---
title: "Compound-to-Assay Workflow With pc_* API"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Compound-to-Assay Workflow With pc_* API}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
```

This vignette demonstrates an end-to-end compound-to-assay flow:

1. Map names to CIDs.
2. Retrieve AIDs from CIDs.
3. Pull assay summaries.

```{r setup}
library(PubChemR)
library(dplyr)
library(tibble)
```

## Step 1: Name to CID

```{r eval=TRUE}
cid_map <- pc_identifier_map(
  identifier = c("aspirin", "ibuprofen", "caffeine"),
  namespace = "name",
  to = "cids",
  domain = "compound",
  cache = TRUE
)

as_tibble(cid_map)
```

## Step 2: CID to AID

```{r eval=TRUE}
aid_map <- pc_identifier_map(
  identifier = c(2244, 3672, 2519),
  namespace = "cid",
  to = "aids",
  domain = "compound",
  cache = TRUE
)

aid_tbl <- as_tibble(aid_map)
aid_tbl
```

## Step 3: Assay summary retrieval

```{r eval=TRUE}
# Select a subset of AIDs for demonstration
sel_aids <- unique(na.omit(unlist(aid_tbl$AID)))
sel_aids <- head(sel_aids, 10)

assay_res <- pc_assay(
  identifier = sel_aids,
  namespace = "aid",
  operation = "summary",
  cache = TRUE
)

as_tibble(assay_res)
```

This pattern composes into larger pipelines with `pc_batch()` for throughput.