Querying Assessment Data

ROAR's assessment data is exported from Firestore to BigQuery. This guide will walk you through the process of querying assessment data from BigQuery, including installation, authentication, understanding schemas, and exporting results to your local machine or a Google Cloud bucket.

How to use this guide

Please read through this entire guide (and work through the examples) before executing your production queries with BigQuery. BigQuery is a very powerful tool but its incorrect use can inflate ROAR's costs so it is important to read through the guide to the end to adopt best practices.

Tables and Views

BigQuery organizes data into datasets and tables (or views). Below are the key views available for querying in our lab's BigQuery project. The diagram below represents the relationships between these different views.

The diagram above only lists a subset of the attributes for each entity. For an exhaustive list of attributes for each view, click on the links below to view schema tables:

• users
• user_runs
• user_trials
• districts
• schools
• classes
• groups
• families
• guests: same as users but with guest_uid as the private key instead of roar_uid
• guest_runs: same as user_runs but with the foreign key guest_uid instead of roar_uid
• guest_trials: same as user_trials but with the foreign key guest_uid instead of roar_uid

In each of these schema tables linked above, the columns "Field name," "Data type," and "Description" are self-explanatory. The "Key type" column indicates whether the field is a primary key (PK), unique key (UK), foreign key (FK), or none. A primary key uniquely identified each row in a table and cannot be NULL. A foreign key is references the primary key of another table. It establishes a relationship between two tables. A unique key is unique across all rows but can allow NULL values.

Installation and initialization

To query assesement data, you will need the bq command line tool to interact with BigQuery from your terminal. To install bq,

1. Install the gcloud CLI

2. Initialize the gcloud CLI. When prompted to log in with your Google account, choose your Stanford-affiliated account. When prompted to select a project, choose gse-roar-assessment.

3. Install the bq tool if it is not already included:

   gcloud components install bq
   

4. Verify installation:

   bq version
   

The initialization step above should have authenticated you into your Google account. But if you need to log in again, use

gcloud auth login

Similarly, the initialization step should set a default project ID. But if you need to reset the project ID, use

gcloud config set project gse-roar-assessment

Querying Data

The bq tool allows you to execute SQL queries against the ROAR BigQuery tables listed above. If you are new to SQL, we recommend viewing the Software Carpentry SQL lessons. Once you are comfortable with SQL, see the examples below to guide you in querying ROAR data.

Querying a single table

Cost Awareness

Queries in BigQuery incur costs based on the amount of data processed. Use filters and limits to minimize costs.

In the examples below, we will use LIMIT 10 to limit our results to only 10 rows. We recommend that you do the same when refining your queries interactively. When you are satisfied with the query that you've built, then you can remove the LIMIT part to get all of the results you want.

Research coordinators often want to query user runs. To pull 10 runs, you would use

bq query --nouse_legacy_sql \
'SELECT * FROM `gse-roar-assessment.assessment.user_runs` LIMIT 10'

The output of this command is written to STDOUT so it can be difficult to parse or feed into downstream analysis. Instead, let's save the output to a JSON file. Use the format prettyjson for a more human readable JSON file.

bq query --nouse_legacy_sql --format=prettyjson \
'SELECT
  *
FROM
  `gse-roar-assessment.assessment.user_runs`
LIMIT
  10' > output.json

Exporting data to CSV

Researchers often want to export data to a CSV file. Let's see what happens when we change the format in that last query to csv:

bq query --nouse_legacy_sql --format=csv \
'SELECT
  *
FROM
  `gse-roar-assessment.assessment.user_runs`
LIMIT
  10' > output.csv

That command does create an ouput.csv file but if we inspect the contents, we see

Error printing table: Cannot print repeated field "assigning_districts" in CSV
format.

The assigning_districts field has the data type ARRAY<STRING>. Since CSV is a flat file format and cannot directly represent nested structures like arrays.

Selecting and excluding fields

One way to get around this limitation is to select only flattened fields. We can explicitly select certain field from the user_runs table:

bq query --nouse_legacy_sql --format=csv \
'SELECT
  roar_uid, run_id, reliable
FROM
  `gse-roar-assessment.assessment.user_runs`
LIMIT
  10' > output.csv

Or we can exclude the troublesome fields and select all remaining fields using EXCEPT:

bq query --nouse_legacy_sql --format=csv \
'SELECT
  * EXCEPT(
    assigning_districts,
    assigning_schools,
    assigning_classes,
    assigning_groups,
    assigning_families
  )
FROM
  `gse-roar-assessment.assessment.user_runs`
LIMIT
  10' > output.csv

