Release/550 (#1567)

* spark-nlp-jsl==5.5.0 requirements (#1544) * bump versions * implemented spark-nlp-jsl==550 requirements --------- Co-authored-by: C-K-Loan <[email protected]> * bump pydantic support to > 2.X, various refactors and deprecation fixes (#1560) * 550 BugFix (#1563) * fix listener config if nlp=False * update conditions * fix deprecated @validator decerator (#1565) * Pydantic2 migration fix env var model parsing (#1566) * fix deprecated @validator decerator * fix env var pydantic model creation bug * bump verisons --------- Co-authored-by: Mehmet Butgul <[email protected]>
JohnSnowLabs · Oct 23, 2024 · 405a223 · 405a223
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diff --git a/docs/en/jsl/jsl_release_notes.md b/docs/en/jsl/jsl_release_notes.md
@@ -16,6 +16,27 @@ sidebar:
 See [Github Releases](https://github.com/JohnSnowLabs/johnsnowlabs/releases) for detailed information on Release History and Features
 
 
+
+## 5.5.0
+Release date: 10-23-2024
+
+The John Snow Labs 5.5.0 Library released with the following pre-installed and recommended dependencies
+
+{:.table-model-big}
+| Library                                                                                 | Version    |
+|-----------------------------------------------------------------------------------------|------------|
+| [Visual NLP](https://nlp.johnsnowlabs.com/docs/en/spark_ocr_versions/ocr_release_notes) | `5.4.1`    |
+| [Enterprise NLP](https://nlp.johnsnowlabs.com/docs/en/licensed_annotators)              | `5.5.0`    |
+| [Finance NLP](https://nlp.johnsnowlabs.com/docs/en/financial_release_notes)             | `1.X.X`    |
+| [Legal NLP](https://nlp.johnsnowlabs.com/docs/en/legal_release_notes)                   | `1.X.X`    |
+| [NLU](https://github.com/JohnSnowLabs/nlu/releases)                                     | `5.4.1` |
+| [Spark-NLP-Display](https://sparknlp.org/docs/en/display)                               | `5.0`      |
+| [Spark-NLP](https://github.com/JohnSnowLabs/spark-nlp/releases/)                        | `5.5.0`    |
+| [Pyspark](https://spark.apache.org/docs/latest/api/python/)                             | `3.4.0`    |
+
+
+
+
 ## 5.4.5
 Release date: 9-27-2024
 

diff --git a/johnsnowlabs/auto_install/jsl_home.py b/johnsnowlabs/auto_install/jsl_home.py
@@ -48,13 +48,15 @@ def download_deps_and_create_info(
     overwrite=False,
 ):
     """Download a list of deps to given lib_dir folder and creates info_file at info_file_path."""
-    info, old_info = {}, {}
+    info, old_info = {}, None
     if os.path.exists(info_file_path):
         #  keep old infos, we assume they are up-to-date and compatible
-        old_info = InstallFolder.parse_file(info_file_path)
+        if os.path.join("java_installs","info.json") in info_file_path:
+            old_info = InstallFolder.java_folder_from_home()
+        elif os.path.join("py_installs","info.json") in info_file_path:
+            old_info = InstallFolder.py_folder_from_home()
 
     for p in deps:
-
         # print_prefix = Software.for_name(p.product_name).logo
         print_prefix = ProductLogo.from_name(p.product_name.name).value
         if p.dependency_type in JvmHardwareTarget:
@@ -88,12 +90,19 @@ def download_deps_and_create_info(
             install_type=p.dependency_type.value,
             product_version=p.dependency_version.as_str(),
         )
+        info[p.file_name].compatible_spark_version = p.spark_version.value.as_str()
+        info[p.file_name].product_version = p.dependency_version.as_str()
+
     if info:
         info = InstallFolder(**{"infos": info})
         if old_info:
             info.infos.update(old_info.infos)
-        info.write(info_file_path, indent=4)
+        with open(info_file_path, "w") as f:
+            for k, v in info.infos.items():
+                v.product_version = str(v.product_version)
+                v.compatible_spark_version = str(v.compatible_spark_version)
 
+            f.write(info.model_dump_json())
 
 def setup_jsl_home(
     secrets: Optional[JslSecrets] = None,
@@ -183,9 +192,10 @@ def setup_jsl_home(
             java_deps, settings.java_dir, settings.java_info_file, overwrite
         )
 
