added tests

app/.streamlit/config.toml

@@ -4,11 +4,8 @@ headless = true
 [client]
 toolbarMode = "viewer"
 
-[deprecation]
-showPyplotGlobalUse = false
-
 [theme]
-primaryColor="#1976d2"
+primaryColor="#004dcf"
 backgroundColor="#181a1e"
 secondaryBackgroundColor="linear-gradient(180deg, rgb(5, 39, 103) 0%, #3a0647 70%)"
 textColor="#fff"

app/components/sidebar.py

@@ -13,7 +13,7 @@
 from utils.species import *
 import numpy as np
 from state.StateManager import StateManager
-from models.ErrorMessage import ErrorMessage, WarningMessage
+from enums.ErrorMessage import ErrorMessage, WarningMessage
 
 
 class Sidebar:
@@ -50,7 +50,7 @@ def show_preview(self, integrate=False):
 
     def delete_experiment_btn(self):
         with st.sidebar:
-            delete_btn = st.button(label="🗑️ Delete Experiment", use_container_width=True, key="btn_delete_adata")
+            delete_btn = st.button(label="🗑️ Delete Experiment", use_container_width=True, key="btn_delete_adata", type='primary')
             if delete_btn:
                 self.state_manager.adata_state() \
                 .delete_record(adata_name=st.session_state.sb_adata_selection)
@@ -151,6 +151,21 @@ def add_experiment(self):
                 except Exception as e:
                     print("Error: ", e)
                     st.error(e)
+
+
+    def steps(self):
+        with st.sidebar:
+            with st.form("form_session_steps"):
+                current_adata_id = self.state_manager.adata_state().current.id
+                sessions = self.conn.query(schemas.Session).filter(schemas.Session.adata_id == current_adata_id).all()
+                if sessions:
+                    session_names = [session.description for session in sessions]
+
+                    steps = st.select_slider(label="Pipeline steps", options=session_names)
+                    submit_btn = st.form_submit_button(label="🔧 Undo", use_container_width=True)
+
+                    if submit_btn:
+                        print("hi")
 
 
     def download_adata(self):
@@ -286,8 +301,7 @@ def change_gene_format():
                 st.toggle(label="Ensembl ID", value=(format == "ensembl"), key="toggle_gene_format", on_change=change_gene_format)
 
         except Exception as e:
-            st.error(e)
-            print("Error: ", e)
+            st.toast(e, icon="❌")
 
 
     def show_version(self):
@@ -394,10 +408,11 @@ def set_adata():
 
 
             self.download_adata()
-
             self.add_experiment()
-
             self.notes()
+            self.show_preview()
+            self.export_script()
+
 
 
 

app/css/common.css

@@ -10,69 +10,19 @@
 
 
 
-footer {visibility: hidden;}
-            .st-emotion-cache-1cypcdb {background: linear-gradient(180deg, rgb(5, 39, 103) 0%, #3a0647 70%); box-shadow: 1px 0 10px -2px #000;}
-            .st-emotion-cache-86cver {color: rgba(250, 250, 250, 0.6)}
-            .stButton button {
-                border-radius: 0.5rem;
-                background: #004dcf;
-                color: #fff;
-                border: 1px solid #004dcf;
-                padding: 0.25rem 0.75rem;
-            }
-
-            .stButton button:hover {
-                background: transparent;
-                color: #004dcf;
-                transition: all 0.1s ease-in-out;
-                border: 1px solid #004dcf;
-            }
-
-            .stButton button:focus {
-                border: 1px solid #004dcf;
-                color: #004dcf;
-            }
-
-            .stButton button:active {
-                border: 1px solid #004dcf;
-                color: #004dcf;
-            }
-
-            .stButton button:visited {
-                border: 1px solid #004dcf;
-                color: #004dcf;
-            }
-
-            .st-emotion-cache-1b9yna5:focus:not(:active) {
-                border: 1px solid #004dcf;
-                color: #004dcf;
-            }
-
-            .st-emotion-cache-1b9yna5:focus:not(:hover) {
-                border: 1px solid #004dcf;
-                color: #fff;
-            }
-
-            .st-emotion-cache-oooxyj:focus:not(:active) {
-                border: 1px solid #004dcf;
-                color: #004dcf;
-            }
+footer {
+    visibility: hidden;
+}
 
