAN testdata/vocabulary-properties/vocabularyTermsHuman.txt -d Humans
common-register-vocabulary-human-add-terms: register-vocabulary USER.HUMAN testdata/vocabulary-properties/vocabularyTermsHumanAdd.txt --add-terms
common-register-vocabulary-human-add-terms-already-existing-term-fail: register-vocabulary USER.HUMAN testdata/vocabulary-properties/vocabularyTermsHumanAdd.txt --add-terms
common-get-vocabulary-info-human: get-vocabulary-info USER.HUMAN 
common-register-vocabulary-plate-geometry-internal-add-terms-fail: register-vocabulary PLATE_GEOMETRY testdata/vocabulary-properties/vocabularyTermsHumanAdd.txt --add-terms
common-register-property-types-vocabulary: register-property-types testdata/vocabulary-properties/examplePropertyTypes.txt
# assign peoperty providing wrong missing values - not from the vocabulaty set.
common-assign-gender-to-bacteria-fail: assign-material-property-type BACTERIUM USER.GENDER -m -f testdata/vocabulary-properties/missing-property-bacteria-wrong-gender.txt
common-assign-gender-to-bacteria: assign-material-property-type BACTERIUM USER.GENDER -m -f testdata/vocabulary-properties/missing-property-bacteria-gender.txt
common-register-bacteria-wrong-gender-fail: register-materials BACTERIUM testdata/vocabulary-properties/bacteriaWrongGender.txt
common-assign-domain-to-bacteria: assign-material-property-type BACTERIUM USER.ORGANISM
common-register-bacteria-vocabulary-props: register-materials BACTERIUM testdata/vocabulary-properties/bacteriaWithVocabularyProps.txt
common-get-material-type-info-with-props: get-material-type-info BACTERIUM
common-list-materials-bacterium-with-props: list-materials BACTERIUM
common-unassign-property-type-bacterium-gender: unassign-material-property-type --force BACTERIUM USER.GENDER
common-fail-unassign-unassigned-property-type-bacterium-gender: unassign-material-property-type BACTERIUM USER.GENDER
common-fail-unassign-unexisting-property-type-bacterium-nonexistent: unassign-material-property-type BACTERIUM USER.NONEXISTENT
common-list-materials-bacterium-without-props: list-materials BACTERIUM
common-list-experiment-property-types: list-experiment-property-types
common-list-experiment-property-types-pretty-print: list-experiment-property-types -P
common-list-plate-property-types-pretty-print: list-plate-property-types -P
common-list-control-layout-property-types-pretty-print: list-control-layout-property-types -P
# ---
common-list-projects: list-projects
common-register-genes: register-materials GENE testdata/register-genes/genes.txt
common-list-genes: list-materials GENE MYGENE*
common-register-oligos-missing-mandatory-column: register-materials OLIGO testdata/register-oligos/oligos-missing-mandatory-column.txt
common-register-oligos-missing-mandatory-value: register-materials OLIGO testdata/register-oligos/oligos-missing-mandatory-value.txt
common-register-oligos-mandatory-only: register-materials OLIGO testdata/register-oligos/oligos-mandatory-only.txt
common-register-oligos-null-values: register-materials OLIGO testdata/register-oligos/oligos-null-values.txt
common-list-oligos-check: list-materials OLIGO XX*
common-register-oligos-fails-duplicated-column-name: register-materials OLIGO testdata/register-oligos/oligos-duplicated-column-name.txt
common-register-oligos-fails-no-code: register-materials OLIGO testdata/register-oligos/oligos-no-code.txt
common-register-oligos-fails-no-inhibitor: register-materials OLIGO testdata/register-oligos/oligos-no-inhibitor.txt
common-register-oligos-fails-unknown-column: register-materials OLIGO testdata/register-oligos/oligos-unknown-column.txt
