build(dev): fetch assets, or source code to build assets, of ketcher2(#…

…2044)

(requires jq or yq, unzip, git)

- default version locked in `.service-dependencies`
- move assets to
  public/editors/ketcher2/{pre}built/{version}/{standalone|remote}
- symlink to `public/editors/default` and
  `public/editors/ketcher2/standalone` (unless real dir present)

Examples:

- install the recommended version from provider artifacts

```sh
bin/chem-ket2-install.sh
```
- build and install the latest version from source

```sh
bin/chem-ket2-install.sh -b -s epam/ketcher@master
```

Usage: bin/chem-ket2-install.sh --package-src <user/repo:version> --artifact-type <type> --build-from-source

  -s, --package-src <src>          Optional: specify the src and version(tag, branch, or commit) for KETCHER2 as defined in the .service-dependencies file.
                                             Default from .service-dependencies file
  -t, --package-type <standalone|remote> Optional: If multiple artifacts are present select the one to use - default 'standalone'
  -b, --build-from-src             Optional: Build from src - default false: get compiled artifacts from src repo
  --options <options>              Optional: Additional options to pass to the build script
  -h, --help                       Display this help message.
  -v, --verbose                    verbose output
```

.gitignore

@@ -100,6 +100,7 @@
 !/public/ontologies/rxno.default.edited.json
 
 /public/data_type.json
+/public/default_editors
 
 /uploads/*
 !/public/attachments/.keep

.service-dependencies

@@ -1,5 +1,5 @@
 #syntax=v1
-CONVERTER=ComPlat/chemotion-converter-app@v1.2.0
+CONVERTER=ComPlat/chemotion-converter-app@1.2.0
 KETCHER=ptrxyz/chemotion-ketchersvc@main
 SPECTRA=ComPlat/[email protected]
 NMRIUMWRAPPER=NFDI4Chem/[email protected]

bin/chem-get-git-src.sh

@@ -0,0 +1,199 @@
+#!/bin/bash
+
+# source utilities function located in the same directory
+source $(dirname $0)/chem-utils.sh
+
+
+# This script reads the version for a package as defined in the ../.service-dependencies file
+# @param $1: the package name
+# @return: the version of the package and the git repository as json or yml object 
+
+function get_git_src() {
+
+ # dependencies lock
+ local dep_filename=".service-dependencies"
+ local dependencies="${app_dir}${dep_filename}"
+ local ref=""
+ local version=""
+ local ref_type=""
+ local repo=""
+ local repo_url=""
+
+# check whether jq or yq are installed. need one of them (jq default) to output json or yml
+# if none installed, exit with error
+# if both installed, use jq as default
+# remember which one is used as $mode
+# local mode="json"
+
+  get_git_src_usage() {
+    echo "Usage: $0 --package-name <name>"
+    echo
+    echo "  -n, --package-name <name>        Specify the package name as defined in the .service-dependencies file - required"
+    echo "  -s, --package-src  <src@version> Set the src and version - optional default from .service-dependencies"
+    echo "  -p, --parse-only                 Do not try to get the assets urls from github"
+    exit 0
+  }
+
+# Initialize variables
+package_name=""
+
+while [[ $# -gt 0 ]]; do
+    case $1 in
+       -n|--package-name)
+            package_name="$2"
+            shift 2
+            ;;
+       -p|--parse-only)
+            parse_only=true
+	    shift
+	;;
+ -s|--package-src)
+            package_src="$2"
+	    shift 2
+	;;
+	-h|--help)
+	  get_git_src_usage
+	  ;;
+
+        *)
+  echo "hello $1"
+            echo "Invalid option: $1"
+  #          usage
+            ;;
+    esac
+done
+
+############################################################################################################
+# Local functions
+############################################################################################################
+
+# Function that extracts a line starting with the package name
+# or build the line if package_src is provided
+# @param $1: the package name
+# @return: the info after the "$package_name=" part if the line is valid
+get_package_src() {
+    local package_name="$1"
+    local line=$(grep -E "^${package_name}=" "$dependencies")	
+    if [[ -z $line ]]; then
+        vecho "No ${package_name} version specified/ in $dep_filename."
+        exit 1
+    fi
+    # package_src=$(echo "$line" | cut -d'=' -f2)
+    package_src=${line#*=}
+    vecho "Package source: $package_src"
+}
+
