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Retrieving Data
🤓 The ultimate guide for data analysts using Isabl!
Filters enable you to subset the data of your interest. For example you can use filters to retrieve all the BAM files of a given project, or get all VCFs from a given variant calling application. Filters are field-value pairs and can be used both in the Command Line and within Python. Check out this examples:
# A request to the API
curl http://{my-isabl-instance}/api/v1/experiments?sample__identifier={the-sample-id}
# Using Isabl CLI
isabl get-outdirs -fi application.name BWA_MEM -fi status SUCCEEDED
# Using Isabl SDK
import isabl_cli as ii
samples = ii.get_instances('samples', individual__species="HUMAN")
Note that fields can traverse the relational model. To do so concatenate the fields with
__ (e.g. samples__disease__acronym=AML, or a dot in the Command Line application.name=PINDEL)As indicated in the previous hint, filter fields can traverse database relationships. However, all filters can be augmented using lookups:
Related Filters
Lookup Types
Datetime Lookups
Full Relational Model
{related_field}__{related_filter}="query"
Here is a quick representation of Isabl's relational model, hence related filters:
Furthermore, all query parameters in this API support advanced lookup types:
Lookup Type | Description | Example |
! | Negate any query | name!=isabel |
[i]exact | Exact match | name__exact=isabl name__iexact=IsAbL |
[i]contains | Value contains query | name__contains=isa name__icontains=iSa |
[i]startswith | Value starts with query | name__startswith=isab name__istartswith=iSab |
[i]endswith | Value starts with query | name__endswith=bl name__iendswith=bL |
in | Comma separated query | name__in=isabl,besuhof |
isnull | Value is null | name__isnull=true |
regex | Use regex pattern | name__regex=isabl |
gt | Greater than | total__gt=1 |
gte | Greater or equal | total__gte=1 |
lt | Less than | total__lt=1 |
lte | Less than or equal | total__lte=1 |
Moreover, Datetime query parameters support extra lookups:
Lookup Type | Description | Example |
`` | No lookup, ISO format required | created= |
date | Filter by date YYYY-MM-DD. | created__date=2016-06-04 created__date__gt=2016-06-04 |
day | Filter by day DD | created__day=04 |
month | Filter by month MM | created__month=06 |
year | Filter by year YYYY | created__year=2016 |
time | Filter by time HH-MM-SS | created__time=21:00:51 |
UML Diagram of the the db schema
To get a full description of all available filters please visit Isabl's Redoc API documentation at https://isabl.github.io/redoc/ or https://isabl.mskcc.org/api/v1 (replacing
isabl.mskcc.org with your own host). Another useful way to explore the relational model is by using isabl get-metadata.Here are some common and useful filters for Isabl.
The filter
count_limit enables you to limit the total number of instances that will be retrieved. For example to get the output directory for the first 10 successful analyses you could do:isabl get-outdirs -fi status SUCCEEDED -fi count_limit 10
On the other side,
limit will determine how many instances should be retrieved at the same time. For example, the following command would retrieve paths to all successful analyses in batches of 10000:isabl get-outdirs -fi status SUCCEEDED -fi limit 100000
To get for example all experiments that have a BAM file for
GRCh37 you could do:experiments = ii.experiments(has_bam_for="GRCh37")
The following filters can be used to (quite dramatically) improve the performance for some queries:
Filter | Description | Usage |
distinct | If you set distinct to false, the each result within the query won't be guaranteed to be unique, yet the response will be faster. | distinct=false |
paginator | By activating the cursor pagination, you would be able to traverse queries results, but you won't know the total number of results. | paginator=cursor |
Filters in the command line are usually provided using the
-fi or --filters flags. Relations or lookups can be provided using double underscores or dots (e.g. application.name or application__name). Here is a list of Isabl commands available to retrieve information:Command | Description | Example |
get-count | Get count of database instances given a particular query. For example, how many failed analyses are in the system? | isabl get-count analyses -fi status FAILED |
get-metadata | Retrieve instances metadata in multiple formats. To limit the number of fields you are interested in use -f (i.e. --fields). | isabl get-metadata samples -fi category TUMOR -f disease |
get-data | This command will retrieved the raw data linked to experiments as imported in Isabl (e.g. BAM, FASTQ, CRAM). Use --verbose to see what experiments have missing data. | isabl get-data -fi projects.pk.in 102,103 |
get-bams | Get the official bam registered for a given list of experiments. Use --assemblyif there are BAMs available for different versions of the genome. Use has_bam_for to filter those experiments with a registered BAM. | isabl get-bams -fi has_bam_for GRCh37 |
get-reference | Isabl supports the linkage of auxiliary resources to the assembly instances. By default get-reference gives you the path to the reference FASTA, however you can retrieve other linked resources. | isabl get-reference GRCh37 |
get-bed | Retrieve a BED file linked to a particular sequencing technique. By default, the targets BED file is returned, to get the baits BED use --bed-type. | isabl get-bed HEMEPACT --assembly GRCh37 |
get-paths | Retrieve the storage directory for any instance in the database. Use --pattern to retrieve files within those directories. | isabl get-paths projects 102 |
get-outdirs | isabl get-outdirs -fi name PINDEL -fi status SUCCEEDED | |
get-results | Retrieve analyses results produced by applications. Use --app-resultsto list all available choices for a given application. | isabl get-results -fi application.pk 1 -r command_script |
Another useful way to explore the relational model is by using
isabl get-metadata:isabl get-metadata experiments --fx
Expand and navigate with arrow keys, press e to expand all and E to minimize. Learn more at
fx documentation. Use --help to learn about other ways to visualize metadata (e.g. tsv).Furthermore, you can limit the amount of information you are retrieving by passing the list of fields you are interested in:
isabl get-metadata analyses -f application.name -f status
By default, the command
get-reference helps you retrieve the assembly reference genome.isabl get-reference GRCh37 # retrieve reference genome
However, by means of the
--data-id flag, the command get-reference also allows you to retrieve the indexes generated during import. To get a list of available files per assembly use --resources:$ isabl get-reference GRCh37 --resources
genome_fasta Reference Genome Fasta File.
