destiny_sdk 0.4.0__tar.gz → 0.5.0__tar.gz

{destiny_sdk-0.4.0 → destiny_sdk-0.5.0}/.gitignore

@@ -186,9 +186,6 @@ cython_debug/
 # Mac Finder config
 .DS_Store
 
-# MinIO presigned URLs
-.minio/presigned_urls.json
-
 # delete-me working files
 tmp-scripts.sh
 infra/app/*.py

{destiny_sdk-0.4.0 → destiny_sdk-0.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: destiny_sdk
-Version: 0.4.0
+Version: 0.5.0
 Summary: A software development kit (sdk) to support interaction with the DESTINY repository
 Author-email: Adam Hamilton <adam@futureevidence.org>, Andrew Harvey <andrew@futureevidence.org>, Daniel Breves <daniel@futureevidence.org>, Jack Walmisley <jack@futureevidence.org>
 License-Expression: Apache-2.0

{destiny_sdk-0.4.0 → destiny_sdk-0.5.0}/pyproject.toml

@@ -33,7 +33,7 @@ license = "Apache-2.0"
 name = "destiny_sdk"
 readme = "README.md"
 requires-python = "~=3.12"
-version = "0.4.0"
+version = "0.5.0"
 
 [tool.pytest.ini_options]
 addopts = ["--color=yes", "--import-mode=importlib", "--verbose"]

{destiny_sdk-0.4.0 → destiny_sdk-0.5.0}/src/destiny_sdk/client.py

@@ -107,14 +107,14 @@ class Client:
         :rtype: RobotEnhancementBatchRead
         """
         response = self.session.post(
-            f"/robot-enhancement-batch/{robot_enhancement_batch_result.request_id}/results/",
+            f"/robot-enhancement-batches/{robot_enhancement_batch_result.request_id}/results/",
             json=robot_enhancement_batch_result.model_dump(mode="json"),
         )
         response.raise_for_status()
         return RobotEnhancementBatchRead.model_validate(response.json())
 
     def poll_robot_enhancement_batch(
-        self, robot_id: UUID4, limit: int = 10
+        self, robot_id: UUID4, limit: int = 10, timeout: int = 60
     ) -> RobotEnhancementBatch | None:
         """
         Poll for a robot enhancement batch.
@@ -127,11 +127,12 @@ class Client:
         :type limit: int
         :return: The RobotEnhancementBatch object from the response, or None if no
             batches available
-        :rtype: RobotEnhancementBatch | None
+        :rtype: destiny_sdk.robots.RobotEnhancementBatch | None
         """
         response = self.session.post(
-            "/robot-enhancement-batch/",
+            "/robot-enhancement-batches/",
             params={"robot_id": str(robot_id), "limit": limit},
+            timeout=timeout,
         )
         # HTTP 204 No Content indicates no batches available
         if response.status_code == httpx.codes.NO_CONTENT:

{destiny_sdk-0.4.0 → destiny_sdk-0.5.0}/src/destiny_sdk/enhancements.py

@@ -15,20 +15,18 @@ class EnhancementType(StrEnum):
     The type of enhancement.
 
     This is used to identify the type of enhancement in the `Enhancement` class.
-
-    **Allowed values**:
-    - `bibliographic`: Bibliographic metadata.
-    - `abstract`: The abstract of a reference.
-    - `annotation`: A free-form enhancement for tagging with labels.
-    - `locations`: Locations where the reference can be found.
-    - `full_text`: The full text of the reference. (To be implemeted)
     """
 
     BIBLIOGRAPHIC = auto()
+    """Bibliographic metadata."""
     ABSTRACT = auto()
+    """The abstract of a reference."""
     ANNOTATION = auto()
+    """A free-form enhancement for tagging with labels."""
     LOCATION = auto()
+    """Locations where the reference can be found."""
     FULL_TEXT = auto()
+    """The full text of the reference. (To be implemented)"""
 
 
 class AuthorPosition(StrEnum):
@@ -36,16 +34,14 @@ class AuthorPosition(StrEnum):
     The position of an author in a list of authorships.
 
     Maps to the data from OpenAlex.
-
-    **Allowed values**:
-    - `first`: The first author.
-    - `middle`: Any middle author
-    - `last`: The last author
     """
 
     FIRST = auto()
+    """The first author."""
     MIDDLE = auto()
+    """Any middle author."""
     LAST = auto()
+    """The last author."""
 
 
 class Authorship(BaseModel):
@@ -104,18 +100,14 @@ other works have cited this work
 
 
 class AbstractProcessType(StrEnum):
-    """
-    The process used to acquire the abstract.
-
-    **Allowed values**:
-    - `uninverted`
-    - `closed_api`
-    - `other`
-    """
+    """The process used to acquire the abstract."""
 
     UNINVERTED = auto()
+    """uninverted"""
     CLOSED_API = auto()
+    """closed_api"""
     OTHER = auto()
+    """other"""
 
 
 class AbstractContentEnhancement(BaseModel):
@@ -142,16 +134,15 @@ class AnnotationType(StrEnum):
     The type of annotation.
 
     This is used to identify the type of annotation in the `Annotation` class.
-
-    **Allowed values**:
-    - `boolean`: An annotation which is the boolean application of a label across a
-    reference.
-    - `score`: An annotation which is a score for a label across a reference,
-    without a boolean value.
     """
 
     BOOLEAN = auto()
+    """An annotation which is the boolean application of a label across a reference."""
     SCORE = auto()
+    """
+    An annotation which is a score for a label across a reference, without a boolean
+    value.
+    """
 
 
 class ScoreAnnotation(BaseModel):
@@ -227,22 +218,22 @@ class DriverVersion(StrEnum):
     The version based on the DRIVER guidelines versioning scheme.
 
     (Borrowed from OpenAlex)
-
-    Allowed values:
-    - `publishedVersion`: The document's version of record. This is the most
-    authoritative version.
-    - `acceptedVersion`: The document after having completed peer review and being
-    officially accepted for publication. It will lack publisher formatting, but the
-    content should be interchangeable with the that of the publishedVersion.
-    - `submittedVersion`: the document as submitted to the publisher by the authors, but
-    before peer-review. Its content may differ significantly from that of the accepted
-    article.
     """
 
     PUBLISHED_VERSION = "publishedVersion"
+    """The document's version of record. This is the most authoritative version."""
     ACCEPTED_VERSION = "acceptedVersion"
+    """
+    The document after having completed peer review and being officially accepted for
+    publication. It will lack publisher formatting, but the content should be
+    interchangeable with that of the publishedVersion.
+    """
     SUBMITTED_VERSION = "submittedVersion"
+    """
+    The document as submitted to the publisher by the authors, but before peer-review.
+    Its content may differ significantly from that of the accepted article."""
     OTHER = "other"
+    """Other version."""
 
 
 class Location(BaseModel):
@@ -360,7 +351,6 @@ class EnhancementFileInput(BaseModel):
     visibility: Visibility = Field(
         description="The level of visibility of the enhancement"
     )
-    enhancement_type: EnhancementType = Field(description="The type of enhancement.")
     robot_version: str | None = Field(
         default=None,
         description="The version of the robot that generated the content.",

{destiny_sdk-0.4.0 → destiny_sdk-0.5.0}/src/destiny_sdk/identifiers.py

@@ -12,19 +12,16 @@ class ExternalIdentifierType(StrEnum):
 
     This is used to identify the type of identifier used in the `ExternalIdentifier`
     class.
-    **Allowed values**:
-    - `doi`: A DOI (Digital Object Identifier) which is a unique identifier for a
-    document.
-    - `pmid`: A PubMed ID which is a unique identifier for a document in PubMed.
-    - `openalex`: An OpenAlex ID which is a unique identifier for a document in
-    OpenAlex.
-    - `other`: Any other identifier not defined. This should be used sparingly.
     """
 
     DOI = auto()
+    """A DOI (Digital Object Identifier) which is a unique identifier for a document."""
     PM_ID = auto()
+    """A PubMed ID which is a unique identifier for a document in PubMed."""
     OPEN_ALEX = auto()
+    """An OpenAlex ID which is a unique identifier for a document in OpenAlex."""
     OTHER = auto()
+    """Any other identifier not defined. This should be used sparingly."""
 
 
 class DOIIdentifier(BaseModel):

{destiny_sdk-0.4.0 → destiny_sdk-0.5.0}/src/destiny_sdk/imports.py

@@ -13,90 +13,52 @@ from pydantic import (
 
 
 class ImportRecordStatus(StrEnum):
-    """
-    Describes the status of an import record.
-
-    - `created`: Created, but no processing has started.
-    - `started`: Processing has started on the batch.
-    - `completed`: Processing has been completed.
-    """
+    """Describes the status of an import record."""
 
