gosset 0.3.2__tar.gz

gosset-0.3.2/LICENSE

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gosset-0.3.2/MANIFEST.in

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+include README.md
+include LICENSE
+include pyproject.toml
+include setup.py
+recursive-include gosset *.py
+recursive-include examples *.py
+include get-token-standalone.py
+
+
+# Internal, live-API tests: not part of the published package (see tests/internal/README.md).
+prune tests/internal

gosset-0.3.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: gosset
+Version: 0.3.2
+Summary: Gosset CLI & SDK - command-line and programmatic access to Gosset drugs, trials, companies, deals, news
+Author-email: Gosset <support@gosset.ai>
+License: Apache-2.0
+Project-URL: Homepage, https://gosset.ai
+Project-URL: Documentation, https://docs.gosset.ai/cli/
+Project-URL: Repository, https://github.com/gosset-ai/gosset
+Project-URL: Bug Tracker, https://github.com/gosset-ai/gosset/issues
+Keywords: gosset,drug-database,biotech,pharmaceutical,mcp,openai-agents
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: requests>=2.25.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
+Requires-Dist: black>=22.0.0; extra == "dev"
+Requires-Dist: flake8>=4.0.0; extra == "dev"
+Requires-Dist: mypy>=0.950; extra == "dev"
+Requires-Dist: python-dotenv>=0.19.0; extra == "dev"
+Provides-Extra: test
+Requires-Dist: pytest>=7.0.0; extra == "test"
+Requires-Dist: pytest-cov>=4.0.0; extra == "test"
+Requires-Dist: python-dotenv>=0.19.0; extra == "test"
+Requires-Dist: numpy>=1.21; extra == "test"
+Requires-Dist: scikit-learn>=1.0; extra == "test"
+Requires-Dist: openai-agents>=0.1.0; extra == "test"
+Requires-Dist: eval_type_backport; python_version < "3.10" and extra == "test"
+Provides-Extra: agents
+Requires-Dist: openai-agents>=0.1.0; extra == "agents"
+Requires-Dist: python-dotenv>=0.19.0; extra == "agents"
+Dynamic: license-file
+Dynamic: requires-python
+
+# Gosset
+
+Command-line and programmatic access to Gosset's database of 100,000+ drug assets — drugs, clinical trials, companies, deals and news.
+
+**The CLI is the main interface.** Search from your terminal, pipe into `jq`, or hand it to an agent. The Python SDK is there when you need programmatic control.
+
+```bash
+pip install gosset
+gosset get-key                        # one-time browser auth
+gosset drugs --target PD-1 --phase 3
+```
+
+---
+
+## Quickstart
+
+### 1. Install
+
+```bash
+pip install gosset
+```
+
+Python 3.9+. For AI-agent support: `pip install "gosset[agents]"`.
+
+### 2. Authenticate
+
+```bash
+gosset get-key                        # opens a browser, prints your API key
+export GOSSET_API_KEY='...'           # add to your shell profile
+```
+
+Or non-interactively, if you already have a key:
+
+```bash
+export GOSSET_API_KEY='your_key_here'
+```
+
+### 3. Ask it something
+
+```bash
+gosset drugs "pembrolizumab"
+```
+
+That's it. Output is JSON by default.
+
+---
+
+## CLI
+
+### The idea: pass names, not ids
+
+Every filter accepts a **name or an id**. The CLI resolves names to ids for you, so you never handle raw ObjectIds.
+
+```bash
+gosset drugs --target PD-1            # "PD-1" is resolved for you
+gosset trials --disease "atopic dermatitis"
+gosset deals --buyer Merck
+```
+
+Add `--debug` to see the resolved request that was actually sent.
+
+### Five entity commands
+
+```bash
+# Drugs — positional NAME, resolved to an id
+gosset drugs "pembrolizumab"
+gosset drugs --target PD-1 --phase 3 --limit 20
+gosset drugs --disease "non-small cell lung cancer" --modality antibody --industry-only
+
+# Trials — positional SEARCH takes an NCT id, acronym, or title text
+gosset trials NCT05599191
+gosset trials "semaglutide phase 3"
+gosset trials --drug semaglutide --phase 3 --status recruiting --has-results
+
+# Companies — positional NAME, resolved to an id
+gosset companies "Merck"
+gosset companies --disease oncology --country US --public
+
+# Deals — filters only, no positional
+gosset deals --drug pembrolizumab --since 2024-01-01
+gosset deals --buyer Merck --deal-type acquisition --min-value 1000
+
+# News — positional SEARCH is free text
+gosset news "GLP-1"
+gosset news --disease "atopic dermatitis" --since 2025-01-01
