Updated the analyse service

e87b66db · Martin Weise · c75d930d · e87b66db · e87b66db · e87b66db
Verified Commit e87b66db authored 8 months ago by Martin Weise
--- a/Pipfile
+++ b/Pipfile
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+mkdocs = "==1.5.3"
+mkdocs-material = "==9.5.17"
+mkdocs-with-pdf = "==0.9.3"
+mkdocs-material-extensions = ">=1.0.3"
+requests = "==2.31.0"
+py-dotenv = ">=0.1"
+python-dotenv = "==1.0.0"
+build = "==1.1.1"
+twine = "==5.0.0"
+furo = "==2024.1.29"
+pika = "==1.3.2"
+pydantic = "==2.6.4"
+tuspy = "==1.0.3"
+mike = "==2.0.0"
+anybadge = "==1.14.0"
+
+[dev-packages]
+
+[requires]
+python_version = "3.11"
--- a/dbrepo-analyse-service/Dockerfile
+++ b/dbrepo-analyse-service/Dockerfile
-FROM pytorch/pytorch:2.4.0-cuda12.4-cudnn9-runtime
+FROM pytorch/pytorch:2.4.0-cuda12.4-cudnn9-runtime AS build
+
+# Build Embeddings
+WORKDIR /app
+
+COPY --chown=1001 ./bge-m3 ./bge-m3
+COPY --chown=1001 ./clients ./clients
+COPY --chown=1001 ./data ./data
+COPY --chown=1001 ./eval ./eval
+COPY --chown=1001 ./matching ./matching
+COPY --chown=1001 ./models ./models
+COPY --chown=1001 ./services ./services
+COPY --chown=1001 ./init.py ./init.py
+
+FROM python:3.11-alpine AS runtime
 LABEL org.opencontainers.image.authors="martin.weise@tuwien.ac.at"

-RUN apt-get update && apt-get install -y bash curl && apt-get clean
+RUN apk --no-cache add py3-h5py bash curl

 WORKDIR /home/alpine

@@ -28,7 +42,7 @@ COPY --chown=1001 ./eval ./eval
 COPY --chown=1001 ./matching ./matching
 COPY --chown=1001 ./models ./models
 COPY --chown=1001 ./services ./services
-COPY --chown=1001 ./*.py ./
+COPY --chown=1001 ./app.py determine_*.py ./

 ENV HF_HOME="/app/ml"
 ENV MPLCONFIGDIR="/app/mpl"

--- a/dbrepo-analyse-service/Pipfile
+++ b/dbrepo-analyse-service/Pipfile
@@ -7,7 +7,6 @@ name = "pypi"
 boto3 = "*"
 exceptiongroup = "*"
 flasgger = "*"
-FlagEmbedding = "*"
 flask = "*"
 flask-caching = "*"
 flask-cors = "*"
@@ -16,23 +15,17 @@ flask-jwt-extended = "*"
 gevent = "*"
 greenlet = "*"
 gunicorn = "*"
-h5py = "*"
 jwt = "*"
 requests = "*"
 matplotlib = "*"
 minio = "*"
-nltk = "*"
 numpy = "*"
 opensearch-py = "*"
-owlready2 = "*"
 prometheus-flask-exporter = "*"
 pandas = "*"
-peft = "*"
 pydantic = "*"
-dbrepo = {path = "./lib/dbrepo-1.4.7.tar.gz"}
-opensearch-py = "*"
-textdistance = "*"
 torch = "*"
+dbrepo = {path = "./lib/dbrepo-1.4.7.tar.gz"}

 [dev-packages]
 coverage = "*"
@@ -40,6 +33,13 @@ pytest = "*"
 requests-mock = "*"
 testcontainers-minio = "*"
 testcontainers-opensearch = "*"
+h5py = "*"
+FlagEmbedding = "*"
+owlready2 = "*"
+peft = "*"
+nltk = "*"
+textdistance = "*"
+sentence-transformers = "*"

