Beginning prelim code cleanup.
This commit is contained in:
lwark
@@ -858,7 +858,7 @@ class SubmissionType(BaseClass):
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id = Column(INTEGER, primary_key=True) #: primary key
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name = Column(String(128), unique=True) #: name of submission type
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info_map = Column(JSON) #: Where basic information is found in the excel workbook corresponding to this type.
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info_map = Column(JSON) #: Where parsable information is found in the excel workbook corresponding to this type.
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defaults = Column(JSON) #: Basic information about this submission type
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instances = relationship("BasicSubmission", backref="submission_type") #: Concrete instances of this type.
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template_file = Column(BLOB) #: Blank form for this type stored as binary.
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@@ -866,6 +866,200 @@ class SubmissionType(BaseClass):
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secondary=submissiontypes_processes) #: Relation to equipment processes used for this type.
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sample_map = Column(JSON) #: Where sample information is found in the excel sheet corresponding to this type.
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"""
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Example info_map (Bacterial Culture)
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NOTE: read locations will be appended to write locations.
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{
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"comment": {
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"read": [
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{
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"column": 2,
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"row": 34,
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"sheet": "Sample List"
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}
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],
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"write": []
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},
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"contact": {
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"read": [
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{
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"column": 2,
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"row": 4,
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"sheet": "Sample List"
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}
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],
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"write": []
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},
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"contact_phone": {
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"read": [],
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"write": [
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{
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"column": 2,
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"row": 5,
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"sheet": "Sample List"
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}
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]
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},
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"cost_centre": {
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"read": [
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{
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"column": 2,
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"row": 6,
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"sheet": "Sample List"
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}
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],
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"write": []
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},
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"custom": {},
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"extraction_kit": {
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"read": [
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{
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"column": 4,
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"row": 5,
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"sheet": "Sample List"
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}
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],
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"write": []
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},
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"rsl_plate_num": {
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"read": [
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{
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"column": 2,
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"row": 13,
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"sheet": "Sample List"
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}
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],
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"write": []
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},
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"sample_count": {
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"read": [
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{
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"column": 4,
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"row": 4,
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"sheet": "Sample List"
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}
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],
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"write": []
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},
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"signed_by": {
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"read": [],
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"write": [
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{
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"column": 2,
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"row": 15,
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"sheet": "Sample List"
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}
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]
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},
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"submission_category": {
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"read": [
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{
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"column": 4,
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"row": 6,
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"sheet": "Sample List"
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}
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],
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"write": []
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},
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"submission_type": {
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"read": [
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{
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"column": 4,
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"row": 3,
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"sheet": "Sample List"
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}
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],
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"write": []
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},
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"submitted_date": {
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"read": [
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{
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"column": 2,
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"row": 3,
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"sheet": "Sample List"
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}
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],
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"write": []
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},
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"submitter_plate_num": {
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"read": [
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{
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"column": 2,
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"row": 2,
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"sheet": "Sample List"
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}
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],
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"write": []
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},
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"submitting_lab": {
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"read": [
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{
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"column": 4,
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"row": 2,
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"sheet": "Sample List"
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}
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],
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"write": []
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},
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"technician": {
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"read": [
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{
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"column": 2,
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"row": 14,
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"sheet": "Sample List"
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}
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],
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"write": []
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}
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}
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"""
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"""
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Example defaults (for Bacterial Culture)
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{
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"abbreviation": "BC",
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"details_ignore": [
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"controls"
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],
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"form_ignore": [
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"controls",
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"cost_centre"
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],
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"regex": "(?P<Bacterial_Culture>RSL(?:-|_)?BC(?:-|_)?20\\d{2}-?\\d{2}-?\\d{2}(?:(_|-)?\\d?([^_0123456789\\sA-QS-Z]|$)?R?\\d?)?)",
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"sample_type": "Bacterial Culture Sample",
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"turnaround_time": 3
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}
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"""
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"""
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Example sample_map (Bacterial Culture)
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{
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"lookup_table": {
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"end_row": 132,
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"merge_on_id": "submitter_id",
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"sample_columns": {
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"column": 6,
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"concentration": 4,
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"organism": 3,
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"row": 5,
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"submitter_id": 2
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},
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"sheet": "Sample List",
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"start_row": 37
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},
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"plate_map": {
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"end_column": 13,
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"end_row": 14,
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"sheet": "Plate Map",
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"start_column": 2,
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"start_row": 7
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}
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}
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"""
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submissiontype_kit_associations = relationship(
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"SubmissionTypeKitTypeAssociation",
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back_populates="submission_type",
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@@ -1218,6 +1412,11 @@ class SubmissionType(BaseClass):
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sample_map=self.sample_map
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)
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@classproperty
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def info_map_json_edit_fields(cls):
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dicto = dict()
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return dicto
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class SubmissionTypeKitTypeAssociation(BaseClass):
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"""
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@@ -1519,7 +1718,7 @@ class KitTypeReagentRoleAssociation(BaseClass):
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case _:
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pass
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setattr(instance, k, v)
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logger.info(f"Instance from query or create: {instance.__dict__}")
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logger.info(f"Instance from query or create: {instance.__dict__}\nis new: {new}")
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# sys.exit()
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return instance, new
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@@ -2196,6 +2395,7 @@ class Process(BaseClass):
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id = Column(INTEGER, primary_key=True) #: Process id, primary key
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name = Column(String(64), unique=True) #: Process name
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# version = Column(String(32))
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submission_types = relationship("SubmissionType", back_populates='processes',
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secondary=submissiontypes_processes) #: relation to SubmissionType
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equipment = relationship("Equipment", back_populates='processes',
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@@ -2209,6 +2409,7 @@ class Process(BaseClass):
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tip_roles = relationship("TipRole", back_populates='processes',
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secondary=process_tiprole) #: relation to KitType
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def __repr__(self) -> str:
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"""
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Returns:
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@@ -2308,6 +2509,7 @@ class Process(BaseClass):
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return OmniProcess(
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instance_object=self,
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name=self.name,
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# version=self.version,
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submission_types=[item.to_omni() for item in self.submission_types],
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equipment_roles=[item.to_omni() for item in self.equipment_roles],
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tip_roles=[item.to_omni() for item in self.tip_roles]
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