| Name | tap-clinicaltrials JSON |
| Version |
0.2.9
JSON |
| download |
| home_page | None |
| Summary | `tap-clinicaltrials` is a Singer tap for ClinicalTrials.gov, built with the Meltano SDK for Singer Taps. |
| upload_time | 2025-10-21 04:41:17 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| license | None |
| keywords |
clinicaltrials.gov
elt
singer.io
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# `tap-clinicaltrials`
Singer tap for [ClinicalTrials.gov](https://clinicaltrials.gov/data-about-studies/learn-about-api) study records data.
Built with the [Meltano Tap SDK](https://sdk.meltano.com) for Singer Taps.
## Capabilities
* `catalog`
* `state`
* `discover`
* `about`
* `stream-maps`
## Settings
| Setting | Required | Default | Description |
|:--------------------|:--------:|:-------:|:------------|
| start_date | False | None | Earliest datetime to get data from |
| condition | False | None | Conditions or disease query |
| sponsor | False | None | Sponsor query |
| stream_maps | False | None | Config object for stream maps capability. For more information check out [Stream Maps](https://sdk.meltano.com/en/latest/stream_maps.html). |
| stream_map_config | False | None | User-defined config values to be used within map expressions. |
| flattening_enabled | False | None | 'True' to enable schema flattening and automatically expand nested properties. |
| flattening_max_depth| False | None | The max depth to flatten schemas. |
| batch_config | False | None | |
A full list of supported settings and capabilities is available by running: `tap-clinicaltrials --about`
## Installation
### In a Meltano project
#### Using a direct reference
```bash
meltano add extractor tap-clinicaltrials --from-ref=https://raw.githubusercontent.com/edgarrmondragon/tap-clinicaltrials/main/plugin.yaml
```
Requires Meltano v3.1.0+.
#### From MeltanoHub
Not yet available.
### From PyPI
```bash
python3 -m pip install --upgrade tap-clinicaltrials
```
### With [pipx][pipx]
```bash
pipx install tap-clinicaltrials
```
[pipx]: https://github.com/pypa/pipx
### From source
```bash
git clone https://github.com/edgarrmondragon/tap-clinicaltrials
cd tap-clinicaltrials
python3 -m pip install .
```
## Usage
You can easily run `tap-clinicaltrials` by itself or in a pipeline using [Meltano](https://meltano.com/).
### With Meltano
1. Clone the repo and `cd` into it:
```bash
git clone https://github.com/edgarrmondragon/tap-clinicaltrials.git
cd tap-clinicaltrials
```
1. Make sure you have [Meltano](https://docs.meltano.com/guide/installation-guide) installed
1. Install all plugins
```bash
meltano install
```
1. Configure the `tap-clinicaltrials` tap:
```bash
meltano config tap-clinicaltrials set start_date '2020-01-01'
meltano config tap-clinicaltrials set condition 'COVID-19'
meltano config tap-clinicaltrials set sponsor 'Pfizer'
```
1. Run a test `tap-clinicaltrials` extraction
```bash
meltano run tap-clinicaltrials target-duckdb
```
1. That's it! Check the data
```console
$ duckdb output/warehouse.duckdb -c "select nctid, lastUpdateSubmitDate, protocolsection->>'$.identificationModule.briefTitle' from clinicaltrials.studies limit 5;
┌─────────────┬──────────────────────┬─────────────────────────────────────────────────────────────────────────────────────────────────────┐
│ nctid │ lastupdatesubmitdate │ (protocolsection ->> '$.identificationModule.briefTitle') │
│ varchar │ varchar │ varchar │
├─────────────┼──────────────────────┼─────────────────────────────────────────────────────────────────────────────────────────────────────┤
│ NCT06156215 │ 2023-12-06 │ PROmotion of COVID-19 BOOSTer VA(X)Ccination in the Emergency Department - PROBOOSTVAXED │
│ NCT05487040 │ 2023-12-06 │ A Study to Measure the Amount of Study Medicine in Blood in Adult Participants With COVID-19 and … │
│ NCT06163677 │ 2023-12-07 │ A Study to Look at the Health Outcomes of Patients With COVID-19 and Influenza. │
│ NCT05032976 │ 2023-12-07 │ Korea Comirnaty Post-marketing Surveillance │
│ NCT05596734 │ 2023-12-11 │ A Study to Evaluate the Safety, Tolerability, and Immunogenicity of Combined Modified RNA Vaccine… │
└─────────────┴──────────────────────┴─────────────────────────────────────────────────────────────────────────────────────────────────────┘
```
### Executing the Tap Directly
```bash
tap-clinicaltrials --version
tap-clinicaltrials --help
tap-clinicaltrials --config CONFIG --discover > ./catalog.json
```
## Developer Resources
### Initialize your Development Environment
```bash
pipx install hatch
```
### Create and Run Tests
Run integration tests:
```bash
hatch run test:integration
```
You can also test the `tap-clinicaltrials` CLI interface directly:
```bash
hatch run sync:console -- --about --format=json
```
### SDK Dev Guide
See the [dev guide](https://sdk.meltano.com/en/latest/dev_guide.html) for more instructions on how to use the SDK to
develop your own taps and targets.