 [requires]
 python_version = "3.11"
--- a/dbrepo-analyse-service/Pipfile.lock
+++ b/dbrepo-analyse-service/Pipfile.lock
--- a/dbrepo-analyse-service/init.py
+++ b/dbrepo-analyse-service/init.py
--- a/dbrepo-analyse-service/lib/dbrepo-1.4.7.tar.gz
+++ b/dbrepo-analyse-service/lib/dbrepo-1.4.7.tar.gz
--- a/dbrepo-analyse-service/matching/embeddings.py
+++ b/dbrepo-analyse-service/matching/embeddings.py
@@ -5,11 +5,17 @@ from sentence_transformers import SentenceTransformer
 from FlagEmbedding import BGEM3FlagModel
 import logging

+from torch import Tensor
+

 class Embedding:
+    """
+    Class to retrieve the embeddings in the runtime
+    """
    # _data: {text:embedding}
    _data: {str: torch.Tensor} = None
    _uris: {str: str}
+    _empty_tensor: None | Tensor = None

    def __init__(self, _data: {str: torch.Tensor}, _uris: {str: str}):
        self._data = _data
@@ -108,6 +114,9 @@ class Encoder:


 class MiniLMEncoder(Encoder):
+    """
+    Class to encode the embeddings during build
+    """

    def __init__(self) -> None:
        super().__init__()
@@ -153,6 +162,9 @@ class MiniLMEncoder(Encoder):


 class NasaSMD(Encoder):
+    """
+    Class to encode the embeddings during build
+    """

    def __init__(self) -> None:
        super().__init__()
@@ -179,6 +191,9 @@ class NasaSMD(Encoder):


 class NasaSMD2(Encoder):
+    """
+    Class to encode the embeddings during build
+    """

    def __init__(self) -> None:
        super().__init__()
@@ -205,6 +220,9 @@ class NasaSMD2(Encoder):


 class BGEMDense(Encoder):
+    """
+    Class to encode the embeddings during build
+    """

    def __init__(self) -> None:
        super().__init__()
@@ -257,6 +275,9 @@ class BGEMDense(Encoder):


 class BGEMMultivector(Encoder):
+    """
+    Class to encode the embeddings during build
+    """

    def __init__(self) -> None:
        super().__init__()

--- a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java
+++ b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java
@@ -13,7 +13,6 @@ import at.tuwien.entities.user.User;
 import at.tuwien.exception.*;
 import at.tuwien.mapper.MetadataMapper;
 import at.tuwien.service.DatabaseService;
-import at.tuwien.service.EntityService;
 import at.tuwien.service.TableService;
 import at.tuwien.service.UserService;
 import at.tuwien.utils.UserUtil;

--- a/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/endpoints/TableEndpointUnitTest.java
+++ b/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/endpoints/TableEndpointUnitTest.java
@@ -64,9 +64,6 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
    @MockBean
    private UserService userService;

-    @MockBean
-    private EntityService entityService;
-
    @Autowired
    private TableEndpoint tableEndpoint;

@@ -560,64 +557,6 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
        generic_findById(DATABASE_3_ID, DATABASE_3, TABLE_8_ID, TABLE_8, USER_1_PRINCIPAL, USER_1, null);
    }

