init

.gitignore

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+*.ipynb
+
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+__pycache__/
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+*.so
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+.Python
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+develop-eggs/
+dist/
+downloads/
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+lib/
+lib64/
+parts/
+sdist/
+var/
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+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
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+
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+pip-log.txt
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+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
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+
+# Django stuff:
+*.log
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+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
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+.scrapy
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+profile_default/
+ipython_config.py
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+cython_debug/
+
+*/env/*

README.md

 # billygene-vue-fastapi-edition
 
+`uvicorn main:app --reload`
\ No newline at end of file

billigene/api/config.py

+from Configs import ConfigBase
+
+
+class DEFAULT(ConfigBase):
+    NEO4J = {}
+    LOG_LEVEL = "INFO"

billigene/api/main.py

+import os
+from typing import Optional, List, Union
+
+from fastapi import FastAPI, Query
+from Configs import getConfig
+from config import DEFAULT
+from py2neo import Graph
+import logging
+
+# logging.basicConfig(level=logging.DEBUG)
+app = FastAPI()
+config: DEFAULT = getConfig(
+    config_classes_pathes=[os.path.join(os.path.dirname(__file__), "config.py")],
+    dotenv_files_dir_path=os.path.join(os.path.dirname(__file__), "env/"),
+)
+
+
+@app.get("/")
+def read_root():
+    return {"Hello": "World"}
+
+
+@app.get("/items/{item_id}")
+def read_item(item_id: Union[int, str], q: Optional[str] = None):
+    return {"item_id": item_id, "q": q}
+
+
+@app.get("/article/{pmid}")
+def articel_by_gene(pmid: Union[int, str]):
+    if isinstance(pmid, int):
+        pmid = str(pmid)
+    g = Graph(**config.NEO4J)
+    query = "MATCH (p:PubMedArticle)  WHERE p.PMID = $pmid RETURN p as article"
+    res = g.run(query, parameters={"pmid": pmid}).data()
+    if res:
+        return res[0]["article"]
+    else:
+        return None
+
+
+###################################################shit
+@app.get("/bygenelist")
+def articel_by_genes(g: Optional[list[str]] = Query(None)):
+    graph = Graph(**config.NEO4J)
+    print("g", g)
+    query = """
+    UNWIND $gene_symbols as x
+        MATCH (g:Gene {sid:x})
+        -[:REPLACED_BY*0..1]-(gs2:Gene)
+        -[:MAPS*0..2]-(gs3:Gene)
+        -[:SYNONYM*0..1]-(gs4:Gene)
+        <-[:MENTIONS]-(at:AbstractText)
+        <-[:ABSTRACT_HAS_ABSTRACTTEXT]-(a:Abstract)
+        <-[:PUBMEDARTICLE_HAS_ABSTRACT]-(p:PubMedArticle)
+        -[:PUBMEDARTICLE_HAS_MESHHEADINGLIST]->
+        (mhl:MeshHeadingList)-[*1..2]->
+        (md:MeshDescriptor)
+    RETURN DISTINCT g.sid,p.ArticleTitle
+    """
+    res = graph.run(query, gene_symbols=g).data()
+    return res

reqs.txt

+fastapi
+uvicorn[standard]
+py2neo
+from Configs import getConfig
\ No newline at end of file