common-register-oligos: register-materials OLIGO testdata/register-oligos/oligos1.txt
common-list-oligos: list-materials OLIGO OL*
common-register-oligos-failed: register-materials OLIGO testdata/register-oligos/oligos2.txt
common-list-oligos-after-rollback: list-materials OLIGO OL*
common-register-master-plate1: register-master-plate -p PLATE_GEOMETRY=384_WELLS_16X24 testdata/register-master-plates/MP001-1.txt xMB1xCode
common-register-master-plate2: register-master-plate -p PLATE_GEOMETRY=384_WELLS_16X24 testdata/register-master-plates/MP002-1.txt xMB2xCode
common-register-master-plate-global: register-master-plate -p PLATE_GEOMETRY=384_WELLS_16X24 testdata/register-master-plates/MP001-1.txt xMB1xCode --sample-identifier /MP
common-check-registered-master-plates: get-plate-info MP001-1
common-fail-get-control-layout-info-because-it-was-a-plate: get-control-layout-info MP001-1
common-register-mp-repeated-well:    register-master-plate -p PLATE_GEOMETRY=384_WELLS_16X24 testdata/register-master-plates/mp-repeated-well.txt xMB5xCode
common-register-mp-unknown-material: register-master-plate -p PLATE_GEOMETRY=384_WELLS_16X24 testdata/register-master-plates/mp-unknown-material.txt xMB6xCode
common-register-mp-unknown-material-type: register-master-plate -p PLATE_GEOMETRY=384_WELLS_16X24 testdata/register-master-plates/mp-unknown-maty.txt xMB6xCode
common-register-mp-wrong-header:     register-master-plate -p PLATE_GEOMETRY=384_WELLS_16X24 testdata/register-master-plates/mp-wrong-header.txt xMB7xCode
common-register-mp-wrong-well-code:  register-master-plate testdata/register-master-plates/mp-wrong-well-code.txt xMBxCode
common-check-unregistered-wrong-mp: list-plates MASTER_PLATE
common-check-unregistered-wrong-mp-pretty-print: list-plates MASTER_PLATE -P
# TODO Tomasz Pylak 2008-07-16: this cmd should test wrong processing instructions, but does not 
common-check-default-strategy: register-experiments SIRNA_HCS testdata/register-experiments/exampleExperiments.txt
common-parse-file-with-extra-column: register-experiments SIRNA_HCS testdata/register-experiments/exampleExperimentsExtraTabs.txt
common-parse-file-with-missing-column: register-experiments SIRNA_HCS testdata/register-experiments/exampleExperimentsMissingColumn.txt
##
# - 3V ----------------------------
##
3V-register-project1: register-project NEMO
3V-register-project2: register-project NOE
3V-list-projects: list-projects
3V-list-projects-pretty-print: list-projects --pretty-print
3V-register-control-layout: register-control-layout -p PLATE_GEOMETRY=384_WELLS_16X24 testdata/register-experiments/CL-3V.txt
3V-list-control-layouts: list-control-layouts
3V-list-control-layouts-pretty-print: list-control-layouts --pretty-print
3V-register-dilution-plate: register-dilution-plates testdata/register-dilutionplate/exampleDilutionPlates.txt
common-assign-plate-description-prop: assign-plate-property-type CELL_PLATE USER.DESCRIPTION -m -g DefaultDescription
common-get-plate-type-info: get-plate-type-info -P CELL_PLATE
3V-register-cell-plate-failed-missing-mandatory-column: register-cell-plates testdata/register-cellplate/exampleCellPlates.txt
3V-register-cell-plate: register-cell-plates testdata/register-cellplate/exampleCellPlatesWithDescriptions.txt --control-layout CL-3V
3V-register-reinfection-plates: register-reinfection-plates testdata/register-reinfectionplate/exampleReinfectionPlates.txt
3V-get-reinfection-plate-info: get-plate-info 3VRP1a
3V-list-reinfection-plates: list-plates REINFECT_PLATE
3V-list-reinfection-plates-pretty-print: list-plates REINFECT_PLATE --pretty-print
3V-list-empty-experiments: list-experiments SIRNA_HCS -P
