reflexive 1.2.2__py3-none-any.whl → 1.2.4__py3-none-any.whl

reflexive/__init__.py

@@ -12,4 +12,8 @@ from reflexive.visualise import (
     Display,
     RES_graph)
 
-__all__ = ["Config","AWS","S3","Comprehend","Nlp","Display","RES_graph"]
+from reflexive.res import (
+    Res_analyse,
+    Res_display)
+
+__all__ = ["Config","AWS","S3","Comprehend","Nlp","Display","RES_graph","Res_analyse","Res_display"]

reflexive/analyse.py

@@ -8,7 +8,7 @@ from reflexive import cfg
 from reflexive import session
 
 import logging
-logging.basicConfig(level=logging.DEBUG)
+#logging.basicConfig(level=logging.DEBUG)
 logger = logging.getLogger(__name__)
 
 

reflexive/res.py

@@ -0,0 +1,198 @@
+import json
+from pandas import DataFrame
+from spacy import displacy
+from time import sleep
+from reflexive import Config
+from reflexive import AWS
+from reflexive import S3
+from reflexive import Comprehend
+from reflexive import Nlp
+from reflexive import Display
+from reflexive import RES_graph
+
+class Res_analyse:
+    
+    config:Config
+    aws:AWS
+    s3:S3
+    comprehend:Comprehend
+    nlp:Nlp
+    
+    def __init__(self,aws_profile="default") -> None:
+        return self._setup(aws_profile)
+    
+    def _setup(self,aws_profile) -> None:
+        self.config = Config(aws_profile)
+        self.config.set_parameters(name_prefix="RES")
+        self.aws = AWS(self.config)
+        return None
+    
+    def set_parameters(self,
+                       s3_access_point:str,
+                       s3_bucket_name:str,
+                       comprehend_service_role_name:str,
+                       reflexive_entity_name:str,
+                       reflexive_entity_version:str) -> str:
+        self.config.set_s3_parameters(s3_access_point,s3_bucket_name)
+        self.config.set_comprehend_parameters(comprehend_service_role_name)
+        self.config.set_comprehend_custom_entity_parameters(reflexive_entity_name,reflexive_entity_version)
+        params = self.config.get_parameters()
+        return json.dumps(params, indent=2)
+    
+    def setup_aws(self) -> None:
+        # Create a new S3 client
+        self.s3 = S3(self.aws)
+        # Create a new Comprehend client
+        self.comprehend = Comprehend(self.aws)
+        # Create an Nlp object to perform analysis on the text
+        self.nlp = Nlp(self.aws)
+        return None
+    
+    def get_basic_analytics(self,df:DataFrame) -> DataFrame:
+        
+        # Text length - this is needed for comprehend analytics
+        df = self.nlp.text_length(df)
+        #df = nlp.remove_IQR_outliers(df)
+        # Comprehend analysis
+        results = self.nlp.comprehend_analysis(self.comprehend,df)
+        #print(results)
+        errors = self.nlp.check_results(results)
+        #print(errors)
+        if errors=={}:
+            print("No errors, so adding results to dataframe")
+            df = self.nlp.add_results_to_df(results,df)
+            df = self.nlp.comprehend_analytics(df)
+        return df
+    
+    def get_reflexive_analytics(self,df:DataFrame) -> DataFrame:
+        # Reflexive expression analysis
+        response = self.nlp.analyse_reflexive_expressions(df,self.s3,self.comprehend)
+        #print(response)
+        job_id = self.comprehend.get_current_job_id()
+        print("Job ID:",job_id)
+        status = self.comprehend.check_job_status()
+        print("Status:",status)
+
+        # Get the details of the job
+        # details = comp.get_job_details()
+        # print("Job details:",details)
+
+        inc = 0
+        while status=="SUBMITTED" or status=="IN_PROGRESS":
+            print("Waiting 10 seconds...")
+            sleep(10)
+            status = self.comprehend.check_job_status()
+            print(f"Job status {inc}:",status)
+            inc += 1
+            
+        # Download from S3 and extract results 
+        print("Downloading and extracting results...")
