From 9a4b91d15d0377eed7b4148d14c0a0d3bffc840b Mon Sep 17 00:00:00 2001
From: nleanba <25827850+nleanba@users.noreply.github.com>
Date: Thu, 29 Feb 2024 18:00:42 +0100
Subject: [PATCH 1/9] initial attempt

---
 src/JobsDataBase.ts  |  9 +++--
 src/action_worker.ts | 79 ++++++++++++++++++++++++++++++++++++++------
 src/deps.ts          |  2 +-
 src/main.ts          |  2 +-
 4 files changed, 78 insertions(+), 14 deletions(-)

diff --git a/src/JobsDataBase.ts b/src/JobsDataBase.ts
index 0d90660..c17eb60 100644
--- a/src/JobsDataBase.ts
+++ b/src/JobsDataBase.ts
@@ -5,12 +5,17 @@ import * as path from "https://deno.land/std@0.209.0/path/mod.ts";
 
 export type Job = {
   id: string;
-  from: string;
-  till: string;
+  from?: string;
+  till?: string;
   author: {
     "name": string;
     "email": string;
   };
+  files?: {
+    // only used for transform_all
+    modified?: string[];
+    removed?: string[];
+  };
 };
 
 export type JobStatus = {
diff --git a/src/action_worker.ts b/src/action_worker.ts
index f669ff2..44700bf 100644
--- a/src/action_worker.ts
+++ b/src/action_worker.ts
@@ -4,7 +4,7 @@
 * The jobs are accepted as messages and stored on disk, when the worker is started uncompleted jobs are picked up and exxecuted.
 
 */
-import { path } from "./deps.ts";
+import { path, walk } from "./deps.ts";
 import { config } from "../config/config.ts";
 import { createBadge } from "./log.ts";
 import { type Job, JobsDataBase } from "./JobsDataBase.ts";
@@ -20,10 +20,14 @@ let isRunning = false;
 await startTask();
 
 self.onmessage = (evt) => {
-  const job = evt.data as Job;
-  queue.addJob(job);
-  if (!isRunning) startTask();
-  else console.log("Already running");
+  const job = evt.data as Job | "FULLUPDATE";
+  if (job === "FULLUPDATE") {
+    gatherJobsForFullUpdate();
+  } else {
+    queue.addJob(job);
+    if (!isRunning) startTask();
+    else console.log("Already running");
+  }
 };
 
 async function startTask() {
@@ -35,6 +39,45 @@ async function startTask() {
   }
 }
 
+async function gatherJobsForFullUpdate() {
+  isRunning = true;
+  try {
+    updateLocalData("source", console.log);
+    const date = (new Date()).toISOString();
+    let block = 0;
+    let files: string[] = [];
+    for await (
+      const walkEntry of walk(Deno.cwd(), {
+        exts: ["xml"],
+        includeDirs: false,
+        includeSymlinks: false,
+      })
+    ) {
+      if (walkEntry.isFile && walkEntry.path.endsWith(".xml")) {
+        files.push(walkEntry.path);
+        if (files.length >= 100) {
+          queue.addJob({
+            author: {
+              name: "GG2RDF Service",
+              email: "gg2rdf@plazi.org",
+            },
+            id: `full update ${date} [${block++}]`,
+            files: {
+              modified: files,
+            },
+          });
+          files = [];
+        }
+      }
+    }
+  } catch (error) {
+    console.error("Could not create full-update jobs\n" + error);
+  } finally {
+    isRunning = false;
+    startTask();
+  }
+}
+
 async function run() {
   while (queue.pendingJobs().length > 0) {
     const jobStatus = queue.pendingJobs()[0];
@@ -47,10 +90,26 @@ async function run() {
     try {
       log("Starting transformation" + JSON.stringify(job, undefined, 2));
 