     CREATED = auto()
+    """Created, but no processing has started."""
     STARTED = auto()
+    """Processing has started on the batch."""
     COMPLETED = auto()
+    """Processing has been completed."""
 
 
 class ImportBatchStatus(StrEnum):
-    """
-    Describes the status of an import batch.
-
-    - `created`: Created, but no processing has started.
-    - `started`: Processing has started on the batch.
-    - `failed`: Processing has failed.
-    - `partially_failed`: Some references succeeded while others failed.
-    - `completed`: Processing has been completed.
-    """
+    """Describes the status of an import batch."""
 
     CREATED = auto()
+    """Created, but no processing has started."""
     STARTED = auto()
+    """Processing has started on the batch."""
     FAILED = auto()
+    """Processing has failed."""
     PARTIALLY_FAILED = auto()
+    """Some references succeeded while others failed."""
     COMPLETED = auto()
-
-
-class CollisionStrategy(StrEnum):
-    """
-    The strategy to use when an identifier collision is detected.
-
-    Identifier collisions are detected on ``identifier_type`` and ``identifier``
-    (and ``other_identifier_name`` where relevant) already present in the database.
-
-    Enhancement collisions are detected on an entry with matching ``enhancement_type``
-    and ``source`` already being present on the collided reference.
-
-    - `discard`: Do nothing with the incoming reference.
-    - `fail`: Do nothing with the incoming reference and mark it as failed. This
-      allows the importing process to "follow up" on the failure.
-    - `merge_aggressive`: Prioritize the incoming reference's identifiers and
-      enhancements in the merge.
-    - `merge_defensive`: Prioritize the existing reference's identifiers and
-      enhancements in the merge.
-    - `append`: Performs an aggressive merge of identifiers, and an append of
-      enhancements.
-    - `overwrite`: Performs an aggressive merge of identifiers, and an overwrite of
-      enhancements (deleting existing and recreating what is imported). This should
-      be used sparingly and carefully.
-    """
-
-    DISCARD = auto()
-    FAIL = auto()
-    MERGE_AGGRESSIVE = auto()
-    MERGE_DEFENSIVE = auto()
-    APPEND = auto()
-    OVERWRITE = auto()
+    """Processing has been completed."""
 
 
 class ImportResultStatus(StrEnum):
-    """
-    Describes the status of an import result.
-
-    - `created`: Created, but no processing has started.
-    - `started`: The reference is currently being processed.
-    - `completed`: The reference has been created.
-    - `partially_failed`: The reference was created but one or more enhancements or
-      identifiers failed to be added. See the result's `failure_details` field for
-      more information.
-    - `failed`: The reference failed to be created. See the result's `failure_details`
-      field for more information.
-    - `retrying`: Processing has failed, but is being retried.
-    """
+    """Describes the status of an import result."""
 
     CREATED = auto()
+    """Created, but no processing has started."""
     STARTED = auto()
+    """The reference is currently being processed."""
     COMPLETED = auto()
+    """The reference has been created."""
     PARTIALLY_FAILED = auto()
+    """
+    The reference was created but one or more enhancements or identifiers failed to
+    be added. See the result's `failure_details` field for more information.
+    """
     FAILED = auto()
+    """
+    The reference failed to be created. See the result's `failure_details` field for
+    more information.
+    """
     RETRYING = auto()
+    """Processing has failed, but is being retried."""
 
 
 class _ImportRecordBase(BaseModel):
@@ -162,13 +124,6 @@ class ImportRecordRead(_ImportRecordBase):
 class _ImportBatchBase(BaseModel):
     """The base class for import batches."""
 
-    collision_strategy: CollisionStrategy = Field(
-        default=CollisionStrategy.FAIL,
-        description="""
-The strategy to use for each reference when an identifier collision occurs.
-Default is `fail`, which allows the importing process to "follow up" on the collision.
-        """,
-    )
     storage_url: HttpUrl = Field(
         description="""
 The URL at which the set of references for this batch are stored. The file is a jsonl
@@ -176,11 +131,6 @@ with each line formatted according to
 :class:`ReferenceFileInput <libs.sdk.src.destiny_sdk.references.ReferenceFileInput>`.
     """,
     )
-    callback_url: HttpUrl | None = Field(
-        default=None,
-        deprecated=True,
-        description="This field is currently a no-op.",
-    )
 
 
 class ImportBatchIn(_ImportBatchBase):

{destiny_sdk-0.4.0 → destiny_sdk-0.5.0}/src/destiny_sdk/parsers/eppi_parser.py

@@ -157,7 +157,6 @@ class EPPIParser:
                     source=parser_source,
                     visibility=Visibility.PUBLIC,
                     content=content,
-                    enhancement_type=content.enhancement_type,
                     robot_version=robot_version,
                 )
                 for content in enhancement_contents

{destiny_sdk-0.4.0 → destiny_sdk-0.5.0}/src/destiny_sdk/robots.py

@@ -140,7 +140,7 @@ reference per line.
 Each reference may have identifiers or enhancements attached, as
 required by the robot.
 If the URL expires, a new one can be generated using
-``GET /robot-enhancement-batch/{batch_id}/``.
+``GET /robot-enhancement-batches/{batch_id}/``.
 """
     )
     result_storage_url: HttpUrl = Field(
@@ -149,7 +149,7 @@ The URL at which the set of enhancements are to be stored. The file is to be a j
 with each line formatted according to
 :class:`EnhancementResultEntry <libs.sdk.src.destiny_sdk.robots.EnhancementResultEntry>`.
 If the URL expires, a new one can be generated using
-``GET /robot-enhancement-batch/{batch_id}/``.
+``GET /robot-enhancement-batches/{batch_id}/``.
 """  # noqa: E501
     )
     extra_fields: dict | None = Field(
@@ -159,32 +159,28 @@ If the URL expires, a new one can be generated using
 
 
 class EnhancementRequestStatus(StrEnum):
-    """
-    The status of an enhancement request.
-
-    **Allowed values**:
-    - `received`: Enhancement request has been received by the repo.
-    - `accepted`: Enhancement request has been accepted by the robot.
-    - `processing`: Enhancement request is being processed by the robot.
-    - `rejected`: Enhancement request has been rejected by the robot.
-    - `partial_failed`: Some enhancements failed to create.
-    - `failed`: All enhancements failed to create.
-    - `importing`: Enhancements have been received by the repo and are being imported.
-    - `indexing`: Enhancements have been imported and are being indexed.
-    - `indexing_failed`: Enhancements have been imported but indexing failed.
-    - `completed`: All enhancements have been created.
-    """
+    """The status of an enhancement request."""
 
