Update UI if pathway mode is set to build

Initial bayer app

Show Pack Classification

Adjusted docker compose to bayer specifics

Adjusted Dockerfile for Bayer

Adding secret flags to group, add secret pools to packages

Adjusted View for Package creation

Prep configs, added Package Create Modal

wip

More on PES

wip

wip

bayer/additional_information/__init__.py

@@ -1,178 +0,0 @@
-import enum
-from typing import Optional
-
-from envipy_additional_information import GroupEnum as G
-from envipy_additional_information import SubcategoryEnum as S
-from envipy_additional_information import (
-    register,
-    register_parser_command,
-    EnviPyModel,
-    # EnviPyModelParser,
-    Interval,
-    UIConfig,
-    IntervalConfig,
-    WidgetType,
-    registry,
-)
-
-
-@register(keyname="compoundlabel", groups=[S.MISC, G.SLUDGE, G.SEDIMENT, G.SOIL])
-class CompoundLabel(EnviPyModel):
-    label: str
-
-    class UI:
-        title = "Compound Label"
-        label = UIConfig(widget=WidgetType.TEXT, label="Label", order=1)
-
-
-# TODO Expose EnviPyModelParser in lib and subclass
-@register_parser_command("compoundlabel")
-class CompoundLabelParser:
-    @staticmethod
-    def from_string(data: str) -> CompoundLabel:
-        return CompoundLabel(label=data)
-
-
-@register(keyname="studywaterstoragecapacity", groups=[S.MISC, G.SLUDGE, G.SEDIMENT, G.SOIL])
-class StudyWaterStorageCapacity(EnviPyModel):
-    capacity: str
-
-    class UI:
-        title = "Study Water Storage Capacity"
-        capacity = UIConfig(widget=WidgetType.TEXT, label="Study Water Storage Capacity", order=1)
-
-
-# TODO Expose EnviPyModelParser in lib and subclass
-@register_parser_command("studywst")
-class StudyWaterStorageCapacityParser:
-    @staticmethod
-    def from_string(data: str) -> StudyWaterStorageCapacity:
-        return StudyWaterStorageCapacity(capacity=data)
-
-
-class ObservationType(enum.Enum):
-    OBSERVED = "observed"
-    APPLIED = "applied"
-    NA = 'NA'
-
-
-@register(keyname="observation", groups=[S.MISC, G.SLUDGE, G.SEDIMENT, G.SOIL])
-class Observation(EnviPyModel):
-    type: ObservationType
-    min_value: Optional[float] = None
-    max_value: Optional[float] = None
-
-    class UI:
-        title = "Observation"
-        type = UIConfig(widget=WidgetType.SELECT, label="Observed or Applied", order=1)
-        min_value = UIConfig(widget=WidgetType.NUMBER, label="Min Value", order=2)
-        max_value = UIConfig(widget=WidgetType.NUMBER, label="Max Value", order=3)
-
-
-# TODO Expose EnviPyModelParser in lib and subclass
-@register_parser_command("observation")
-class ObservationParser:
-    @staticmethod
-    def from_string(data: str) -> Observation:
-        parts = data.split(";")
-
-        observation_type = ObservationType(parts[0])
-        min_value = None
-        if parts[1]:
-            try:
-                min_value = float(parts[1])
-            except ValueError:
-                pass
-
-        max_value = None
-        if parts[2]:
-            try:
-                max_value = float(parts[2])
-            except ValueError:
-                pass
-
-        return Observation(type=observation_type, min_value=min_value, max_value=max_value)
-
-
-@register(keyname="kinetics", groups=[S.MISC, G.SLUDGE, G.SEDIMENT, G.SOIL])
-class Kinetics(EnviPyModel):
-    dt50: Interval[float]
-    normalized_dt50: bool
-    chi2err: Optional[float] = None
-    t_test: Optional[float] = None
-    swarc: Optional[float] = None
-    visual_fit: Optional[int] = None
-    comment: str
-    source: str
-    kinetic_model: str
-    k1: Optional[float] = None
-    k2: Optional[float] = None
-    g: Optional[float] = None
-    tb: Optional[float] = None
-    alpha: Optional[float] = None
-    beta: Optional[float] = None
-
-    class UI:
-        title = "Kinetics"
-
-        # Field config
