Merge branch 'list-system-ms' into 'main'

List system ms

See merge request !161

components/PfamChips.vue

@@ -3,21 +3,21 @@ import { usePfamStore } from "@/stores/pfam";
 
 const { pfam: pfamStore } = usePfamStore();
 export interface Props {
-  pfamString: string | null;
+  pfams: Record<string, any>[];
   itemsToDisplay?: number;
 }
 
 const props = withDefaults(defineProps<Props>(), {
-  pfamString: null,
+  pfams: [],
   itemsToDisplay: 2,
 });
-const pfams = computed(() => {
-  if (props.pfamString === null) {
-    return [];
-  } else {
-    return props.pfamString.split(",").map((pfam) => pfam.trim());
-  }
-});
+// const pfams = computed(() => {
+//   if (props.pfamString === null) {
+//     return [];
+//   } else {
+//     return props.pfamString.split(",").map((pfam) => pfam.trim());
+//   }
+// });
 const show = ref(false);
 
 const pfamBaseUrl = ref(new URL("https://www.ebi.ac.uk/interpro/entry/pfam/"));
@@ -31,11 +31,11 @@ function constructPfamUrl(pfam: string) {
     <v-col>
       <v-card flat color="transparent" density="compact" rounded="false">
         <template v-for="(pfam, index) in pfams" :key="pfam">
-          <v-chip v-if="index < itemsToDisplay || itemsToDisplay < 0" :href="constructPfamUrl(pfam)" target="_blank"
+          <v-chip v-if="index < itemsToDisplay || itemsToDisplay < 0" :href="constructPfamUrl(pfam.AC)" target="_blank"
             color="info" class="mr-1 mb-1">
-            {{ pfam }}
+            {{ pfam.DE }}
             <v-tooltip activator="parent" location="top">{{
-              pfamStore.get(pfam)?.DE ?? "none"
+              pfam.AC
             }}</v-tooltip></v-chip>
 
           <template v-if="index === itemsToDisplay">
@@ -51,11 +51,11 @@ function constructPfamUrl(pfam: string) {
         </template>
         <template v-if="pfams.length > itemsToDisplay && show">
           <template v-for="(pfam, index) in pfams" :key="pfam">
-            <v-chip v-if="index >= itemsToDisplay" :href="constructPfamUrl(pfam)" target="_blank" color="info"
+            <v-chip v-if="index >= itemsToDisplay" :href="constructPfamUrl(pfam.AC)" target="_blank" color="info"
               class="mr-1 mb-1">
-              {{ pfam }}
+              {{ pfam.DE }}
               <v-tooltip activator="parent" location="top">{{
-                pfamStore.get(pfam)?.DE ?? "none"
+                pfam.AC
               }}</v-tooltip></v-chip>
           </template>
         </template>

components/content/SystemDb.vue

+<script setup lang="ts">
+import type { SortItem } from "@/components/ServerDbTable.vue"
+import { ServerDbTable } from "#components"
+const sortBy: Ref<SortItem[]> = ref([{ key: 'title', order: "asc" }])
+const itemValue = ref("title");
+const facets: Ref<string[]> = ref(["title", "Sensor", "Activator"])
+const headers: Ref<Object[]> = ref([
+    { title: "System", key: "title", removable: false },
+    { title: "Article", key: "doi", removable: false },
+    { title: "Sensor", key: "Sensor", removable: false },
+    { title: "Activator", key: "Activator", removable: false },
+    { title: "Effector", key: "Effector", removable: false },
+
+    { title: "PFAM", key: "PFAM", removable: false },
+    { title: "Contributors", key: "contributors", removable: false },
+
+
+])
+const { search: msSearch, result: msResult } = useMeiliSearch('systems')
+
+const defaultDataTableServerProps = ref({
+    showExpand: false
+})
+
+const dataTableServerProps = computed(() => {
+    return {
+        ...toValue(defaultDataTableServerProps),
+        headers: toValue(headers),
+        itemValue: toValue(itemValue)
+    }
+})
+
+</script>
+<template>
+    <ServerDbTable title="systems" db="systems" :sortBy="sortBy" :facets="facets"
+        :data-table-server-props="dataTableServerProps">
+
+        <template #top>
+            <v-toolbar><v-toolbar-title class="text-capitalize">
+                    List Systems </v-toolbar-title><v-spacer></v-spacer>
+            </v-toolbar>
+        </template>
+
+        <template #[`item.title`]="{ item }">
+            <v-chip color="info" link :to="`/defense-systems/${item.title.toLowerCase()}`">{{
+                item.title
+            }}</v-chip>
+        </template>
+
+        <template #[`item.doi`]="{ item }">
+            <ArticleDoi v-if="item?.doi" :doi="item.doi" :abstract="item?.abstract" :divider="false" :enumerate="false" />
+        </template>
+        <template #[`item.PFAM`]="{ item }">
+
+            <pfam-chips v-if="item?.PFAM" :pfams="item.PFAM"></pfam-chips>
+        </template>
+    </ServerDbTable>
+</template>
\ No newline at end of file

content/3.defense-systems/0.index.md

@@ -11,8 +11,8 @@ The knowledge of anti-phage defense systems is ever expanding. The spectacular i
 