-    @Test
-    @WithAnonymousUser
-    public void analyseTable_anonymous_fails() {
-
-        /* test */
-        assertThrows(org.springframework.security.access.AccessDeniedException.class, () -> {
-            analyseTable_generic(DATABASE_1_ID, TABLE_1_ID, TABLE_1);
-        });
-    }
-
-    @Test
-    @WithMockUser(username = USER_4_USERNAME)
-    public void findAll_noRole_fails() {
-
-        /* test */
-        assertThrows(org.springframework.security.access.AccessDeniedException.class, () -> {
-            analyseTable_generic(DATABASE_1_ID, TABLE_1_ID, TABLE_1);
-        });
-    }
-
-    @Test
-    @WithMockUser(username = USER_1_USERNAME, authorities = {"table-semantic-analyse"})
-    public void findAll_hasRole_succeeds() throws MalformedException, TableNotFoundException,
-            DatabaseNotFoundException {
-
-        /* test */
-        analyseTable_generic(DATABASE_1_ID, TABLE_1_ID, TABLE_1);
-    }
-
-    @Test
-    @WithAnonymousUser
-    public void analyseTableColumn_anonymous_fails() {
-
-        /* test */
-        assertThrows(org.springframework.security.access.AccessDeniedException.class, () -> {
-            analyseTableColumn_generic(DATABASE_1_ID, TABLE_1_ID, TABLE_1_COLUMNS.get(0).getId(), TABLE_1_COLUMNS.get(0));
-        });
-    }
-
-    @Test
-    @WithMockUser(username = USER_4_USERNAME)
-    public void analyseTableColumn_noRole_fails() {
-
-        /* test */
-        assertThrows(org.springframework.security.access.AccessDeniedException.class, () -> {
-            analyseTableColumn_generic(DATABASE_1_ID, TABLE_1_ID, TABLE_1_COLUMNS.get(0).getId(), TABLE_1_COLUMNS.get(0));
-        });
-    }
-
-    @Test
-    @WithMockUser(username = USER_1_USERNAME, authorities = {"table-semantic-analyse"})
-    public void analyseTableColumn_hasRole_succeeds() throws MalformedException, TableNotFoundException,
-            DatabaseNotFoundException {
-
-        /* test */
-        analyseTableColumn_generic(DATABASE_1_ID, TABLE_1_ID, TABLE_1_COLUMNS.get(0).getId(), TABLE_1_COLUMNS.get(0));
-    }
-
    @Test
    @WithAnonymousUser
    public void update_publicAnonymous_fails() {
@@ -1002,34 +941,6 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
    /* ## GENERIC TEST CASES                                                                            ## */
    /* ################################################################################################### */

-    public void analyseTable_generic(Long databaseId, Long tableId, Table table) throws MalformedException,
-            TableNotFoundException, DatabaseNotFoundException {
-
-        /* mock */
-        when(entityService.suggestByTable(table))
-                .thenReturn(List.of());
-
-        /* test */
-        final ResponseEntity<List<EntityDto>> response = tableEndpoint.analyseTable(databaseId, tableId);
-        assertEquals(HttpStatus.OK, response.getStatusCode());
-        final List<EntityDto> body = response.getBody();
-        assertNotNull(body);
-    }
-
-    public void analyseTableColumn_generic(Long databaseId, Long tableId, Long columnId, TableColumn tableColumn)
-            throws MalformedException, TableNotFoundException, DatabaseNotFoundException {
-
-        /* mock */
-        when(entityService.suggestByColumn(tableColumn))
-                .thenReturn(List.of());
-
-        /* test */
-        final ResponseEntity<List<TableColumnEntityDto>> response = tableEndpoint.analyseTableColumn(databaseId, tableId, columnId);
-        assertEquals(HttpStatus.OK, response.getStatusCode());
-        final List<TableColumnEntityDto> body = response.getBody();
-        assertNotNull(body);
-    }
-
    protected ResponseEntity<List<TableBriefDto>> generic_list(Long databaseId, Database database, Principal principal,
                                                               User user, DatabaseAccess access)
            throws NotAllowedException, DatabaseNotFoundException, AccessNotFoundException, UserNotFoundException {

