PHC SDK for Python¶

Source location - lifeomic/phc-sdk-py

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

(NOTE: All examples use fictious data or freely available data sets.)

0.23.1 - 2021-07-26¶

Fixed¶

Fix import error because of missing __init__ file for summary API folder

0.23.0 - 2021-07-23¶

Fixed¶

phc.Project now operates properly when one of the accounts only has limited access
phc.Observation, phc.Condition, and phc.Procedures's get_codes method now uses the new summary APIs to return better results.

Added¶

Summary APIs (PR #150)
phc.SummaryClinicalCounts - Retrieve all clinical counts (across tables like observation, conditions, procedures, and medications)
phc.SummaryOmicsCounts - Retrieve summaries across genomic data (counts of clinvar_significance, gene_variant, sequence, test, etc)
phc.SummaryCounts - Retrieve all summaries (across omics and clinical)
phc.SummaryItemCounts - Retrieve counts for a specific table (e.g. condition, procedure)

Example

phc.SummaryClinicalCounts.get_data_frame(match="fuzzy", system=["snomed.info", "loinc.org"])
#        summary       code                           display  patient_count                  system   count media_type  media_type_count

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 0    procedure  406505007       modified radical mastectomy          322.0  http://snomed.info/sct   322.0        NaN               NaN

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 1    procedure  392090004                             other          272.0  http://snomed.info/sct   272.0        NaN               NaN

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 2  observation    21975-8              Date of Last Contact         1094.0        http://loinc.org  1094.0        NaN               NaN

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 3   medication  387420009                           cytoxan          514.0  http://snomed.info/sct   523.0        NaN               NaN

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 4   medication  372817009       doxorubicin+cyclophosphamid          364.0  http://snomed.info/sct   371.0        NaN               NaN

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 5    condition  254837009                              None         1086.0  http://snomed.info/sct  1086.0        NaN               NaN

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 6    condition   82711006  Infiltrating duct carcinoma, NOS          778.0  http://snomed.info/sct   778.0        NaN               NaN

Source location - <https://github.com/lifeomic/phc-sdk-py/>

0.22.2 - 2021-04-30¶

Fixed¶

Make token optional when using a custom adapter that doesn't support refreshing the token

0.22.1 - 2021-04-27¶

Added¶

Added ability to use custom adapter for sending/receiving underlying data (e.g. for tests)

0.22.0 - 2021-03-24¶

Fixed¶

Bug that caused error related to printing progress

Added¶

Added lots of Ocr functionality and a Composition module in the easy namespace.

phc.Ocr.Config - Create and update PrecisionOCR config within a project
phc.Ocr.Document - Retrieve PrecisionOCR documents
phc.Ocr.DocumentComposition - Retrieve metadata by page for PrecisionOCR documents
phc.Ocr.Block - Retrieve the text and layout metadata from a PrecisionOCR document
phc.Ocr.Suggestion - Retrieve all permutations of PrecisionOCR medical suggestions
phc.Composition - Base FHIR class for retrieving Composition resources from the FHIR Search Service

Added the ability to create, read, update, and delete using the FHIR DSTU3 API by appending .DSTU3 to any easy module that supports it.

phc.Patient.DSTU3.create(...)
phc.Patient.DSTU3.get(...)
phc.Patient.DSTU3.update(...)
phc.Patient.DSTU3.put(...)
phc.Patient.DSTU3.delete(...)

0.21.1 - 2020-12-17¶

Fixed¶

Updated API calls to the data-lake to use correct endpoints.

0.21.0 - 2020-12-10¶

Added¶

Tools - A service to manager resources in the tool registry service
tools.create - Adds a tool to the registry
tools.download - Downloads a tool
tools.get - Gets the default verson or a specific version of a tool
tools.add_version - Adds a verson to an existing tool
tools.delete - Deletes the tool or a specific version of a tool
tools.get_list - Returns tools from the registry and allows for optional filters
Workflows - A service to manager workflows
workflows.run - Runs a workflow using a provided tool from the registry
workflows.get - Gets a workflow run
workflows.get_list - Returns all workflows for a project
workflows.describe - Returns a list of the inputs and types the workflow requires to run a tool
Added filtering by id for all phc.easy modules

# By single ID

Source location - <https://github.com/lifeomic/phc-sdk-py/>
phc.Patient.get_data_frame(id="<value>")

# Or by multiple IDs

Source location - <https://github.com/lifeomic/phc-sdk-py/>
phc.Observation.get_data_frame(ids=["<value1>", "<value2>"])

Added getting all pages of results for phc.Project

Fixed¶

Genomics modules (phc.easy) now handle an out of range date via a warning (and auto-conversion to NaT)
Setting and retrieving projects now works properly again (Previously, projects were inaccurate or sometimes missing.)

