brapi_put_studies_studyDbId_observationunits: put /studies/{studyDbId}/observationunits

In mverouden/brapir: Client to Access BrAPI Compliant Plant Breeding Databases

put /studies/{studyDbId}/observationunits

Description

Update the Observation Units or upload new Observation Units for a specific Study

Usage

brapi_put_studies_studyDbId_observationunits(
  con = NULL,
  studyDbId = "",
  observationUnits = "",
  observationUnitXrefList = list(),
  treatmentList = list(),
  observationsList = list(),
  seasonList = list()
)

Arguments

con	list; required: TRUE; BrAPI connection object
studyDbId	character; required: TRUE; The internal study database identifier of which these observation units are updated or addded.
observationUnits	data.frame; required: TRUE; Data.frame of observation units. Each row in the observationUnits data.frame corresponds to a single observation unit. The following columns are required in the observationUnits argument data.frame: blockNumber vector of type character; The block number for each observation unit. Different systems may use different block designs. entryNumber vector of type character; The entry number for each observation unit. Different systems may use different entry systems. entryType vector of type character; The type of entry for each observation unit with possible values: "CHECK" | "FILLER" | "TEST" germplasmDbId vector of type character; The internal database identifier of a germplasm for each observation unit observationLevel vector of type character; The level of each observation unit, e.g. "plot", "plant" observationUnitDbId vector of type character; The internal database identifier for each observation unit in case of updating observationUnitName vector of type character; A human readable name for each observation unit plantNumber vector of type character; The plant number in a field. Applicable for observationLevel: "plant" plotNumber vector of type character: The plot number in a field. Applicable for observationLevel: "plot" positionCoordinateX vector of type character; to specify the X position coordinate for each observation unit. Different systems may use different coordinate systems. positionCoordinateXType vector of type character; to specify the type of X positional coordinate used for each observation unit. Must be one of the following values: LONGITUDE ISO 6709 standard, WGS84 geodetic datum. See Location Coordinate Encoding for details LATITUDE ISO 6709 standard, WGS84 geodetic datum. See Location Coordinate Encoding for details PLANTED_ROW The physical planted row number PLANTED_INDIVIDUAL The physical counted number, could be independEnt or within a planted row GRID_ROW The row index number of a square grid overlay GRID_COL The column index number of a square grid overlay MEASURED_ROW The distance in meters from a defined 0th row MEASURED_COL The distance in meters from a defined 0th column positionCoordinateY vector of type character; to specify the Y position coordinate for each observation unit. Different systems may use different coordinate systems. positionCoordinateYType vector of type character; to specify the type of positional Y coordinate used for each observation unit. Must be one of the following values: LONGITUDE ISO 6709 standard, WGS84 geodetic datum. See Location Coordinate Encoding for details LATITUDE ISO 6709 standard, WGS84 geodetic datum. See Location Coordinate Encoding for details PLANTED_ROW The physical planted row number PLANTED_INDIVIDUAL The physical counted number, could be independEnt or within a planted row GRID_ROW The row index number of a square grid overlay GRID_COL The column index number of a square grid overlay MEASURED_ROW The distance in meters from a defined 0th row MEASURED_COL The distance in meters from a defined 0th column replicate vector of type character; To specify the replicate number of each observation unit. May be the same as blockNumber. studyDbId vector of type character; The internal study database identifier each observation unit is related to. Must be the same as provided as the studyDbId argument in the function. The Examples Section shows an example of how to construct the observationUnits argument as a data.frame object.
observationUnitXrefList	list; required: FALSE; List of data frames, where each element of the list contains the cross references (as a data.frame) to a single observation unit, i.e. a single row in the obeservationUnits argument data.frame. Each observationUnitXref data.frame requires the following columns: id vector of type character; The unique identifier in the external reference 'source' system for each cross reference. source vector of type character; The system identifier (name, URL, etc) which has an external reference to the observation unit The Examples Section shows an example of how to construct the observationUnitXrefList argument as a list of data.frame objects.
treatmentList	list; required: FALSE; List of data frames, where each element of the list contains the treatments (as a data.frame) applied to a single observation unit, i.e. a single row in the observationUnits argument data.frame. Each treatment data.frame requires the following columns: factor vector of type character; The type of treatment/factor. e.g. 'fertilizer', 'inoculation', 'irrigation', etc modality vector of type character; The treatment/factor descritpion. e.g. 'low fertilizer', 'yellow rust inoculation', 'high water', etc The Examples Section shows an example of how to construct the treatmentList argument as a list of data.frame objects.
observationsList	list; required: FALSE; List of data frames, where each element of the list contains the observations (as a data.frame) of a single observation unit, i.e. a single row in the observationUnits argument data.frame. Each observations data.frame requires the following columns: germplasmDbId vector of type character; The internal database identifier, which uniquely identifies a germplasm which the observations have been done on. Must have the same value as the germplasmDbId in the row of the observationUnits data.frame, which the observations belong to. germplasmName vector of type character; Name of the germplasm. It can be the preferred name and does not have to be unique. observationDbId vector of type character; The internal database identifier which uniquely identifies an observation. observationLevel vector of type character; The level of an observation unit, e.g. "plot" or "plant". observationTimeStamp vector of type character; The date and time when this observation was made specified in the ISO 8601 format. observationUnitDbId vector of type character; The internal database identifier which uniquely identifies an observation unit. Must have the same value as the observationUnitDbId in the row of the observationUnits data.frame, which the observations belong to. observationUnitName vector of type character; A human readable name for an observation unit as defined earlier in the observationUnits data.frame the observations belong to. observationVariableDbId vector of type character; The internal database identifier which uniquely identifies an observation variable. observationVariableName vector of type character; A human readable name for an observation variable. operator vector of type character; The name or identifier of the entity which collected the observation. studyDbId vector of type character; The internal study database identifier each observation unit is related to. Must be the same as provided as the studyDbId argument in the function. uploadedBy vector of type character; The name or identifier of the user who uploaded the observation to the database system. value vector of type character; The value of the data collected as an observation. The Examples Section shows an example of how to construct the observationsList argument as a list of data.frame objects.
seasonList	list; required: FALSE; List of data frames, where each element of the list specifies seasonal information in which observations have been made. Therefore, the number of rows in an element of the list must match the number of rows in the linked element of the observationsList. Each season data.frame requires the following columns: season vector of type character; Name of the season. ex. 'Spring', 'Q2', 'Season A', etc. seasonDbId vector of type character; The internal database identifier which uniquely identifies a season. year vector of type character; The 4 digit year of the season. The Examples Section shows an example of how to construct the seasonList argument as a list of data.frame objects.