     RECEIVED = auto()
+    """Enhancement request has been received by the repo."""
     ACCEPTED = auto()
+    """Enhancement request has been accepted by the robot."""
     PROCESSING = auto()
+    """Enhancement request is being processed by the robot."""
     REJECTED = auto()
+    """Enhancement request has been rejected by the robot."""
     PARTIAL_FAILED = auto()
+    """Some enhancements failed to create."""
     FAILED = auto()
+    """All enhancements failed to create."""
     IMPORTING = auto()
+    """Enhancements have been received by the repo and are being imported."""
     INDEXING = auto()
+    """Enhancements have been imported and are being indexed."""
     INDEXING_FAILED = auto()
+    """Enhancements have been imported but indexing failed."""
     COMPLETED = auto()
+    """All enhancements have been created."""
 
 
 class _EnhancementRequestBase(BaseModel):
@@ -302,7 +298,7 @@ with each line formatted according to
 :class:`EnhancementResultEntry <libs.sdk.src.destiny_sdk.robots.EnhancementResultEntry>`.
 This field is only relevant to robots.
 If the URL expires, a new one can be generated using
-``GET /robot-enhancement-batch/{batch_id}/``.
+``GET /robot-enhancement-batches/{batch_id}/``.
         """,  # noqa: E501
     )
     validation_result_url: HttpUrl | None = Field(
@@ -312,7 +308,7 @@ The URL at which the result of the enhancement request is stored.
 This file is a txt file, one line per reference, with either an error
 or a success message.
 If the URL expires, a new one can be generated using
-``GET /robot-enhancement-batch/{batch_id}/``.
+``GET /robot-enhancement-batches/{batch_id}/``.
         """,
     )
     error: str | None = Field(
@@ -334,10 +330,6 @@ class _RobotBase(BaseModel):
     model_config = ConfigDict(extra="forbid")  # Forbid extra fields on robot models
 
     name: str = Field(description="The name of the robot, must be unique.")
-    base_url: HttpUrl = Field(
-        description="The base url of the robot. The robot must implement endpoint"
-        "base_url/batch for batch enhancements of references.",
-    )
     description: str = Field(
         description="Description of the enhancement the robot provides."
     )

{destiny_sdk-0.4.0 → destiny_sdk-0.5.0}/src/destiny_sdk/visibility.py

@@ -9,16 +9,11 @@ class Visibility(StrEnum):
 
     This is used to manage whether information should be publicly available or
     restricted (generally due to copyright constraints from publishers).
-
-    TODO: Implement data governance layer to manage this.
-
-    **Allowed values**:
-
-    - `public`: Visible to the general public without authentication.
-    - `restricted`: Requires authentication to be visible.
-    - `hidden`: Is not visible, but may be passed to data mining processes.
     """
 
     PUBLIC = auto()
+    """Visible to the general public without authentication."""
     RESTRICTED = auto()
+    """Requires authentication to be visible."""
     HIDDEN = auto()
+    """Is not visible, but may be passed to data mining processes."""

{destiny_sdk-0.4.0 → destiny_sdk-0.5.0}/tests/unit/test_client.py

@@ -50,7 +50,7 @@ def test_verify_hmac_headers_sent(
 
     httpx_mock.add_response(
         url=fake_destiny_repository_url
-        + "/robot-enhancement-batch/"
+        + "/robot-enhancement-batches/"
         + f"{fake_batch_result.request_id}/results/",
         method="POST",
         match_headers={