-      const files = getModifiedAfter(job.from, job.till, log);
-
-      const modified = [...files.added, ...files.modified];
-      const removed = files.removed;
+      let modified: string[] = [];
+      let removed: string[] = [];
+      let message = "";
+
+      if (job.files) {
+        modified = job.files.modified || [];
+        removed = job.files.removed || [];
+        message =
+          `committed by action runner ${config.sourceRepository} ${job.id}`;
+      } else if (job.from) {
+        const files = getModifiedAfter(job.from, job.till, log);
+        modified = [...files.added, ...files.modified];
+        removed = files.removed;
+        message =
+          `committed by action runner ${config.sourceRepository}@${job.id}`;
+      } else {
+        throw new Error(
+          "Could not start job, neither explicit file list nor from-commit specified",
+        );
+      }
 
       updateLocalData("source", log);
 
@@ -126,7 +185,7 @@ async function run() {
       const gitCommands = `git config --replace-all user.name ${job.author.name}
       git config --replace-all user.email ${job.author.email}
       git add -A
-      git commit --quiet -m "committed by action runner ${config.sourceRepository}@${job.id}"
+      git commit --quiet -m "${message}"
       git push --quiet ${
         config.targetRepositoryUri.replace(
           "https://",
diff --git a/src/deps.ts b/src/deps.ts
index 3393791..a3c403b 100644
--- a/src/deps.ts
+++ b/src/deps.ts
@@ -9,7 +9,7 @@ export {
   serveFile,
 } from "https://deno.land/std@0.202.0/http/file_server.ts";
 
-export { existsSync } from "https://deno.land/std@0.202.0/fs/mod.ts";
+export { existsSync, walk } from "https://deno.land/std@0.202.0/fs/mod.ts";
 export * as path from "https://deno.land/std@0.209.0/path/mod.ts";
 
 export { parseArgs } from "https://deno.land/std@0.215.0/cli/parse_args.ts";
diff --git a/src/main.ts b/src/main.ts
index 98ef7cc..dbedd22 100644
--- a/src/main.ts
+++ b/src/main.ts
@@ -78,7 +78,7 @@ const webhookHandler = async (request: Request) => {
     }
     if (pathname === "/full_update") {
       console.log("· got full_update request");
-      // TODO
+      worker.postMessage("FULLUPDATE");
       return new Response("Not Implemented", {
         status: Status.NotImplemented,
         statusText: STATUS_TEXT[Status.NotImplemented],

From 30b65a0df36f2c6218253f35e2f7380916edea7f Mon Sep 17 00:00:00 2001
From: nleanba <25827850+nleanba@users.noreply.github.com>
Date: Thu, 29 Feb 2024 18:02:11 +0100
Subject: [PATCH 2/9] cleanup

---
 src/action_worker.ts | 2 +-
 src/main.ts          | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/action_worker.ts b/src/action_worker.ts
index 44700bf..8aaf0f5 100644
--- a/src/action_worker.ts
+++ b/src/action_worker.ts
@@ -78,7 +78,7 @@ async function gatherJobsForFullUpdate() {
   }
 }
 
-async function run() {
+function run() {
   while (queue.pendingJobs().length > 0) {
     const jobStatus = queue.pendingJobs()[0];
     const job = jobStatus.job;
diff --git a/src/main.ts b/src/main.ts
index dbedd22..f14e2af 100644
--- a/src/main.ts
+++ b/src/main.ts
@@ -79,9 +79,9 @@ const webhookHandler = async (request: Request) => {
     if (pathname === "/full_update") {
       console.log("· got full_update request");
       worker.postMessage("FULLUPDATE");
-      return new Response("Not Implemented", {
-        status: Status.NotImplemented,
-        statusText: STATUS_TEXT[Status.NotImplemented],
+      return new Response(undefined, {
+        status: Status.Accepted,
+        statusText: STATUS_TEXT[Status.Accepted],
       });
     } else {
       if (WEBHOOK_SECRET && !(await verifySignature(request))) {