+```
+
+### Two prediction commands
+
+```bash
+gosset ptrs NCT05599191               # probability of technical & regulatory success
+gosset timeline NCT05599191           # predicted primary-completion date
+gosset timeline NCT05599191 --as-of 2025-06-01   # point-in-time, no lookahead
+```
+
+### Flags every entity command shares
+
+| Flag | Purpose |
+| --- | --- |
+| `--limit`, `--offset` | Page through results |
+| `--sort` | Order results |
+| `--fields a,b,c` | Return only these fields |
+| `--table` | Human-readable table |
+| `--json` | JSON (the default) |
+| `--debug` | Print the resolved request |
+| `--api-key`, `--base-url` | Override auth / endpoint |
+
+Per-command filters differ — `gosset <command> --help` lists them.
+
+### Built for pipes and agents
+
+JSON on stdout by default, so it composes:
+
+```bash
+# Every phase-3 PD-1 asset, names only
+gosset drugs --target PD-1 --phase 3 --fields name --limit 100 | jq -r '.[].name'
+
+# Score every recruiting trial for a drug
+gosset trials --drug semaglutide --status recruiting --fields nct_id \
+  | jq -r '.[].nct_id' \
+  | xargs -I{} gosset ptrs {}
+```
+
+Use `--table` when a human is reading:
+
+```bash
+gosset drugs --target PD-1 --phase 3 --table
+```
+
+---
+
+## SDK
+
+When you need programmatic control, the same data is available from Python.
+
+```python
+from gosset import GossetClient
+
+client = GossetClient()                    # reads GOSSET_API_KEY
+
+drugs = client.find_drugs(targets="PD-1", latest_phase="3")
+trials = client.find_trials(drug="semaglutide", phase="3")
+
+ptrs = client.estimate_ptrs({"nct_id": "NCT05599191"})
+print(ptrs["probability"])
+```
+
+### Search
+
+| Method | Returns |
+| --- | --- |
+| `find_drugs(**filters)` | Drug assets |
+| `find_trials(**filters)` | Clinical trials |
+| `find_companies(**filters)` | Companies |
+| `find_deals(**filters)` | Deals |
+| `find_news(**filters)` | News and press releases |
+| `query(entity, where=...)` | Structured predicate queries |
+| `get_trials(...)`, `get_similar_trials(...)` | Trial lookup and similarity |
+
+### Prediction
+
+| Method | Returns |
+| --- | --- |
+| `estimate_ptrs(params)` | Probability of success for a trial or described asset |
+| `estimate_program_ptrs(...)` | Program-level success estimate |
+| `estimate_remaining_time(...)` | Predicted time to completion |
+| `benchmark_ptrs(...)` | Benchmark a prediction against comparables |
+| `get_trial_params(nct_id)` | The feature set behind a trial's prediction |
+
+### Resolution and schema
+
+| Method | Returns |
+| --- | --- |
+| `classify_disease(text)` | Disease name → ontology class ids |
+| `classify_modality(text)` | Modality name → ontology class ids |
+| `get_schema()` | Field schema for the query API |
+
+`estimate_ptrs` accepts either a trial (`{"nct_id": ...}`) or a described asset built from `get_trial_params`, so you can score hypothetical designs, not just registered trials.
+
+### Errors
+
+```python
+from gosset import GossetClient, GossetAPIError
+
+try:
+    client.estimate_ptrs({"nct_id": "NCT00000000"})
+except GossetAPIError as e:
+    print(f"request failed: {e}")
+```
+
+---
+
+## Authentication
+
+The CLI and SDK read the same credential, checked in this order:
+
+1. `--api-key` (CLI) or `GossetClient(api_key=...)` (SDK)
+2. `GOSSET_API_KEY`
+3. `GOSSET_OAUTH_TOKEN`
+
+Get one with `gosset get-key`, which opens a browser and prints your API key. Use `--quiet` to print only the key, for scripting:
+
+```bash
+export GOSSET_API_KEY="$(gosset get-key --quiet)"
+```
+
+`gosset get-token` returns a raw **OAuth** token instead. That is what MCP
+clients need, and it is *not* accepted by this API — the REST endpoints
+validate bearers against your account's API key, so an OAuth token fails every
+call with "Authentication failed". Use `get-key` unless you specifically want
+the OAuth credential.
+
+Point at a different environment with `--base-url` or `GOSSET_API_URL`.
+
+---
+
+## Links
+
+- **Documentation** — https://docs.gosset.ai/cli/
+- **Homepage** — https://gosset.ai
+- **Issues** — https://github.com/gosset-ai/gosset/issues
+
+## License
+
+Apache License 2.0 — see [LICENSE](LICENSE).