-            .st-emotion-cache-oooxyj:focus:not(:hover) {
-                border: 1px solid #004dcf;
-                color: #fff;
-            }
+.st-emotion-cache-1cypcdb {
+    background: linear-gradient(180deg, rgb(5, 39, 103) 0%, #3a0647 70%); box-shadow: 1px 0 10px -2px #000;
 
-            .st-emotion-cache-1ts31n5:focus:not(:active) {
-                border: 1px solid #004dcf;
-                color: #004dcf;
-            }
+}
+.st-emotion-cache-86cver {
+    color: rgba(250, 250, 250, 0.6)
+}
 
-            .st-emotion-cache-1ts31n5:focus:not(:hover) {
-                border: 1px solid #004dcf;
-                color: #fff;
-            }
+.st-emotion-cache-z5fcl4 {
+    padding-top: 2rem;
+}
 
-            .st-emotion-cache-z5fcl4 {
-                padding-top: 2rem;
-            }

app/css/workspace.css

@@ -24,7 +24,7 @@
     }
 }
 
-.st-emotion-cache-1qcb9zv, .st-emotion-cache-1ts31n5 {
+.st-emotion-cache-1h7cibc {
     width: 100%;
     font-size: 48px;
     font-weight: 800;
@@ -48,7 +48,7 @@
 }
 
 
-.st-emotion-cache-1qcb9zv:hover, .st-emotion-cache-1ts31n5:hover {
+.st-emotion-cache-1h7cibc:hover {
 
     background-position: 10% 0;
     moz-transition: all .8s ease-in-out;
@@ -61,7 +61,7 @@
     color: #fff;
 }
 
-.st-emotion-cache-1qcb9zv:focus, .st-emotion-cache-1ts31n5:focus {
+.st-emotion-cache-1h7cibc:focus {
     border: rgba(255,255,255,0.8) 2px solid;
 }
 

app/database/schemas/schemas.py

@@ -12,7 +12,6 @@ class Workspaces(Base):
     data_dir = Column(String, nullable=False, unique=True)
     created = Column(TIMESTAMP(timezone=True), nullable=False, server_default=text('now()'))
     description = Column(String, nullable=True)
-    cache_file = Column(String, nullable=True)
 
 class Adata(Base):
     __tablename__ = "adata"
@@ -31,4 +30,14 @@ class Scripts(Base):
     id = Column(Integer, primary_key=True, nullable=False, autoincrement=True)
     script = Column(String, nullable=False)
     language = Column(String, nullable=False)
-    created = Column(TIMESTAMP(timezone=True), nullable=False, server_default=text('now()'))
+    created = Column(TIMESTAMP(timezone=True), nullable=False, server_default=text('now()'))
+
+class Session(Base):
+    __tablename__ = "sessions"
+
+    id = Column(Integer, primary_key=True, nullable=False, autoincrement=True)
+    adata_id = Column(Integer, ForeignKey("adata.id", ondelete="CASCADE"), nullable=False)
+    session_id = Column(String, nullable=False)
+    filename = Column(String, nullable=False) 
+    description = Column(String, nullable=True)
+    created = Column(TIMESTAMP(timezone=True), nullable=False, server_default=text('now()'))

app/models/ErrorMessage.py → app/enums/ErrorMessage.py

@@ -12,4 +12,3 @@ class ErrorMessage(Enum):
 
 class WarningMessage(Enum):
     DATASET_ALREADY_EXISTS = "Dataset already exists in workspace, using original."
-

app/enums/Language.py

@@ -0,0 +1,6 @@
+from enum import Enum
+
+class Language(Enum):
+    python = "python"
+    R = "R"
+    ALL_SUPPORTED = ["python", "R"]

app/models/ScriptModel.py

@@ -1,7 +1,6 @@
 from typing import Optional
 from pydantic import BaseModel, ConfigDict, ValidationError
 from datetime import date
-from enum import Enum
 
 class ScriptModel(BaseModel):
     adata_id: int
@@ -10,7 +9,3 @@ class ScriptModel(BaseModel):
     language: str
     created: Optional[date]
 