Details

Use this call for updating the Observation Units or uploading new Observation Units for a specific Study. The following rules are used:

• If observationUnitDbId or observationDbId is populated, they should be considered updates to existing records.

• If an existing record of a observationUnitDbId or observationDbId is not found, the entered data should be treated as new records and assign new internal database identifiers.

• If observationUnitDbId or observationDbId is un-populated (empty string or null) the entered data should be treated as new records and assign new internal database identifiers.

Value

data.frame

Author(s)

brapir generator package

References

BrAPI SwaggerHub

See Also

Other brapi_1.3: brapi_get_allelematrices_search(), brapi_get_allelematrices(), brapi_get_attributes_categories(), brapi_get_attributes(), brapi_get_breedingmethods_breedingMethodDbId(), brapi_get_breedingmethods(), brapi_get_calls(), brapi_get_commoncropnames(), brapi_get_germplasm_germplasmDbId_attributes(), brapi_get_germplasm_germplasmDbId_markerprofiles(), brapi_get_germplasm_germplasmDbId_mcpd(), brapi_get_germplasm_germplasmDbId_pedigree(), brapi_get_germplasm_germplasmDbId_progeny(), brapi_get_germplasm_germplasmDbId(), brapi_get_germplasm(), brapi_get_images_imageDbId(), brapi_get_images(), brapi_get_lists_listDbId(), brapi_get_lists(), brapi_get_locations_locationDbId(), brapi_get_locations(), brapi_get_maps_mapDbId_positions_linkageGroupName(), brapi_get_maps_mapDbId_positions(), brapi_get_maps_mapDbId(), brapi_get_maps(), brapi_get_markerprofiles_markerProfileDbId(), brapi_get_markerprofiles(), brapi_get_markers_markerDbId(), brapi_get_markers(), brapi_get_methods_methodDbId(), brapi_get_methods(), brapi_get_observationlevels(), brapi_get_observationunits(), brapi_get_ontologies(), brapi_get_people_personDbId(), brapi_get_people(), brapi_get_programs(), brapi_get_samples_sampleDbId(), brapi_get_samples(), brapi_get_scales_scaleDbId(), brapi_get_scales(), brapi_get_search_germplasm_searchResultsDbId(), brapi_get_search_images_searchResultsDbId(), brapi_get_search_markers_searchResultsDbId(), brapi_get_search_observationtables_searchResultsDbId(), brapi_get_search_observationunits_searchResultsDbId(), brapi_get_search_programs_searchResultsDbId(), brapi_get_search_samples_searchResultsDbId(), brapi_get_search_studies_searchResultsDbId(), brapi_get_search_variables_searchResultsDbId(), brapi_get_seasons(), brapi_get_studies_studyDbId_germplasm(), brapi_get_studies_studyDbId_layouts(), brapi_get_studies_studyDbId_observations(), brapi_get_studies_studyDbId_observationunits(), brapi_get_studies_studyDbId_observationvariables(), brapi_get_studies_studyDbId_table(), brapi_get_studies_studyDbId(), brapi_get_studies(), brapi_get_studytypes(), brapi_get_traits_traitDbId(), brapi_get_traits(), brapi_get_trials_trialDbId(), brapi_get_trials(), brapi_get_variables_observationVariableDbId(), brapi_get_variables(), brapi_get_vendor_orders_orderId_plates(), brapi_get_vendor_orders_orderId_results(), brapi_get_vendor_orders_orderId_status(), brapi_get_vendor_orders(), brapi_get_vendor_plates_submissionId(), brapi_get_vendor_specifications(), brapi_post_allelematrices_search(), brapi_post_images(), brapi_post_lists_listDbId_items(), brapi_post_lists(), brapi_post_methods(), brapi_post_people(), brapi_post_phenotypes(), brapi_post_scales(), brapi_post_search_germplasm(), brapi_post_search_images(), brapi_post_search_markers(), brapi_post_search_observationtables(), brapi_post_search_observationunits(), brapi_post_search_programs(), brapi_post_search_samples(), brapi_post_search_studies(), brapi_post_search_variables(), brapi_post_studies_studyDbId_table(), brapi_post_traits(), brapi_post_vendor_orders(), brapi_post_vendor_plates(), brapi_put_images_imageDbId_imagecontent(), brapi_put_images_imageDbId(), brapi_put_lists_listDbId(), brapi_put_methods_methodDbId(), brapi_put_people_personDbId(), brapi_put_samples(), brapi_put_scales_scaleDbId(), brapi_put_studies_studyDbId_layouts(), brapi_put_studies_studyDbId_observations(), brapi_put_traits_traitDbId()