destiny_sdk-0.5.0/tests/unit/test_data/eppi_import.jsonl

@@ -0,0 +1,4 @@
+{"visibility":"public","identifiers":[{"identifier":"10.1016/j.eclinm.2024.102524","identifier_type":"doi"}],"enhancements":[{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"abstract","process":"other","abstract":"Background\nWhile human papillomavirus (HPV) vaccines have been available since 2006, the coverage has varied among countries. Our aim is to analyse the equity impact of HPV vaccination on the lifetime projections of cervical cancer burden among vaccinated cohorts of 2010–22 in 84 countries.\n\nMethods\nWe used WHO and UNICEF estimates of national immunisation coverage for HPV vaccination in 84 countries during 2010–22. We used PRIME (Papillomavirus Rapid Interface for Modelling and Economics) to estimate the lifetime health impact of HPV vaccination on cervical cancer burden in terms of deaths, cases, and disability-adjusted life years (DALYs) averted by vaccination in their respective countries. We generated concentration indices and curves to assess the equity impact of HPV vaccination across 84 countries.\n\nFindings\nThe health impact of HPV vaccination varied across the 84 countries and ranged from Switzerland to Tanzania at 2 to 34 deaths, 4 to 47 cases, and 40 to 735 DALYs averted per 1000 vaccinated adolescent girls over the lifetime of the vaccinated cohorts of 2010–22. The concentration index for the distribution of average coverage during 2010–22 among the 84 countries ranked by vaccine impact was 0.33 (95% CI: 0.27–0.40) and highlights the wide inequities in HPV vaccination coverage.\n\nInterpretation\nOur findings suggested that countries with a relatively higher cervical cancer burden and thereby a relatively higher need for HPV vaccination had relatively lower coverage during 2010–22. Further, there were significant inequities in HPV vaccination coverage within the Americas, Europe, and Western Pacific regions, and in high- and low-income countries with a pro-advantaged and regressive distribution favouring countries with lower vaccine impact."}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"bibliographic","authorship":[{"display_name":"Abbas Kaja","position":"first"},{"display_name":"Yoo Katelyn","position":"middle"},{"display_name":"Prem Kiesha","position":"middle"},{"display_name":"Jit Mark","position":"last"}],"publication_year":2024,"publisher":"Elsevier BV","title":"Equity impact of HPV vaccination on lifetime projections of cervical cancer burden among cohorts in 84 countries by global, regional, and income levels, 2010–22: a modelling study"}}]}
+{"visibility":"public","identifiers":[{"identifier":"10.1016/j.jvacx.2024.100459","identifier_type":"doi"}],"enhancements":[{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"abstract","process":"other","abstract":"The World Health Organization has recommended the inclusion of human papillomavirus (HPV) vaccines in national immunization programs to address the global problem of cervical cancer. In the Philippines, HPV vaccination was introduced in a phased approach in 2015. This study seeks to estimate the cost of delivery of the HPV vaccination program and its operational context in the Philippines.\n\nMethods\nThis was a retrospective, cross-sectional micro-costing study focused on ongoing HPV vaccination delivery and its operational context across all levels of the health system. Using structured questionnaires and data collection from secondary sources, the weighted mean financial and economic costs and costs per dose at the national, subnational, and health facility levels were estimated.\nResults\nThe weighted mean financial and economic costs per dose of the HPV vaccination program aggregated across all levels of the health system were $US3.72and $29.74, respectively. Activities contributing most significantly to costs were service delivery and vaccine collection or distribution and storage at the health facility and administrative levels, respectively. The opportunity costs for health worker and non-health worker time accounted for 77% of the economic cost per dose.\nConclusion\nThe total weighted mean financial and economic costs of HPV delivery are within range of those reported in other countries. Costing studies can help identify cost drivers with local operational context to help inform policymakers and program managers in budgeting and planning interventions to improve program implementation."}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"bibliographic","authorship":[{"display_name":"Aldaba Josephine","position":"first"},{"display_name":"Llave Cecilia","position":"middle"},{"display_name":"Uy Ma","position":"middle"},{"display_name":"Tejano Kim","position":"middle"},{"display_name":"Aquino Ma","position":"middle"},{"display_name":"Catalig Migel","position":"middle"},{"display_name":"Sy Alvin","position":"middle"},{"display_name":"Valverde Haidee","position":"middle"},{"display_name":"Mooney Jessica","position":"middle"},{"display_name":"Slavkovsky Rose","position":"last"}],"publication_year":2024,"publisher":"Elsevier BV","title":"The cost of human papillomavirus vaccination delivery at the administrative and health facility levels in the Philippines"}}]}
+{"visibility":"public","identifiers":[{"identifier":"10.1016/j.vaccine.2019.12.013","identifier_type":"doi"}],"enhancements":[{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"abstract","process":"other","abstract":"Human papillomavirus (HPV) vaccination has not been introduced in many countries in South-Central Asia, including Afghanistan, despite the sub-region having the highest incidence rate of cervical cancer in Asia. This study estimates the potential health impact and cost-effectiveness of HPV vaccination in Afghanistan to inform national decision-making. An Excel-based static cohort model was used to estimate the lifetime costs and health outcomes of vaccinating a single cohort of 9-year-old girls in the year 2018 with the bivalent HPV vaccine, compared to no vaccination. We also explored a scenario with a catch-up campaign for girls aged 10–14 years. Input parameters were based on local sources, published literature, or assumptions when no data was available. The primary outcome measure was the discounted cost per disability-adjusted life-year (DALY) averted, evaluated from both government and societal perspectives. Vaccinating a single cohort of 9-year-old girls against HPV in Afghanistan could avert 1718 cervical cancer cases, 125 hospitalizations, and 1612 deaths over the lifetime of the cohort. The incremental cost-effectiveness ratio was US$426 per DALY averted from the government perspective and US$400 per DALY averted from the societal perspective. The estimated annual cost of the HPV vaccination program (US$3,343,311) represents approximately 3.53% of the country′s total immunization budget for 2018 or 0.13% of total health expenditures. In Afghanistan, HPV vaccine introduction targeting a single cohort is potentially cost-effective (0.7 times the GDP per capita of $586) from both the government and societal perspective with additional health benefits generated by a catch-up campaign, depending on the government′s willingness to pay for the projected health outcomes."}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"bibliographic","authorship":[{"display_name":"Anwari Palwasha","position":"first"},{"display_name":"Debellut Frédéric","position":"middle"},{"display_name":"Vodicka Elisabeth","position":"middle"},{"display_name":"Clark Andrew","position":"middle"},{"display_name":"Farewar Farhad","position":"middle"},{"display_name":"Zhwak Zubiada","position":"middle"},{"display_name":"Nazary Dastagger","position":"middle"},{"display_name":"Pecenka Clint","position":"middle"},{"display_name":"LaMontagne D","position":"middle"},{"display_name":"Safi Najibullah","position":"last"}],"publication_year":2019,"publisher":"Elsevier BV","title":"Potential health impact and cost-effectiveness of bivalent human papillomavirus (HPV) vaccination in Afghanistan"}}]}
+{"visibility":"public","identifiers":[{"identifier":"10.1016/j.cct.2021.106266","identifier_type":"doi"}],"enhancements":[{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"abstract","process":"other","abstract":"Human papillomavirus (HPV) infection is the primary cause of cervical cancer. In 2018, the World Health Organization (WHO) Director General announced his commitment to eliminate cervical cancer, with HPV vaccination as a priority. However, the costs of setting up a multi-dose HPV vaccination programme remain a barrier to its introduction. We are conducting a randomised-controlled trial of reduced dose schedules of HPV vaccine in Tanzania to establish whether a single dose produces immune responses that will be effective in preventing cervical cancer. 930 girls aged 9–14 years in Mwanza, Tanzania, were randomised to one of 6 arms, comprising 3 different dose schedules of the 2-valent (Cervarix) and 9-valent (Gardasil-9) HPV vaccines: 3 doses; 2 doses given 6 months apart; or a single dose. All participants will be followed for 36 months; those in the 1 and 2 dose arms will be followed for 60 months. Trial outcomes focus on vaccine immune responses including HPV 16/18-specific antibody levels, antibody avidity, and memory B cell responses. Results will be immunobridged to historical cohorts of girls and young women in whom efficacy has been demonstrated. This is the first randomised trial of the single dose HPV vaccine schedule in the target age group. The trial will allow us to examine the quality and durability of immune responses of reduced dose schedules in a population with high burden of malaria and other infections that may affect vaccine immune responses. Initial results (24 months) are expected to be published in early 2021."}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"bibliographic","authorship":[{"display_name":"Baisley Kathy","position":"first"},{"display_name":"Whitworth Hilary","position":"middle"},{"display_name":"Changalucha John","position":"middle"},{"display_name":"Pinto Lígia","position":"middle"},{"display_name":"Dillner Joakim","position":"middle"},{"display_name":"Kapiga Saidi","position":"middle"},{"display_name":"de Sanjosé Sílvia","position":"middle"},{"display_name":"Mayaud Philippe","position":"middle"},{"display_name":"Hayes Richard","position":"middle"},{"display_name":"Lacey Charles","position":"middle"},{"display_name":"Watson‐Jones Deborah","position":"last"}],"publication_year":2021,"publisher":"Elsevier BV","title":"A dose-reduction HPV vaccine immunobridging trial of two HPV vaccines among adolescent girls in Tanzania (the DoRIS trial) – Study protocol for a randomised controlled trial"}}]}

