Merge branch 'master' of github.com:informatics-isi-edu/ermrestjs int…

…o alt-fk-syntax

.github/workflows/unit-test.yml

@@ -11,18 +11,19 @@ jobs:
     timeout-minutes: 15
     steps:
       - name: Checkout repository code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           path: ermrestjs
       - name: Setup the system
         run: |
+          whoami
           echo "npm version:"
           npm --version
           echo "node version:"
           node --version
           sudo timedatectl set-timezone America/Los_Angeles
           export PATH="$(systemd-path user-binaries):$PATH"
-          sudo apt-get update
+          sudo apt-get -y update
           sudo apt-get -y install libcurl4-openssl-dev libjson-c-dev
           sudo service postgresql stop || true
           sudo service postgresql start 12
@@ -31,18 +32,19 @@ jobs:
           sudo a2enmod ssl
           sudo a2ensite default-ssl
           sudo groupadd -o -g $(id -g www-data) apache
+          sudo apt-get install -y python3-setuptools python3-ply
           sudo python3 --version
           sudo pip3 --version
-          sudo apt-get install -y python3-setuptools python3-ply
+          sudo su -c 'echo /usr/lib/python3.8/site-packages > /usr/local/lib/python3.8/dist-packages/sys-site-packages.pth'
           sudo su -c 'python3 -c "import site;print(site.PREFIXES);"'
           sudo su -c 'python3 -c "import site;print(site.getsitepackages())"'
+          : # the line below will make sure pyopenssl and cryptography have compatible versions
+          sudo pip3 install -U pyopenssl cryptography
+          sudo pip3 install flask
           sudo pip3 install requests
+          sudo pip3 install globus_sdk
           sudo pip3 install psycopg2-binary
-          sudo pip3 install git+https://github.com/informatics-isi-edu/webpy.git
-      - name: Set up JDK 1.8
-        uses: actions/setup-java@v1
-        with:
-          java-version: 1.8
+          sudo pip3 install oauth2client
       - name: Install webauthn
         run: |
           sudo useradd -m -r webauthn
@@ -83,8 +85,7 @@ jobs:
       - name: Install ermrestjs
         run: |
           cd ermrestjs
-          make dist
-          sudo make deploy
+          sudo make root-install
       - name: Add tests users
         run: |
           sudo -H -u webauthn webauthn2-manage adduser test1

Makefile

@@ -83,6 +83,7 @@ LIB=$(VENDOR)/lz-string.min.js \
 	$(VENDOR)/markdown-it-sub.min.js \
 	$(VENDOR)/markdown-it-sup.min.js \
 	$(VENDOR)/markdown-it-span.js \
+	$(VENDOR)/markdown-it-escape.js \
 	$(VENDOR)/markdown-it-attrs.js \
 	$(VENDOR)/markdown-it-container.min.js
 
@@ -221,17 +222,31 @@ deploy: dont_deploy_in_root
 	$(info - deploying the package)
 	@rsync -avz --exclude=$(MAKEFILE_VAR) $(DIST)/ $(ERMRESTJSDIR)
 
+# run dist and deploy with proper uesrs (GNU). only works with root user
+.PHONY: root-install
+root-install:
+	su $(shell stat -c "%U" Makefile) -c "make dist"
+	make deploy
+
+# run dist and deploy with proper uesrs (FreeBSD and MAC OS X). only works with root user
+.PHONY: root-install-alt
+root-install-alt:
+	su $(shell stat -f '%Su' Makefile) -c "make dist"
+	make deploy
+
 # Rules for help/usage
 .PHONY: help usage
 help: usage
 usage:
 	@echo "Available 'make' targets:"
-	@echo "    all           - run linter, build the pacakge andand docs"
-	@echo "    dist   	     - local install of node dependencies, and build the pacakge"
-	@echo "    deploy   	   - deploy the package to $(ERMRESTJSDIR)"
-	@echo "    deps          - local install of node dependencies"
-	@echo "    deps-test     - local install of dev node dependencies"
-	@echo "    lint          - lint the source"
-	@echo "    test          - run tests"
-	@echo "    clean         - remove the files and folders created during build"
-	@echo "    distclean     - the same as clean, and also removes npm dependencies"
+	@echo "    all               - run linter, build the pacakge andand docs"
+	@echo "    dist   	         - local install of node dependencies, and build the package"
+	@echo "    deploy   	       - deploy the package to $(ERMRESTJSDIR)"
+	@echo "    deps              - local install of node dependencies"
+	@echo "    deps-test         - local install of dev node dependencies"
+	@echo "    lint              - lint the source"
+	@echo "    test              - run tests"
+	@echo "    clean             - remove the files and folders created during build"
+	@echo "    distclean         - the same as clean, and also removes npm dependencies"
+	@echo "    root-install      - should only be used as root. will use dist with proper user and then deploy, for GNU systems"
+	@echo "    root-install-alt  - should only be used as root. will use dist with proper user and then deploy, for FreeBSD and MAC OS X"

RELEASE.md

@@ -10,6 +10,55 @@ This document is a summary of code changes in ERMRestJS. This is the vocabulary
   - `[Annotation]`: when the describe modification is related to annotation.
   - `[No changes]`: means that ERMRestJS hasn't been changed in the described duration.
 