From 89ac68aec21d1fa67b8bd7c49e2fccf8c2b7e827 Mon Sep 17 00:00:00 2001
From: nleanba <25827850+nleanba@users.noreply.github.com>
Date: Thu, 29 Feb 2024 18:10:20 +0100
Subject: [PATCH 3/9] changed to type import

---
 src/gg2rdf.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/gg2rdf.ts b/src/gg2rdf.ts
index ea6904b..20707f8 100644
--- a/src/gg2rdf.ts
+++ b/src/gg2rdf.ts
@@ -1,5 +1,5 @@
 import { DOMParser, parseArgs } from "./deps.ts";
-import { Element } from "https://esm.sh/v135/linkedom@0.16.8/types/interface/element.d.ts";
+import type { Element } from "https://esm.sh/v135/linkedom@0.16.8/types/interface/element.d.ts";
 
 class Subject {
   properties: { [key: string]: Set<string> } = {};

From 94c10ace6d06dbe9ca7c7e2d24ce3b027ab2fed8 Mon Sep 17 00:00:00 2001
From: nleanba <25827850+nleanba@users.noreply.github.com>
Date: Thu, 29 Feb 2024 18:21:41 +0100
Subject: [PATCH 4/9] various fixes

---
 src/action_worker.ts | 11 +++++++++--
 src/repoActions.ts   |  3 ++-
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/src/action_worker.ts b/src/action_worker.ts
index 8aaf0f5..17d94fc 100644
--- a/src/action_worker.ts
+++ b/src/action_worker.ts
@@ -42,12 +42,14 @@ async function startTask() {
 async function gatherJobsForFullUpdate() {
   isRunning = true;
   try {
-    updateLocalData("source", console.log);
+    console.log("gathering jobs for full update");
+    updateLocalData("source");
+    console.log("pull complete");
     const date = (new Date()).toISOString();
     let block = 0;
     let files: string[] = [];
     for await (
-      const walkEntry of walk(Deno.cwd(), {
+      const walkEntry of walk(`${config.workDir}/repo/source/`, {
         exts: ["xml"],
         includeDirs: false,
         includeSymlinks: false,
@@ -55,6 +57,7 @@ async function gatherJobsForFullUpdate() {
     ) {
       if (walkEntry.isFile && walkEntry.path.endsWith(".xml")) {
         files.push(walkEntry.path);
+        console.log("added", walkEntry.path);
         if (files.length >= 100) {
           queue.addJob({
             author: {
@@ -66,10 +69,14 @@ async function gatherJobsForFullUpdate() {
               modified: files,
             },
           });
+          console.log("added Job");
           files = [];
         }
+      } else {
+        console.log("skipped", walkEntry.path);
       }
     }
+    console.log(`succesfully created full-update jobs (${block} jobs)`);
   } catch (error) {
     console.error("Could not create full-update jobs\n" + error);
   } finally {
diff --git a/src/repoActions.ts b/src/repoActions.ts
index 149e6f2..cabb059 100644
--- a/src/repoActions.ts
+++ b/src/repoActions.ts
@@ -49,8 +49,9 @@ const cloneRepo = (which: "source" | "target", log = console.log) => {
 // Function to update local data
 export function updateLocalData(
   which: "source" | "target",
-  log = console.log,
+  log: (msg: string) => void = console.log,
 ) {
+  log("starting git pull...");
   Deno.mkdirSync(`${config.workDir}/repo/${which}/.git`, { recursive: true });
   const p = new Deno.Command("git", {
     args: ["pull"],

From 86967cbfd4e8fd80f6047f38f618ae2fa58ef411 Mon Sep 17 00:00:00 2001
From: nleanba <25827850+nleanba@users.noreply.github.com>
Date: Thu, 29 Feb 2024 18:46:24 +0100
Subject: [PATCH 5/9] updated readme

---
 README.md | 24 ++++++++++++++----------
 1 file changed, 14 insertions(+), 10 deletions(-)

diff --git a/README.md b/README.md
index 75ff655..3bfbbab 100644
--- a/README.md
+++ b/README.md
@@ -12,31 +12,34 @@ This Docker Image exposes a server on port `4505` which:
 This webserver also exposes the follwing paths:
 
