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Long-Running Integration Tests

This document describes tests that are excluded from the normal ./gradlew test run because they require network access and take significant time (10–30 minutes).

MmCifDownloadParseAllTest

File: mollib/src/test/java/com/bammellab/mollib/data/MmCifDownloadParseAllTest.kt

What it does:

  1. Collects every PDB ID from mollib/src/main/java/com/bammellab/mollib/data/PDBs.kt
  2. Deduplicates them (~500–600 unique IDs from ~1 700 list entries)
  3. Downloads each one from RCSB as https://files.rcsb.org/download/<ID>.cif.gz
  4. Decompresses with GZIPInputStream and parses with ParserMmCifFile
  5. Reports a per-run summary: pass / fail / HTTP 404 counts
  6. Fails the test if any structure parses with 0 atoms or throws an exception (404s are warnings only)

How to run:

./gradlew.bat :mollib:testLongRunning

Output appears in the Gradle console and in the HTML report:

mollib/build/reports/tests/testLongRunning/index.html

Skipping behavior:

  • If the network is unreachable the test prints a skip message and exits cleanly (no failure).
  • HTTP 404 responses are logged but do not count as failures — some legacy PDB entries have been removed from RCSB.

Why it is excluded from the default test run:

The test is tagged @Tag("long-running"). The default :mollib:test Gradle task is configured to excludeTags("long-running") in mollib/build.gradle.kts.

Running all tests (unit + long-running)

# Fast: unit tests only (default)
./gradlew.bat :mollib:test

# Slow: long-running network tests only
./gradlew.bat :mollib:testLongRunning