Flattening nested fields

That works, but what if we actually want the data in those nested fields? We have options here as well. We can "stringify" the array fields, converting them into a JSON-like string:

bq query --nouse_legacy_sql --format=csv \
'SELECT
  * EXCEPT(
    assigning_districts,
    assigning_schools,
    assigning_classes,
    assigning_groups,
    assigning_families
  ),
  TO_JSON_STRING(assigning_districts) as assigning_districts,
  TO_JSON_STRING(assigning_schools) as assigning_schools,
  TO_JSON_STRING(assigning_classes) as assigning_classes,
  TO_JSON_STRING(assigning_groups) as assigning_groups,
  TO_JSON_STRING(assigning_families) as assigning_families,
FROM
  `gse-roar-assessment.assessment.user_runs`
LIMIT
  10' > output.csv

Using the WHERE clause

You can use the WHERE clause to filter results. For example, to select only runs with the task ID "swr", use

bq query --nouse_legacy_sql --format=csv \
'SELECT
  roar_uid, run_id, task_id
FROM
  `gse-roar-assessment.assessment.user_runs`
WHERE
  task_id = "swr"
LIMIT
  10' > output.csv

You can use the AND keywork to create compound filters. For example, you could query all "swr" runs that were started after a certain date using

bq query --nouse_legacy_sql --format=csv \
'SELECT
  roar_uid, run_id, task_id, time_started
FROM
  `gse-roar-assessment.assessment.user_runs`
WHERE
  task_id = "swr"
AND
  time_started > "2024-08-08"
LIMIT
  10' > output.csv

Sorting results

You can use the ORDER BY clause to sort your results. For example, you can sort the results in the last query by time_started using

bq query --nouse_legacy_sql --format=csv \
'SELECT
  roar_uid, run_id, task_id, time_started
FROM
  `gse-roar-assessment.assessment.user_runs`
WHERE
  task_id = "swr"
AND
  time_started > "2024-08-08"
ORDER BY
  time_started ASC
LIMIT
  10' > output.csv

Note that we used the ASC keyword to sort the results in ascending order. To reverse that and sort results in descending order, use DESC. For example, a very popular and useful query for researchers it to request the 10 most recent runs for a given task ID:

bq query --nouse_legacy_sql --format=csv \
'SELECT
  roar_uid, run_id, task_id, time_started
FROM
  `gse-roar-assessment.assessment.user_runs`
WHERE
  task_id = "swr"
ORDER BY
  time_started DESC
LIMIT
  10' > output.csv

Querying array fields

You can use the UNNEST() keyword to access the elements of an array field. This will allow you to query based on values that appear in those arrays. In this example, we want to retireve 10 records from the user_runs table where the user was assigned to the school with ID "uSpviE1t4lUzH8J7I9aQ".

bq query --nouse_legacy_sql --format=csv \
'SELECT
  roar_uid, run_id, task_id, time_started,
  TO_JSON_STRING(assigning_schools) as assigning_school
FROM
  `gse-roar-assessment.assessment.user_runs`
WHERE
  "uSpviE1t4lUzH8J7I9aQ" IN UNNEST(assigning_schools)
ORDER BY
  time_started DESC
LIMIT
  10' > output.csv

Note that we use UNNEST in the WHERE clause and still have to use TO_JSON_STRING to flatten the assigning_schools column as above.

Advanced queries that use multiple tables

All of our examples so far have queried only one table at a time. However, some queries require referencing multiple tables. For example, the user_trials table has a foreign key called roar_uid that references the private key roar_uid in the users table. But researchers don't always know the roar_uid of a particular user. They may instead want to query by the assessment_pid in the users table.

To query across multiple tables in BigQuery where you need to match a foreign key (roar_uid) from one table (user_trials) with a private key in another table (users), and filter based on a unique key (assessment_pid), you can use a JOIN clause. In the below example, we query for 10 trials from the user with PID "efschl-shs-a05c9862".

bq query --nouse_legacy_sql --format=csv \
'SELECT ut.*, u.assessment_pid
 FROM `gse-roar-assessment.assessment.user_trials` AS ut
 JOIN `gse-roar-assessment.assessment.users` AS u
   ON ut.roar_uid = u.roar_uid
 WHERE u.assessment_pid = "efschl-shs-a05c9862"
 LIMIT 10' > output.csv

This last query introduced a few new concepts so let's break it down.

• The SELECT clause selects which columns to include in the results.
• We use the JOIN keyword to join two tables together into one.
• While doing so, we use the AS keyword to refer to each table by a shortened variable name. So the user_trials table is assigned the alias ut and the users table is assigned the alias u.
• We use the ON keyword to identify the column names on which to join the two tables.
• The JOIN, AS, and ON clauses combine to defined a new table from which to select data. This joined table becomes the argument to the FROM keyword.
• Finally, we use the WHERE keyword as before to filter results to the requested PID.

