🔖Release 0.0.4

EhsanBitaraf · Oct 16, 2023 · a85390f · a85390f
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diff --git a/.github/workflows/python-flake.yml b/.github/workflows/python-flake.yml
@@ -29,6 +29,7 @@ jobs:
         pip install flake8
     - name: Lint with flake8
       run: |
+        flake8 ./triplea/ --count --no-show-source --statistics
         flake8 ./triplea/  --count --exit-zero  --max-complexity=20 --max-line-length=90 --no-show-source  --statistics
     - name: Fail if there are linting errors
       if: ${{ failure() }}

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,17 @@
 # Changelog
 All notable changes to this project will be documented in this file.
 
+
+## v0.0.4 2023-10-14
+### Improvements
+- Add FlagAffiliationMining_TITIPATA from Api
+- Add ParseMethod field in Affiliation
+
+
+### Bug Fixes
+- Fix GitHub Action `pyhton-flake`
+
+
 ## v0.0.3 - 2023-09-27
 ### Improvements
 - Add micro version

diff --git a/README.md b/README.md
@@ -77,6 +77,10 @@ https://badge.fury.io/for/py/Triple-a -->
 - Dynamic citations deep definition for meta data fetch
 - Network Analysis (Per Node/Overall Graph)
 - Import bibliography file
+- Use for [Bibliometric Analysis](https://researchguides.uic.edu/bibliometrics)
+
+
+
 # How to use 
 
 ## Setup
@@ -268,8 +272,8 @@ List of Custom Pipeline
 |------|--------|-----------|
 |Triple extraction from article abstract|FlagExtractKG||
 |Topic extraction from article abstract|FlagExtractTopic||
-|Convert Affiliation text to structural data|FlagAffiliationMining| |
-
+|Convert Affiliation text to structural data|FlagAffiliationMining|This is simple way for parse Affiliation text |
+|Convert Affiliation text to structural data|FlagAffiliationMining_Titipata|use [Titipat Achakulvisut Repo](https://github.com/titipata/affiliation_parser) for parsing Affiliation text|
 
 #### NER Article Title
 You can try the NER method to extract the major topic of the article's title by using the following command. This command is independent and is used for testing and is not stored in the Arepo.

diff --git a/docs/code-quality.md b/docs/code-quality.md
@@ -86,7 +86,7 @@ Flake8 Rules
 
 https://www.flake8rules.com/
 
-Sample command:
+## Sample command:
 
 ```
 flake8 --show-source .\triplea\cli\main.py
@@ -158,4 +158,200 @@ flake8 --config=.flake8 --output-file out-flake8.txt .\triplea\cli\
 