Raw data
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"description": "# `tap-clinicaltrials`\n\nSinger tap for [ClinicalTrials.gov](https://clinicaltrials.gov/data-about-studies/learn-about-api) study records data.\n\nBuilt with the [Meltano Tap SDK](https://sdk.meltano.com) for Singer Taps.\n\n## Capabilities\n\n* `catalog`\n* `state`\n* `discover`\n* `about`\n* `stream-maps`\n\n## Settings\n\n| Setting | Required | Default | Description |\n|:--------------------|:--------:|:-------:|:------------|\n| start_date | False | None | Earliest datetime to get data from |\n| condition | False | None | Conditions or disease query |\n| sponsor | False | None | Sponsor query |\n| stream_maps | False | None | Config object for stream maps capability. For more information check out [Stream Maps](https://sdk.meltano.com/en/latest/stream_maps.html). |\n| stream_map_config | False | None | User-defined config values to be used within map expressions. |\n| flattening_enabled | False | None | 'True' to enable schema flattening and automatically expand nested properties. |\n| flattening_max_depth| False | None | The max depth to flatten schemas. |\n| batch_config | False | None | |\n\nA full list of supported settings and capabilities is available by running: `tap-clinicaltrials --about`\n\n## Installation\n\n### In a Meltano project\n\n#### Using a direct reference\n\n```bash\nmeltano add extractor tap-clinicaltrials --from-ref=https://raw.githubusercontent.com/edgarrmondragon/tap-clinicaltrials/main/plugin.yaml\n```\n\nRequires Meltano v3.1.0+.\n\n#### From MeltanoHub\n\nNot yet available.\n\n### From PyPI\n\n```bash\npython3 -m pip install --upgrade tap-clinicaltrials\n```\n\n### With [pipx][pipx]\n\n```bash\npipx install tap-clinicaltrials\n```\n\n[pipx]: https://github.com/pypa/pipx\n\n### From source\n\n```bash\ngit clone https://github.com/edgarrmondragon/tap-clinicaltrials\ncd tap-clinicaltrials\npython3 -m pip install .\n```\n\n## Usage\n\nYou can easily run `tap-clinicaltrials` by itself or in a pipeline using [Meltano](https://meltano.com/).\n\n### With Meltano\n\n1. Clone the repo and `cd` into it:\n\n ```bash\n git clone https://github.com/edgarrmondragon/tap-clinicaltrials.git\n cd tap-clinicaltrials\n ```\n\n1. Make sure you have [Meltano](https://docs.meltano.com/guide/installation-guide) installed\n\n1. Install all plugins\n\n ```bash\n meltano install\n ```\n\n1. Configure the `tap-clinicaltrials` tap:\n\n ```bash\n meltano config tap-clinicaltrials set start_date '2020-01-01'\n meltano config tap-clinicaltrials set condition 'COVID-19'\n meltano config tap-clinicaltrials set sponsor 'Pfizer'\n ```\n\n1. Run a test `tap-clinicaltrials` extraction\n\n ```bash\n meltano run tap-clinicaltrials target-duckdb\n ```\n\n1. That's it! Check the data\n\n ```console\n $ duckdb output/warehouse.duckdb -c \"select nctid, lastUpdateSubmitDate, protocolsection->>'$.identificationModule.briefTitle' from clinicaltrials.studies limit 5;\n \u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u252c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u252c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n \u2502 nctid \u2502 lastupdatesubmitdate \u2502 (protocolsection ->> '$.identificationModule.briefTitle') \u2502\n \u2502 varchar \u2502 varchar \u2502 varchar \u2502\n \u251c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u253c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u253c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2524\n \u2502 NCT06156215 \u2502 2023-12-06 \u2502 PROmotion of COVID-19 BOOSTer VA(X)Ccination in the Emergency Department - PROBOOSTVAXED \u2502\n \u2502 NCT05487040 \u2502 2023-12-06 \u2502 A Study to Measure the Amount of Study Medicine in Blood in Adult Participants With COVID-19 and \u2026 \u2502\n \u2502 NCT06163677 \u2502 2023-12-07 \u2502 A Study to Look at the Health Outcomes of Patients With COVID-19 and Influenza. \u2502\n \u2502 NCT05032976 \u2502 2023-12-07 \u2502 Korea Comirnaty Post-marketing Surveillance \u2502\n \u2502 NCT05596734 \u2502 2023-12-11 \u2502 A Study to Evaluate the Safety, Tolerability, and Immunogenicity of Combined Modified RNA Vaccine\u2026 \u2502\n \u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\n ```\n\n### Executing the Tap Directly\n\n```bash\ntap-clinicaltrials --version\ntap-clinicaltrials --help\ntap-clinicaltrials --config CONFIG --discover > ./catalog.json\n```\n\n## Developer Resources\n\n### Initialize your Development Environment\n\n```bash\npipx install hatch\n```\n\n### Create and Run Tests\n\nRun integration tests:\n\n```bash\nhatch run test:integration\n```\n\nYou can also test the `tap-clinicaltrials` CLI interface directly:\n\n```bash\nhatch run sync:console -- --about --format=json\n```\n\n### SDK Dev Guide\n\nSee the [dev guide](https://sdk.meltano.com/en/latest/dev_guide.html) for more instructions on how to use the SDK to\ndevelop your own taps and targets.\n",
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