 - `/status`: Serves a Badge (svg) to show the current pipeline status
-- `/logs`: List of logs of past runs
-- `/logs/[id]`: Log of past run with that id.
-- `/update?from=[from-commit-id]&till=[till-commit-id]`: send a `POST` here to update all files modified since from-commit-id up till-commit-id or HEAD if not specified
-- `/full_update`: send a `POST` here to run the full_update script. (Not
-  implemented yet, continue using the scripts in the "manual run" directory)
+- `/workdir/jobs/`: List of runs
+- `/workdir/jobs/[id]/status.json`: Status of run with that id
+- `/workdir/jobs/[id]/log.txt`: Log of run with that id
+- `/update?from=[from-commit-id]&till=[till-commit-id]`: send a `POST` here to
+  update all files modified since from-commit-id up till-commit-id or HEAD if
+  not specified
+- `/full_update`: send a `POST` here to run the full_update script.
 
 ## Usage
 
 Build as a docker container.
+
 ```sh
 docker build . -t gg2rdf
 ```
 
-Requires a the environment-variable `GHTOKEN` as `username:<personal-acces-token>`
-to authenticate the pushing into the target-repo.
+Requires a the environment-variable `GHTOKEN` as
+`username:<personal-acces-token>` to authenticate the pushing into the
+target-repo.
 
 Then run using a volume
+
 ```sh
 docker run --name gg2rdf --env GHTOKEN=username:<personal-acces-token> -p 4505:4505 -v gg2rdf:/app/workdir gg2rdf
 ```
 
 Exposes port `4505`.
 