+        results = self.comprehend.download_and_extract(self.s3)
+        print("RESULTS:")
+        print(results)
+        
+        # Extract output of analysis and add to df
+        return self.nlp.add_to_dataframe(df,results)
+
+class Res_display:
+    
+    res_analyse:Res_analyse
+    vis:Display
+    
+    def __init__(self,res:Res_analyse) -> None:
+        return self._setup(res)
+    
+    def _setup(self,res:Res_analyse) -> None:
+        self.res_analyse = res
+        self.vis = Display(res.aws)
+        return None  
+    
+    def show_text(self,df:DataFrame,inline=True) -> str:
+        df = self.vis.add_offsets(df)
+        disp_data = self.vis.create_displacy(df)
+        if inline:
+            displacy.render(disp_data,manual=True,style="ent", options=self.res_analyse.config.display_options)
+            html_out = "Set inline to false to produce HTML"
+        else:
+            html_out = displacy.render(disp_data,manual=True,style="ent", options=self.res_analyse.config.display_options,page=True,jupyter=False)
+        return html_out
+    
+    def get_interactions(self,df:DataFrame) -> DataFrame:
+        #Get RE sequence
+        df = self._add_res_sequence(df)
+        df = self._add_res_interactions(df)
+        df = self._add_res_adj_matrix(df)
+        return df
+    
+    def show_graph(self,df:DataFrame,inline=True) -> str:
+        for am in df.res_adj_matrix:
+            g = RES_graph(am)
+            g.show()
+        return("nothing yet")
+    
+    def _add_res_sequence(self,df):
+        temp_df = df.copy()
+        temp_df['res_sequence'] = temp_df.reflexive_expressions.apply(self._get_res_sequence)
+        return temp_df
+    
+    def _add_res_interactions(self,df):
+        temp_df = df.copy()
+        temp_df['res_interactions'] = temp_df.res_sequence.apply(self._count_res_interactions)
+        return temp_df
+    
+    def _add_res_adj_matrix(self,df):
+        temp_df = df.copy()
+        temp_df['res_adj_matrix'] = temp_df.res_interactions.apply(self._create_adj_matrix)
+        return temp_df
+    
+    def _get_res_sequence(self,reflexive_expressions):
+        re_seq = [label for re,label in reflexive_expressions]
+        res_seq = []
+        # Need to substitute new RES labels for old RE labels
+        for re in re_seq:
+            if re=='ER' or re=='VR':
+                res_seq.append('NR')
+            elif re=='EV':
+                res_seq.append('EP')
+            elif re=='CN':
+                res_seq.append('AF')
+            else:
+                res_seq.append(re)
+        return res_seq
+    
+    def _empty_res_interactions(self) -> dict[tuple,int]:
+        RE_types = ['RR','NR','AR','AF','EP']
+        RE_interactions:dict[tuple,int] = dict()
+        for t1 in RE_types:
+            for t2 in RE_types:
+                entry = tuple(sorted((t1,t2)))
+                if entry not in RE_interactions.keys():
+                    RE_interactions[entry] = 0
+        return RE_interactions
+    
+    def _count_res_interactions(self,re_sequence:list[str]) -> dict[tuple,int]:
+        re_ints = self._empty_res_interactions()
+        limit = len(re_sequence)-1
+        for i,s in enumerate(re_sequence):
+            if i < limit:
+                rei = tuple(sorted((s,re_sequence[i+1])))
+                #print(i,rei)
+                re_ints[rei] += 1 
+        return re_ints
+    
+    def _create_adj_matrix(self,interactions:dict[tuple,int])->list[list[int]]:
+        re_types = ["RR","NR","AR","AF","EP"]
+        matrix = []
+        for r in re_types:
+            row = []
+            for c in re_types:
+                key = tuple(sorted((r,c)))
+                #print(key)
+                weight = interactions.get(key,0)
+                row.append(weight)
+            matrix.append(row)
+        return matrix
+        
+        
+        
+        