--- a/dbrepo-search-service/Pipfile.lock
+++ b/dbrepo-search-service/Pipfile.lock
--- a/dbrepo-search-service/init/Pipfile.lock
+++ b/dbrepo-search-service/init/Pipfile.lock
@@ -282,7 +282,7 @@
        },
        "dbrepo": {
            "hashes": [
-                "sha256:84607677b0826bb9b2fa120aacdf56d16c8d9ae423f435b2bd2c22b1c965a33c"
+                "sha256:eaaa149c6e121ed1f280712c52bea22f0d70a5bc4593710b213683a17b659f8c"
            ],
            "path": "./lib/dbrepo-1.4.7.tar.gz"
        },
@@ -392,6 +392,14 @@
            "markers": "python_version >= '3.8'",
            "version": "==1.4.1"
        },
+        "html5lib-modern": {
+            "hashes": [
+                "sha256:1fadbfc27ea955431270e4e79a4a4c290ba11c3a3098a95cc22dc73e312a1768",
+                "sha256:3458b6e31525ede4fcaac0ff42d9eeb5efaf755473768103cb56e0275caa8d99"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==1.2"
+        },
        "idna": {
            "hashes": [
                "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9",
@@ -408,13 +416,6 @@
            "markers": "python_version >= '3.7'",
            "version": "==2.0.0"
        },
-        "isodate": {
-            "hashes": [
-                "sha256:0751eece944162659049d35f4f549ed815792b38793f07cf73381c1c87cbed96",
-                "sha256:48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9"
-            ],
-            "version": "==0.6.1"
-        },
        "itsdangerous": {
            "hashes": [
                "sha256:c6242fc49e35958c8b15141343aa660db5fc54d4f13a1db01a3f5891b98700ef",
@@ -965,7 +966,7 @@
                "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3",
                "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"
            ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
            "version": "==2.9.0.post0"
        },
        "python-dotenv": {
@@ -986,12 +987,12 @@
        },
        "rdflib": {
            "hashes": [
-                "sha256:0438920912a642c866a513de6fe8a0001bd86ef975057d6962c79ce4771687cd",
-                "sha256:9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae"
+                "sha256:240c25c6e1b573ffa67aed23aae128e253c443c15291c9a01d8d392ea80c05b6",
+                "sha256:a29a8fccebd3d3a5f1b7e88d92dace1c89829018c7d29a6114fff4449c188b3b"
            ],
            "index": "pypi",
            "markers": "python_full_version >= '3.8.1' and python_full_version < '4.0.0'",
-            "version": "==7.0.0"
+            "version": "==7.1.0"
        },
        "requests": {
            "hashes": [
@@ -1006,7 +1007,7 @@
                "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926",
                "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"
            ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
            "version": "==1.16.0"
        },
        "testcontainers-core": {
@@ -1150,107 +1151,91 @@
        },
        "yarl": {
            "hashes": [
-                "sha256:0545de8c688fbbf3088f9e8b801157923be4bf8e7b03e97c2ecd4dfa39e48e0e",
-                "sha256:076b1ed2ac819933895b1a000904f62d615fe4533a5cf3e052ff9a1da560575c",
-                "sha256:0afad2cd484908f472c8fe2e8ef499facee54a0a6978be0e0cff67b1254fd747",
-                "sha256:0ccaa1bc98751fbfcf53dc8dfdb90d96e98838010fc254180dd6707a6e8bb179",
-                "sha256:0d3105efab7c5c091609abacad33afff33bdff0035bece164c98bcf5a85ef90a",
-                "sha256:0e1af74a9529a1137c67c887ed9cde62cff53aa4d84a3adbec329f9ec47a3936",
-                "sha256:136f9db0f53c0206db38b8cd0c985c78ded5fd596c9a86ce5c0b92afb91c3a19",
-                "sha256:156ececdf636143f508770bf8a3a0498de64da5abd890c7dbb42ca9e3b6c05b8",
-                "sha256:15c87339490100c63472a76d87fe7097a0835c705eb5ae79fd96e343473629ed",
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            ],
-            "markers": "python_version >= '3.8'",
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        }
    },
    "develop": {

--- a/dbrepo-search-service/init/lib/dbrepo-1.4.7.tar.gz
+++ b/dbrepo-search-service/init/lib/dbrepo-1.4.7.tar.gz
--- a/dbrepo-search-service/lib/dbrepo-1.4.7.tar.gz
+++ b/dbrepo-search-service/lib/dbrepo-1.4.7.tar.gz