Repository: Australian-Text-Analytics-Platform/atap-corpus-slicer
Issue category: Performance Issue

Numeric slicing operation with NA values to be improved.
![image](https://github.com/user-attachments/assets/cc4f4c4a-6550-479c-aa0c-148605ab2613)



Functions to edit:
atap_corpus_slicer/CorpusSlicer.py:CorpusSlicer.corpus_run_spacy
atap_corpus_slicer/Operation.py:DefaultOperations.call_operation
atap_corpus_slicer/Operation.py:TextOperations.call_operation
atap_corpus_slicer/Operation.py:IntegerOperations.call_operation
atap_corpus_slicer/Operation.py:FloatOperations.call_operation
atap_corpus_slicer/Operation.py:BooleanOperations.call_operation
atap_corpus_slicer/Operation.py:DateOperations.call_operation
atap_corpus_slicer/Operation.py:CategoryOperations.call_operation
atap_corpus_slicer/Operation.py:SpacyTokenOperations.call_operation
atap_corpus_slicer/Operation.py:SpacyPhraseOperations.call_operation

Patch:
diff --git a/atap_corpus_slicer/CorpusSlicer.py b/atap_corpus_slicer/CorpusSlicer.py
index 2c6fa97..7b828ba 100644
--- a/atap_corpus_slicer/CorpusSlicer.py
+++ b/atap_corpus_slicer/CorpusSlicer.py
@@ -363,7 +363,8 @@ def corpus_run_spacy(self, corpus):
 
             progress_bar = self.corpus_loader.controller.get_build_progress_bar()
             docs_ls = []
-            for doc in progress_bar(self.model.pipe(docs), total=len(run_spacy_on), desc="Processing with NLP model", unit="files", leave=True):
+            for text in progress_bar(docs, total=len(run_spacy_on), desc="Processing with NLP model", unit="files", leave=True):
+                doc = self.model(text)
                 docs_ls.append(doc)
             run_spacy_on._df[run_spacy_on._COL_DOC] = Series(docs_ls)
         except Exception as e:
diff --git a/atap_corpus_slicer/Operation.py b/atap_corpus_slicer/Operation.py
index b6c7dd4..006c2bc 100644
--- a/atap_corpus_slicer/Operation.py
+++ b/atap_corpus_slicer/Operation.py
@@ -8,7 +8,7 @@
 from spacy.tokens import Doc
 import pandas as pd
 import panel as pn
-from pandas import Series
+from pandas import Series, isna
 
 pn.extension()
 
@@ -33,6 +33,8 @@ def __init__(self, data_series: Series, **params):
         self.panel.objects = ["is equal to", self.query_value]
 
     def call_operation(self, data_value: Any) -> bool:
+        if isna(data_value) or isna(self.query_value.value_input):
+            return False
         return str(data_value) == self.query_value.value_input
 
 
@@ -122,6 +124,8 @@ def toggle_count_inputs(self, *_):
         self.count_threshold.visible = count_op
 
     def call_operation(self, data_value: Union[str, Doc]) -> bool:
+        if isna(data_value) or isna(self.query_value.value_input):
+            return False
         if isinstance(data_value, Doc):
             data_value = data_value.text_with_ws
         if self.operation.value == self.text_contains:
@@ -140,7 +144,11 @@ def __init__(self, data_series: Series, **params):
         self.panel.objects = [self.data_range]
 
     def call_operation(self, data_value: int) -> bool:
-        return self.data_range.value[0] <= data_value <= self.data_range.value[1]
+        range_start = self.data_range.value[0]
+        range_end = self.data_range.value[1]
+        if isna(data_value) or isna(range_start) or isna(range_end):
+            return False
+        return bool(range_start <= data_value <= range_end)
 
 
 class FloatOperations(Operations):
@@ -154,7 +162,11 @@ def __init__(self, data_series: Series, **params):
         self.panel.objects = [self.data_range]
 
     def call_operation(self, data_value: float) -> bool:
-        return self.data_range.value[0] <= data_value <= self.data_range.value[1]
+        range_start = self.data_range.value[0]
+        range_end = self.data_range.value[1]
+        if isna(data_value) or isna(range_start) or isna(range_end):
+            return False
+        return bool(range_start <= data_value <= range_end)
 
 
 class BooleanOperations(Operations):
@@ -165,7 +177,9 @@ def __init__(self, data_series: Series, **params):
         self.panel.objects = [self.query_value]
 
     def call_operation(self, data_value: bool) -> bool:
-        return data_value == self.query_value.value
+        if isna(data_value) or isna(self.query_value.value):
+            return False
+        return bool(data_value == self.query_value.value)
 
 
 class DateOperations(Operations):
@@ -179,6 +193,10 @@ def __init__(self, data_series: Series, **params):
         self.panel.objects = [self.date_range]
 
     def call_operation(self, data_value: pd.Timestamp) -> bool:
+        range_start = self.date_range.value[0]
+        range_end = self.date_range.value[1]
+        if isna(data_value) or isna(range_start) or isna(range_end):
+            return False
         data_value = data_value.to_pydatetime()
         return self.date_range.value[0] <= data_value <= self.date_range.value[1]
 