3V-register-experiments: register-experiments SIRNA_HCS testdata/register-experiments/example3VExperiments.txt
3V-register-experiment-with-group: register-experiments SIRNA_HCS testdata/register-experiments/example3VExperimentsInGroup.txt
3V-fail-assign-experiment-property: assign-experiment-property-type SIRNA_HCS USER.GENDER -m \
-f testdata/assign-experiment-property/wrong-example-properties.txt
3V-assign-experiment-property-with-global: assign-experiment-property-type SIRNA_HCS USER.GENDER \
-g male
3V-list-experiments: list-experiments SIRNA_HCS
3V-list-experiments-with-project: list-experiments SIRNA_HCS -p NEMO --time-interval :now
3V-get-plate-locations: get-plate-locations -e NEMO/EXP1 -i 1
3V-get-plate-locations-by-symbol: get-plate-locations A1BG
3V-register-data-set: register-data-set  3VCP1 xxx/yyy/zzz PROPRIETARY
3V-register-analysis-data-set: register-data-set -p IMAGE_ANALYSIS -f 3VPROPRIETARY 3VCP1 analysis/result PROPRIETARY
3V-list-experiments-with-last-dataset-date: list-experiments SIRNA_HCS
3V-get-experiment: get-experiment-info NEMO/EXP1
3V-list-cell-plates: list-plates CELL_PLATE 
3V-list-cell-plates-with-no-experiment: list-plates CELL_PLATE -n
3V-list-dilution-plates: list-plates DILUTION_PLATE 
3V-list-dilution-plates-pretty-print: list-plates DILUTION_PLATE --pretty-print
3V-get-dilution-plate-info: get-plate-info 3V-125
3V-get-cell-plate-info: get-plate-info 3VCP2
3V-invalidate-cell-plates: invalidate-plates 3VCP1 3VCP2 --invalidation-reason wrong-code
3V-invalidate-cell-plates-from-file: invalidate-plates -f testdata/register-cellplate/invalidate_plates.txt
3V-invalidate-master-plate: invalidate-plates MP001-1 -r Reason.
3V-list-master-plates-show-invalidated: list-plates MASTER_PLATE -a
3V-list-dilution-plates-show-invalidated: list-plates DILUTION_PLATE -a
3V-list-cell-plates-show-invalidated: list-plates CELL_PLATE -a
3V-list-reinfection-plates-show-invalidated: list-plates REINFECT_PLATE -a
3V-list-master-plates-dont-show-invalidated: list-plates MASTER_PLATE
3V-list-dilution-plates-dont-show-invalidated: list-plates DILUTION_PLATE
3V-list-cell-plates-dont-show-invalidated: list-plates CELL_PLATE -P
3V-list-reinfection-plates-dont-show-invalidated-tsv: list-plates REINFECT_PLATE
3V-list-reinfection-plates-dont-show-invalidated: list-plates REINFECT_PLATE -P
3V-get-experiment-with-invalid-plate-dont-show-invalid: list-experiment-plates NEMO/EXP1
3V-get-experiment-with-invalid-plate-show-invalid: list-experiment-plates -a NEMO/EXP1
3V-list-experiment-datasets: list-experiment-datasets NEMO/EXP1 -P -a
3V-get-invalid-dilution-plate-info: get-plate-info 3V-123
3V-get-invalid-cell-plate-info: get-plate-info 3VCP2
3V-get-plate-location-dont-show-invalid:get-plate-locations -e NEMO/EXP1 AMPD2
3V-get-plate-location-show-invalid:get-plate-locations -a -e NEMO/EXP1 AMPD2
3V-unassign-plate-property-type: unassign-plate-property-type --force CELL_PLATE USER.DESCRIPTION
3V-register-cell-plate-with-invalid-dilution:register-cell-plates testdata/register-cellplate/invalid_dilution.txt
3V-register-dilution-plate-with-invalid-master:register-dilution-plates testdata/register-dilutionplate/invalid_master.txt
3V-register-reinfection-plate-with-invalid-cell:register-reinfection-plates testdata/register-reinfectionplate/invalid_cell.txt
3V-register-experiment-with-invalid-plate: register-experiments SIRNA_HCS testdata/register-experiments/example3VExperimentsWithInvalidPlate.txt
3V-register-data-set-with-invalid-plate: register-data-set  3VCP1 xxx/yyy/zzz2 PROPRIETARY
##
# - common ----------------------------
##
common-multiCL-register-CL-1: register-control-layout -p PLATE_GEOMETRY=384_WELLS_16X24 testdata/register-controllayouts/B1B3.txt