genome_fasta_fai Index generated by: samtools faidx
...
Then get the one you are interested in with:
isabl get-reference GRCh37 --data-id genome_fasta_fai
You can use
get-outdirs within the command line to systematically explore output directories. For example:isabl get-outdirs -fi status FAILED | xargs tree -L 2
Further more you can retrieve files within those directories by using
--pattern:isabl get-outdirs -fi status FAILED --pattern 'head_job.*'
Additionally, you can retrieve results directly registered by the application:
for i in `isabl get-results -fi status FAILED -r command_err`; do
echo exploring $i;
cat $i;
done
To visualize what results are available for a given application run:
isabl get-results --app-results <application primary key>
You can retrieve the application primary key from the front end.
Importantly,
isabl-cli can also be used as a Software Development Kit within python:Try from an ipython session
import isabl_cli as ii # ii stands for `interactive isabl` 😎
If you are using
ipython, use ? to get help on a method (e.g. ii.get_instances?)To get started, we can retrieve specific instances from the database:
# retrieve an experiment with a system id (primary keys also work)
experiment = ii.Experiment("DEM_10000_T01_01_TD1")
# we can also get an analysis using it's primary key (we'll limit retrieved fields)
analysis = ii.Analysis(10235, fields="status,application")
# same thing for assemblies
assembly = ii.Assembly("GRCh37")
These instances are
Munch, in other words they are dot-dicts (like javascript). So you can do both analysis["status"] or analysis.status.A more general way to retrieve any object in the database is using
get_instance:project = ii.get_instance("projects", 100) # the signature is (endpoint, identifier)
Some examples of things you can do with these instances:
# get the target experiment or tumor
target = analysis.targets[0]
# print the experiment sample class
print(experiment.sample.category)
# see available analysis fields
print(analysis.keys())
# see all available data
print(vars(assembly))
To get multiple instances you can do:
# get all TUMOR experiments in project 102
experiments = ii.get_experiments(projects=102, sample__category="TUMOR")
# get the first 10 SUCCEEDED analyses in the same project
analyses = ii.get_experiments(projects=102, status="SUCCEEDED", count_limit=10)
# get all the projects where I'm the owner
projects = ii.get_projects(owner__startswith="besuhof")
Similarly to
isabl get-count , you can determine the number of available results for a given query:ii.get_instances_count("analyses", status="FAILED")
To retrieve all samples and experiments for a given individual:
# you can also use the individual system_id
individual = ii.get_tree(10000)
# them all samples are available at
samples = individual.sample_set
# and all experiments for a given sample
experiments = samples[0].experiment_set
You can also retrieve multiple trees:
individuals = ii.get_trees(projects=267)
If you have permissions, you will be able to systematically alter instances in the database:
# create a disease
ii.create_instance("diseases", name="Osteosarcoma", acrynom="OS")
# update an individual's gender
ii.patch_instance(individual.pk, gender="UNKNOWN")
# delete an analysis
ii.delete_instance("analyses", analysis.pk)
With great power, comes... yeah you know how it goes. Just be careful.
Here are other useful utilities available in
isabl-cli:Method | Description |
ii.api.chunks | Given a list of elements, return a list of chunks of n elements from the original list. |
ii.api.api_request | Perform an authenticated request to Isabl API. |
ii.api.retry_request | Retry an HTTP request multiple times with a delay between each failure. |
Isabl Web is a great tool to retrieve information and understand the state of affairs within the system. Simply type something in the search bar to retrieve instances across multiple schemas:
Multiple panels will be stacked horizontally as you request more information:
image
The projects detail panel conveys all assets and stakeholders linked to a particular project:
Live Tables are directly wired to the API and will enable you to search and filter on specific columns. For the later, simply click in the column name:
Directly searching on the sample Identifier column.
The samples tree panel provides access to all assets generated on a given individual.
A data generation process tree that resulted in 4 experiments (or ultimately bams), produced from two samples of the same individual.
By clicking on a given node in the tree, you can retrieve more metadata, filter out available analyses on that instance, and even get access to BAM files:
Although the BAM file is an output of the bwa-mem analysis, Isabl enables registering default bams to an experiment. Thus a link is available in the sample panel.
We can retrieve different types of results for all analyses generated by Isabl. For example accessing a project level quality control report:
A project level Quality Control report. Can you find the Experiment and Individual-level reports?
Similarly we can retrieve other types of results such as a VCF:
Last modified 7mo ago