destiny_sdk-0.5.0/tests/unit/test_data/eppi_import_with_annotations.jsonl

@@ -0,0 +1,4 @@
+{"visibility":"public","identifiers":[{"identifier":"10.1016/j.eclinm.2024.102524","identifier_type":"doi"}],"enhancements":[{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"abstract","process":"other","abstract":"Background\nWhile human papillomavirus (HPV) vaccines have been available since 2006, the coverage has varied among countries. Our aim is to analyse the equity impact of HPV vaccination on the lifetime projections of cervical cancer burden among vaccinated cohorts of 2010–22 in 84 countries.\n\nMethods\nWe used WHO and UNICEF estimates of national immunisation coverage for HPV vaccination in 84 countries during 2010–22. We used PRIME (Papillomavirus Rapid Interface for Modelling and Economics) to estimate the lifetime health impact of HPV vaccination on cervical cancer burden in terms of deaths, cases, and disability-adjusted life years (DALYs) averted by vaccination in their respective countries. We generated concentration indices and curves to assess the equity impact of HPV vaccination across 84 countries.\n\nFindings\nThe health impact of HPV vaccination varied across the 84 countries and ranged from Switzerland to Tanzania at 2 to 34 deaths, 4 to 47 cases, and 40 to 735 DALYs averted per 1000 vaccinated adolescent girls over the lifetime of the vaccinated cohorts of 2010–22. The concentration index for the distribution of average coverage during 2010–22 among the 84 countries ranked by vaccine impact was 0.33 (95% CI: 0.27–0.40) and highlights the wide inequities in HPV vaccination coverage.\n\nInterpretation\nOur findings suggested that countries with a relatively higher cervical cancer burden and thereby a relatively higher need for HPV vaccination had relatively lower coverage during 2010–22. Further, there were significant inequities in HPV vaccination coverage within the Americas, Europe, and Western Pacific regions, and in high- and low-income countries with a pro-advantaged and regressive distribution favouring countries with lower vaccine impact."}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"bibliographic","authorship":[{"display_name":"Abbas Kaja","position":"first"},{"display_name":"Yoo Katelyn","position":"middle"},{"display_name":"Prem Kiesha","position":"middle"},{"display_name":"Jit Mark","position":"last"}],"publication_year":2024,"publisher":"Elsevier BV","title":"Equity impact of HPV vaccination on lifetime projections of cervical cancer burden among cohorts in 84 countries by global, regional, and income levels, 2010–22: a modelling study"}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"annotation","annotations":[{"annotation_type":"boolean","scheme":"destiny_sdk.eppi_parser@1.0","label":"test-tag","value":true,"data":{}},{"annotation_type":"boolean","scheme":"destiny_sdk.eppi_parser@1.0","label":"another-tag","value":true,"data":{}}]}}]}
+{"visibility":"public","identifiers":[{"identifier":"10.1016/j.jvacx.2024.100459","identifier_type":"doi"}],"enhancements":[{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"abstract","process":"other","abstract":"The World Health Organization has recommended the inclusion of human papillomavirus (HPV) vaccines in national immunization programs to address the global problem of cervical cancer. In the Philippines, HPV vaccination was introduced in a phased approach in 2015. This study seeks to estimate the cost of delivery of the HPV vaccination program and its operational context in the Philippines.\n\nMethods\nThis was a retrospective, cross-sectional micro-costing study focused on ongoing HPV vaccination delivery and its operational context across all levels of the health system. Using structured questionnaires and data collection from secondary sources, the weighted mean financial and economic costs and costs per dose at the national, subnational, and health facility levels were estimated.\nResults\nThe weighted mean financial and economic costs per dose of the HPV vaccination program aggregated across all levels of the health system were $US3.72and $29.74, respectively. Activities contributing most significantly to costs were service delivery and vaccine collection or distribution and storage at the health facility and administrative levels, respectively. The opportunity costs for health worker and non-health worker time accounted for 77% of the economic cost per dose.\nConclusion\nThe total weighted mean financial and economic costs of HPV delivery are within range of those reported in other countries. Costing studies can help identify cost drivers with local operational context to help inform policymakers and program managers in budgeting and planning interventions to improve program implementation."}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"bibliographic","authorship":[{"display_name":"Aldaba Josephine","position":"first"},{"display_name":"Llave Cecilia","position":"middle"},{"display_name":"Uy Ma","position":"middle"},{"display_name":"Tejano Kim","position":"middle"},{"display_name":"Aquino Ma","position":"middle"},{"display_name":"Catalig Migel","position":"middle"},{"display_name":"Sy Alvin","position":"middle"},{"display_name":"Valverde Haidee","position":"middle"},{"display_name":"Mooney Jessica","position":"middle"},{"display_name":"Slavkovsky Rose","position":"last"}],"publication_year":2024,"publisher":"Elsevier BV","title":"The cost of human papillomavirus vaccination delivery at the administrative and health facility levels in the Philippines"}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"annotation","annotations":[{"annotation_type":"boolean","scheme":"destiny_sdk.eppi_parser@1.0","label":"test-tag","value":true,"data":{}},{"annotation_type":"boolean","scheme":"destiny_sdk.eppi_parser@1.0","label":"another-tag","value":true,"data":{}}]}}]}
+{"visibility":"public","identifiers":[{"identifier":"10.1016/j.vaccine.2019.12.013","identifier_type":"doi"}],"enhancements":[{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"abstract","process":"other","abstract":"Human papillomavirus (HPV) vaccination has not been introduced in many countries in South-Central Asia, including Afghanistan, despite the sub-region having the highest incidence rate of cervical cancer in Asia. This study estimates the potential health impact and cost-effectiveness of HPV vaccination in Afghanistan to inform national decision-making. An Excel-based static cohort model was used to estimate the lifetime costs and health outcomes of vaccinating a single cohort of 9-year-old girls in the year 2018 with the bivalent HPV vaccine, compared to no vaccination. We also explored a scenario with a catch-up campaign for girls aged 10–14 years. Input parameters were based on local sources, published literature, or assumptions when no data was available. The primary outcome measure was the discounted cost per disability-adjusted life-year (DALY) averted, evaluated from both government and societal perspectives. Vaccinating a single cohort of 9-year-old girls against HPV in Afghanistan could avert 1718 cervical cancer cases, 125 hospitalizations, and 1612 deaths over the lifetime of the cohort. The incremental cost-effectiveness ratio was US$426 per DALY averted from the government perspective and US$400 per DALY averted from the societal perspective. The estimated annual cost of the HPV vaccination program (US$3,343,311) represents approximately 3.53% of the country′s total immunization budget for 2018 or 0.13% of total health expenditures. In Afghanistan, HPV vaccine introduction targeting a single cohort is potentially cost-effective (0.7 times the GDP per capita of $586) from both the government and societal perspective with additional health benefits generated by a catch-up campaign, depending on the government′s willingness to pay for the projected health outcomes."}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"bibliographic","authorship":[{"display_name":"Anwari Palwasha","position":"first"},{"display_name":"Debellut Frédéric","position":"middle"},{"display_name":"Vodicka Elisabeth","position":"middle"},{"display_name":"Clark Andrew","position":"middle"},{"display_name":"Farewar Farhad","position":"middle"},{"display_name":"Zhwak Zubiada","position":"middle"},{"display_name":"Nazary Dastagger","position":"middle"},{"display_name":"Pecenka Clint","position":"middle"},{"display_name":"LaMontagne D","position":"middle"},{"display_name":"Safi Najibullah","position":"last"}],"publication_year":2019,"publisher":"Elsevier BV","title":"Potential health impact and cost-effectiveness of bivalent human papillomavirus (HPV) vaccination in Afghanistan"}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"annotation","annotations":[{"annotation_type":"boolean","scheme":"destiny_sdk.eppi_parser@1.0","label":"test-tag","value":true,"data":{}},{"annotation_type":"boolean","scheme":"destiny_sdk.eppi_parser@1.0","label":"another-tag","value":true,"data":{}}]}}]}
+{"visibility":"public","identifiers":[{"identifier":"10.1016/j.cct.2021.106266","identifier_type":"doi"}],"enhancements":[{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"abstract","process":"other","abstract":"Human papillomavirus (HPV) infection is the primary cause of cervical cancer. In 2018, the World Health Organization (WHO) Director General announced his commitment to eliminate cervical cancer, with HPV vaccination as a priority. However, the costs of setting up a multi-dose HPV vaccination programme remain a barrier to its introduction. We are conducting a randomised-controlled trial of reduced dose schedules of HPV vaccine in Tanzania to establish whether a single dose produces immune responses that will be effective in preventing cervical cancer. 930 girls aged 9–14 years in Mwanza, Tanzania, were randomised to one of 6 arms, comprising 3 different dose schedules of the 2-valent (Cervarix) and 9-valent (Gardasil-9) HPV vaccines: 3 doses; 2 doses given 6 months apart; or a single dose. All participants will be followed for 36 months; those in the 1 and 2 dose arms will be followed for 60 months. Trial outcomes focus on vaccine immune responses including HPV 16/18-specific antibody levels, antibody avidity, and memory B cell responses. Results will be immunobridged to historical cohorts of girls and young women in whom efficacy has been demonstrated. This is the first randomised trial of the single dose HPV vaccine schedule in the target age group. The trial will allow us to examine the quality and durability of immune responses of reduced dose schedules in a population with high burden of malaria and other infections that may affect vaccine immune responses. Initial results (24 months) are expected to be published in early 2021."}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"bibliographic","authorship":[{"display_name":"Baisley Kathy","position":"first"},{"display_name":"Whitworth Hilary","position":"middle"},{"display_name":"Changalucha John","position":"middle"},{"display_name":"Pinto Lígia","position":"middle"},{"display_name":"Dillner Joakim","position":"middle"},{"display_name":"Kapiga Saidi","position":"middle"},{"display_name":"de Sanjosé Sílvia","position":"middle"},{"display_name":"Mayaud Philippe","position":"middle"},{"display_name":"Hayes Richard","position":"middle"},{"display_name":"Lacey Charles","position":"middle"},{"display_name":"Watson‐Jones Deborah","position":"last"}],"publication_year":2021,"publisher":"Elsevier BV","title":"A dose-reduction HPV vaccine immunobridging trial of two HPV vaccines among adolescent girls in Tanzania (the DoRIS trial) – Study protocol for a randomised controlled trial"}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","content":{"enhancement_type":"annotation","annotations":[{"annotation_type":"boolean","scheme":"destiny_sdk.eppi_parser@1.0","label":"test-tag","value":true,"data":{}},{"annotation_type":"boolean","scheme":"destiny_sdk.eppi_parser@1.0","label":"another-tag","value":true,"data":{}}]}}]}