-        dt50 = IntervalConfig(label="DT50 Range", order=1, unit="d")
-        normalized_dt50 = UIConfig(widget=WidgetType.CHECKBOX, label="Normalized DT50", order=2)
-        chi2err = UIConfig(widget=WidgetType.NUMBER, label="Chi2err", order=3)
-        t_test = UIConfig(widget=WidgetType.NUMBER, label="T-Test", order=4)
-        swarc = UIConfig(widget=WidgetType.NUMBER, label="SWARC", order=5)
-        visual_fit = UIConfig(widget=WidgetType.NUMBER, label="Visual Fit", order=6)
-        comment = UIConfig(widget=WidgetType.TEXTAREA, label="Comments", order=7)
-        source = UIConfig(widget=WidgetType.TEXT, label="Source", order=8)
-        kinetic_model = UIConfig(widget=WidgetType.SELECT, label="Kinetic Model", order=9)
-        k1 = UIConfig(widget=WidgetType.NUMBER, label="K1", order=10)
-        k2 = UIConfig(widget=WidgetType.NUMBER, label="K2", order=11)
-        g = UIConfig(widget=WidgetType.NUMBER, label="G", order=12)
-        tb = UIConfig(widget=WidgetType.NUMBER, label="TB", order=13)
-        alpha = UIConfig(widget=WidgetType.NUMBER, label="Alpha", order=14)
-        beta = UIConfig(widget=WidgetType.NUMBER, label="Beta", order=15)
-
-
-# TODO Expose EnviPyModelParser in lib and subclass
-@register_parser_command("kineticevaluation")
-class KinecticsParser:
-    @staticmethod
-    def from_string(data: str) -> Kinetics:
-        parts = data.split(";")
-        dt50 = registry.get_parser("interval").from_string(parts[0])
-        normalized_dt50 = parts[1] == "true"
-        chi2err = float(parts[2]) if parts[2] else None
-        t_test = float(parts[3]) if parts[3] else None
-        swarc = float(parts[4]) if parts[4] else None
-        visual_fit = int(parts[5]) if parts[5] else None
-        comment = parts[6]
-        source = parts[7]
-        kinetic_model = parts[8]
-        k1 = float(parts[9]) if parts[9] else None
-        k2 = float(parts[10]) if parts[10] else None
-        g = float(parts[11]) if parts[11] else None
-        tb = float(parts[12]) if parts[12] else None
-        alpha = float(parts[13]) if parts[13] else None
-        beta = float(parts[14]) if parts[14] else None
-
-        return Kinetics(
-            dt50=dt50,
-            normalized_dt50=normalized_dt50,
-            chi2err=chi2err,
-            t_test=t_test,
-            swarc=swarc,
-            visual_fit=visual_fit,
-            comment=comment,
-            source=source,
-            kinetic_model=kinetic_model,
-            k1=k1,
-            k2=k2,
-            g=g,
-            tb=tb,
-            alpha=alpha,
-            beta=beta,
-        )
-
-
-if __name__ == '__main__':
-    print(KinecticsParser.from_string("187.0 - 187.0;false;;;;;;;AFO;;;;;;"))

bayer/epdb_hooks.py

@@ -1,6 +1,5 @@
 import logging
 
-from bayer import additional_information  # noqa: F401
 from epdb.template_registry import register_template
 
 logger = logging.getLogger(__name__)
@@ -37,4 +36,4 @@ register_template(
 register_template(
     "epdb.objects.node.viz",
     "objects/node_viz.html",
-)
+)

epdb/models.py

@@ -2174,7 +2174,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
         smiles: str,
         name: Optional[str] = None,
         description: Optional[str] = None,
-        depth: Optional[int] = -1,
+        depth: Optional[int] = 0,
     ):
         return Node.create(self, smiles, depth, name=name, description=description)
 
@@ -2381,7 +2381,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
         "epdb.Pathway", verbose_name="belongs to", on_delete=models.CASCADE, db_index=True
     )
     edge_label = models.ForeignKey(
-        "epdb.Reaction", verbose_name="Edge label", null=True, on_delete=models.CASCADE
+        "epdb.Reaction", verbose_name="Edge label", null=True, on_delete=models.SET_NULL
     )
     start_nodes = models.ManyToManyField(
         "epdb.Node", verbose_name="Start Nodes", related_name="edge_educts"