 
 
-
-
+::system-db
+::
 
 
 

packages/df-wiki-cli/df_wiki_cli/content/main.py

 import typer
 import sys
-import re
+import json
+import pandas as pd
 import shutil
 import csv
 import yaml
@@ -11,10 +12,6 @@ from pydantic import BaseModel, ValidationError
 import frontmatter
 from enum import Enum
 from rich.console import Console
-from rich import print as rprint
-from rich.layout import Layout
-from rich.panel import Panel
-
 
 console = Console()
 app = typer.Typer()
@@ -130,10 +127,8 @@ def structure(
 
     with open(stat, "r") as stat_f:
         reader = csv.DictReader(stat_f)
-
         for row in reader:
             dir_name = system_to_dir[row["system"]]
-            # console.rule(f"[bold blue]{dir_name}", style="blue")
             pdb_path_file = Path(row["pdb"])
             cif_file_name = Path(str(pdb_path_file).split(".pdb")[0] + ".cif")
             files = [
@@ -157,3 +152,80 @@ def structure(
                         console.print(
                             f"[red] file {str(file_to_copy.name)} does not exist"
                         )
+
+
+@app.command()
+def systems(
+    dir: Annotated[
+        Path,
+        typer.Option(exists=False, file_okay=False, readable=True, dir_okay=True),
+    ],
+    pfam: Annotated[
+        Path,
+        typer.Option(
+            exists=False,
+            file_okay=True,
+            writable=True,
+        ),
+    ],
+    output: Annotated[
+        Path,
+        typer.Option(
+            file_okay=True,
+            dir_okay=False,
+            writable=True,
+            resolve_path=True,
+        ),
+    ],
+):
+    with open(pfam, "r") as pf:
+        pfam_df = pd.read_csv(pf, index_col="AC", keep_default_na=False)
+        systems = []
+        with open(output, "a") as ty:
+            for file in dir.iterdir():
+                if file.suffix == ".md":
+                    console.rule(f"[bold blue]{file.name}", style="blue")
+                    with open(file) as f:
+                        metadata, _ = frontmatter.parse(f.read())
+                        del metadata["layout"]
+                        if "tableColumns" in metadata:
+                            table_data = metadata["tableColumns"]
+                            if "PFAM" in table_data:
+                                # print(table_data["PFAM"])
+                                pfams_list = [
+                                    pfam.strip()
+                                    for pfam in table_data["PFAM"].split(",")
+                                ]
+                                pfam_metadata = list()
+                                for pfam in pfams_list:
+                                    try:
+                                        pfam_obj = pfam_df.loc[[pfam]]
+                                        # print(pfam_obj)
+                                        pfam_to_dict = pfam_obj.to_dict(orient="index")
+                                        pfam_to_dict[pfam]["AC"] = pfam
+                                        flatten_value = pfam_to_dict[pfam]
+                                        pfam_metadata.append(flatten_value)
+
+                                    except KeyError as err:
+                                        console.print(f"[bold red]{err}", style="red")
+                                        console.print(
+                                            f"[bold red]No pfam entry or {pfam}",
+                                            style="red",
+                                        )
+                                        continue
+                                del metadata["tableColumns"]
+
+                                if "article" in table_data:
+                                    metadata["doi"] = table_data["article"]["doi"]
+                                    if "abstract" in table_data["article"]:
+                                        metadata["abstract"] = table_data["article"][
+                                            "abstract"
+                                        ]
+                                    del table_data["article"]
+                                sanitizedMetadata = {**metadata, **table_data}
+
+                                sanitizedMetadata["PFAM"] = pfam_metadata
+                                systems.append(sanitizedMetadata)
+
+            json_object = json.dumps(systems, indent=2)
+            ty.write(json_object)

packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py

 import meilisearch
 from pathlib import Path
 import csv
-
+import json
 from typing import Annotated, List, Optional
 from pydantic import BaseModel, Field, BeforeValidator
 from enum import Enum
@@ -175,6 +175,37 @@ def update_structure(
     index.update_typo_tolerance({"enabled": False})
 