-        RootInfo(version=settings.raw_version_jsl_lib, run_from=sys.executable).write(
-            settings.root_info_file, indent=4
-        )
+        root_info = RootInfo(version=settings.raw_version_jsl_lib, run_from=sys.executable)
+        root_info.version = root_info.version.as_str()
+        with open(settings.root_info_file, "w") as f:
+            f.write(root_info.model_dump_json())
         print(f"🙆 JSL Home setup in {settings.root_dir}")
 
         return
@@ -258,9 +268,8 @@ def get_install_suite_from_jsl_home(
     if os.path.exists(settings.py_info_file):
         py_folder = InstallFolder.py_folder_from_home()
 
-    info = RootInfo.parse_file(settings.root_info_file)
+    info = RootInfo.get_from_jsl_home()
     # Read all dependencies from local ~/.johnsnowlabs folder
-
     suite = InstallSuite(
         nlp=LocalPy4JLib(
             java_lib=java_folder.get_product_entry(ProductName.nlp, jvm_hardware_target)

diff --git a/johnsnowlabs/finance.py b/johnsnowlabs/finance.py
@@ -123,6 +123,8 @@
             LargeFewShotClassifierModel,
             Mapper2Chunk,
             DocumentFiltererByNER,
+            REChunkMerger,
+            ContextualEntityFilterer,
         )
 
         from sparknlp_jsl.modelTracer import ModelTracer

diff --git a/johnsnowlabs/legal.py b/johnsnowlabs/legal.py
@@ -121,6 +121,8 @@
             LargeFewShotClassifierModel,
             Mapper2Chunk,
             DocumentFiltererByNER,
+            REChunkMerger,
+            ContextualEntityFilterer,
         )
         from sparknlp_jsl.modelTracer import ModelTracer
         from sparknlp_jsl.pipeline_tracer import PipelineTracer

diff --git a/johnsnowlabs/medical.py b/johnsnowlabs/medical.py
@@ -98,6 +98,8 @@
             LargeFewShotClassifierModel,
             Mapper2Chunk,
             DocumentFiltererByNER,
+            REChunkMerger,
+            ContextualEntityFilterer,
         )
         from sparknlp_jsl.structured_deidentification import StructuredDeidentification
         from sparknlp_jsl.text_to_documents_columns import TextToDocumentsColumns
@@ -130,6 +132,7 @@
             TextMatcherInternalModel as TextMatcherModel,
             RegexMatcherInternal as RegexMatcher,
             RegexMatcherInternalModel as RegexMatcherModel,
+            MedicalLLM as AutoGGUFModel,
         )
         from sparknlp_jsl.compatibility import Compatibility
         from sparknlp_jsl.pretrained import InternalResourceDownloader

diff --git a/johnsnowlabs/py_models/install_info.py b/johnsnowlabs/py_models/install_info.py
@@ -9,7 +9,7 @@
 from johnsnowlabs.py_models.lib_version import LibVersion
 from johnsnowlabs.utils.enums import JvmHardwareTarget, ProductName, PyInstallTypes
 
-
+import json
 class InstallFileInfoBase(WritableBaseModel):
     file_name: str
     product: ProductName
@@ -71,7 +71,12 @@ def __init__(self, *args, **kwargs):
 
     @staticmethod
     def get_from_jsl_home():
-        return RootInfo.parse_file(settings.root_info_file)
+        import json
+        if os.path.exists(settings.root_info_file):
+            with open(settings.root_info_file, "r") as f:
+                json_data = json.loads(f.read())
+            return RootInfo(run_from=json_data["run_from"],
+                            version=json_data["version"])
 
 
 class InstallFolder(WritableBaseModel):
@@ -93,13 +98,26 @@ def get_product_entry(
     @staticmethod
     def java_folder_from_home():
         if os.path.exists(settings.java_info_file):
-            return InstallFolder.parse_file(settings.java_info_file)
+            with open(settings.java_info_file, "r") as f:
+                json_data = json.loads(f.read())
+            infos = {}
+            for k,v in json_data['infos'].items():
+                if k.endswith(".jar"):
+                    infos[k] = JvmInstallInfo(**v)
+            return InstallFolder(infos=infos)
         return False
 
     @staticmethod
     def py_folder_from_home():
         if os.path.exists(settings.py_info_file):
-            return InstallFolder.parse_file(settings.py_info_file)
+            with open(settings.py_info_file, "r") as f:
+                json_data = json.loads(f.read())
+            infos = {}
+            for k,v in json_data['infos'].items():
+                if k.endswith(".whl") or k.endswith(".tar.gz"):
+                    infos[k] = PyInstallInfo(**v)
+
+            return InstallFolder(infos=infos)
         return False
 
 

diff --git a/johnsnowlabs/py_models/jsl_secrets.py b/johnsnowlabs/py_models/jsl_secrets.py
@@ -4,7 +4,7 @@
 from pathlib import Path
 from typing import Dict, List, Optional, Union
 
