feat: porting over test_hgvs_variantmapper_gcp (#21)

.gitattributes

@@ -3,3 +3,5 @@ tests/data/*.gz filter=lfs diff=lfs merge=lfs -text
 tests/data/*/*.gz filter=lfs diff=lfs merge=lfs -text
 tests/data/*.fasta filter=lfs diff=lfs merge=lfs -text
 tests/data/*/*.fasta filter=lfs diff=lfs merge=lfs -text
+tests/data/*/*.tsv filter=lfs diff=lfs merge=lfs -text
+tests/data/*/*/*.tsv filter=lfs diff=lfs merge=lfs -text

.github/workflows/rust.yml

@@ -50,6 +50,12 @@ jobs:
     needs: Formatting
     runs-on: ubuntu-latest
 
+    strategy:
+      matrix:
+        include:
+          - label: fast
+          - label: full
+
     services:
       # The tests need a postgres server;  the data will be loaded later
       # after checkout.
@@ -90,20 +96,34 @@ jobs:
 
       - uses: Swatinem/rust-cache@v1.3.0
 
-      - name: Run cargo-tarpaulin
+      - name: Run cargo-tarpaulin with fast tests
         uses: actions-rs/tarpaulin@v0.1
         with:
           version: 0.21.0
-          args: "-- --test-threads 1"
+          args: "-- --test-threads 1 ${{ matrix.flag }}"
+        env:
+          TEST_UTA_DATABASE_URL: postgres://uta_admin:uta_admin@0.0.0.0/uta
+          TEST_UTA_DATABASE_SCHEMA: uta_20210129
+          TEST_SEQREPO_CACHE_MODE: read
+          TEST_SEQREPO_CACHE_PATH: tests/data/seqrepo_cache.fasta
+        if: ${{ matrix.label == 'fast' }}
+
+      - name: Run cargo-test with full tests
+        uses: actions-rs/cargo@v1
+        with:
+          command: test
+          args: "--release -- ${{ matrix.flag }}"
         env:
           TEST_UTA_DATABASE_URL: postgres://uta_admin:uta_admin@0.0.0.0/uta
           TEST_UTA_DATABASE_SCHEMA: uta_20210129
           TEST_SEQREPO_CACHE_MODE: read
           TEST_SEQREPO_CACHE_PATH: tests/data/seqrepo_cache.fasta
+        if: ${{ matrix.label == 'full' }}
 
-      - name: Codecov
+      - name: Codecov submission of fast test results
         uses: codecov/codecov-action@v3
         with:
           verbose: true
           fail_ci_if_error: true
           token: ${{ secrets.CODECOV_TOKEN }}
+        if: ${{ matrix.label == 'fast' }}

.gitignore

@@ -4,3 +4,5 @@
 *~
 .*.sw?
 /.vscode
+
+*.lock

Cargo.toml

@@ -18,6 +18,7 @@ nom = "7.1.3"
 phf = { version = "0.11.1", features = ["macros"] }
 postgres = { version = "0.19.4", features = ["with-chrono-0_4"] }
 pretty_assertions = "1.3.0"
+quick_cache = "0.2.2"
 regex = "1.7.1"
 seqrepo = { git = "https://github.com/bihealth/seqrepo-rs.git", branch = "27-whole-fasta-sequences-are-read" }
 serde = { version = "1.0.152", features = ["derive"] }

README.md

@@ -31,6 +31,7 @@ export TEST_SEQREPO_CACHE_PATH=tests/data/seqrepo_cache.fasta
 ```
 
 When running the tests with `cargo test`, the cache file will be (re-)written.
+Note that you have to use `cargo test --release -- --test-threads 1 --ignored` when writing the cache for enforcing a single test writing to the cache at any time.
 If you don't want to regenerate the cache then you can use the following settings.
 With these settings, the cache will only be read.
 
@@ -45,7 +46,7 @@ After either this, you can run the tests.
 cargo test
 ```
 
-## Creating Recuded UTA Databases
+## Creating Reduced UTA Databases
 
 The script `tests/data/data/bootstrap.sh` allows to easily build a reduced set of the UTA database given a list of genes.
 The process is as follows:

src/data/interface.rs

@@ -178,7 +178,7 @@ pub struct TxMappingOptionsRecord {
 
 /// Interface for data providers.
 pub trait Provider {
-    /// Return the data version, e.g., `uta_20180821`.
+    /// Return the data version, e.g., `uta_20210129`.
     fn data_version(&self) -> &str;
 
     /// Return the schema version, e.g., `"1.1"`.