@@ -191,6 +209,8 @@ def __init__(self, data_series: Series, **params):
         self.panel.objects = [self.category]
 
     def call_operation(self, data_value: Any) -> bool:
+        if isna(data_value) or isna(self.category.value):
+            return False
         return bool(data_value in self.category.value)
 
 
@@ -251,6 +271,8 @@ def update_tag_values(self, *_):
         self.attribute_values.value = []
 
     def call_operation(self, data_value: Doc) -> bool:
+        if isna(data_value) or isna(self.attribute_values.value):
+            return False
         if len(self.attribute_values.value) == 0:
             return True
         regex_flag = 0
@@ -311,6 +333,8 @@ def _set_search_doc(self, *_):
         self.search_doc = self.model(self.search.value)
 
     def call_operation(self, data_value: Doc) -> bool:
+        if isna(data_value) or isna(self.attribute.value):
+            return False
         matcher: PhraseMatcher = PhraseMatcher(self.model.vocab, self.attribute.value)
         matcher.add('pattern', [self.search_doc])
 
diff --git a/corpus-slicer.ipynb b/corpus-slicer.ipynb
index e5f7813..cd213cb 100644
--- a/corpus-slicer.ipynb
+++ b/corpus-slicer.ipynb
@@ -8,7 +8,7 @@
     "from atap_corpus_slicer import CorpusSlicer\n",
     "from atap_corpus_loader import CorpusLoader\n",
     "\n",
-    "loader = CorpusLoader(root_directory='corpus_data', include_meta_loader=True)\n",
+    "loader = CorpusLoader(root_directory='corpus_data', include_meta_loader=True, run_logger=True)\n",
     "corpus_slicer: CorpusSlicer = CorpusSlicer(corpus_loader=loader, run_logger=True)\n",
     "corpus_slicer"
    ],
diff --git a/poetry.lock b/poetry.lock
index 9ad6293..ff33689 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -13,13 +13,13 @@ files = [
 
 [[package]]
 name = "anyio"
-version = "4.5.0"
+version = "4.6.0"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "anyio-4.5.0-py3-none-any.whl", hash = "sha256:fdeb095b7cc5a5563175eedd926ec4ae55413bb4be5770c424af0ba46ccb4a78"},
-    {file = "anyio-4.5.0.tar.gz", hash = "sha256:c5a275fe5ca0afd788001f58fca1e69e29ce706d746e317d660e21f70c530ef9"},
+    {file = "anyio-4.6.0-py3-none-any.whl", hash = "sha256:c7d2e9d63e31599eeb636c8c5c03a7e108d73b345f064f1c19fdc87b79036a9a"},
+    {file = "anyio-4.6.0.tar.gz", hash = "sha256:137b4559cbb034c477165047febb6ff83f390fc3b20bf181c1fc0a728cb8beeb"},
 ]
 
 [package.dependencies]
@@ -154,13 +154,13 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "atap-corpus"
-version = "0.1.13"
+version = "0.1.15"
 description = "Corpus mini-framework allowing for memory-efficient slicing and provides a standardised base corpus structure for the collection of ATAP tools. "
 optional = false
-python-versions = ">=3.10,<3.13"
+python-versions = "<3.13,>=3.10"
 files = [
-    {file = "atap_corpus-0.1.13-py3-none-any.whl", hash = "sha256:cb1308bcbfe6ab9a999e0e6f734bc6f1215a9dba5119913275335c4c295f5bfc"},
-    {file = "atap_corpus-0.1.13.tar.gz", hash = "sha256:3710e18ef6540bfcb29bd7a7f6b685de96c388e43fe92a643e6cd299d52f9e87"},
+    {file = "atap_corpus-0.1.15-py3-none-any.whl", hash = "sha256:dc7a06e315dbe7ef39992bc8d310874a175c7860e9e9b9dd184cc353d84a89d8"},
+    {file = "atap_corpus-0.1.15.tar.gz", hash = "sha256:cd7a15177c4636899f90fed708de7d5280a89839258101b2ab3954e03580015e"},
 ]
 
 [package.dependencies]
@@ -177,17 +177,17 @@ tqdm = ">=4.64.0,<5.0.0"
 
 [package.extras]
 apple = ["thinc-apple-ops[apple] (>=0.1.0,<0.2.0)", "urllib3 (>=1.26.18,<2.0.0)"]
-viz = ["ipywidgets (>=7.7.2,<8.0.0)", "matplotlib (>=3.5.2,<4.0.0)", "panel (>=1.2.3,<2.0.0)", "plotly (>=5.11.0,<6.0.0)"]
+viz = ["ipywidgets (>=8.0)", "matplotlib (>=3.5.2,<4.0.0)", "panel (>=1.2.3,<2.0.0)", "plotly (>=5.11.0,<6.0.0)"]
 