common-multiCL-register-CL-2: register-control-layout -p PLATE_GEOMETRY=384_WELLS_16X24 testdata/register-controllayouts/C1.txt
common-multiCL-register-CL-3: register-control-layout -p PLATE_GEOMETRY=384_WELLS_16X24 testdata/register-controllayouts/C2.txt
common-multiCL-register-CL-4: register-control-layout -p PLATE_GEOMETRY=384_WELLS_16X24 testdata/register-controllayouts/C3.txt
common-multiCL-register-MP-overlapping-CL-fails: register-master-plate -p PLATE_GEOMETRY=384_WELLS_16X24 testdata/register-master-plates/MP1-mixed.txt batch-code --control-layout CL1
common-multiCL-register-MP1-with-CL-fails: register-master-plate -p PLATE_GEOMETRY=384_WELLS_16X24 testdata/register-master-plates/MP1-mixed.txt batch-code -c MP001-1
common-multiCL-register-MP1-with-CL: register-master-plate -p PLATE_GEOMETRY=384_WELLS_16X24 testdata/register-master-plates/MP1-mixed.txt batch-code -c C1
common-multiCL-register-MP2-no-CL: register-master-plate -p PLATE_GEOMETRY=384_WELLS_16X24 testdata/register-master-plates/MP2-no-CL.txt batch-code
common-multiCL-register-dilution-plates: register-dilution-plates testdata/multi-cl-plates/dilution-plates.txt
common-multiCL-register-cell-plates-fails: register-cell-plates testdata/multi-cl-plates/cell-plates-fails.txt --control-layout C1
common-multiCL-register-cell-plates: register-cell-plates testdata/multi-cl-plates/cell-plates.txt
common-multiCL-reinf-plates-overlap-MP-fails: register-reinfection-plates testdata/multi-cl-plates/reinfection-plates-overlap-MP-fails.txt -c CISD:/CISD/C1
common-multiCL-reinf-plates-overlap-DP-fails: register-reinfection-plates testdata/multi-cl-plates/reinfection-plates-overlap-DP-fails.txt -c C2
common-multiCL-register-reinf-plates: register-reinfection-plates testdata/multi-cl-plates/reinfection-plates.txt
common-multiCL-get-MP-plate-info: get-plate-info MP1-mixed
common-multiCL-get-DP-plate-info: get-plate-info DP1-A
common-multiCL-get-CP-plate-info: get-plate-info CP1-A1
common-multiCL-get-RP-plate-info: get-plate-info RP1-A2x
common-multiCL-register-experiments: register-experiments SIRNA_HCS testdata/multi-cl-plates/experiment.txt
common-multiCL-list-experiment-plates: list-experiment-plates DEFAULT/EXP-X
# - reuse screenable plates from invalidated experiments
common-resue-plates-register-experiments-fail: register-experiments SIRNA_HCS testdata/multi-cl-plates/experimentWithReusedPlates.txt
common-resue-plates-invalidate-experiment: invalidate-experiment DEFAULT/EXP-X
common-resue-plates-list-cell-plates-no-exp: list-plates CELL_PLATE CP1*
common-resue-plates-register-experiments: register-experiments SIRNA_HCS testdata/multi-cl-plates/experimentWithReusedPlates.txt
common-resue-plates-experiment-info: list-experiment-plates DEFAULT/EXP-REUSE
common-resue-plates-list-cell-plates-with-exp: list-plates CELL_PLATE CP1*
# - end reuse
common-register-empty-master-plate: register-master-plate x-Batch-x -p PLATE_GEOMETRY=384_WELLS_16X24 --empty empty-MP
common-get-empty-master-plate-info: get-plate-info empty-MP -P
common-list-experiments-project-group: list-experiments SIRNA_HCS --project /CISD/NEMO
common-list-experiments-group: list-experiments SIRNA_HCS --group /NEMO
list-master-plates-group-pattern: list-plates MASTER_PLATE -P /MP cisd:/cisd/*1*
common-register-experiments-inconsistent-group-fail: register-experiments SIRNA_HCS testdata/multi-cl-plates/experimentInconsistentPlates.txt
common-register-experiments-inconsistent-group-default-fail: register-experiments SIRNA_HCS testdata/multi-cl-plates/experimentInconsistentGroupNotFound.txt
common-logout2: logout