 
+def update_systems(
+    host: str,
+    key: str,
+    file: Path,
+    document: str,
+):
+    client = meilisearch.Client(host, key)
+    index = client.index(document.lower())
+    with open(file, "r") as jsonfile:
+        json_object = json.load(jsonfile)
+        tasks = index.add_documents_in_batches(json_object, primary_key="title")
+        for task in tasks:
+            print(task)
+    pagination_settings_task = index.update_pagination_settings(
+        {"maxTotalHits": 100000}
+    )
+    print(pagination_settings_task)
+    attr_task = index.update_filterable_attributes(
+        body=["title", "Sensor", "Activator", "Effector", "PFAM.AC"]
+    )
+    params = {
+        "maxValuesPerFacet": 1000000,
+        "sortFacetValuesBy": {"*": "count"},
+    }
+    index.update_faceting_settings(params)
+
+    print(attr_task)
+    index.update_sortable_attributes(["title", "Sensor", "Activator", "Effector"])
+    index.update_typo_tolerance({"enabled": False})
+
+
 def split_on_comma(str_val: str) -> List[str]:
     for val in str_val.split(","):
         yield val.strip()

packages/df-wiki-cli/df_wiki_cli/meilisearch/main.py

@@ -2,7 +2,7 @@ import typer
 import meilisearch
 from typing_extensions import Annotated
 from pathlib import Path
-from df_wiki_cli.meilisearch import update_refseq, update_structure
+from df_wiki_cli.meilisearch import update_refseq, update_structure, update_systems
 from enum import Enum
 from types import SimpleNamespace
 
@@ -12,6 +12,7 @@ app = typer.Typer()
 class Documents(str, Enum):
     refseq = "refseq"
     structure = "structure"
+    systems = "systems"
 
 
 @app.callback()
@@ -54,6 +55,8 @@ def update(
         update_refseq(ctx.obj.host, ctx.obj.key, file, document)
     if document == "structure":
         update_structure(ctx.obj.host, ctx.obj.key, file, document)
+    if document == "systems":
+        update_systems(ctx.obj.host, ctx.obj.key, file, document)
 
 
 @app.command()

packages/df-wiki-cli/df_wiki_cli/pfam/__init__.py

@@ -26,7 +26,10 @@ def fetch_pfam(output):
                     else:
                         kk, v = line.split("   ")
                         g, k = kk.split()
-                        d[pfID][k] = v
+                        if (k == 'AC'):
+                            d[pfID][k] = v.split(".")[0]
+                        else: 
+                            d[pfID][k] = v
 
         df = pd.DataFrame(d).T
         df.index.name = "ID"

pages/defense-systems.vue

-<script setup lang="ts">
-import { useDisplay, useLayout } from "vuetify";
-
-const { height } = useDisplay();
-// const { getLayoutItem } = useLayout()
-// console.log(getLayoutItem('app-bar'))
-const { data, error, pending } = await useAsyncData(
-  "list-defense-systems",
-  () => queryContent("/defense-systems").where({ _partial: false }).find()
-);
-const defaultHeaders = ref([{ title: "System", key: "system" }]);
-const tableKey = "tableColumns";
-
-const sanitizedData = computed(() => {
-  if (data?.value && data.value?.length > 0) {
-    return data.value?.filter((entry) => {
-      if (entry._dir === "old" || entry._dir === "") {
-        return false;
-      }
-      return true;
-    });
-  } else {
-    return [];
-  }
-});
-
-const headers = computed(() => {
-  const uniqHeaders = Array.from(
-    sanitizedData.value.reduce((headerSet, df) => {
-      if (df?.[tableKey]) {
-        return new Set([...headerSet, ...Object.keys(df[tableKey])]);
-      } else {
-        return headerSet;
-      }
-    }, new Set())
-  );
-  return [
-    ...defaultHeaders.value,
-    ...uniqHeaders.map((value) => {
-      return { title: value, key: value };
-    }),
-  ];
-});
-const systems = computed(() => {
-  return sanitizedData.value.map((content) => {
-    return {
-      system: { name: content.title, path: content._path },
-      ...content[tableKey],
-    };
-  });
-});
-
-
-</script>
-<template>
-  <v-card flat color="transparent">
-    <ListSystems :headers="headers" :systems="systems" :height="height - 220"></ListSystems>
-  </v-card>
-</template>
\ No newline at end of file