0.20.0 - 2020-11-19¶

Added¶

Auto-retrieve GenomicTests for each type of variant (short, copy number, structural, and expression) if no variant_set_ids passed

# Specify the specific sets within a test

Source location - <https://github.com/lifeomic/phc-sdk-py/>
phc.GenomicShortVariant.get_data_frame(variant_set_ids)

# ...or have it auto-fetch the relevant tests (uses a sample if executed with

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# no arguments)

Source location - <https://github.com/lifeomic/phc-sdk-py/>
phc.GenomicShortVariant.get_data_frame()

- Added GenomicExpression

phc.GenomicExpression.get_data_frame(
    expression=">=4000",
    gene=["B2M", "MIR663B", "MT-CYB"],
    order_by="expression:desc",
    in_ckb=True,
    all_results=True,
    log=True
)

Added GenomicCopyNumberVariant

phc.GenomicCopyNumberVariant.get_data_frame(
    effect=[phc.Option.CopyNumberStatus.AMPLIFICATION],
    in_ckb=True
)

Added GenomicStructuralVariant

phc.GenomicStructuralVariant.get_data_frame(
    patient_id="2c8660b4-1e63-403e-b52b-55c290072a66",
    effect=[phc.Option.StructuralType.TRANSLOCATION],
    gene=["TNRC6B", "CTD-2616J11.4"],
    max_pages=2,
    page_size=100
)

Added Gene and GeneClass from the knowledge APIs

phc.Gene.get_data_frame()
phc.GeneSet.get_data_frame()

Added abstract class GenomicVariant from which these specific classes inherit
Added a whole host of options for these variant/expression classes
phc.Option.Chromosome
phc.Option.ClinVarReview
phc.Option.ClinvarSignificance
phc.Option.CodingEffect
phc.Option.Common
phc.Option.CopyNumberStatus
phc.Option.GeneClass
phc.Option.Zygosity
Added run-time validation of variant/expression options using these classes
phc.easy.omics.option.genomic_copy_number_variant.GenomicCopyNumberVariant
phc.easy.omics.option.genomic_expression.GenomicExpression
phc.easy.omics.option.genomic_short_variant.GenomicShortVariant
phc.easy.omics.option.genomic_structural_variant.GenomicStructuralVariant
phc.easy.omics.option.genomic_test.GenomicTest

Changed¶

Updated options for GenomicShortVariant

phc.GenomicShortVariant.get_data_frame(
    patient_id="2c8660b4-1e63-403e-b52b-55c290072a66",
    chromosome=[phc.Option.Chromosome.CHR_19],
    gene_class=[phc.Option.GeneClass.PROTEIN_CODING],
    zygosity=[phc.Option.Zygosity.HETEROZYGOUS],
    rs_id=["rs11324363", "rs36247", "rs77134098"],
    min_allele_frequency="0.2-1",
    log=True,
    all_results=True
)

0.19.0 - 2020-10-23¶

Added¶

Added GenomicTest and GenomicShortVariant

# Get genomic tests and the associated sets

Source location - <https://github.com/lifeomic/phc-sdk-py/>
set_ids = phc.GenomicTest.get_data_frame(
    patient_id="8cb82aa0-7f2c-4fdb-bf91-0ed1b315392c",
    status="ACTIVE",
    test_type="shortVariant",
    all_results=True,
).id.values.tolist()

# Pull first 1000 short variants on chr1

Source location - <https://github.com/lifeomic/phc-sdk-py/>
phc.GenomicShortVariant.get_data_frame(
    variant_set_ids=set_ids,
    chromosome=["chr1"],
    page_size=1000,
    log=True
)

Added filtering by exact code, system, and/or display

phc.Condition.get_data_frame(code=["25910003", "30156004"], system="http://snomed.info/sct")

Fixed¶

Sped up finding projects - phc.Project.set_current()

Changed¶

Overhauled get_codes to make results more accurate and allow searching by display (See #93 for full discussion)

# 1. Get display values and number of records they occur in

Source location - <https://github.com/lifeomic/phc-sdk-py/>
phc.Observation.get_codes()
# =>    doc_count                       display                        field

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# => 0      1094.0          Date of Last Contact                  code.coding

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# => ...