Similarly, you could combine three different tables by chaining multiple JOIN clauses together. Let's combine the users, user_runs, and user_trials tables. Start by recognizing that the users and user_runs tables are linked by the roar_uid column. Similarly, the user_runs and user_trials columns are linked by the run_id column. Then the order of these joins should reflect the logical relationships between these tables:

bq query --nouse_legacy_sql --format=csv \
'SELECT ut.*, u.assessment_pid, ur.scores
FROM `gse-roar-assessment.assessment.users` AS u
JOIN `gse-roar-assessment.assessment.user_runs` AS ur
  ON u.roar_uid = ur.roar_uid
JOIN `gse-roar-assessment.assessment.user_trials` AS ut
  ON ur.run_id = ut.run_id
LIMIT 10' > output.csv

Exporting large queries to a google cloud bucket

For large datasets, it’s more efficient to export query results directly to a Google Cloud Storage (GCS) bucket. This has a few benefits

• Handling of large datasets: GCS can handle large datasets that might exceed the limits of local storage or network speed. Large files won't impact local disk space or system performance.
• Cost-effectiveness: Avoid repeated query costs by exporting the results once and reusing data.
• Sharing and collaboration: GCS facilitates data sharing with team members or external collaborators. You can grant specific access to a GCS bucket or file to external collaborators without sharing your local system.

Follow the naming conventions

In the steps below, you will create GCS buckets to which to export data. In order to avoid name collisions, please read the below naming conventions thoroughly and follow the conventions strictly. The ROAR dev team will periodically audit the bucket names reserves the right to delete any buckets that do not follow the naming convention.

Exporting to a GCS Bucket requires a few steps.

1. Create a Google Cloud Storage bucket

   The first step in exporting query results to a GCS bucket is to create a bucket. You MUST adopt the following naming convention when creating export buckets: BUCKET_NAME = roar-bq-export_[IDENTIFIER]. If your GCS bucket is for your own personal use, IDENTIFIER must be the string internal_ followed by your SUNet ID. For example, Adam's bucket name would be roar-bq-export_internal_adamrh. If the bucket is for export to an external collaborator, the IDENTIFIER must be the string external_ followed by the name of that organization. For example, a bucket that will be shared with collaborators at the Basque Center on Cognition, Brain, and Language (BCBL) would be named roar-bq-export_external_bcbl. In the commands below, replace BUCKET_NAME with the actual bucket name.

   gcloud storage buckets create gs://[BUCKET_NAME]
   

2. Export query results to the bucket

   Next, we use the EXPORT DATA keywords to tell BigQuery where to export the data. We can pass export options using the OPTIONS keyword. In the example below, we tell BigQuery to export a csv file, overwrite existing files if necessary, and we specificy a wildcard pattern to use to name the exported files. You MUST use the following filename format: FILENAME = [DATE]_[DESCRIPTION]_*.[EXT], where DATE is an ISO 8601 date string for the export date in the format "YYYY-MM-DD", DESCRIPTION is a hyphen-delimited human readable description of the file contents, and EXT is a fiile extension, usually csv but it could also be avro, json, or parquet if desired.

   Note that the filename must contain a single wildcard character *. This requirement comes from Google's BigQuery and cannot be avoided. BigQuery will "shard" your exported data into multiple files if the exported data is greater than 1GB in size. So the parameter uri="gs://bucket-name/YYYY-MM-DD_description_*.csv" will create the files

   gs://bucket-name/YYYY-MM-DD_description_000000000000.csv
   gs://bucket-name/YYYY-MM-DD_description_000000000001.csv
   gs://bucket-name/YYYY-MM-DD_description_000000000002.csv
   ...
   

   Let's put this all together by taking the UNNEST example query from above and exporting it to a bucket.

   bq query --nouse_legacy_sql \
   'EXPORT DATA
   OPTIONS(
     uri="gs://[BUCKET_NAME]/2024-12-11_school-name-export_*.csv",
     format="csv",
     overwrite=true
   ) AS
   SELECT
     roar_uid, run_id, task_id, time_started,
     TO_JSON_STRING(assigning_schools) as assigning_school
   FROM
     `gse-roar-assessment.assessment.user_runs`
   WHERE
     "uSpviE1t4lUzH8J7I9aQ" IN UNNEST(assigning_schools)
   ORDER BY
     time_started DESC
   LIMIT
     10'
   

   If the query results are less than 1GB in size, this will create one file at gs://[BUCKET_NAME]/2024-12-11_school-name-export_000000000000.csv with the query results.