-from pydantic import validator
+from pydantic import field_validator
 
 from johnsnowlabs import settings
 from johnsnowlabs.abstract_base.pydantic_model import WritableBaseModel
@@ -62,17 +62,17 @@ class JslSecrets(WritableBaseModel):
     methods for reading/storing found_secrets and managing .jslhome folder
     """
 
-    HC_SECRET: Secret = None
-    HC_LICENSE: Secret = None
+    HC_SECRET: Optional[str] = None
+    HC_LICENSE: Optional[str] = None
     HC_VERSION: Optional[LibVersionIdentifier] = None
-    OCR_SECRET: Secret = None
-    OCR_LICENSE: Secret = None
+    OCR_SECRET: Optional[str] = None
+    OCR_LICENSE: Optional[str] = None
     OCR_VERSION: Optional[LibVersionIdentifier] = None
-    AWS_ACCESS_KEY_ID: Secret = None
-    AWS_SECRET_ACCESS_KEY: Secret = None
+    AWS_ACCESS_KEY_ID: Optional[str] = None
+    AWS_SECRET_ACCESS_KEY: Optional[str] = None
     NLP_VERSION: Optional[LibVersionIdentifier] = None
-    JSL_LEGAL_LICENSE: Secret = None
-    JSL_FINANCE_LICENSE: Secret = None
+    JSL_LEGAL_LICENSE: Optional[str] = None
+    JSL_FINANCE_LICENSE: Optional[str] = None
 
     @staticmethod
     def raise_invalid_version():
@@ -82,7 +82,7 @@ def raise_invalid_version():
         )
         raise ValueError("Invalid secrets")
 
-    @validator("HC_SECRET")
+    @field_validator("HC_SECRET")
     def hc_version_check(cls, HC_SECRET):
         global hc_validation_logged
         try:
@@ -114,7 +114,7 @@ def is_ocr_secret_correct_version(ocr_secret: Optional[str]) -> bool:
     def is_hc_secret_correct_version(hc_secret: Optional[str]) -> bool:
         return hc_secret and hc_secret.split("-")[0] == settings.raw_version_medical
 
-    @validator("OCR_SECRET")
+    @field_validator("OCR_SECRET")
     def ocr_version_check(cls, OCR_SECRET):
         global ocr_validation_logged
         try:
@@ -123,6 +123,8 @@ def ocr_version_check(cls, OCR_SECRET):
                 and not ocr_validation_logged
             ):
                 ocr_validation_logged = True
+                if not OCR_SECRET:
+                    return OCR_SECRET
                 print(
                     f"🚨 Outdated OCR Secrets in license file. Version={(OCR_SECRET.split('-')[0] if OCR_SECRET else None)} but should be Version={settings.raw_version_ocr}"
                 )
@@ -424,6 +426,13 @@ def search_env_vars() -> Union["JslSecrets", bool]:
             ]
         ):
             print("👌 License detected in Environment Variables")
+            if isinstance(hc_version,str):
+                hc_version = LibVersionIdentifier(hc_version)
+            if isinstance(ocr_version,str):
+                ocr_version = LibVersionIdentifier(ocr_version)
+            if isinstance(nlp_version,str):
+                nlp_version = LibVersionIdentifier(nlp_version)
+
             return JslSecrets(
                 HC_SECRET=hc_secret,
                 HC_LICENSE=hc_license,
@@ -631,6 +640,13 @@ def from_json_dict(secrets, secrets_metadata: Optional = None) -> "JslSecrets":
             secrets["JSL_FINANCE_LICENSE"] if "JSL_FINANCE_LICENSE" in secrets else None
         )
 
+        if isinstance(hc_version,str):
+            hc_version = LibVersionIdentifier(hc_version)
+        if isinstance(ocr_version,str):
+            ocr_version = LibVersionIdentifier(ocr_version)
+        if isinstance(nlp_version,str):
+            nlp_version = LibVersionIdentifier(nlp_version)
+
         return JslSecrets(
             HC_SECRET=hc_secret,
             HC_LICENSE=hc_license,
@@ -659,8 +675,9 @@ def from_jsl_home(
             return False
 