-
-
 ### Docker-Compose
 
 ```yml
@@ -57,7 +60,8 @@ Edit the file `config/config.ts`. Should be self-explanatory what goes where.
 
 ## Development
 
-The repo comes with vscode devcontaioner configurations. Some tweaks to allow using git from inside the devcontainer.
+The repo comes with vscode devcontaioner configurations. Some tweaks to allow
+using git from inside the devcontainer.
 
 To start from the terminal in vscode:
 

From 03161e0a697d550cbcc5e2d7155f707eb79950fd Mon Sep 17 00:00:00 2001
From: nleanba <25827850+nleanba@users.noreply.github.com>
Date: Thu, 29 Feb 2024 19:02:27 +0100
Subject: [PATCH 6/9] should work

---
 src/JobsDataBase.ts  |  6 +++---
 src/action_worker.ts | 22 ++++++++++++++--------
 src/main.ts          | 10 ++++++++--
 3 files changed, 25 insertions(+), 13 deletions(-)

diff --git a/src/JobsDataBase.ts b/src/JobsDataBase.ts
index c17eb60..b959394 100644
--- a/src/JobsDataBase.ts
+++ b/src/JobsDataBase.ts
@@ -60,13 +60,13 @@ export class JobsDataBase {
     );
   }
 
-  allJobs(): JobStatus[] {
+  allJobs(oldestFirst = false): JobStatus[] {
     const jobDirs = [];
     for (const jobDir of Deno.readDirSync(this.jobsDir)) {
       jobDirs.push(jobDir);
     }
     return jobDirs.filter((entry) => entry.isDirectory).sort((a, b) =>
-      b.name.localeCompare(a.name)
+      oldestFirst ? a.name.localeCompare(b.name) : b.name.localeCompare(a.name)
     ).map((jobDir) => {
       const statusFile = path.join(this.jobsDir, jobDir.name, "status.json");
       try {
@@ -98,6 +98,6 @@ export class JobsDataBase {
     }).filter(notEmpty);
   }
   pendingJobs() {
-    return this.allJobs().filter((js) => js.status === "pending");
+    return this.allJobs(true).filter((js) => js.status === "pending");
   }
 }
diff --git a/src/action_worker.ts b/src/action_worker.ts
index 17d94fc..6d9df02 100644
--- a/src/action_worker.ts
+++ b/src/action_worker.ts
@@ -44,9 +44,9 @@ async function gatherJobsForFullUpdate() {
   try {
     console.log("gathering jobs for full update");
     updateLocalData("source");
-    console.log("pull complete");
     const date = (new Date()).toISOString();
     let block = 0;
+    const jobs: Job[] = [];
     let files: string[] = [];
     for await (
       const walkEntry of walk(`${config.workDir}/repo/source/`, {
@@ -56,26 +56,32 @@ async function gatherJobsForFullUpdate() {
       })
     ) {
       if (walkEntry.isFile && walkEntry.path.endsWith(".xml")) {
-        files.push(walkEntry.path);
-        console.log("added", walkEntry.path);
-        if (files.length >= 100) {
-          queue.addJob({
+        files.push(
+          walkEntry.path.replace(`${config.workDir}/repo/source/`, ""),
+        );
+        if (files.length >= 500) {
+          jobs.push({
             author: {
               name: "GG2RDF Service",
               email: "gg2rdf@plazi.org",
             },
-            id: `full update ${date} [${block++}]`,
+            id: `full update ${date} [${
+              (++block).toString(10).padStart(4, "0")
+            }`,
             files: {
               modified: files,
             },
           });
-          console.log("added Job");
           files = [];
         }
       } else {
         console.log("skipped", walkEntry.path);
       }
     }
+    jobs.forEach((j) => {
+      j.id += ` of ${block.toString(10).padStart(4, "0")}]`;
+      queue.addJob(j);
+    });
     console.log(`succesfully created full-update jobs (${block} jobs)`);
   } catch (error) {
     console.error("Could not create full-update jobs\n" + error);
@@ -95,7 +101,7 @@ function run() {
       });
     };
     try {
-      log("Starting transformation" + JSON.stringify(job, undefined, 2));