+
+# 1/31/24
+
+- [Improved] added the `flags` optional parameter to regular expression handlebar functions ([link](https://github.com/informatics-isi-edu/ermrestjs/commit/d6690571e767a3b2dfe1caa5a5cee02c337ed8a0))
+- [Added] support for markdown values in comment ([link](https://github.com/informatics-isi-edu/ermrestjs/pull/1000))
+- [Changed] how `.comment` API works to be similar to `.displayname` API (link above)
+- [Added] support for contextualized `comment` (link above)
+- [Fixed] the inheritance of `comment_display` from the parent catalog, schema, or table (link above)
+- [Changed] `comment`, `comment_display`, and `comment_render_markdown` can come from different levels and don't affect each other. Before, we used to only get the `comment_display` from where the `comment` was defined. But now `comment_display` can come from the column directive while the comment is derived from the table, or vice versa (link above)
+
+# 11/30/23
+
+- [Fixed] spacing issue in the full-screen-btn of iframes ([link](https://github.com/informatics-isi-edu/ermrestjs/pull/994))
+- [Improved] visible-columns and rowname heuristics ([link](https://github.com/informatics-isi-edu/ermrestjs/pull/995))
+- [Changed] how data can be accessed through `page_markdown_pattern` for consistency (link above) 
+
+# 9/30/23
+
+- [Added][Annotation] `input_iframe` property to column-directives ([link](https://github.com/informatics-isi-edu/ermrestjs/pull/988))
+- [Added][Annotation] `selector_ux_mode` property to visible-columns, foreign-ke, table-display, and display annotations ([link](https://github.com/informatics-isi-edu/ermrestjs/pull/986))
+- [Improved] default presentation of asset columns and its metadata ([link](https://github.com/informatics-isi-edu/ermrestjs/pull/985))
+- [Added][Annotation] asset related propreties to the column-defaults (link above)
+- [Added][Annotation] `data-chaise-tooltip` attribute to our markdown rendering that can be used for showing tooltips (link above)
+- [Improved][Annotation] add a new argument to the `huamnizeBytes` handlebars function to show the raw value in the tooltip (link above)
+- [Fixed] issues in parser related to search ([link](https://github.com/informatics-isi-edu/ermrestjs/commit/3268586e0ca8cead6337c5701a808e329cff72c0))
+- [Fixed] issues related to uncontextualized reference ([link](https://github.com/informatics-isi-edu/ermrestjs/commit/af9e210d6df7e79b52299767abcba67b516ba382))
+- [Fixed] avoid adding non-sortable shortest key columns to the default sort ([link](https://github.com/informatics-isi-edu/ermrestjs/commit/e0f6e9d27500b10fd2c01bcf0d72f0942e2c7ab1))
+- [Improved] allow other ways of using encodeFacet and jsonStringify handlebar helpers ([link](https://github.com/informatics-isi-edu/ermrestjs/commit/e490a86533bcf7af38327d91805bdbedba83feec))
+- [Added] `root-intall` make target ([link](https://github.com/informatics-isi-edu/ermrestjs/commit/e0f6c38043e0b2ad19aa9b0a5df12ee888891195))
+- [Improved] allow `entity`, `aggregate`, and `self_link` to be defined at the same type as `sourcekey` ([link](https://github.com/informatics-isi-edu/ermrestjs/pull/992))
+- [Improved] default visible columns heuristics regarding the display key (link above)
+
+# 7/31/23
+
+- [Added][Annotation] `humanizeBytes` handlebars function ([link](https://github.com/informatics-isi-edu/ermrestjs/pull/978))
+- [Added][Annotation] `skip_root_path` to allow export template to skip adding the root path ([link](https://github.com/informatics-isi-edu/ermrestjs/pull/980))
+- [Improved][Annotation] how export annotation handles `limit` query parameter (link above)
+
+# 5/31/23
+
+- [Improved] properly handle URL length limitation while validating facet filters ([link](https://github.com/informatics-isi-edu/ermrestjs/pull/975))
+- [Improved] how ermrest-data-utils is used for testing ([link](https://github.com/informatics-isi-edu/ermrestjs/pull/974))
+
+# 3/31/23
+
+- [Added] support for immutable, generated, and non-deletable annotations on catalog ([link](https://github.com/informatics-isi-edu/ermrestjs/commit/ab249623a19afa5e2e260a6c473c0901c80f7ca3))
+- [Added][Annotation] support for column-defaults annotation ([link](https://github.com/informatics-isi-edu/ermrestjs/pull/972))
+- [Added][Annotation] support for `image_preview` to `asset` annotation ([link](https://github.com/informatics-isi-edu/ermrestjs/pull/973))
+
 # 1/31/23
 
 - [Improved] make sure fast_filter_source is honored for urls with join ([link](https://github.com/informatics-isi-edu/ermrestjs/commit/a2a234534ca120a1308027a443c96d158fd5a130)).