 ```
 black .\triplea\cli\
-```
+```
+
+
+## History
+
+### All
+
+```sh
+flake8 --config=.flake8 --count --output-file out-flake8.txt .\triplea\ --no-show-source  --statistics
+```
+
+
+2023-10-15
+```
+4     C901 'export_rayyan_csv' is too complex (21)
+24    E116 unexpected indentation (comment)
+6     E117 over-indented
+3     E122 continuation line missing indentation or outdented
+3     E125 continuation line with same indent as next logical line
+14    E127 continuation line over-indented for visual indent
+8     E128 continuation line under-indented for visual indent
+1     E131 continuation line unaligned for hanging indent
+17    E201 whitespace after '('
+14    E202 whitespace before ')'
+38    E203 whitespace before ':'
+1     E211 whitespace before '('
+6     E221 multiple spaces before operator
+7     E222 multiple spaces after operator
+24    E225 missing whitespace around operator
+43    E231 missing whitespace after ','
+4     E251 unexpected spaces around keyword / parameter equals
+4     E252 missing whitespace around parameter equals
+15    E261 at least two spaces before inline comment
+5     E262 inline comment should start with '# '
+24    E265 block comment should start with '# '
+1     E271 multiple spaces after keyword
+1     E301 expected 1 blank line, found 0
+32    E302 expected 2 blank lines, found 1
+84    E303 too many blank lines (3)
+1     E402 module level import not at top of file
+143   E501 line too long (112 > 90 characters)
+1     E711 comparison to None should be 'if cond is None:'
+4     E712 comparison to False should be 'if cond is False:' or 'if not cond:'
+11    E722 do not use bare 'except'
+1     E741 ambiguous variable name 'l'
+78    F401 'json' imported but unused
+1     F821 undefined name 'topics'
+29    F841 local variable 'output_data' is assigned to but never used
+63    W291 trailing whitespace
+13    W292 no newline at end of file
+84    W293 blank line contains whitespace
+11    W391 blank line at end of file
+```
+
+select
+```sh
+flake8 --config=.flake8 --count --output-file out-flake8.txt .\triplea\ --no-show-source  --statistics --select E501
+```
+
+ignore
+```sh
+flake8 --config=.flake8 --count --output-file out-flake8.txt .\triplea\ --no-show-source  --statistics --ignore E501,W503,E722
+```
+
+
+```sh
+black .\triplea\the_private_backyard.py
+
+black .\triplea\the_private_backyard1.py
+
+black .\triplea\the_private_backyard2.py
+
+black .\triplea\the_private_backyard3.py
+
+black .\triplea\the_private_backyard3.py
+
+black .\triplea\the_private_backyard_mongodb.py
+
+```
+
+2023-10-16
+```
+4     C901 'export_rayyan_csv' is too complex (21)
+1     E303 too many blank lines (3)
+82    E501 line too long (110 > 90 characters)
+10    E722 do not use bare 'except'
+1     E741 ambiguous variable name 'l'
+1     F821 undefined name 'topics'
+5     F841 local variable 'city' is assigned to but never used
+104
+```
+104
+
+### cli
+
+```sh
+black .\triplea\cli\
+```
+
+```sh
+flake8 --config=.flake8 --output-file out-flake8.txt .\triplea\cli\ --no-show-source  --statistics
+```
+
+0
+
+### client
+
+```sh
+black .\triplea\client\
+```
+
+```sh
+flake8 --config=.flake8 --output-file out-flake8.txt .\triplea\client\ --no-show-source  --statistics
+```
+
+0
+
+### config
+
+
+```sh
+black .\triplea\config\
+```
+
+```sh
+flake8 --config=.flake8 --output-file out-flake8.txt .\triplea\config\ --no-show-source  --statistics
+```
+
+0
+
+### db
+
+```sh
+black .\triplea\db\
+```
+
+```sh
+flake8 --config=.flake8 --output-file out-flake8.txt .\triplea\db\ --no-show-source  --statistics
+```
+0
+
+
+### schemas
+
+
+```sh
+black .\triplea\schemas\
+```
+
+```sh
+flake8 --config=.flake8 --output-file out-flake8.txt .\triplea\schemas\ --no-show-source  --statistics
+```
+
+0
+
+### service
+
+```sh
+black .\triplea\service\
+```
+
+```sh
+flake8 --config=.flake8 --count --output-file out-flake8.txt .\triplea\service\ --no-show-source  --statistics --ignore E501,W503,E722
+
+flake8 --config=.flake8 --count --output-file out-flake8.txt .\triplea\service\ --no-show-source  --statistics
+
+```
+
+510
+137
+113
+
+```
+4     C901 'export_rayyan_csv' is too complex (21)
+1     E303 too many blank lines (3)
+1     E402 module level import not at top of file
+82    E501 line too long (110 > 90 characters)
+2     E712 comparison to False should be 'if cond is False:' or 'if not cond:'
+10    E722 do not use bare 'except'
+1     E741 ambiguous variable name 'l'
+5     F401 'networkx.classes.function.is_directed' imported but unused
+1     F821 undefined name 'topics'
+6     F841 local variable 'elapsed' is assigned to but never used
+```
+
+### utils
+
+
+```sh
+black .\triplea\utils\
+```
+
+```sh
+flake8 --config=.flake8 --output-file out-flake8.txt .\triplea\utils\ --no-show-source  --statistics
+```
+
+0
diff --git a/docs/related-work.md b/docs/related-work.md
@@ -90,6 +90,26 @@ https://pubmed.ncbi.nlm.nih.gov/30678631/
 
 https://github.com/NeuroMorphoOrg/PaperBot
 
+## Paperfetcher
+Paperfetcher: A tool to automate handsearching and citation searching for systematic reviews
+
+https://onlinelibrary.wiley.com/doi/epdf/10.1002/jrsm.1604
+
+https://paperfetcher.github.io/
+
+https://github.com/paperfetcher/paperfetcher-web-app
+
+https://github.com/paperfetcher/paperfetcher
+
+
+## paperscraper
+![Awesome Badges](https://img.shields.io/badge/badges-awesome-green.svg)
+Tools to scrape publication metadata from pubmed, arxiv, medrxiv and chemrxiv. 
+
+Since v0.2.4 paperscraper also supports scraping PDF files directly! Thanks to @daenuprobst for suggestions!
+
+https://github.com/PhosphorylatedRabbits/paperscraper
+
 ## bibliometrix: An R-tool for comprehensive science mapping analysis
 