Source location - <https://github.com/lifeomic/phc-sdk-py/>

# 2. Get full code values that match this text (case-insensitive)

Source location - <https://github.com/lifeomic/phc-sdk-py/>
phc.Observation.get_codes(display_query="date of")
# ...

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# Retrieved 2332/2394 results

Source location - <https://github.com/lifeomic/phc-sdk-py/>
#
# =>           field            system     code                      display     doc_count

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# =>  0  code.coding  http://loinc.org  63931-0            Date of Diagnosis       1094.0

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# =>  1  code.coding  http://loinc.org  21975-8         Date of Last Contact       1094.0

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# =>  2  code.coding  http://loinc.org  21981-6  Date of Disease Progression        144.0

Source location - <https://github.com/lifeomic/phc-sdk-py/>

# 3. Get full code values but restrict number of records to find the associated system and code

Source location - <https://github.com/lifeomic/phc-sdk-py/>
phc.Observation.get_codes("status", sample_size=10)
# ...

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# Retrieved 10/3017 results

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# Records with missing system/code values were not retrieved.

Source location - <https://github.com/lifeomic/phc-sdk-py/>

# =>           field     code            system                       display     doc_count

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# =>  0  code.coding  85337-4  http://loinc.org      Estrogen Receptor Status        1048.0

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# =>  1  code.coding  85339-0  http://loinc.org  Progesterone Receptor Status        1047.0

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# =>  2          NaN      NaN               NaN      HER2/neu receptor status         919.0

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# =>  3          NaN      NaN               NaN                    TMB Status           3.0

Source location - <https://github.com/lifeomic/phc-sdk-py/>

0.18.1 - 2020-10-09¶

Fixed¶

Fixed Genomics.update_set use of readgroupsets API

0.18.0 - 2020-10-09¶

Added¶

Added Genomics.update_set method for updating genomic sets

0.17.1 - 2020-09-17¶

Added¶

Paging requests with all_results=True now automatically retries to the server with an exponentially smaller batch size on error (pow(limit, 0.85)). We can't tell what the error is, but we can retry with a smaller page size.
Added page_size to the easy modules for a custom batch size
Added max_pages to the easy modules for capping the number of pages returned
Added pretty print to FHIR Search Service queries when passing log=True
Warn and convert out of range date times (e.g. 0217-01-01) to NaT

Fixed¶

Properly parse date columns with positive time zones into the local time and time zone
Resolved a KeyError issue with coding where the valueCodeableConcept didn't have a system or url
Passing patient_id / patient_ids with a must FHIR Search Service query now works as expected

Changed¶

[BREAKING] The expanded columns have changed to more reflect the location of the value. All systems and URLs are separated by __ and prefixed with either url or system. Here is an example:

input_dict = [
    {
        "url": "http://hl7.org/fhir/StructureDefinition/us-core-race",
        "valueCodeableConcept": {
            "text": "race",
            "coding": [
                {
                    "code": "2106-3",
                    "system": "http://hl7.org/fhir/v3/Race",
                    "display": "white",
                }
            ],
        },
    },
    {
        "url": "http://hl7.org/fhir/StructureDefinition/us-core-ethnicity",
        "valueCodeableConcept": {
            "text": "ethnicity",
            "coding": [
                {
                    "code": "2186-5",
                    "system": "http://hl7.org/fhir/v3/Ethnicity",
                    "display": "not hispanic or latino",
                }
            ],
        },
    },
]

