From 21e4640249224fecfcbda0629ac09dde17451a2b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karl=20Sv=C3=A4rd?= <60181709+Karl-Svard@users.noreply.github.com> Date: Fri, 22 Nov 2024 08:38:03 +0100 Subject: [PATCH] Update and refactor pooling map EPP (#559)(patch) ### Changed - Added pool sorting to the pooling map - Changed the color set - Added new flag, '-r' / '--round-decimals' for determining the amount of rounding - Made the coloring truly container-specific, and not pool-container as it was before --- .../files/pooling_map/make_pooling_map.py | 85 +++++++++++-------- cg_lims/options.py | 6 ++ 2 files changed, 54 insertions(+), 37 deletions(-) diff --git a/cg_lims/EPPs/files/pooling_map/make_pooling_map.py b/cg_lims/EPPs/files/pooling_map/make_pooling_map.py index 77d57d48..0712af9f 100644 --- a/cg_lims/EPPs/files/pooling_map/make_pooling_map.py +++ b/cg_lims/EPPs/files/pooling_map/make_pooling_map.py @@ -1,7 +1,7 @@ import logging import sys from datetime import date -from typing import List, Tuple +from typing import Dict, List, Optional, Tuple import click from cg_lims import options @@ -18,20 +18,25 @@ ) from cg_lims.exceptions import LimsError from cg_lims.get.artifacts import get_artifacts -from genologics.entities import Artifact, Process +from genologics.entities import Artifact, Process, Sample from matplotlib import colors -COLORS = list(colors.TABLEAU_COLORS.values()) +COLORS: List[str] = list(colors.XKCD_COLORS.values()) LOG = logging.getLogger(__name__) -def add_pool_info(pool_udfs: List[str], pool: Artifact) -> str: +def add_pool_info( + pool_udfs: List[str], + pool: Artifact, + round_decimals: Optional[int], +) -> str: """Adding info about the pool""" - - html = [] + html: List[str] = [] for udf in pool_udfs: value = pool.udf.get(udf) if value is not None: + if round_decimals and type(value) is float: + value: float = round(value, round_decimals) html.append( f'{udf}: {value}' ) @@ -40,18 +45,17 @@ def add_pool_info(pool_udfs: List[str], pool: Artifact) -> str: def add_sample_info_headers(udfs_headers: List[str]) -> str: """Adding headers for more info about samples in the pool""" - - html = [f'{header}' for header in udfs_headers] - + html: List[str] = [f'{header}' for header in udfs_headers] return "".join(html) -def add_sample_info(artifact: Artifact, udfs: List[str]) -> str: +def add_sample_info(artifact: Artifact, udfs: List[str], round_decimals: Optional[int]) -> str: """Adding info about samples in the pool""" - - html = [] + html: List[str] = [] for udf in udfs: - value = artifact.udf.get(udf, "") + value = artifact.udf.get(udf) + if round_decimals and type(value) is float: + value: float = round(value, round_decimals) html.append(f'{value}') return "".join(html) @@ -61,13 +65,13 @@ def make_html( process: Process, pool_udfs: List[str], sample_udfs: List[str], + round_decimals: Optional[int], ) -> str: """Building the html for the pooling map""" - - html = [] + html: List[str] = [] header_info = PlacementMapHeader(process_type=process.type.name, date=date.today().isoformat()) html.append(PLACEMENT_MAP_HEADER.format(**header_info.dict())) - + source_containers: Dict[str, str] = {} for pool in pools: artifacts: List[Tuple[str, Artifact]] = [ (artifact.location[1], artifact) for artifact in pool.input_artifact_list() @@ -79,54 +83,61 @@ def make_html( nr_samples=len(artifacts), pool_name=pool.name, pool_id=pool.id, - pools_information=add_pool_info(pool_udfs, pool), + pools_information=add_pool_info( + pool_udfs=pool_udfs, pool=pool, round_decimals=round_decimals + ), ) html.append(POOL_HEADER.format(**pool_info.dict())) extra_sample_columns: str = add_sample_info_headers(sample_udfs) html.append(SAMPLE_COLUMN_HEADERS.format(extra_sample_columns=extra_sample_columns)) html.append("""""") - source_containers = [] for location, artifact in artifacts: - sample = artifact.samples[0] - sample_warning_color = "#F08080" if artifact.udf.get("Warning") else "#FFFFFF" - if artifact.container.name not in source_containers: - source_container_color = COLORS[0] - COLORS.pop(0) - source_containers.append(artifact.container.name) + sample: Sample = artifact.samples[0] + sample_warning_color: str = "#F08080" if artifact.udf.get("Warning") else "#FFFFFF" + if artifact.container.name not in source_containers.keys(): + source_container_color: str = COLORS.pop(0) + source_containers[artifact.container.name] = source_container_color sample_table_values = SampleTableSection( sample_id=sample.id, sample_warning_color=sample_warning_color, source_well=location, source_container=artifact.container.name, - source_container_color=source_container_color, + source_container_color=source_containers[artifact.container.name], pool_name=pool.name, - extra_sample_values=add_sample_info(artifact, sample_udfs), + extra_sample_values=add_sample_info( + artifact=artifact, udfs=sample_udfs, round_decimals=round_decimals + ), ) html.append(SAMPLE_COLUMN_VALUES.format(**sample_table_values.dict())) html.append("""

""") - - html = "".join(html) - return html + return "".join(html) @click.command() @options.file_placeholder(help="File placeholder name.") @options.pool_udfs(help="Pool UDFs to show in the placement map.") @options.sample_udfs(help="Sample UDFs to show in the placement map.") +@options.round_decimals() @click.pass_context -def pool_map(ctx, file: str, sample_udfs: List[str], pool_udfs: List[str]): +def pool_map( + ctx, file: str, sample_udfs: List[str], pool_udfs: List[str], round_decimals: str = None +): """Create a pool placement map.""" LOG.info(f"Running {ctx.command_path} with params: {ctx.params}") - process = ctx.obj["process"] + process: Process = ctx.obj["process"] try: - pools = get_artifacts(process=process, input=False) - html = make_html( - pools, - process, - pool_udfs, - sample_udfs, + if round_decimals: + round_decimals: int = int(round_decimals) + pools: List[Artifact] = get_artifacts(process=process, input=False) + pools.sort(key=lambda x: x.id) + html: str = make_html( + pools=pools, + process=process, + pool_udfs=pool_udfs, + sample_udfs=sample_udfs, + round_decimals=round_decimals, ) with open(f"{file}.html", "w") as file: file.write(html) diff --git a/cg_lims/options.py b/cg_lims/options.py index 5973560f..2a93a935 100644 --- a/cg_lims/options.py +++ b/cg_lims/options.py @@ -717,3 +717,9 @@ def minimum_volume( help: str = "Minimum volume", ) -> click.option: return click.option("--min-volume", required=False, default=0, help=help) + + +def round_decimals( + help: str = "The number of decimals you want to round to.", +) -> click.option: + return click.option("-r", "--round-decimals", required=False, help=help)