geomedb (version 2.0.1)

queryMetadata: Query metadata from the GEOME database.

Description

`queryMetadata` uses HTTP to query metadata from the GEOME database. If you are looking to download associated sequences from the SRA, you must include 'fastqMetadata' as one of the entities searched (this is done by default) and you should include "_exists_:bioSample" within your query statement to find only samples with associated SRA sequences

Usage

queryMetadata(entity = "Sample", projects = list(),
  expeditions = list(), select = list("fastqMetadata"), query = "",
  source = NULL, page = 0, limit = "10000")

Arguments

entity

String. The entity or entities (tables) to query. One of ('Event', 'Sample', 'Tissue', 'Sample_Photo', 'Event_Photo','fastqMetadata'). Default is to query 'Sample'

projects

List of projects to include in the query. The default is all projects

expeditions

Only applicable if projects are specified. list of expeditions to include in the query. The default is all expeditions

select

List of entities to include in the response. One of ('Event', 'Sample', 'Tissue', 'Sample_Photo', 'Event_Photo','fastqMetadata') The @param `entity` will always be included in the response. `fastqMetadata` included by default.

query

FIMS Query statement http://fims.readthedocs.io/en/latest/fims/query.html query string. Ex. 'yearCollected >= 2017 and country = "Indonesia"'. Your query must include "_exists_:bioSample" to find samples that have associated data in the SRA.

source

List of column names to include in the data.frame results. If there is no entity prefix, the column is assumed to belong to the @param `entity`. Ex. list('Event.eventID', 'Event.locality', 'materialSampleID', 'bcid', 'Event.bcid') 'materialSampleID' and 'bcid' in the above list are assumed to belong to the @param `entity`

page

The results page to return. Used to offset the page for large result sets. Defaults to 0.

limit

The number of results to include in the response. Defaults to 10000

Value

a list object with each entity (table) as a dataframe object

Examples

# NOT RUN {
df <- queryMetadata('Sample', projects=list(1), expeditions=list("acaach_CyB_JD", "acajap_CyB_JD"))
df <- queryMetadata('Sample', names=list("materialSampleID", "bcid"), query="Chordata")
df <- queryMetadata('Sample', projects=list(1), expeditions=list("acajap_CyB_JD"),
                    names=list("bcid"), query="yearCollected=2008")
df <- queryMetadata('Sample', select=list('Event', 'Tissue'), names=list("bcid"),
                    query="yearCollected=2008")
df <- queryMetadata('fastqMetadata', select=list('Event', 'Sample', 'Tissue'),
                    query="_exists_:bioSample")
acaoli <- queryMetadata(
    entity = "fastqMetadata", 
    query = "genus = Acanthurus AND specificEpithet = olivaceus AND _exists_:bioSample",
    select=c("Event"))
# }