Other Studies: brapi_get_search_studies_searchResultsDbId(), brapi_get_seasons(), brapi_get_studies_studyDbId_germplasm(), brapi_get_studies_studyDbId_layouts(), brapi_get_studies_studyDbId_observations(), brapi_get_studies_studyDbId_observationunits(), brapi_get_studies_studyDbId_observationvariables(), brapi_get_studies_studyDbId_table(), brapi_get_studies_studyDbId(), brapi_get_studies(), brapi_get_studytypes(), brapi_post_search_studies(), brapi_post_studies_studyDbId_table(), brapi_put_studies_studyDbId_layouts(), brapi_put_studies_studyDbId_observations()

Other Observations: brapi_get_observationlevels(), brapi_get_observationunits(), brapi_get_search_observationtables_searchResultsDbId(), brapi_get_search_observationunits_searchResultsDbId(), brapi_get_studies_studyDbId_observations(), brapi_get_studies_studyDbId_observationunits(), brapi_get_studies_studyDbId_table(), brapi_post_phenotypes(), brapi_post_search_observationtables(), brapi_post_search_observationunits(), brapi_post_studies_studyDbId_table(), brapi_put_studies_studyDbId_observations()

Examples

## Not run: 

# Create a connection object
con <- brapi_db()$testserver

# Create an observationUnits data.frame object
# with 4 observation units
observationUnits <- data.frame(
  blockNumber = c("1", "1", "1", "1"),
  entryNumber = c("5", "6", "7", "8"),
  entryType = c("TEST", "TEST", "TEST", "CHECK"),
  germplasmDbId = c("1", "1", "3", "3"),
  observationLevel = c("plot", "plant",  "plot", "plant"),
  observationUnitDbId = c("5", "6", "7", "8"),
  observationUnitName = c("Plot 3", "Plant 3", "Plot 4", "Plant 4"),
  plantNumber = c("0", "3", "0", "4"),
  plotNumber = c("3", "3", "4", "4"),
  positionCoordinateX = c("1", "1", "1", "1"),
  positionCoordinateXType = c("GRID_COL", "GRID_COL", "GRID_COL", "GRID_COL"),
  positionCoordinateY = c("1", "1", "2", "2"),
  positionCoordinateYType = c("GRID_ROW", "GRID_ROW", "GRID_ROW", "GRID_ROW"),
  replicate = c("0", "0", "0", "0"),
  studyDbId = c("1002", "1002", "1002", "1002")
)

# Create an observationUnitXref list
# with 4 element, because of 4 observation units
observationUnitXref1 <- data.frame(
  id = c(),
  source = c()
)
observationUnitXref2 <- data.frame(
  id = c("unit6id1", "unit6id2"),
  source = c("unit6src1", "unit6src2")
)
observationUnitXref3 <- data.frame(
  id = c(),
  source = c()
)
observationUnitXref4 <- data.frame(
  id = c("unit8id1"),
  source = c("unit8src1")
)
observationUnitXrefList <- list(
  observationUnitXref1, observationUnitXref2,
  observationUnitXref3, observationUnitXref4)
rm(observationUnitXref1, observationUnitXref2,
   observationUnitXref3, observationUnitXref4)