assert generic_codeable_to_dict(input_dict) == {
    "url__hl7.org/fhir/StructureDefinition/us-core-race__valueCodeableConcept_text": "race",
    "url__hl7.org/fhir/StructureDefinition/us-core-race__valueCodeableConcept_coding_system__hl7.org/fhir/v3/Race__code": "2106-3",
    "url__hl7.org/fhir/StructureDefinition/us-core-race__valueCodeableConcept_coding_system__hl7.org/fhir/v3/Race__display": "white",
    "url__hl7.org/fhir/StructureDefinition/us-core-ethnicity__valueCodeableConcept_text": "ethnicity",
    "url__hl7.org/fhir/StructureDefinition/us-core-ethnicity__valueCodeableConcept_coding_system__hl7.org/fhir/v3/Ethnicity__code": "2186-5",
    "url__hl7.org/fhir/StructureDefinition/us-core-ethnicity__valueCodeableConcept_coding_system__hl7.org/fhir/v3/Ethnicity__display": "not hispanic or latino",
}

0.16.0 - 2020-08-27¶

Added¶

Added most of remaining FSS entities:
AuditEvent
CarePlan
DiagnosticReport
DocumentReference
Encounter
ImagingStudy
Immunization
Media
MedicationAdministration
MedicationDispense
MedicationRequest
MedicationStatement
Person
Practitioner
Procedure
ProcedureRequest
Provenance
ReferralRequest
Sequence
Specimen
Add abstract Item class for entities that don't relate to a patient (e.g. Organization and Practitioner)

Changed¶

All date columns now return two columns--one for the local time (with time zone removed) and one for the time zone offset in hours. Consider the onsetDateTime column from BRCA's Condition table:

   onsetDateTime.tz       onsetDateTime.local
0               0.0 1998-01-01 00:00:00+00:00
1               0.0 2010-01-01 00:00:00+00:00
2               0.0 2008-01-01 00:00:00+00:00
3               0.0 1994-01-01 00:00:00+00:00
4               0.0 2008-01-01 00:00:00+00:00
5               0.0 2012-01-01 00:00:00+00:00
6               0.0 2017-06-27 04:00:00+00:00

0.15.0 - 2020-08-05¶

Includes more work on the easy modules (imported via import phc.easy as phc).

Added¶

Added phc.easy.Query.execute_ga4gh that auto-scrolls GA4GH results
Added phc.easy.Sequence as another entity module
Added generic methods on phc.easy.Query
get_count_by_field
get_codes
execute_composite_aggregations (used by get_count_by_field and get_codes)
Added phc.easy.PatientItem.get_count_by_patient (Observation, Procedure, Specimen, etc.)

# Example: Get number of procedures by patient

Source location - <https://github.com/lifeomic/phc-sdk-py/>
phc.Procedure.get_count_by_patient()

#                                      doc_count

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# subject.reference

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 518eb55d-adbf-42c3-8aed-68176d0ed4b7        334

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 67233488-ddd6-46e1-88cc-a93140b86c02       2088

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# b41f8107-85e1-42c3-b36e-400085799ab5        176

Source location - <https://github.com/lifeomic/phc-sdk-py/>

Added phc.easy.PatientItem.get_count_by_field (Observation, Procedure, Specimen, etc.)

# Example: Get count of unique procedure display codes

Source location - <https://github.com/lifeomic/phc-sdk-py/>
phc.Procedure.get_count_by_field("code.coding.display")

#                      code.coding.display  doc_count

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 0                             lumpectomy        247

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 1            modified radical mastectomy        322

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 2                                  other        272

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 3                      simple mastectomy        200

Source location - <https://github.com/lifeomic/phc-sdk-py/>

Added phc.easy.PatientItem.get_codes (Observation, Procedure, Specimen, etc.)

