feat: add "serve" command (#24) (#35)

Makefile

@@ -1,6 +1,9 @@
 .PHONY: default
 default:
 
+.PHONY: format
+format: black isort
+
 .PHONY: black
 black:
 	black -l 100 .

chew/cli.py

@@ -1,9 +1,17 @@
 import typing
 
 import click
+from logzero import logger
 
 from chew import __version__, compare, fingerprint, plot_compare, plot_var_het, stats
 
+try:
+    import dash  # noqa
+
+    have_dash_installed = True
+except ImportError:
+    have_dash_installed = False
+
 
 @click.group()
 @click.version_option(__version__)
@@ -171,3 +179,39 @@ def cli_plot_var_het(
         stats_out=stats_out,
     )
     plot_var_het.run(config)
+
+
+if have_dash_installed:
+
+    @cli.command("serve", help="Run report server")  # type: ignore[attr-defined]
+    @click.option(
+        "--annos-tsv",
+        default=None,
+        required=False,
+        help="Optional TSV file with further annotations",
+    )
+    @click.option("--strip-suffix", default="", help="Suffix to strip from sample names")
+    @click.argument("cohort_ped")
+    @click.argument("fingerprints", nargs=-1)
+    @click.pass_context
+    def cli_serve(
+        ctx: click.Context,
+        annos_tsv: typing.Optional[str],
+        strip_suffix: str,
+        cohort_ped: str,
+        fingerprints: typing.List[str],
+    ):
+        if not fingerprints:
+            logger.warn("No fingerprints given!")
+            return
+
+        from chew import serve
+
+        config = serve.Config(
+            verbosity=2 if ctx.obj["verbose"] else 1,
+            strip_suffix=strip_suffix,
+            cohort_ped=cohort_ped,
+            fingerprints=fingerprints,
+            annos_tsv=annos_tsv,
+        )
+        serve.run(config)

chew/common.py

@@ -1,5 +1,6 @@
 """Commonly used code"""
 
+import enum
 import gzip
 import os
 import typing
@@ -67,6 +68,55 @@
 }
 
 
+class Sex(enum.Enum):
+    UNKNOWN = "unknown"
+    MALE = "male"
+    FEMALE = "female"
+
+
+PED_SEX_MAP = {
+    "0": Sex.UNKNOWN,
+    "1": Sex.MALE,
+    "2": Sex.FEMALE,
+}
+
+
+class DiseaseState(enum.Enum):
+    UNKNOWN = "unknown"
+    UNAFFECTED = "affected"
+    AFFECTED = "unaffected"
+
+
+PED_DISEASE_MAP = {
+    "0": DiseaseState.UNKNOWN,
+    "1": DiseaseState.UNAFFECTED,
+    "2": DiseaseState.AFFECTED,
+}
+
+
+@attrs.frozen
+class PedigreeMember:
+    family_name: str
+    name: str
+    father: str
+    mother: str
+    sex: Sex
+    disease_state: DiseaseState
+
+
+def pedigree_member_from_tsv(arr: typing.List[str]) -> PedigreeMember:
+    if len(arr) < 6:
+        raise Exception("TSV array must have at least 6 fields")
+    return PedigreeMember(
+        family_name=arr[0],
+        name=arr[1],
+        father=arr[2],
+        mother=arr[3],
+        sex=PED_SEX_MAP.get(arr[4], Sex.UNKNOWN),
+        disease_state=PED_DISEASE_MAP.get(arr[5], DiseaseState.UNKNOWN),
+    )
+
+
 @attrs.frozen
 class Site:
     chrom: str