# Create a treatment list
# with 4 element, because of 4 observation units
treatment1 <- data.frame(
  factor = c("water regimen"),
  modality = c("deficit"))
treatment2 <- data.frame(
  factor = c("water regimen"),
  modality = c("deficit"))
treatment3 <- data.frame(
  factor = c("water regimen", "Phosphate level"),
  modality = c("deficit", "high"))
treatment4 <- data.frame(
  factor = c("water regimen", "Phosphate level"),
  modality = c("deficit", "high"))
treatmentList <- list(
  treatment1, treatment2,
  treatment3, treatment4)
rm(treatment1, treatment2,
   treatment3, treatment4)

# Create an observations list
# with 4 element, because of 4 observation units
observations1 <- data.frame(
  # two observation on the first observation unit!
  germplasmDbId = c("1", "1"),
  germplasmName = c("Name001", "Name001"),
  # one existing observation with specified DbId
  # one new observation, where a new DbId will be assigned
  observationDbId = c("9", ""),
  observationLevel = c("plot", "plot"),
  observationTimeStamp = c("2013-06-14T22:11:51Z", "2020-06-18T15:22:15Z"),
  observationUnitDbId = c("5", "5"),
  observationUnitName = c("Plot 3", "Plot 3"),
  observationVariableDbId = c("MO_123:100002", "MO_123:100003"),
  observationVariableName = c("Plant height", "Carotenoid"),
  operator = c("Bob", "Bob"),
  studyDbId = c("1002", "1002"),
  uploadedBy = c("Bob", "Bob"),
  value = c("2.1", "1.86"))
observations2 <- data.frame(
  germplasmDbId = c("1"),
  germplasmName = c("Name001"),
  observationDbId = c("10"),
  observationLevel = c("plant"),
  observationTimeStamp = c("2013-06-14T22:12:51Z"),
  observationUnitDbId = c("6"),
  observationUnitName = c("Plant 3"),
  observationVariableDbId = c("MO_123:100006"),
  observationVariableName = c("Virus severity"),
  operator = c("Bob"),
  studyDbId = c("1002"),
  uploadedBy = c("Bob"),
  value = c("4.5"))
observations3 <- data.frame(
  germplasmDbId = c("3"),
  germplasmName = c("Name003"),
  observationDbId = c("11"),
  observationLevel = c("plot"),
  observationTimeStamp = c("2013-06-14T22:13:51Z"),
  observationUnitDbId = c("7"),
  observationUnitName = c("Plot 4"),
  observationVariableDbId = c("MO_123:100003"),
  observationVariableName = c("Carotenoid"),
  operator = c("Bob"),
  studyDbId = c("1002"),
  uploadedBy = c("Bob"),
  value = c("1.4"))
observations4 <- data.frame(
  germplasmDbId = c("3"),
  germplasmName = c("Name003"),
  observationDbId = c("12"),
  observationLevel = c("plant"),
  observationTimeStamp = c("2013-06-14T22:14:51Z"),
  observationUnitDbId = c("8"),
  observationUnitName = c("Plant 4"),
  observationVariableDbId = c("MO_123:100005"),
  observationVariableName = c("Root color"),
  operator = c("Bob"),
  studyDbId = c("1002"),
  uploadedBy = c("Bob"),
  value = c("red"))
observationsList <- list(
  observations1, observations2,
  observations3, observations4)
rm(observations1, observations2,
   observations3, observations4)

# Create a season list
# with 4 element, because of 4 observation units
season1 <- data.frame(
 # two rows because observations1 has two observations!
 season = c("spring", "summer"),
 seasonDbId = c("3", "4"),
 year = c("2012", "2012"))
season2 <- data.frame(
  season = c("spring"),
  seasonDbId = c("3"),
  year = c("2012"))
season3 <- data.frame(
  season = c("spring"),
  seasonDbId = c("3"),
  year = c("2012"))
season4 <- data.frame(
  season = c("spring"),
  seasonDbId = c("3"),
  year = c("2012"))
seasonList <- list(
  season1, season2,
  season3, season4)
rm(season1, season2,
   season3, season4)

# Make put /studies/{studyDbId}/observationunits call
brapi_put_studies_studyDbId_observationunits(
  con = con,
  studyDbId = "1002",
  observationUnits = observationUnits,
  observationUnitXrefList = observationUnitXrefList,
  treatmentList = treatmentList,
  observationsList = observationsList,
  seasonList = seasonList)

## End(Not run)

mverouden/brapir documentation built on April 10, 2022, 5:36 p.m.