{destiny_sdk-0.4.0 → destiny_sdk-0.5.0}/tests/unit/test_robots.py

@@ -2,13 +2,12 @@ import uuid
 
 import destiny_sdk
 import pytest
-from pydantic import HttpUrl, ValidationError
+from pydantic import ValidationError
 
 
 def test_provisioned_robot_valid():
     provisioned_robot = destiny_sdk.robots.ProvisionedRobot(
         id=uuid.uuid4(),
-        base_url=HttpUrl("https://www.domo-arigato-mr-robo.to"),
         name="Mr. Roboto",
         description="I have come to help you with your problems",
         owner="Styx",
@@ -21,7 +20,6 @@ def test_provisioned_robot_valid():
 def test_robot_models_reject_any_extra_fields():
     with pytest.raises(ValidationError):
         destiny_sdk.robots.Robot(
-            base_url=HttpUrl("https://www.domo-arigato-mr-robo.to"),
             name="Mr. Roboto",
             description="I have come to help you with your problems",
             owner="Styx",

{destiny_sdk-0.4.0 → destiny_sdk-0.5.0}/uv.lock

@@ -63,7 +63,7 @@ wheels = [
 
 [[package]]
 name = "destiny-sdk"
-version = "0.4.0"
+version = "0.5.0"
 source = { editable = "." }
 dependencies = [
     { name = "cachetools" },

destiny_sdk-0.4.0/tests/unit/test_data/eppi_import.jsonl

@@ -1,4 +0,0 @@
-{"visibility":"public","identifiers":[{"identifier":"10.1016/j.eclinm.2024.102524","identifier_type":"doi"}],"enhancements":[{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"abstract","content":{"enhancement_type":"abstract","process":"other","abstract":"Background\nWhile human papillomavirus (HPV) vaccines have been available since 2006, the coverage has varied among countries. Our aim is to analyse the equity impact of HPV vaccination on the lifetime projections of cervical cancer burden among vaccinated cohorts of 2010–22 in 84 countries.\n\nMethods\nWe used WHO and UNICEF estimates of national immunisation coverage for HPV vaccination in 84 countries during 2010–22. We used PRIME (Papillomavirus Rapid Interface for Modelling and Economics) to estimate the lifetime health impact of HPV vaccination on cervical cancer burden in terms of deaths, cases, and disability-adjusted life years (DALYs) averted by vaccination in their respective countries. We generated concentration indices and curves to assess the equity impact of HPV vaccination across 84 countries.\n\nFindings\nThe health impact of HPV vaccination varied across the 84 countries and ranged from Switzerland to Tanzania at 2 to 34 deaths, 4 to 47 cases, and 40 to 735 DALYs averted per 1000 vaccinated adolescent girls over the lifetime of the vaccinated cohorts of 2010–22. The concentration index for the distribution of average coverage during 2010–22 among the 84 countries ranked by vaccine impact was 0.33 (95% CI: 0.27–0.40) and highlights the wide inequities in HPV vaccination coverage.\n\nInterpretation\nOur findings suggested that countries with a relatively higher cervical cancer burden and thereby a relatively higher need for HPV vaccination had relatively lower coverage during 2010–22. Further, there were significant inequities in HPV vaccination coverage within the Americas, Europe, and Western Pacific regions, and in high- and low-income countries with a pro-advantaged and regressive distribution favouring countries with lower vaccine impact."}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"bibliographic","content":{"enhancement_type":"bibliographic","authorship":[{"display_name":"Abbas Kaja","position":"first"},{"display_name":"Yoo Katelyn","position":"middle"},{"display_name":"Prem Kiesha","position":"middle"},{"display_name":"Jit Mark","position":"last"}],"publication_year":2024,"publisher":"Elsevier BV","title":"Equity impact of HPV vaccination on lifetime projections of cervical cancer burden among cohorts in 84 countries by global, regional, and income levels, 2010–22: a modelling study"}}]}
-{"visibility":"public","identifiers":[{"identifier":"10.1016/j.jvacx.2024.100459","identifier_type":"doi"}],"enhancements":[{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"abstract","content":{"enhancement_type":"abstract","process":"other","abstract":"The World Health Organization has recommended the inclusion of human papillomavirus (HPV) vaccines in national immunization programs to address the global problem of cervical cancer. In the Philippines, HPV vaccination was introduced in a phased approach in 2015. This study seeks to estimate the cost of delivery of the HPV vaccination program and its operational context in the Philippines.\n\nMethods\nThis was a retrospective, cross-sectional micro-costing study focused on ongoing HPV vaccination delivery and its operational context across all levels of the health system. Using structured questionnaires and data collection from secondary sources, the weighted mean financial and economic costs and costs per dose at the national, subnational, and health facility levels were estimated.\nResults\nThe weighted mean financial and economic costs per dose of the HPV vaccination program aggregated across all levels of the health system were $US3.72and $29.74, respectively. Activities contributing most significantly to costs were service delivery and vaccine collection or distribution and storage at the health facility and administrative levels, respectively. The opportunity costs for health worker and non-health worker time accounted for 77% of the economic cost per dose.\nConclusion\nThe total weighted mean financial and economic costs of HPV delivery are within range of those reported in other countries. Costing studies can help identify cost drivers with local operational context to help inform policymakers and program managers in budgeting and planning interventions to improve program implementation."}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"bibliographic","content":{"enhancement_type":"bibliographic","authorship":[{"display_name":"Aldaba Josephine","position":"first"},{"display_name":"Llave Cecilia","position":"middle"},{"display_name":"Uy Ma","position":"middle"},{"display_name":"Tejano Kim","position":"middle"},{"display_name":"Aquino Ma","position":"middle"},{"display_name":"Catalig Migel","position":"middle"},{"display_name":"Sy Alvin","position":"middle"},{"display_name":"Valverde Haidee","position":"middle"},{"display_name":"Mooney Jessica","position":"middle"},{"display_name":"Slavkovsky Rose","position":"last"}],"publication_year":2024,"publisher":"Elsevier BV","title":"The cost of human papillomavirus vaccination delivery at the administrative and health facility levels in the Philippines"}}]}
-{"visibility":"public","identifiers":[{"identifier":"10.1016/j.vaccine.2019.12.013","identifier_type":"doi"}],"enhancements":[{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"abstract","content":{"enhancement_type":"abstract","process":"other","abstract":"Human papillomavirus (HPV) vaccination has not been introduced in many countries in South-Central Asia, including Afghanistan, despite the sub-region having the highest incidence rate of cervical cancer in Asia. This study estimates the potential health impact and cost-effectiveness of HPV vaccination in Afghanistan to inform national decision-making. An Excel-based static cohort model was used to estimate the lifetime costs and health outcomes of vaccinating a single cohort of 9-year-old girls in the year 2018 with the bivalent HPV vaccine, compared to no vaccination. We also explored a scenario with a catch-up campaign for girls aged 10–14 years. Input parameters were based on local sources, published literature, or assumptions when no data was available. The primary outcome measure was the discounted cost per disability-adjusted life-year (DALY) averted, evaluated from both government and societal perspectives. Vaccinating a single cohort of 9-year-old girls against HPV in Afghanistan could avert 1718 cervical cancer cases, 125 hospitalizations, and 1612 deaths over the lifetime of the cohort. The incremental cost-effectiveness ratio was US$426 per DALY averted from the government perspective and US$400 per DALY averted from the societal perspective. The estimated annual cost of the HPV vaccination program (US$3,343,311) represents approximately 3.53% of the country′s total immunization budget for 2018 or 0.13% of total health expenditures. In Afghanistan, HPV vaccine introduction targeting a single cohort is potentially cost-effective (0.7 times the GDP per capita of $586) from both the government and societal perspective with additional health benefits generated by a catch-up campaign, depending on the government′s willingness to pay for the projected health outcomes."}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"bibliographic","content":{"enhancement_type":"bibliographic","authorship":[{"display_name":"Anwari Palwasha","position":"first"},{"display_name":"Debellut Frédéric","position":"middle"},{"display_name":"Vodicka Elisabeth","position":"middle"},{"display_name":"Clark Andrew","position":"middle"},{"display_name":"Farewar Farhad","position":"middle"},{"display_name":"Zhwak Zubiada","position":"middle"},{"display_name":"Nazary Dastagger","position":"middle"},{"display_name":"Pecenka Clint","position":"middle"},{"display_name":"LaMontagne D","position":"middle"},{"display_name":"Safi Najibullah","position":"last"}],"publication_year":2019,"publisher":"Elsevier BV","title":"Potential health impact and cost-effectiveness of bivalent human papillomavirus (HPV) vaccination in Afghanistan"}}]}
-{"visibility":"public","identifiers":[{"identifier":"10.1016/j.cct.2021.106266","identifier_type":"doi"}],"enhancements":[{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"abstract","content":{"enhancement_type":"abstract","process":"other","abstract":"Human papillomavirus (HPV) infection is the primary cause of cervical cancer. In 2018, the World Health Organization (WHO) Director General announced his commitment to eliminate cervical cancer, with HPV vaccination as a priority. However, the costs of setting up a multi-dose HPV vaccination programme remain a barrier to its introduction. We are conducting a randomised-controlled trial of reduced dose schedules of HPV vaccine in Tanzania to establish whether a single dose produces immune responses that will be effective in preventing cervical cancer. 930 girls aged 9–14 years in Mwanza, Tanzania, were randomised to one of 6 arms, comprising 3 different dose schedules of the 2-valent (Cervarix) and 9-valent (Gardasil-9) HPV vaccines: 3 doses; 2 doses given 6 months apart; or a single dose. All participants will be followed for 36 months; those in the 1 and 2 dose arms will be followed for 60 months. Trial outcomes focus on vaccine immune responses including HPV 16/18-specific antibody levels, antibody avidity, and memory B cell responses. Results will be immunobridged to historical cohorts of girls and young women in whom efficacy has been demonstrated. This is the first randomised trial of the single dose HPV vaccine schedule in the target age group. The trial will allow us to examine the quality and durability of immune responses of reduced dose schedules in a population with high burden of malaria and other infections that may affect vaccine immune responses. Initial results (24 months) are expected to be published in early 2021."}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"bibliographic","content":{"enhancement_type":"bibliographic","authorship":[{"display_name":"Baisley Kathy","position":"first"},{"display_name":"Whitworth Hilary","position":"middle"},{"display_name":"Changalucha John","position":"middle"},{"display_name":"Pinto Lígia","position":"middle"},{"display_name":"Dillner Joakim","position":"middle"},{"display_name":"Kapiga Saidi","position":"middle"},{"display_name":"de Sanjosé Sílvia","position":"middle"},{"display_name":"Mayaud Philippe","position":"middle"},{"display_name":"Hayes Richard","position":"middle"},{"display_name":"Lacey Charles","position":"middle"},{"display_name":"Watson‐Jones Deborah","position":"last"}],"publication_year":2021,"publisher":"Elsevier BV","title":"A dose-reduction HPV vaccine immunobridging trial of two HPV vaccines among adolescent girls in Tanzania (the DoRIS trial) – Study protocol for a randomised controlled trial"}}]}