 [[package]]
 name = "atap-corpus-loader"
-version = "1.7.2"
+version = "1.7.3"
 description = "A GUI loader for atap_corpus using the Panel library."
 optional = false
 python-versions = "<3.13,>=3.10"
 files = [
-    {file = "atap_corpus_loader-1.7.2-py3-none-any.whl", hash = "sha256:0908365f542b30fbb995a428139b89c189dfbdae43ced71fb6624bda4b9457e3"},
-    {file = "atap_corpus_loader-1.7.2.tar.gz", hash = "sha256:545ebc244c1360644fd0df01d6ab161abe8381a8f6bec95375d499a83aff0116"},
+    {file = "atap_corpus_loader-1.7.3-py3-none-any.whl", hash = "sha256:03f8089cb0660f4e8c26649946d30e1a68fda328c9f91203b3e39ced0909cd2e"},
+    {file = "atap_corpus_loader-1.7.3.tar.gz", hash = "sha256:24ee8c1fec5d4004da616c53215e345159a029ab35c4297bbbfbca3151c12b37"},
 ]
 
 [package.dependencies]
@@ -197,6 +197,7 @@ odfpy = ">=1.4.0,<1.5.0"
 pandas = ">2.0"
 panel = ">=1.4.0,<1.5.0"
 python-docx = ">=1.1.0,<1.2.0"
+XlsxWriter = ">=3.2.0,<3.3.0"
 
 [[package]]
 name = "attrs"
@@ -839,33 +840,33 @@ files = [
 
 [[package]]
 name = "debugpy"
-version = "1.8.5"
+version = "1.8.6"
 description = "An implementation of the Debug Adapter Protocol for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
@@ -2227,40 +2228,53 @@ files = [
 
 [[package]]
 name = "pandas"
-version = "2.2.2"
+version = "2.2.3"
 description = "Powerful data structures for data analysis, time series, and statistics"
 optional = false
 python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -2566,13 +2580,13 @@ murmurhash = ">=0.28.0,<1.1.0"
 
 [[package]]
 name = "prometheus-client"
-version = "0.20.0"
+version = "0.21.0"
 description = "Python client for the Prometheus monitoring system."
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "prometheus_client-0.20.0.tar.gz", hash = "sha256:287629d00b147a32dcb2be0b9df905da599b2d82f80377083ec8463309a4bb89"},
+    {file = "prometheus_client-0.21.0-py3-none-any.whl", hash = "sha256:4fa6b4dd0ac16d58bb587c04b1caae65b8c5043e85f778f42f5f632f6af2e166"},
+    {file = "prometheus_client-0.21.0.tar.gz", hash = "sha256:96c83c606b71ff2b0a433c98889d275f51ffec6c5e267de37c7a2b5c9aa9233e"},
 ]
 
 [package.extras]
@@ -4032,13 +4046,13 @@ files = [
 
 [[package]]
 name = "tzdata"
-version = "2024.1"
+version = "2024.2"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
 files = [
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-    {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"},
+    {file = "tzdata-2024.2-py2.py3-none-any.whl", hash = "sha256:a48093786cdcde33cad18c2555e8532f34422074448fbc874186f0abd79565cd"},
+    {file = "tzdata-2024.2.tar.gz", hash = "sha256:7d85cc416e9382e69095b7bdf4afd9e3880418a2413feec7069d533d6b4e31cc"},
 ]
 
 [[package]]
@@ -4306,4 +4320,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.10.0,<3.12.0"
-content-hash = "0c7c9070c2ca3f49be51e93c68efd9e2e52042aaca452845e588350d0e0ae5d8"
+content-hash = "3806e05481dceb58797116ae78ea1a12f08e2f99bfb51b64dcbfcdcb9c725dfa"
diff --git a/pyproject.toml b/pyproject.toml
index 6ba65af..de8ae8a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "atap-corpus-slicer"
-version = "0.3.1"
+version = "0.3.2"
 description = "A GUI corpus filter built with the Panel library."
 authors = ["Hamish Croser <hamish.croser@sydney.edu.au>"]
 readme = "README.md"
@@ -13,7 +13,7 @@ exclude = ["*/.ipynb_checkpoints/*", "*log.txt"]
 [tool.poetry.dependencies]
 python = ">=3.10.0,<3.12.0"
 atap_corpus = "~=0.1.13"
-atap-corpus-loader = "~=1.7.2"
+atap-corpus-loader = "~=1.7.3"
 pandas = "~=2.0"
 panel = "~=1.4"
 numpy = "<2.0"