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Global Search with SolveBio clients

Global Search allows you to search for vaults, files, folders, and datasets by name, tags, user, date, and other metadata which can be customized. For more information about Global Search please look at Global Search Overview section.

Similarly to Global Search on the web application, the search functionality is available through SolveBio Python and R clients as well.

Please upgrade your Python and R clients

Search functionality is available with the latest versions of the Python client (v2.18.0 or higher) and R client (v2.12.0 or higher).

  • To upgrade Python client, run pip install --upgrade solvebio
  • To upgrade R client, run install.packages("solvebio")

Global Search basics

GlobalSearch performs search based on the provided set of parameters (filters, entities, query, limit, ordering, etc.):

  • query: Advanced search query string
  • filters: Filters to apply
  • entities: List of entity tuples to filter on (entity type, entity)
  • limit: Maximum number of query results to return

Note: Please see the documentation for the client you're using to find more about the search parameters and functionality.

When no search parameters are provided, it's equivalent to the Global Search page results, on the SolveBio Mesh web application, when no filters, queries or entities are selected:

Python R 
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from solvebio import GlobalSearch

# Search returns all objects by default
results = GlobalSearch()

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library("solvebio")

# By default it limits the number of objects in search result to 100
results <- GlobalSearch.search()

# To return all objects set parameter paginate to TRUE
results <- GlobalSearch.search(paginate = TRUE)

You may use the limit parameter to limit the number of returned objects:

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# No filters applied with limit parameter
results = GlobalSearch(limit = 200)

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# No filters applied with limit parameter
results <- GlobalSearch.search(limit = 200)

Similar as in the web application, where you can apply filters from Filter Dropdown, you can do the same operation with Python and R clients:

Python R 
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from solvebio import GlobalSearch

# Global Search object
search = GlobalSearch()

# Searching only for vaults
vaults = search.filter(type__in=["vault"])

# Searching based on date created
objects = search.filter(created_at__range=["2021-11-28","2021-12-28"])

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library("solvebio")

# Searching only for vaults
response <- GlobalSearch.search(filters = '[{"and":[["type__in",["vault"]]]}]')

# Searching based on date created
response <- GlobalSearch.search(filters = '[{"and":[{"and":[["created_at__range",["2021-11-21","2021-12-28"]]]}]}]')

Advanced Search query

In the Advanced Search it is explained how users can write their own query using the Query String syntax.

That is also possible to do using Python and R clients by providing query parameter:

Python R 
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from solvebio import GlobalSearch

# Advanced search (using keyword argument)
results = GlobalSearch(query="test")

# Advanced search (using positional argument)
results = GlobalSearch("fuji")

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library("solvebio")

# Advanced search (using keyword argument)
results <- GlobalSearch.search(query = "test", paginate = TRUE)

# Advanced search (using positional argument)
results <- GlobalSearch.search("fuji", paginate = TRUE)

Global Beacon Search, that is explained in the Global Beacon Search section, can be performed as well with both clients by using entities parameter:

Python R 
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# Entity search example
GlobalSearch(entities=[["gene", "BRCA2"]])

# Entity search example
GlobalSearch(entities=[["variant", "GRCH38-7-140753336-140753336-T"]])

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# Entity search example
GlobalSearch.search(entities = '[["gene","BRCA2"]]')

# Entity search example
GlobalSearch.search(entities = '[["variant", "GRCH38-7-140753336-140753336-T"]]')

Getting the Global Search subjects

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# Getting the subjects
search = GlobalSearch(entities=[["gene","BRCA2"]])
search.subjects()

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# Getting the subjects
GlobalSearch.subjects(entities = '[["gene","BRCA2"]]')

Additional examples

To see some additional examples and more details about Python and R client functionality please see the Examples section:

Last updated 2022-12-07.

Have questions or comments about this article? Get in touch with SolveBio Support by submitting a ticket or by sending us an email.