destiny_sdk-0.4.0/tests/unit/test_data/eppi_import_with_annotations.jsonl

@@ -1,4 +0,0 @@
-{"visibility":"public","identifiers":[{"identifier":"10.1016/j.eclinm.2024.102524","identifier_type":"doi"}],"enhancements":[{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"abstract","content":{"enhancement_type":"abstract","process":"other","abstract":"Background\nWhile human papillomavirus (HPV) vaccines have been available since 2006, the coverage has varied among countries. Our aim is to analyse the equity impact of HPV vaccination on the lifetime projections of cervical cancer burden among vaccinated cohorts of 2010–22 in 84 countries.\n\nMethods\nWe used WHO and UNICEF estimates of national immunisation coverage for HPV vaccination in 84 countries during 2010–22. We used PRIME (Papillomavirus Rapid Interface for Modelling and Economics) to estimate the lifetime health impact of HPV vaccination on cervical cancer burden in terms of deaths, cases, and disability-adjusted life years (DALYs) averted by vaccination in their respective countries. We generated concentration indices and curves to assess the equity impact of HPV vaccination across 84 countries.\n\nFindings\nThe health impact of HPV vaccination varied across the 84 countries and ranged from Switzerland to Tanzania at 2 to 34 deaths, 4 to 47 cases, and 40 to 735 DALYs averted per 1000 vaccinated adolescent girls over the lifetime of the vaccinated cohorts of 2010–22. The concentration index for the distribution of average coverage during 2010–22 among the 84 countries ranked by vaccine impact was 0.33 (95% CI: 0.27–0.40) and highlights the wide inequities in HPV vaccination coverage.\n\nInterpretation\nOur findings suggested that countries with a relatively higher cervical cancer burden and thereby a relatively higher need for HPV vaccination had relatively lower coverage during 2010–22. Further, there were significant inequities in HPV vaccination coverage within the Americas, Europe, and Western Pacific regions, and in high- and low-income countries with a pro-advantaged and regressive distribution favouring countries with lower vaccine impact."}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"bibliographic","content":{"enhancement_type":"bibliographic","authorship":[{"display_name":"Abbas Kaja","position":"first"},{"display_name":"Yoo Katelyn","position":"middle"},{"display_name":"Prem Kiesha","position":"middle"},{"display_name":"Jit Mark","position":"last"}],"publication_year":2024,"publisher":"Elsevier BV","title":"Equity impact of HPV vaccination on lifetime projections of cervical cancer burden among cohorts in 84 countries by global, regional, and income levels, 2010–22: a modelling study"}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"annotation","content":{"enhancement_type":"annotation","annotations":[{"annotation_type":"boolean","scheme":"destiny_sdk.eppi_parser@1.0","label":"test-tag","value":true,"data":{}},{"annotation_type":"boolean","scheme":"destiny_sdk.eppi_parser@1.0","label":"another-tag","value":true,"data":{}}]}}]}
-{"visibility":"public","identifiers":[{"identifier":"10.1016/j.jvacx.2024.100459","identifier_type":"doi"}],"enhancements":[{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"abstract","content":{"enhancement_type":"abstract","process":"other","abstract":"The World Health Organization has recommended the inclusion of human papillomavirus (HPV) vaccines in national immunization programs to address the global problem of cervical cancer. In the Philippines, HPV vaccination was introduced in a phased approach in 2015. This study seeks to estimate the cost of delivery of the HPV vaccination program and its operational context in the Philippines.\n\nMethods\nThis was a retrospective, cross-sectional micro-costing study focused on ongoing HPV vaccination delivery and its operational context across all levels of the health system. Using structured questionnaires and data collection from secondary sources, the weighted mean financial and economic costs and costs per dose at the national, subnational, and health facility levels were estimated.\nResults\nThe weighted mean financial and economic costs per dose of the HPV vaccination program aggregated across all levels of the health system were $US3.72and $29.74, respectively. Activities contributing most significantly to costs were service delivery and vaccine collection or distribution and storage at the health facility and administrative levels, respectively. The opportunity costs for health worker and non-health worker time accounted for 77% of the economic cost per dose.\nConclusion\nThe total weighted mean financial and economic costs of HPV delivery are within range of those reported in other countries. Costing studies can help identify cost drivers with local operational context to help inform policymakers and program managers in budgeting and planning interventions to improve program implementation."}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"bibliographic","content":{"enhancement_type":"bibliographic","authorship":[{"display_name":"Aldaba Josephine","position":"first"},{"display_name":"Llave Cecilia","position":"middle"},{"display_name":"Uy Ma","position":"middle"},{"display_name":"Tejano Kim","position":"middle"},{"display_name":"Aquino Ma","position":"middle"},{"display_name":"Catalig Migel","position":"middle"},{"display_name":"Sy Alvin","position":"middle"},{"display_name":"Valverde Haidee","position":"middle"},{"display_name":"Mooney Jessica","position":"middle"},{"display_name":"Slavkovsky Rose","position":"last"}],"publication_year":2024,"publisher":"Elsevier BV","title":"The cost of human papillomavirus vaccination delivery at the administrative and health facility levels in the Philippines"}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"annotation","content":{"enhancement_type":"annotation","annotations":[{"annotation_type":"boolean","scheme":"destiny_sdk.eppi_parser@1.0","label":"test-tag","value":true,"data":{}},{"annotation_type":"boolean","scheme":"destiny_sdk.eppi_parser@1.0","label":"another-tag","value":true,"data":{}}]}}]}