+      log("Starting transformation\n" + JSON.stringify(job, undefined, 2));
 
       let modified: string[] = [];
       let removed: string[] = [];
diff --git a/src/main.ts b/src/main.ts
index f14e2af..f64ee5a 100644
--- a/src/main.ts
+++ b/src/main.ts
@@ -33,7 +33,14 @@ const WEBHOOK_SECRET: string | undefined = Deno.env.get("WEBHOOK_SECRET");
 await Deno.mkdir(`${config.workDir}/repo`, { recursive: true });
 await Deno.mkdir(`${config.workDir}/tmprdf`, { recursive: true });
 await Deno.mkdir(`${config.workDir}/tmpttl`, { recursive: true });
-await createBadge("Unknown");
+
+const db = new JobsDataBase(`${config.workDir}/jobs`);
+const latest =
+  db.allJobs().find((j) => j.status === "completed" || j.status === "failed")
+    ?.status || "Unknown";
+if (latest === "failed") createBadge("Failed");
+else if (latest === "completed") createBadge("OK");
+else createBadge("Unknown");
 
 const worker = new Worker(
   new URL("./action_worker.ts", import.meta.url).href,
@@ -136,7 +143,6 @@ const webhookHandler = async (request: Request) => {
     response.headers.set("Content-Type", "image/svg+xml");
     return response;
   } else if (pathname === "/jobs.json") {
-    const db = new JobsDataBase(`${config.workDir}/jobs`);
     const json = JSON.stringify(db.allJobs(), undefined, 2);
     const response = new Response(json);
     response.headers.set("Content-Type", "application/json");

From 2e12f26d1b01bbd69c6f4df152f9475c530998f5 Mon Sep 17 00:00:00 2001
From: nleanba <25827850+nleanba@users.noreply.github.com>
Date: Thu, 29 Feb 2024 19:10:43 +0100
Subject: [PATCH 7/9] moved datestamp to front for correct ordering of jobs

---
 src/action_worker.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/action_worker.ts b/src/action_worker.ts
index 6d9df02..2e0fe40 100644
--- a/src/action_worker.ts
+++ b/src/action_worker.ts
@@ -65,7 +65,7 @@ async function gatherJobsForFullUpdate() {
               name: "GG2RDF Service",
               email: "gg2rdf@plazi.org",
             },
-            id: `full update ${date} [${
+            id: `${date} full update [${
               (++block).toString(10).padStart(4, "0")
             }`,
             files: {

From 419459906c517ff70ee557a56e90fd69e83c9500 Mon Sep 17 00:00:00 2001
From: nleanba <25827850+nleanba@users.noreply.github.com>
Date: Thu, 29 Feb 2024 19:16:23 +0100
Subject: [PATCH 8/9] added note about not removing files

---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 3bfbbab..735f682 100644
--- a/README.md
+++ b/README.md
@@ -18,7 +18,8 @@ This webserver also exposes the follwing paths:
 - `/update?from=[from-commit-id]&till=[till-commit-id]`: send a `POST` here to
   update all files modified since from-commit-id up till-commit-id or HEAD if
   not specified
-- `/full_update`: send a `POST` here to run the full_update script.
+- `/full_update`: send a `POST` here to run the full_update script. Note that
+  this will not delete any files (yet).
 
 ## Usage
 

From 4bcec72334bebd7a2e9ebd56b6212761fad9aaac Mon Sep 17 00:00:00 2001
From: nleanba <25827850+nleanba@users.noreply.github.com>
Date: Thu, 29 Feb 2024 19:20:33 +0100
Subject: [PATCH 9/9] removed obsolete manual run

---
 manual run/main-on-all-wrapper.sh | 28 ----------------
 manual run/main-on-all.sh         | 55 -------------------------------
 manual run/readme                 |  7 ----
 3 files changed, 90 deletions(-)
 delete mode 100755 manual run/main-on-all-wrapper.sh
 delete mode 100755 manual run/main-on-all.sh
 delete mode 100644 manual run/readme

diff --git a/manual run/main-on-all-wrapper.sh b/manual run/main-on-all-wrapper.sh
deleted file mode 100755