+# Function that validates the package info
+# @param $1: the package name src info
+validate_package_info() {
+    local info_src="$1"
+    if [[ ! $info_src =~ ^[a-zA-Z0-9_-]+/[a-zA-Z0-9_-]+@[a-zA-Z0-9_.-]+$ ]]; then
+      # echo invalid version and exit
+      vecho "Invalid version format for $package_name in $dep_filename."
+      # return empty string
+      exit 1
+    fi
+    vecho "Valid version format: $info_src"
+    repo=${info_src%@*}  # part before '@' (user/repo)
+    repo_url="https://github.com/$repo"
+    version=${info_src#*@}  # part after '@' (version)
+    ref=${info_src#*@}   # part after '@' (branch/version/revision)
+    ref_type="tag"
+
+    # if ref is an hexademical string, it is a revision
+    # otherwise it is a branch or a tag
+    if [[ $ref =~ ^[0-9a-fA-F]+$ ]]; then
+	type="revision"
+    fi
+    # if ref is like a version number, it is a tag otherwise it is a branch
+    # A version number  is semantic, can start with v or a number, and can have dots
+
+    if [[ $ref =~ ^v?[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
+	type="tag"
+    else
+	type="branch"
+    fi
+    vecho "Repo: $repo, Ref: $ref, Type: $type"
+
+}	
+
+
+# function to get the assets from the release by the tag
+# @param $1: the git repository
+# @param $2: the tag
+# @return: the url to the assets from the release tag
+get_assets_urls() {
+    # if mode is json, use jq to get the assets url
+    vecho "Getting assets urls from $repo_url/releases/tag/$ref"
+    if [[ $mode == "json" ]]; then
+      local assets_url=$(curl -L -H "Accept: application/vnd.github+json" -s "https://api.github.com/repos/${repo}/releases/tags/$ref" | jq -r '.assets_url')
+      assets_urls=$(curl -L -H "Accept: application/vnd.github+json" -s $assets_url | jq -r '[.[] | .browser_download_url]') jq -r ".$package_name.assets_urls = ( env.assets_urls | fromjson)" $dep_json > tmp/.tmp.json
+      mv tmp/.tmp.json $dep_json
+
+    elif [[ $mode == "yml" ]]; then
+      local assets_url=$(curl -L -H "Accept: application/vnd.github+json" -s "https://api.github.com/repos/${repo}/releases/tags/$ref" | yq -r '.assets_url')
+      local assets_urls=$(curl -L -H "Accept: application/vnd.github+json" -s $assets_url | yq -p=json '[.[] | .browser_download_url]')
+      assus="$assets_urls" yq  ".${package_name}.assets_urls = env(assus)" -i $dep_yml
+    fi
+}
+
+
+# Function that echoes a json object with the version and the git repository
+#  from the package info
+# @param $1: the package_info
+# @param $2: the git repository of the package
+# @return: the json or yml object
+get_service_info() {
+    # define the repo_url on github based on $repo
+   local result=""
+   local base_info="{\"$package_name\": {\"repo\": \"$repo\", \"repo_url\": \"$repo_url\", \"version\": \"$ref\", \"ref_type\": \"$ref_type\", \"assets_urls\": []}}"
+
+    if [[ $mode == "json" ]]; then
+      # build the json object from the base_info and the assets_urls
+      vecho "Building json object with base_info: $base_info"
+      echo $base_info | jq -r | tee $dep_json
+    elif [[ $mode == "yml" ]]; then
+       local cmd="yq -n '$base_info' > $dep_yml"
+       eval $cmd
+       cp $dep_yml $dep_yml.bak
+    fi
+}
+
+
+############################################################################################################
+# Main
+############################################################################################################
+
+# Check if the file exists in the current directory
+# if no package_name is provided, exit with error
+if [ -z "$package_name" ]; then
+  echo "Error: No package name provided"
+  get_git_src_usage
+fi
+# if no package_src is provided, and $dependencies does not exist, exit with error
+if [ -z "$package_src" ] && [ ! -f "$dependencies" ]; then
+  echo "Error: No package source provided and no dependencies file found"
+  get_git_src_usage
+fi
+
+
+if [ -z "$package_src" ]; then
+  get_package_src $package_name
+fi
+
+# if validate_package_info returns false, exit with error
+if ! validate_package_info $package_src; then
+  vecho "Error: Invalid package source provided"
+  get_git_src_usage
+fi
+
+get_service_info $package_src
+# get type of version from the package info
+# if the version is a tag, get the assets urls
+if [[ $ref_type == "tag" && -z $parse_only ]]; then
+	vecho "Getting assets urls for $package_name"
+  get_assets_urls
+fi
+
+}
+