 https://www.sciencedirect.com/science/article/abs/pii/S1751157717300500

diff --git a/out-flake8.txt b/out-flake8.txt
@@ -1,46 +0,0 @@
-.\triplea\cli\export_graph.py:121: [E127] continuation line over-indented for visual indent
-1     E127 continuation line over-indented for visual indent
-.\triplea\cli\export_graph.py:121: [E127] continuation line over-indented for visual indent
-                        "graphjson",
-                        ^
-1     E127 continuation line over-indented for visual indent
-.\triplea\cli\export_graph.py:121: [E128] continuation line under-indented for visual indent
-                    "graphjson",
-                    ^
-.\triplea\cli\export_graph.py:122: [E128] continuation line under-indented for visual indent
-                    "gson",
-                    ^
-.\triplea\cli\export_graph.py:123: [E128] continuation line under-indented for visual indent
-                    "gpickle",
-                    ^
-.\triplea\cli\export_graph.py:124: [E128] continuation line under-indented for visual indent
-                    "graphml",
-                    ^
-.\triplea\cli\export_graph.py:125: [E128] continuation line under-indented for visual indent
-                    "gexf"]),
-                    ^
-5     E128 continuation line under-indented for visual indent
-.\triplea\cli\export_graph.py:121: [E127] continuation line over-indented for visual indent
-                        "graphjson",
-                        ^
-1     E127 continuation line over-indented for visual indent
-.\triplea\cli\export_graph.py:121: [E128] continuation line under-indented for visual indent
-        "graphjson",
-        ^
-.\triplea\cli\export_graph.py:122: [E128] continuation line under-indented for visual indent
-        "gson",
-        ^
-.\triplea\cli\export_graph.py:123: [E128] continuation line under-indented for visual indent
-        "gpickle",
-        ^
-.\triplea\cli\export_graph.py:124: [E128] continuation line under-indented for visual indent
-        "graphml",
-        ^
-.\triplea\cli\export_graph.py:125: [E128] continuation line under-indented for visual indent
-        "gexf"]),
-        ^
-5     E128 continuation line under-indented for visual indent
-.\triplea\cli\export_graph.py:123: [E127] continuation line over-indented for visual indent
-                        "gpickle",
-                        ^
-1     E127 continuation line over-indented for visual indent

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "triplea"
-version = "0.0.3"
+version = "0.0.4"
 license = "Apache-2.0"
 description = "Article Analysis Assistant"
 authors = ["Ehsan Bitaraf <bitaraf.e@iums.ac.ir>", "Maryam Jafarpour <maryam.jafarpoor@gmail.com>"]

diff --git a/triplea/cli/aaa.py b/triplea/cli/aaa.py
@@ -11,7 +11,7 @@
 from triplea.cli.export_graph import export_graph  # exportgraph # noqa: F401
 from triplea.cli.export import export  # export # noqa: F401
 from triplea.cli.export_pretrain_llm import export_llm  # exportllm # noqa: F401
-from triplea.cli.export_article import cli_export_article # export_article # noqa: F401
+from triplea.cli.export_article import cli_export_article  # export_article # noqa: F401
 from triplea.cli.visualize import visualize  # visualize # noqa: F401
 from triplea.cli.visualize import visualize_file  # visualize_file # noqa: F401
 from triplea.cli.analysis import analysis  # analysis # noqa: F401

diff --git a/triplea/cli/config.py b/triplea/cli/config.py
@@ -84,19 +84,27 @@ def configuration(command):
                         f"""AAA_MONGODB_CONNECTION_URL=
                         {AAA_MONGODB_CONNECTION_URL} \n"""
                     )
-                    file.writelines(f"""AAA_MONGODB_DB_NAME=
-                                    {AAA_MONGODB_DB_NAME} \n""")
+                    file.writelines(
+                        f"""AAA_MONGODB_DB_NAME=
+                                    {AAA_MONGODB_DB_NAME} \n"""
+                    )
                 elif TRIPLEA_DB_TYPE == "TinyDB":
-                    file.writelines(f"""AAA_TINYDB_FILENAME=
-                                    {AAA_TINYDB_FILENAME} \n""")
+                    file.writelines(
+                        f"""AAA_TINYDB_FILENAME=
+                                    {AAA_TINYDB_FILENAME} \n"""
+                    )
 
                 file.writelines(f"AAA_TPS_LIMIT={AAA_TPS_LIMIT} \n")
                 file.writelines(f"AAA_PROXY_HTTP={AAA_PROXY_HTTP} \n")
                 file.writelines(f"AAA_PROXY_HTTPS={AAA_PROXY_HTTPS} \n")
-                file.writelines(f"""AAA_REFF_CRAWLER_DEEP=
-                                {AAA_REFF_CRAWLER_DEEP} \n""")
-                file.writelines(f"""AAA_CITED_CRAWLER_DEEP=
-                                {AAA_CITED_CRAWLER_DEEP} \n""")
+                file.writelines(
+                    f"""AAA_REFF_CRAWLER_DEEP=
+                                {AAA_REFF_CRAWLER_DEEP} \n"""
+                )
+                file.writelines(
+                    f"""AAA_CITED_CRAWLER_DEEP=
+                                {AAA_CITED_CRAWLER_DEEP} \n"""
+                )
 
     else:
         raise NotImplementedError