         try:
+
             # Try/Catch incase we get validation errors from outdated files
-            license_infos = LicenseInfos.parse_file(settings.creds_info_file)
+            license_infos = LicenseInfos.from_home()
             if log and not already_logged:
                 already_logged = True
                 print(
@@ -692,7 +709,7 @@ def update_outdated_lib_secrets(
         for license in os.listdir(settings.license_dir):
             if license == "info.json":
                 continue
-            secrets = JslSecrets.parse_file(os.path.join(settings.license_dir, license))
+            secrets = JslSecrets.from_json_file_path(os.path.join(settings.license_dir, license))
             if (
                 secrets.HC_SECRET
                 and hc_secrets
@@ -768,7 +785,7 @@ def are_credentials_known(found_secrets: "JslSecrets") -> bool:
         # Return True, if secrets are already stored in JSL-Home, otherwise False
         Path(settings.py_dir).mkdir(parents=True, exist_ok=True)
         if os.path.exists(settings.creds_info_file):
-            license_infos = LicenseInfos.parse_file(settings.creds_info_file)
+            license_infos = LicenseInfos.from_home()
         else:
             # If license dir did not exist yet, secrets are certainly new
             return False
@@ -786,13 +803,13 @@ def are_lib_secrets_an_upgrade(found_secrets: "JslSecrets") -> bool:
         # Return True, if lib are newer than existing ones, if yes upgrade locally stored secrets
         Path(settings.py_dir).mkdir(parents=True, exist_ok=True)
         if os.path.exists(settings.creds_info_file):
-            license_infos = LicenseInfos.parse_file(settings.creds_info_file)
+            license_infos = LicenseInfos.from_home()
         else:
             # If license dir did not exist yet, secrets are certainly new
             return False
 
         # if any stored secrets equal to found_secrets, then we already know them
-        # check OCR secrets
+
         if found_secrets.HC_SECRET:
             if any(
                 map(
@@ -837,7 +854,7 @@ def store_in_jsl_home_if_new(secrets: "JslSecrets") -> None:
         file_name = file_name + "_".join(products) + f".json"
 
         if os.path.exists(settings.creds_info_file):
-            license_infos = LicenseInfos.parse_file(settings.creds_info_file)
+            license_infos =  LicenseInfos.from_home()
             file_name = file_name.format(number=str(len(license_infos.infos)))
             license_info = LicenseInfo(
                 jsl_secrets=secrets, products=products, id=str(len(license_infos.infos))
@@ -848,13 +865,16 @@ def store_in_jsl_home_if_new(secrets: "JslSecrets") -> None:
             secrets.write(out_dir)
             print(f"📋 Stored new John Snow Labs License in {out_dir}")
         else:
-            file_name = file_name.format(number="0")
             license_info = LicenseInfo(jsl_secrets=secrets, products=products, id="0")
-            LicenseInfos(infos={file_name: license_info}).write(
-                settings.creds_info_file
-            )
+            license_infos = LicenseInfos(infos={file_name: license_info})
+            with open(settings.creds_info_file, "w") as f:
+                f.write(license_infos.model_dump_json())
+
+            file_name = file_name.format(number="0")
             out_dir = os.path.join(settings.license_dir, file_name)
-            secrets.write(out_dir)
+            with open(out_dir, "w") as f:
+                f.write(secrets.model_dump_json())
+            #secrets.write(out_dir)
             print(f"📋 Stored John Snow Labs License in {out_dir}")
             # We might load again JSL-Secrets from local
             already_logged = True
@@ -877,6 +897,7 @@ class LicenseInfo(WritableBaseModel):
     products: List[ProductName]
 
 
+
 class LicenseInfos(WritableBaseModel):
     """Representation of a LicenseInfo in ~/.johnsnowlabs/licenses/info.json
     Maps file_name to LicenseInfo
@@ -886,6 +907,15 @@ class LicenseInfos(WritableBaseModel):
 
     @staticmethod
     def from_home() -> Optional["LicenseInfos"]:
-        if os.path.exists(settings.creds_info_file):
-            return LicenseInfos.parse_file(settings.creds_info_file)
-        return None
+        if not os.path.exists(settings.creds_info_file):
+            return None
+        data = json.load(open(settings.creds_info_file))
+        infos = {}
+        for info in data['infos']:
+            secret = JslSecrets.from_json_dict(data['infos'][info]['jsl_secrets'])
+            i = LicenseInfo(id=info, jsl_secrets=secret,
+                            products=data['infos'][info]['products'],
+                            )
+            infos[info] = i
+        license_infos = LicenseInfos(infos=infos)
+        return license_infos
diff --git a/johnsnowlabs/py_models/lib_version.py b/johnsnowlabs/py_models/lib_version.py
@@ -133,3 +133,6 @@ def as_str(self) -> str:
         """Return LibVersion object as canonical str representation"""
         # We filter out all values != None soo version checks match up
         return ".".join(filter(lambda x: x, [self.major, self.minor, self.patch]))
+
+    def __str__(self):
+        return self.as_str()