index 32ebc6b..0000000
--- a/manual run/main-on-all-wrapper.sh	
+++ /dev/null
@@ -1,28 +0,0 @@
-#! /bin/bash
-
-#TODO VARS
-GITHUB_WORKSPACE=`pwd`
-GITHUB_ACTION_PATH=`pwd`
-
-echo "GG-XML input : $GITHUB_WORKSPACE/xml"
-echo "Turtle output: $GITHUB_WORKSPACE/ttl"
-echo "xslt         : $GITHUB_WORKSPACE/gg2rdf.xslt"
-echo "saxon        : $GITHUB_WORKSPACE/saxon-he-10.8.jar"
-echo "script       : $GITHUB_WORKSPACE/main-on-all.sh"
-
-[[ ! -d "$GITHUB_WORKSPACE/xml" ]] && echo -e "\e[1;31mno exists: $GITHUB_WORKSPACE/xml\e[0m" && exit 1
-[[ -d "$GITHUB_WORKSPACE/ttl" ]] && echo -e "\e[1;31mexists: $GITHUB_WORKSPACE/ttl\e[0m" && exit 1
-[[ ! -f "$GITHUB_WORKSPACE/gg2rdf.xslt" ]] && echo -e "\e[1;31mno exists: $GITHUB_WORKSPACE/gg2rdf.xslt\e[0m" && exit 1
-[[ ! -f "$GITHUB_WORKSPACE/saxon-he-10.8.jar" ]] && echo -e "\e[1;31mno exists: $GITHUB_WORKSPACE/saxon-he-10.8.jar\e[0m" && exit 1
-[[ ! -f "$GITHUB_WORKSPACE/main-on-all.sh" ]] && echo -e "\e[1;31mno exists: $GITHUB_WORKSPACE/main-on-all.sh\e[0m" && exit 1
-
-
-mkdir "$GITHUB_WORKSPACE/ttl"
-
-docker run\
-  -v "$GITHUB_WORKSPACE"/xml:/workspace/xml\
-  -v "$GITHUB_WORKSPACE"/ttl:/workspace/ttl\
-  -v "$GITHUB_WORKSPACE"/gg2rdf.xslt:/workspace/gg2rdf.xslt\
-  -v "$GITHUB_WORKSPACE"/saxon-he-10.8.jar:/workspace/saxon-he-10.8.jar\
-  -v "$GITHUB_WORKSPACE"/main-on-all.sh:/workspace/main-on-all.sh\
-  ubuntu /workspace/main-on-all.sh
diff --git a/manual run/main-on-all.sh b/manual run/main-on-all.sh
deleted file mode 100755
index ac18d36..0000000
--- a/manual run/main-on-all.sh	
+++ /dev/null
@@ -1,55 +0,0 @@
-#! /bin/bash
-
-## ./xml ----> ./ttl
-
-#TODO VARS
-GITHUB_WORKSPACE=/workspace/
-GITHUB_ACTION_PATH=/workspace/
-GITHUB_ACTOR=retog
-
-apt update
-DEBIAN_FRONTEND=noninteractive apt install -y raptor2-utils openjdk-11-jdk git curl
-  # This is assuming that /usr/bin is in the path
-ls -l $GITHUB_ACTION_PATH
-ls -l $GITHUB_WORKSPACE
-
-#git clone --depth 1 git@github.com:plazi/treatments-xml.git $GITHUB_WORKSPACE/xml
-
-# Run saxon on all files
-cd $GITHUB_WORKSPACE/xml
-mkdir $GITHUB_WORKSPACE/rdf
-for file in $(find . -type f); do
-  if [[ $file == *.xml ]]; then
-    echo "$file is xml, applying saxon"
-    mkdir -p $GITHUB_WORKSPACE/rdf/${file%/*}
-    java -jar $GITHUB_ACTION_PATH/saxon-he-10.8.jar -s:$file -o:$GITHUB_WORKSPACE/rdf/${file:0:-4}.rdf -xsl:$GITHUB_ACTION_PATH/gg2rdf.xslt
-  fi
-done
-
-# Convert all generated RDF-XML files to TTL
-cd $GITHUB_WORKSPACE/rdf
-mkdir -p $GITHUB_WORKSPACE/ttl
-for file in $(find . -type f); do
-  echo "$file in generated rdf-xml folder"
-  relative_file=`realpath -m --relative-to=$GITHUB_WORKSPACE/rdf $file`
-  mkdir -p $GITHUB_WORKSPACE/ttl/${relative_file%/*}
-  # $file → $GITHUB_WORKSPACE/ttl/${file:0:-4}.ttl
-  rapper -e -w -q $file --output turtle > $GITHUB_WORKSPACE/ttl/${file:0:-4}.ttl
-done
-
-#git clone --depth 1 git@github.com:plazi/treatments-rdf.git $GITHUB_WORKSPACE/ttl-repo
-#
-## Remove
-#cd $GITHUB_WORKSPACE/ttl-repo
-#rm -rf data
-#
-## Move
-#cd $GITHUB_WORKSPACE
-#mv ttl ttl-repo
-#
-#cd $GITHUB_WORKSPACE/ttl-repo
-#git config user.name $GITHUB_ACTOR
-#git config user.email $GITHUB_ACTOR@users.noreply.github.com
-#git add -A
-#git commit -m "manual conversion of all files"
-#git push origin main
diff --git a/manual run/readme b/manual run/readme
deleted file mode 100644
index bdc046f..0000000
--- a/manual run/readme	
+++ /dev/null
@@ -1,7 +0,0 @@
-# this is outdated, do not use
-
-Run the ./main-on-all-wrapper.sh skript to convert everything in pwd/xml to ttl (placed into pwd/ttl)
-
-`pwd`/xml must exist & contain xml data
-`pwd`/ttl must not exist
-`pwd`/gg2rdf.xslt must exist
\ No newline at end of file