-{"visibility":"public","identifiers":[{"identifier":"10.1016/j.vaccine.2019.12.013","identifier_type":"doi"}],"enhancements":[{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"abstract","content":{"enhancement_type":"abstract","process":"other","abstract":"Human papillomavirus (HPV) vaccination has not been introduced in many countries in South-Central Asia, including Afghanistan, despite the sub-region having the highest incidence rate of cervical cancer in Asia. This study estimates the potential health impact and cost-effectiveness of HPV vaccination in Afghanistan to inform national decision-making. An Excel-based static cohort model was used to estimate the lifetime costs and health outcomes of vaccinating a single cohort of 9-year-old girls in the year 2018 with the bivalent HPV vaccine, compared to no vaccination. We also explored a scenario with a catch-up campaign for girls aged 10–14 years. Input parameters were based on local sources, published literature, or assumptions when no data was available. The primary outcome measure was the discounted cost per disability-adjusted life-year (DALY) averted, evaluated from both government and societal perspectives. Vaccinating a single cohort of 9-year-old girls against HPV in Afghanistan could avert 1718 cervical cancer cases, 125 hospitalizations, and 1612 deaths over the lifetime of the cohort. The incremental cost-effectiveness ratio was US$426 per DALY averted from the government perspective and US$400 per DALY averted from the societal perspective. The estimated annual cost of the HPV vaccination program (US$3,343,311) represents approximately 3.53% of the country′s total immunization budget for 2018 or 0.13% of total health expenditures. In Afghanistan, HPV vaccine introduction targeting a single cohort is potentially cost-effective (0.7 times the GDP per capita of $586) from both the government and societal perspective with additional health benefits generated by a catch-up campaign, depending on the government′s willingness to pay for the projected health outcomes."}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"bibliographic","content":{"enhancement_type":"bibliographic","authorship":[{"display_name":"Anwari Palwasha","position":"first"},{"display_name":"Debellut Frédéric","position":"middle"},{"display_name":"Vodicka Elisabeth","position":"middle"},{"display_name":"Clark Andrew","position":"middle"},{"display_name":"Farewar Farhad","position":"middle"},{"display_name":"Zhwak Zubiada","position":"middle"},{"display_name":"Nazary Dastagger","position":"middle"},{"display_name":"Pecenka Clint","position":"middle"},{"display_name":"LaMontagne D","position":"middle"},{"display_name":"Safi Najibullah","position":"last"}],"publication_year":2019,"publisher":"Elsevier BV","title":"Potential health impact and cost-effectiveness of bivalent human papillomavirus (HPV) vaccination in Afghanistan"}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"annotation","content":{"enhancement_type":"annotation","annotations":[{"annotation_type":"boolean","scheme":"destiny_sdk.eppi_parser@1.0","label":"test-tag","value":true,"data":{}},{"annotation_type":"boolean","scheme":"destiny_sdk.eppi_parser@1.0","label":"another-tag","value":true,"data":{}}]}}]}
-{"visibility":"public","identifiers":[{"identifier":"10.1016/j.cct.2021.106266","identifier_type":"doi"}],"enhancements":[{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"abstract","content":{"enhancement_type":"abstract","process":"other","abstract":"Human papillomavirus (HPV) infection is the primary cause of cervical cancer. In 2018, the World Health Organization (WHO) Director General announced his commitment to eliminate cervical cancer, with HPV vaccination as a priority. However, the costs of setting up a multi-dose HPV vaccination programme remain a barrier to its introduction. We are conducting a randomised-controlled trial of reduced dose schedules of HPV vaccine in Tanzania to establish whether a single dose produces immune responses that will be effective in preventing cervical cancer. 930 girls aged 9–14 years in Mwanza, Tanzania, were randomised to one of 6 arms, comprising 3 different dose schedules of the 2-valent (Cervarix) and 9-valent (Gardasil-9) HPV vaccines: 3 doses; 2 doses given 6 months apart; or a single dose. All participants will be followed for 36 months; those in the 1 and 2 dose arms will be followed for 60 months. Trial outcomes focus on vaccine immune responses including HPV 16/18-specific antibody levels, antibody avidity, and memory B cell responses. Results will be immunobridged to historical cohorts of girls and young women in whom efficacy has been demonstrated. This is the first randomised trial of the single dose HPV vaccine schedule in the target age group. The trial will allow us to examine the quality and durability of immune responses of reduced dose schedules in a population with high burden of malaria and other infections that may affect vaccine immune responses. Initial results (24 months) are expected to be published in early 2021."}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"bibliographic","content":{"enhancement_type":"bibliographic","authorship":[{"display_name":"Baisley Kathy","position":"first"},{"display_name":"Whitworth Hilary","position":"middle"},{"display_name":"Changalucha John","position":"middle"},{"display_name":"Pinto Lígia","position":"middle"},{"display_name":"Dillner Joakim","position":"middle"},{"display_name":"Kapiga Saidi","position":"middle"},{"display_name":"de Sanjosé Sílvia","position":"middle"},{"display_name":"Mayaud Philippe","position":"middle"},{"display_name":"Hayes Richard","position":"middle"},{"display_name":"Lacey Charles","position":"middle"},{"display_name":"Watson‐Jones Deborah","position":"last"}],"publication_year":2021,"publisher":"Elsevier BV","title":"A dose-reduction HPV vaccine immunobridging trial of two HPV vaccines among adolescent girls in Tanzania (the DoRIS trial) – Study protocol for a randomised controlled trial"}},{"source":"destiny_sdk.eppi_parser@1.0","visibility":"public","enhancement_type":"annotation","content":{"enhancement_type":"annotation","annotations":[{"annotation_type":"boolean","scheme":"destiny_sdk.eppi_parser@1.0","label":"test-tag","value":true,"data":{}},{"annotation_type":"boolean","scheme":"destiny_sdk.eppi_parser@1.0","label":"another-tag","value":true,"data":{}}]}}]}