# Example: Get observation codes for specific patients

Source location - <https://github.com/lifeomic/phc-sdk-py/>
phc.Observation.get_codes(patient_ids=[
    "e296f292-230f-444c-887f-0b213bde90fa",
    "78adf262-c77e-4cb3-8435-034bd9e73b64"
])

#    doc_count            system     code                                     display        field

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 0        1.0  http://loinc.org  21893-3  Regional lymph nodes positive [#] Specimen  code.coding

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 1        2.0  http://loinc.org  21975-8                        Date of Last Contact  code.coding

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 2        1.0  http://loinc.org  21981-6                 Date of Disease Progression  code.coding

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 3        2.0  http://loinc.org  49683-6                    HER2/neu receptor status  code.coding

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 4        2.0  http://loinc.org  63931-0                           Date of Diagnosis  code.coding

Source location - <https://github.com/lifeomic/phc-sdk-py/>
# 5        2.0  http://loinc.org  85337-4                    Estrogen Receptor Status  code.coding

Source location - <https://github.com/lifeomic/phc-sdk-py/>

Changed¶

Passing log to any PatientItem entities now logs the FSS query being run
For aggregations, phc.Query.execute_fhir_dsl now returns a FhirAggregation if an aggregation is specified in the query
phc.Query.execute_fhir_dsl_with_options now caches aggregation queries in JSON format
Specifying patient_id and/or patient_ids is now properly supported with a custom FHIR query.

# Example: Get observations tagged with loinc for a specific patient

Source location - <https://github.com/lifeomic/phc-sdk-py/>

phc.Observation.get_data_frame(patient_id="<id>", query_overrides={
    "where": {
        "type": "elasticsearch",
        "query": {
            "term": {
                "code.coding.system.keyword": "http://loinc.org"
            }
        }
    }
})

Fixed¶

Fix phc.easy.Procedure not inheriting new phc.easy.PatientItem behavior

0.14.1 - 2020-07-15¶

Fixed¶

Fixed missing trust_env args in created client objects

0.14.0 - 2020-07-14¶

Added¶

All-new easy module for faster analysis! Simply import phc.easy as phc.
Add Auth for shared authentication details (account, project, and token)
Add Query for scrolling through FHIR Search Service (FSS) data
Add Frame for expanding columns that contain FHIR data and parsing dates
Add APICache for auto-caching results from easy modules
Add CSVWriter for intelligently writing batches O(1) without having memory grow
Includes Project, Patient, Observation, Procedure, Condition, Goal, and Specimen

0.13.0 - 2020-04-17¶

Added¶

Switched build over to github actions

0.12.3 - 2020-04-13¶

Added¶

Adds dsl and sql methods to phc.services.Fhir

Changed¶

Deprecates execute_sql and execute_es methods in phc.services.Fhir

0.12.2 - 2020-03-25¶

Fixed¶

Added retries to file download requests

0.12.1 - 2020-03-25¶

Fixed¶

Fixed retry logic to include OS level errors.

0.12.0 - 2020-03-23¶

Added¶

Added retry support for failed API requests.

0.11.0 - 2020-03-17¶

Added¶

Added the trust_env parameter to all service classes to enable http proxy support.

0.10.0 - 2020-03-10¶

Added¶

Added execute_sql to phc.services.Analytics.

0.9.2 - 2020-02-19¶

Added¶

Added scroll support to phc.services.Fhir via the scroll param.

0.9.1 - 2019-12-17¶

Changed¶

Fixed phc.services.Genomics.Status enum.

0.9.0 - 2019-12-16¶

Changed¶

Added phc.services.Genomics for performing genomic related operations.

0.8.1 - 2019-11-27¶

Changed¶

In Analytics.load_data_lake_result_to_dataframe increased the amount of time it takes to wait for a results file.

0.8.0 - 2019-11-25¶

Added¶

Added Analytics.list_data_lake_schemas to fetch the schemas of each data lake table.
Added Analytics.get_data_lake_schema to fetch the schema of a single data lake table.
Added Analytics.execute_data_lake_query_to_dataframe to execute a data lake query and load the results to a Pandas dataframe.
Added Analytics.load_data_lake_result_to_dataframe to load the results of a previously executed data lake query to a Pandas dataframe.
Added Files.exists to check if a file exists.

0.7.1 - 2019-11-21¶

Fixed¶

Fixed issue with Files.download to create target directories if they do not exist.

0.7.0 - 2019-11-20¶

Added¶

Added optional pandas setup install
Added ApiResponse.get_as_dataframe to return a response item as a Pandas DataFrame.

0.6.0 - 2019-11-01¶

Added¶

Added the phc.services.Files submodule that provides actions for files in PHC projects.
Added the phc.services.Cohorts submodule that provides actions for files in PHC cohorts.

Last update: 2021-08-02