reflexive/session.py

@@ -7,7 +7,7 @@ import json
 from reflexive import cfg
 
 import logging
-logging.basicConfig(level=logging.DEBUG)
+#logging.basicConfig(level=logging.DEBUG)
 logger = logging.getLogger(__name__)
 
 class AWS:

reflexive/util.py

@@ -3,7 +3,7 @@ import json
 import pandas as pd
 from sklearn.preprocessing import MinMaxScaler
 import logging
-logging.basicConfig(level=logging.DEBUG)
+#logging.basicConfig(level=logging.DEBUG)
 logger = logging.getLogger(__name__)
 
 

{reflexive-1.2.2.dist-info → reflexive-1.2.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: reflexive
-Version: 1.2.2
+Version: 1.2.4
 Summary: Supports AWS Reflexive Expressions Systems (RES) Analysis
 Project-URL: Repository, https://github.com/nlytx/reflexive.git
 Author-email: Andrew Gibson <andrew@nlytx.io>

reflexive-1.2.4.dist-info/RECORD

@@ -0,0 +1,11 @@
+reflexive/__init__.py,sha256=x5l8GV_9yC8yJyjTLqiM_WkfuPMLuNgQxF6PIz5MfFU,422
+reflexive/analyse.py,sha256=CU6mQ8PxQrkOvuSe4mmnuI18jGMkuxql3zLZ1vEeMEY,17466
+reflexive/cfg.py,sha256=tDPiC9NwpEVoT05_831sMsMfHhJt8pVrSOsgbtzTNDM,4267
+reflexive/res.py,sha256=eXqdd9g24AoPcXLdddM9iE85Fx8iucZN6ODHnRsuRa4,6937
+reflexive/session.py,sha256=8STWo8sqmWn-1PHcloFbgmLEvd7lsiFTU4t7ESRTsvw,10046
+reflexive/util.py,sha256=uU7-lqUmiCiCaR85AdNFKXrdrBspjb1Rmd-yThA3fRU,3699
+reflexive/visualise.py,sha256=pVnsPJOnHiLAIvDDm9P0u6-sGQINC4GVOY9b0GrzTK4,11725
+reflexive-1.2.4.dist-info/METADATA,sha256=mibCUwBnfR03eOBn4vbNMbyAY2wDhfVU6RPeg0D5qc4,574
+reflexive-1.2.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+reflexive-1.2.4.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+reflexive-1.2.4.dist-info/RECORD,,

reflexive-1.2.2.dist-info/RECORD

@@ -1,10 +0,0 @@
-reflexive/__init__.py,sha256=i503RuB3poQF-9otbkxPBD2GnqEBpFSn1TnIyx5DxME,331
-reflexive/analyse.py,sha256=LsDgFI_UUlK88ecQc19iPdcweAvT11CZCqtWtCsevC8,17465
-reflexive/cfg.py,sha256=tDPiC9NwpEVoT05_831sMsMfHhJt8pVrSOsgbtzTNDM,4267
-reflexive/session.py,sha256=ttyUAowaKgkwAgejRb_af5nZruKeH_kn3NB1NtitYUk,10045
-reflexive/util.py,sha256=zwlFncsWrRSuK8rsQaZKFNVLTkRySb1WPeY6Hz6qHhc,3698
-reflexive/visualise.py,sha256=pVnsPJOnHiLAIvDDm9P0u6-sGQINC4GVOY9b0GrzTK4,11725
-reflexive-1.2.2.dist-info/METADATA,sha256=stD6fGt19L8kTosYXpahYcCJroFCdeep6IhYCODbt7I,574
-reflexive-1.2.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-reflexive-1.2.2.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-reflexive-1.2.2.dist-info/RECORD,,