-class Language(Enum):
-    python = "python"
-    R = "R"
-    ALL_SUPPORTED = ["python", "R"]

app/models/SessionModel.py

@@ -0,0 +1,11 @@
+from typing import Optional
+from pydantic import BaseModel, ConfigDict, ValidationError
+from datetime import date
+
+class SessionModel(BaseModel):
+    id: Optional[int] #Uses autoincrement when not included
+    adata_id: int
+    session_id: str
+    filename: str
+    description: Optional[str]
+    created: Optional[date]

app/pages/11_Plotly_3D.py

@@ -121,7 +121,7 @@ def change_embeddings():
                 break
         st.selectbox(label="Embedding colors", options=adata.obs_keys(), key="plotly_embedding_color", index=cluster_color_index)
         st.slider(label="Point size", min_value=0.5, max_value=5.0, step=0.1, value=1.0, key="plotly_point_size")
-        st.button(label="Plot chart", use_container_width=True, on_click=change_embeddings)
+        st.button(label="Plot chart", use_container_width=True, on_click=change_embeddings, type='primary')
 
 
     if 'plotly_df' in st.session_state:

app/pages/1_Upload.py

@@ -1,8 +1,6 @@
-from pydantic import ValidationError
 import streamlit as st
 import scanpy as sc
 import squidpy as sq
-import pickle
 import os
 from models.AdataModel import AdataModel
 from models.WorkspaceModel import WorkspaceModel
@@ -11,8 +9,6 @@
 from database.schemas import schemas
 from state.AdataState import AdataState
 from state.StateManager import StateManager
-from state.ScriptState import ScriptState
-from utils.session_cache import load_data_from_cache, cache_data_to_session
 import loompy as lmp
 import glob
 from components.sidebar import Sidebar
@@ -40,6 +36,7 @@ class Upload:
     """
     def __init__(self):
         self.conn: Session = SessionLocal()
+        self.state_manager = StateManager()
         self.upload_file()
         self.scanpy_dataset()
         self.external_sources()
@@ -279,33 +276,48 @@ def var_unique(self):
 
 
     def show_anndata(self, adata, f = None, filename = ""):
-        #upload raw adata
-        # If there are already a file in this location. If so, don't overwrite. 
-        if not os.path.isfile(os.path.join(os.getenv('WORKDIR'), 'adata', f'{filename}.h5ad')):
+        """upload raw adata. If there are already a file in this location. If so, don't overwrite. """
 
-            if filename == "":
-                filename = f.name.split(".")[0]
-
-            filename = filename.replace(" ", "_") #files must not contain spaces
+        if filename == "":
+            filename = f.name.split(".")[0]
+        filename = filename.replace(" ", "_") # files must not contain spaces
+        filepath = os.path.join(os.getenv('WORKDIR'), 'adata', f'{filename}.h5ad')
+
+        if not os.path.isfile(filepath):
 
             sc.write(filename=os.path.join(os.getenv('WORKDIR'), 'uploads', f'{filename}.h5ad'), adata=adata)
-
+                        
             adata.raw = adata
             active_adata = AdataModel(
                 work_id = st.session_state.current_workspace.id, 
                 adata_name=f"{filename}", adata=adata, 
-                filename=os.path.join(os.getenv('WORKDIR'), 'adata', f'{filename}.h5ad')
+                filename=filepath
             )
             st.session_state["adata_state"] = AdataState(active=active_adata)
+
+            self.state_manager \
+            .add_adata(adata) \
+            .add_description("Raw") \
+            .save_session()
+
             st.toast("Successfully uploaded file", icon='✅')
 
         else:
-            st.warning("A dataset with the same name already exists, will not overwrite.")
+
+            existing_adata = sc.read_h5ad(filename=filepath)
+
+            active_adata = AdataModel(
+                work_id = st.session_state.current_workspace.id, 
+                adata_name=f"{filename}", adata=existing_adata, 
+                filename=filepath
+            )
+
+            st.session_state["adata_state"] = AdataState(active=active_adata)
 
         self.show_sidebar_preview(f)
-
 
 
+
     def show_sidebar_preview(self, file):
 
         with st.sidebar: