From e2714ff082cf9cea8d69687b147347a885714723 Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Thu, 12 Dec 2024 17:32:10 +0100 Subject: [PATCH 01/20] =?UTF-8?q?=E2=9C=A8=20wizard=20data=20step?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit From d942e84a06a3e82307f60141a8bcf9cf73e13563 Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Fri, 13 Dec 2024 11:11:20 +0100 Subject: [PATCH 02/20] chore: update dependencies --- pyproject.toml | 1 + uv.lock | 3294 ++++++++++++++++++++++++------------------------ 2 files changed, 1644 insertions(+), 1651 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index ca6c8ecde91..d3e4559afa1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -66,6 +66,7 @@ dependencies = [ "scikit-learn>=1.5.2", "geopy>=2.4.1", "py7zr>=0.22.0", + "streamlit>=1.41.0", ] [tool.uv.sources] diff --git a/uv.lock b/uv.lock index 2f4ecd7dbac..d7b37e44faf 100644 --- a/uv.lock +++ b/uv.lock @@ -17,16 +17,16 @@ wheels = [ 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minor tweaks to expert --- apps/wizard/app_pages/expert/app.py | 299 ++++++++++++++-------------- apps/wizard/config/__init__.py | 10 +- apps/wizard/config/config.yml | 70 ++++--- 3 files changed, 206 insertions(+), 173 deletions(-) diff --git a/apps/wizard/app_pages/expert/app.py b/apps/wizard/app_pages/expert/app.py index 929a40e5439..f1fa89f1abf 100644 --- a/apps/wizard/app_pages/expert/app.py +++ b/apps/wizard/app_pages/expert/app.py @@ -20,6 +20,7 @@ SYSTEM_PROMPT_START, ) from apps.wizard.utils import set_states +from apps.wizard.utils.components import st_horizontal from apps.wizard.utils.db import DB_IS_SET_UP, WizardDB from etl.config import load_env @@ -34,7 +35,7 @@ # CONFIG ## Title/subtitle -st.title("**Expert** 🧙") +st.title(":rainbow[:material/lightbulb_2:] Expert") st.markdown( "Ask the Expert any questions about ETL! Alternatively, visit [**our documentation ↗**](https://docs.owid.io/projects/etl])." ) @@ -131,6 +132,8 @@ def reset_messages() -> None: ) +container_chat = st.container() + # Category for the chat options = [ Options.FULL, @@ -140,14 +143,9 @@ def reset_messages() -> None: Options.GUIDES, Options.PRINCIPLES, ] -# captions = [ -# "The most complete chat. Use all our documentation.", -# "Specific queries about the metadata, yaml files, etc.", -# "Create SQL queries on our Datasette instance.", -# "Specific queries about setting up your environment.", -# ] # NOTE: using pills is a good viz (https://github.com/jrieke/streamlit-pills). however, existing tool does not have an on_change options, which is basic if we want to reset some values from session_state with st.container(border=True): + st.markdown("**Settings**") st.radio( label="Choose a category for the question", options=options, @@ -158,60 +156,73 @@ def reset_messages() -> None: horizontal=True, ) -## EXAMPLE QUERIES -if st.session_state["category_gpt"] == Options.DATASETTE: - EXAMPLE_QUERIES = [ - "> Which are our top 10 articles by pageviews?", - "> How many charts do we have that use only a single indicator?", - "> Do we have datasets whose indicators are not used in any chart?", - ] -else: - EXAMPLE_QUERIES = [ - "> In the metadata yaml file, which field should I use to disable the map tap view?", - "> In the metadata yaml file, how can I define a common `description_processing` that affects all indicators in a specific table?" - "> What is the difference between `description_key` and `description_from_producer`? Be concise.", - "> Is the following snapshot title correct? 'Cherry Blossom Full Blook Dates in Kyoto, Japan'", - "> What is the difference between an Origin and Dataset?", - ] -with st.popover("See examples"): - for example in EXAMPLE_QUERIES: - st.markdown(example) - -# Sidebar with GPT config -st.session_state.analytics = st.session_state.get("analytics", True) -with st.sidebar: + ## EXAMPLE QUERIES + if st.session_state["category_gpt"] == Options.DATASETTE: + EXAMPLE_QUERIES = [ + "> Which are our top 10 articles by pageviews?", + "> How many charts do we have that use only a single indicator?", + "> Do we have datasets whose indicators are not used in any chart?", + ] + else: + EXAMPLE_QUERIES = [ + "> In the metadata yaml file, which field should I use to disable the map tap view?", + "> In the metadata yaml file, how can I define a common `description_processing` that affects all indicators in a specific table?" + "> What is the difference between `description_key` and `description_from_producer`? Be concise.", + "> Is the following snapshot title correct? 'Cherry Blossom Full Blook Dates in Kyoto, Japan'", + "> What is the difference between an Origin and Dataset?", + ] + with st.popover("See examples"): + for example in EXAMPLE_QUERIES: + st.markdown(example) + + # Sidebar with GPT config + st.session_state.analytics = st.session_state.get("analytics", True) + # with st.container(): + st.divider() st.button( label="Clear chat", on_click=reset_messages, ) - st.divider() - st.toggle( - label="Collect data for analytics", - value=True, - on_change=lambda: set_states( - { - "analytics": not st.session_state.analytics, - } - ), - help="If enabled, we will collect usage data to improve the app. \n\nThis **is really helpful to improve** how we query chat GPT: E.g. which system prompt to use, optimise costs, and much more 😊. \n\nData collected: questions, responses and feedback submitted. \n\nYou can see how this data is collected [here](https://github.com/owid/etl/blob/master/apps/wizard/utils/db.py). \n\nRecords are anonymous.", - ) - st.divider() - st.markdown("## GPT Configuration") - model_name = st.selectbox( - label="Select GPT model", - options=MODELS_AVAILABLE_LIST, - format_func=lambda x: MODELS_AVAILABLE[x], - index=MODELS_AVAILABLE_LIST.index(MODEL_DEFAULT), - help="[Pricing](https://openai.com/api/pricing) | [Model list](https://platform.openai.com/docs/models/)", - ) + # st.divider() + # st.toggle( + # label="Collect data for analytics", + # value=True, + # on_change=lambda: set_states( + # { + # "analytics": not st.session_state.analytics, + # } + # ), + # help="If enabled, we will collect usage data to improve the app. \n\nThis **is really helpful to improve** how we query chat GPT: E.g. which system prompt to use, optimise costs, and much more 😊. \n\nData collected: questions, responses and feedback submitted. \n\nYou can see how this data is collected [here](https://github.com/owid/etl/blob/master/apps/wizard/utils/db.py). \n\nRecords are anonymous.", + # ) + col1, col2, col3 = st.columns(3, vertical_alignment="center") + with col1: + model_name = st.selectbox( + label="Select GPT model", + options=MODELS_AVAILABLE_LIST, + format_func=lambda x: MODELS_AVAILABLE[x], + index=MODELS_AVAILABLE_LIST.index(MODEL_DEFAULT), + help="[Pricing](https://openai.com/api/pricing) | [Model list](https://platform.openai.com/docs/models/)", + ) ## See pricing list: https://openai.com/api/pricing (USD) ## See model list: https://platform.openai.com/docs/models/ + with col2: + max_tokens = int( + st.number_input( + "Max tokens", + min_value=32, + max_value=4096, + value=4096, + step=32, + help="The maximum number of tokens in the response.", + ) + ) - use_reduced_context = st.toggle( - "Reduced context window", - value=False, - help="If checked, only the last user message will be accounted (i.e less tokens and therefore cheaper).", - ) + with col3: + use_reduced_context = st.toggle( + "Reduced context window", + value=False, + help="If checked, only the last user message will be accounted (i.e less tokens and therefore cheaper).", + ) temperature = st.slider( "Temperature", min_value=0.0, @@ -220,94 +231,94 @@ def reset_messages() -> None: step=0.01, help="What sampling temperature to use, between 0 and 2. Higher values like 0.8 will make the output more random, while lower values like 0.2 will make it more focused and deterministic.", ) - max_tokens = int( - st.number_input( - "Max tokens", - min_value=32, - max_value=4096, - value=4096, - step=32, - help="The maximum number of tokens in the response.", - ) - ) - -# API with OPENAI -api = OpenAIWrapper() - -# ACTUAL APP -# Initialize chat history -if "messages" not in st.session_state: - reset_messages() - -# DEGUG -# st.write([m for m in st.session_state.messages if m["role"] != "system"]) - -# Display chat messages from history on app rerun -for message in st.session_state.messages: - if message["role"] != "system": - with st.chat_message(message["role"]): - st.markdown(message["content"]) - -# Initialise session state -st.session_state.response = st.session_state.get("response", None) -st.session_state.prompt = st.session_state.get("prompt", None) -st.session_state.feedback_key = st.session_state.get("feedback_key", 0) -st.session_state.cost_last = st.session_state.get("cost_last", 0) - -# React to user input -if prompt := st.chat_input("Ask me!"): - st.session_state.feedback_key += 1 - print("asking GPT...") - # Display user message in chat message container - with st.chat_message("user"): - st.markdown(prompt) - - # Add user message to chat history - st.session_state.messages.append({"role": "user", "content": prompt}) - - # Build GPT query (only use the system prompt and latest user input) - if use_reduced_context: - messages = [{"role": "system", "content": get_system_prompt()}, {"role": "user", "content": prompt}] - else: - messages = st.session_state.messages - - # Display assistant response in chat message container - with st.chat_message("assistant"): - # Ask GPT (stream) - stream = api.chat.completions.create( - model=cast(str, model_name), - messages=messages, # type: ignore - temperature=temperature, - max_tokens=max_tokens, - stream=True, - ) - st.session_state.response = cast(str, st.write_stream(stream)) - - # Add new response by the System - st.session_state.messages.append({"role": "assistant", "content": st.session_state.response}) - - # Add prompt to session state - st.session_state.prompt = prompt - - print("finished asking GPT...") - -if st.session_state.response: - # Get cost & tokens - text_in = "\n".join([m["content"] for m in st.session_state.messages]) - cost, num_tokens = get_cost_and_tokens(text_in, st.session_state.response, cast(str, model_name)) - cost_msg = f"**Cost**: ≥{cost} USD.\n\n **Tokens**: ≥{num_tokens}." - st.session_state.cost_last = cost - - if DB_IS_SET_UP and st.session_state.analytics: - # Get feedback only if DB is properly setup - feedback = streamlit_feedback( - feedback_type="thumbs", - optional_text_label="[Optional] Please provide an explanation", - key=f"feedback_{st.session_state.feedback_key}", - on_submit=handle_feedback, - ) - # Show cost below feedback - st.info(cost_msg) -# DEBUG -# st.write([m for m in st.session_state.messages if m["role"] != "system"]) +with container_chat: + # API with OPENAI + api = OpenAIWrapper() + + # ACTUAL APP + # Initialize chat history + if "messages" not in st.session_state: + reset_messages() + + # DEGUG + # st.write([m for m in st.session_state.messages if m["role"] != "system"]) + + # Display chat messages from history on app rerun + for message in st.session_state.messages: + if message["role"] != "system": + avatar = None + if message["role"] == "user": + avatar = ":material/person:" + with st.chat_message(message["role"], avatar=avatar): + st.markdown(message["content"]) + + # Initialise session state + st.session_state.response = st.session_state.get("response", None) + st.session_state.prompt = st.session_state.get("prompt", None) + st.session_state.feedback_key = st.session_state.get("feedback_key", 0) + st.session_state.cost_last = st.session_state.get("cost_last", 0) + + # Placeholder for response + container_response = st.container() + + # React to user input + if prompt := st.chat_input("Ask me any question!"): + st.session_state.feedback_key += 1 + print("asking GPT...") + # Display user message in chat message container + with container_response: + with st.chat_message("user", avatar=":material/person:"): + st.markdown(prompt) + + # Add user message to chat history + st.session_state.messages.append({"role": "user", "content": prompt}) + + # Build GPT query (only use the system prompt and latest user input) + if use_reduced_context: + messages = [{"role": "system", "content": get_system_prompt()}, {"role": "user", "content": prompt}] + else: + messages = st.session_state.messages + + # Display assistant response in chat message container + with container_response: + with st.chat_message("assistant"): + # Ask GPT (stream) + stream = api.chat.completions.create( + model=cast(str, model_name), + messages=messages, # type: ignore + temperature=temperature, + max_tokens=max_tokens, + stream=True, + ) + st.session_state.response = cast(str, st.write_stream(stream)) + + # Add new response by the System + st.session_state.messages.append({"role": "assistant", "content": st.session_state.response}) + + # Add prompt to session state + st.session_state.prompt = prompt + + print("finished asking GPT...") + + if st.session_state.response: + # Get cost & tokens + text_in = "\n".join([m["content"] for m in st.session_state.messages]) + cost, num_tokens = get_cost_and_tokens(text_in, st.session_state.response, cast(str, model_name)) + cost_msg = f"**Cost**: ≥{cost} USD.\n\n **Tokens**: ≥{num_tokens}." + st.session_state.cost_last = cost + + if DB_IS_SET_UP and st.session_state.analytics: + # Get feedback only if DB is properly setup + feedback = streamlit_feedback( + feedback_type="thumbs", + optional_text_label="[Optional] Please provide an explanation", + key=f"feedback_{st.session_state.feedback_key}", + on_submit=handle_feedback, + ) + # Show cost below feedback + with container_response: + st.info(cost_msg) + + # DEBUG + # st.write([m for m in st.session_state.messages if m["role"] != "system"]) diff --git a/apps/wizard/config/__init__.py b/apps/wizard/config/__init__.py index 0366998ded4..dde01aa05c1 100644 --- a/apps/wizard/config/__init__.py +++ b/apps/wizard/config/__init__.py @@ -75,7 +75,15 @@ def _check_wizard_config(config: dict): assert "description" in config["etl"], "`etl.description` property is required in wizard config!" assert "steps" in config["etl"], "`etl.steps` property is required in wizard config!" steps = config["etl"]["steps"] - steps_expected = ["snapshot", "express", "meadow", "garden", "fasttrack", "grapher"] + steps_expected = [ + "snapshot", + "data", + # "express", + # "meadow", + # "garden", + # "grapher", + "fasttrack", + ] for step_expected in steps_expected: assert step_expected in steps, f"{step_expected} property is required in etl.steps property in wizard config!" for prop in etl_steps_properties_expected: diff --git a/apps/wizard/config/config.yml b/apps/wizard/config/config.yml index ca80284a32b..c28e8ab6d4f 100644 --- a/apps/wizard/config/config.yml +++ b/apps/wizard/config/config.yml @@ -36,7 +36,7 @@ main: - "@lucas" - "@daniel" entrypoint: app_pages/expert/app.py - icon: ":material/hotel_class:" + icon: ":material/lightbulb_2:" analytics: title: "Analytics (external)" description: "Learn more about OWID in Data!" @@ -58,34 +58,13 @@ etl: image_url: "https://greatescapepublishing.com/wp-content/uploads/2019/11/30463274482_90aff8a230_c.jpg" disable: "production": True - express: - title: "Express" - entrypoint: etl_steps/express.py - icon: ":material/bolt:" + data: + title: "Data step" + entrypoint: etl_steps/data.py + icon: ":material/table:" image_url: "https://upload.wikimedia.org/wikipedia/commons/b/b3/Indochinese_leopard.jpg" disable: "production": True - meadow: - title: "Meadow" - entrypoint: etl_steps/meadow.py - icon: ":material/nature:" - image_url: "https://upload.wikimedia.org/wikipedia/commons/thumb/5/5e/Blumenwiese_bei_Obermaiselstein05.jpg/1024px-Blumenwiese_bei_Obermaiselstein05.jpg" - disable: - "production": True - garden: - title: "Garden" - entrypoint: etl_steps/garden.py - icon: ":material/deceased:" - image_url: "https://upload.wikimedia.org/wikipedia/commons/2/27/Butchart_gardens.JPG" - disable: - "production": True - grapher: - title: "Grapher" - entrypoint: etl_steps/grapher.py - icon: ":material/database:" - image_url: "https://pbs.twimg.com/media/EbHwdjwUcAEfen4?format=jpg&name=large" - disable: - "production": True fasttrack: title: "Fast Track" alias: fasttrack @@ -94,6 +73,41 @@ etl: image_url: "https://upload.wikimedia.org/wikipedia/commons/b/be/Alonso_%28Renault%29_qualifying_at_USGP_2005.jpg" sections: + - title: "ETL Steps (legacy)" + description: "Keeping this temporary" + apps: + - alias: express + title: "Express" + description: "Add all data steps." + entrypoint: etl_steps/express.py + icon: ":material/bolt:" + image_url: "https://upload.wikimedia.org/wikipedia/commons/b/b3/Indochinese_leopard.jpg" + disable: + "production": True + - alias: meadow + title: "Meadow" + description: "Add meadow step." + entrypoint: etl_steps/meadow.py + icon: ":material/nature:" + image_url: "https://upload.wikimedia.org/wikipedia/commons/thumb/5/5e/Blumenwiese_bei_Obermaiselstein05.jpg/1024px-Blumenwiese_bei_Obermaiselstein05.jpg" + disable: + "production": True + - alias: garden + title: "Garden" + description: "Add garden step." + entrypoint: etl_steps/garden.py + icon: ":material/deceased:" + image_url: "https://upload.wikimedia.org/wikipedia/commons/2/27/Butchart_gardens.JPG" + disable: + "production": True + - alias: grapher + title: "Grapher" + description: "Add grapher step." + entrypoint: etl_steps/grapher.py + icon: ":material/database:" + image_url: "https://pbs.twimg.com/media/EbHwdjwUcAEfen4?format=jpg&name=large" + disable: + "production": True - title: "Data curation" description: |- Updates, data edits, etc. @@ -156,7 +170,7 @@ sections: description: "Extract analytics to share with data producers" maintainer: "@pablo" entrypoint: app_pages/producer_analytics.py - icon: ":material/developer_board:" + icon: ":material/analytics:" image_url: "https://upload.wikimedia.org/wikipedia/commons/thumb/c/ce/Wikimedia_Product_Analytics_team_logo.svg/512px-Wikimedia_Product_Analytics_team_logo.svg.png" - title: "Explorers" @@ -194,7 +208,7 @@ sections: description: "Data insights with GPT" maintainer: "@daniel" entrypoint: app_pages/datainsight_robot.py - icon: ":material/lightbulb:" + icon: ":material/stylus_note:" image_url: "https://cdn.cpdonline.co.uk/wp-content/uploads/2023/08/03153310/Starting-To-Become-A-Writer-1200x350.jpg" - title: "Misc" From 8138f7fb903572546c8bf666bfd8352832b672d2 Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Fri, 13 Dec 2024 14:17:13 +0100 Subject: [PATCH 04/20] wip: data step --- apps/wizard/etl_steps/data.py | 602 ++++++++++++++++++++++++++++++++++ apps/wizard/home.py | 39 +-- 2 files changed, 617 insertions(+), 24 deletions(-) create mode 100644 apps/wizard/etl_steps/data.py diff --git a/apps/wizard/etl_steps/data.py b/apps/wizard/etl_steps/data.py new file mode 100644 index 00000000000..7e44ae62a40 --- /dev/null +++ b/apps/wizard/etl_steps/data.py @@ -0,0 +1,602 @@ +"""Garden phase.""" + +from datetime import date, datetime, timedelta +from pathlib import Path +from typing import Any, Dict, List + +import streamlit as st +from rapidfuzz import fuzz +from sqlalchemy.exc import OperationalError +from typing_extensions import Self + +import etl.grapher_model as gm +from apps.utils.files import add_to_dag, generate_step_to_channel +from apps.wizard import utils +from apps.wizard.etl_steps.utils import TAGS_DEFAULT, remove_playground_notebook +from apps.wizard.utils import set_states +from apps.wizard.utils.components import st_horizontal +from etl.config import DB_HOST, DB_NAME +from etl.db import get_session +from etl.paths import DAG_DIR + +######################################################### +# CONSTANTS ############################################# +######################################################### +st.set_page_config( + page_title="Wizard: Data Step", + page_icon="🪄", +) +st.session_state.submit_form = st.session_state.get("submit_form", False) +st.session_state.data_steps_to_create = st.session_state.get("data_steps_to_create", []) +st.session_state.data_express_mode = st.session_state.get("data_express_mode") +st.session_state.update_steps_selection = st.session_state.get("update_steps_selection", False) + +# Available namespaces +OPTIONS_NAMESPACES = utils.get_namespaces("all") + + +# Get current directory +CURRENT_DIR = Path(__file__).parent +# FIELDS FROM OTHER STEPS +st.session_state["step_name"] = "express" +APP_STATE = utils.AppState() +APP_STATE._previous_step = "snapshot" +# Config style +utils.config_style_html() +# DUMMY defaults +dummy_values = { + "namespace": "dummy", + "version": utils.DATE_TODAY, + "short_name": "dummy", + "snapshot_version": "2020-01-01", + "topic_tags": ["Uncategorized"], +} + +# Get list of available tags from DB (only those used as topic pages) +# If can't connect to DB, use TAGS_DEFAULT instead +# USING_TAGS_DEFAULT = False +# try: +# with get_session() as session: +# tag_list = gm.Tag.load_tags(session) +# tag_list = ["Uncategorized"] + sorted([tag.name for tag in tag_list]) +# except OperationalError: +# USING_TAGS_DEFAULT = True +# tag_list = TAGS_DEFAULT +# TODO: Remove following lines, uncomment lines above +USING_TAGS_DEFAULT = True +tag_list = TAGS_DEFAULT + + +######################################################### +# FUNCTIONS & CLASSES ################################### +######################################################### +class DataForm(utils.StepForm): + """express step form.""" + + step_name: str = "express" + + namespace: str + short_name: str + version: str + update_period_days: int + topic_tags: List[str] + add_to_dag: bool + dag_file: str + # Others + is_private: bool + # Snapshot + snapshot_version: str + file_extension: str + + # Others + namespace_custom: str | None = None + update_period_date: date + + def __init__(self: Self, **data: str | date | bool | int) -> None: # type: ignore[reportInvalidTypeVarUse] + """Construct class.""" + data["add_to_dag"] = data["dag_file"] != utils.ADD_DAG_OPTIONS[0] + + # Handle custom namespace + if ("namespace_custom" in data) and data["namespace_custom"] is not None: + data["namespace"] = str(data["namespace_custom"]) + + # Handle update_period_days. Obtain from date. + if "update_period_date" in data: + assert isinstance(data["update_period_date"], date) + update_period_days = (data["update_period_date"] - date.today()).days + + data["update_period_days"] = update_period_days + + super().__init__(**data) # type: ignore + + def validate(self: Self) -> None: + """Check that fields in form are valid. + + - Add error message for each field (to be displayed in the form). + - Return True if all fields are valid, False otherwise. + """ + # Check other fields (non meta) + fields_required = ["namespace", "short_name", "version", "topic_tags", "snapshot_version", "file_extension"] + fields_snake = ["namespace", "short_name"] + fields_version = ["version", "snapshot_version"] + + self.check_required(fields_required) + self.check_snake(fields_snake) + self.check_is_version(fields_version) + + # Check tags + if (len(self.topic_tags) > 1) and ("Uncategorized" in self.topic_tags): + self.errors["topic_tags"] = "If you choose multiple tags, you cannot choose `Uncategorized`." + + @property + def base_step_name(self) -> str: + """namespace/version/short_name""" + return f"{form.namespace}/{form.version}/{form.short_name}" + + @property + def snapshot_step_uri(self) -> str: + """Get snapshot step URI.""" + return f"snapshot{self.private_suffix}://{self.namespace}/{self.snapshot_version}/{self.short_name}.{self.file_extension}" + + @property + def meadow_step_uri(self) -> str: + """Get garden step name.""" + return f"data{self.private_suffix}://meadow/{self.base_step_name}" + + @property + def garden_step_uri(self) -> str: + """Get garden step name.""" + return f"data{self.private_suffix}://garden/{self.base_step_name}" + + @property + def grapher_step_uri(self) -> str: + """Get garden step name.""" + return f"data{self.private_suffix}://grapher/{self.base_step_name}" + + @property + def dag_path(self) -> Path: + """Get DAG path.""" + return DAG_DIR / self.dag_file + + @property + def private_suffix(self) -> str: + return "-private" if self.is_private else "" + + @property + def meadow_dict(self): + """Get meadow dictionary.""" + return { + "namespace": self.namespace, + "short_name": self.short_name, + "version": self.version, + "add_to_dag": self.add_to_dag, + "dag_file": self.dag_file, + "is_private": self.is_private, + "snapshot_version": self.snapshot_version, + "file_extension": self.file_extension, + "channel": "meadow", + } + + @property + def garden_dict(self): + """Get meadow dictionary.""" + ## HOTFIX 1: filter topic_tags if empty + if self.topic_tags is None or self.topic_tags == []: + topic_tags = "" + ## HOTFIX 2: For some reason, when using cookiecutter only the first element in the list is taken? + ## Hence we need to convert the list to an actual string + else: + topic_tags = "- " + "\n- ".join(self.topic_tags) + return { + "namespace": self.namespace, + "short_name": self.short_name, + "version": self.version, + "meadow_version": self.version, + "add_to_dag": self.add_to_dag, + "dag_file": self.dag_file, + "is_private": self.is_private, + "update_period_days": self.update_period_days, + "topic_tags": topic_tags, + "channel": "garden", + } + + @property + def grapher_dict(self): + """Get meadow dictionary.""" + return { + "namespace": self.namespace, + "short_name": self.short_name, + "version": self.version, + "garden_version": self.version, + "add_to_dag": self.add_to_dag, + "dag_file": self.dag_file, + "is_private": self.is_private, + "channel": "grapher", + } + + def to_dict(self, channel: str): + match channel: + case "meadow": + return self.meadow_dict + case "garden": + return self.garden_dict + case "grapher": + return self.grapher_dict + case _: + raise ValueError(f"Channel `{channel}` not recognized.") + + def create_files(self, channel: str) -> List[Dict[str, Any]]: + # Generate files + DATASET_DIR = generate_step_to_channel( + cookiecutter_path=utils.COOKIE_STEPS[channel], data=self.to_dict(channel) + ) + # Remove playground (by default it is created, we no longer want it) + remove_playground_notebook(DATASET_DIR) + # Add to generated files + generated_files = [ + { + "path": DATASET_DIR / (self.short_name + ".py"), + "language": "python", + "channel": "meadow", + } + ] + if channel == "garden": + generated_files.append( + { + "path": DATASET_DIR / (self.short_name + ".meta.yml"), + "language": "yaml", + "channel": "garden", + } + ) + return generated_files + + def add_steps_to_dag(self) -> str: + if form.add_to_dag: + dag_content = add_to_dag( + dag={ + self.meadow_step_uri: [ + self.snapshot_step_uri, + ], + self.garden_step_uri: [ + self.meadow_step_uri, + ], + self.grapher_step_uri: [ + self.garden_step_uri, + ], + }, + dag_path=self.dag_path, + ) + else: + dag_content = "" + + return dag_content + + +def submit_form() -> None: + """Submit form.""" + # Create form + form = DataForm.from_state() + # Update states with values from form + APP_STATE.update_from_form(form) + + # Submit + utils.set_states({"submit_form": True}) + + +def edit_field() -> None: + """Submit form.""" + utils.set_states({"submit_form": False}) + + +def render_step_selection(): + """Render step selection.""" + name_mapping = { + "meadow": ":material/nature: Meadow", + "garden": ":material/deceased: Garden", + "grapher": ":material/database: Grapher", + } + + # st.write(st.session_state) + with st_horizontal("center"): + # Multi-select (data steps) + with st.container(): + if (st.session_state.update_steps_selection) and (st.session_state.data_express_mode is not None): + st.session_state.data_steps_to_create = ["meadow", "garden", "grapher"] + st.session_state.update_steps_selection = False + + st.segmented_control( + label="Select the steps you want to create", + options=["meadow", "garden", "grapher"], + format_func=lambda option: name_mapping[option], + selection_mode="multi", + help="You can select multiple steps to create.", + key="data_steps_to_create", + ) + # Express mode + with st.container(): + if (st.session_state.data_express_mode is not None) and (len(st.session_state.data_steps_to_create) != 3): + st.session_state.data_express_mode = None + + # Set to false if: data_express_mode is "express" & len(st.session_state.data_steps_to_create) is not 3 + st.segmented_control( + "Express?", + ["express"], + format_func=lambda _: ":material/bolt: Use express mode", + label_visibility="hidden", + help="Express mode will create all steps at once.", + # default=default, + key="data_express_mode", + on_change=lambda: set_states({"update_steps_selection": True}), + ) + + if len(st.session_state.data_steps_to_create) > 0: + return True + return False + + +def render_form(): + """Render form.""" + with form_widget.container(border=True): + if (default_version := APP_STATE.default_value("version", previous_step="snapshot")) == "": + default_version = APP_STATE.default_value("snapshot_version", previous_step="snapshot") + + # Namespace + custom_label = "Custom namespace..." + APP_STATE.st_selectbox_responsive( + st_widget=st.selectbox, + custom_label=custom_label, + key="namespace", + label="Namespace", + help="Institution or topic name", + options=OPTIONS_NAMESPACES, + default_last=dummy_values["namespace"] if APP_STATE.args.dummy_data else OPTIONS_NAMESPACES[0], + on_change=edit_field, + ) + if APP_STATE.vars.get("namespace") == custom_label: + namespace_key = "namespace_custom" + else: + namespace_key = "namespace" + + # Short name (meadow, garden, grapher) + APP_STATE.st_widget( + st_widget=st.text_input, + key="short_name", + label="short name", + help="Dataset short name using [snake case](https://en.wikipedia.org/wiki/Snake_case). Example: natural_disasters", + placeholder="Example: 'cherry_blossom'", + value=dummy_values["short_name"] if APP_STATE.args.dummy_data else None, + on_change=edit_field, + ) + + # Version (meadow, garden, grapher) + APP_STATE.st_widget( + st_widget=st.text_input, + label="version", + help="Version of the dataset (by default, the current date, or exceptionally the publication date).", + key="version", + default_last=default_version, + value=dummy_values["version"] if APP_STATE.args.dummy_data else default_version, + on_change=edit_field, + ) + + # Add to DAG + sorted_dag = sorted( + utils.dag_files, + key=lambda file_name: fuzz.ratio(file_name.replace(".yml", ""), APP_STATE.vars[namespace_key]), + reverse=True, + ) + sorted_dag = [ + utils.dag_not_add_option, + *sorted_dag, + ] + if sorted_dag[1].replace(".yml", "") == APP_STATE.vars[namespace_key]: + default_value = sorted_dag[1] + else: + default_value = "" + APP_STATE.st_widget( + st.selectbox, + label="Add to DAG", + options=sorted_dag, + key="dag_file", + help="Add ETL step to a DAG file. This will allow it to be tracked and executed by the `etl` command.", + default_value=default_value, + on_change=edit_field, + ) + + if "garden" in st.session_state.data_steps_to_create: + # Indicator tags + label = "Indicators tag" + if USING_TAGS_DEFAULT: + label += f"\n\n:red[Using a 2024 March snapshot of the tags. Couldn't connect to database `{DB_NAME}` in host `{DB_HOST}`.]" + + namespace = APP_STATE.vars[namespace_key].replace("_", " ") + default_last = None + for tag in tag_list: + if namespace.lower() == tag.lower(): + default_last = tag + break + APP_STATE.st_widget( + st_widget=st.multiselect, + label=label, + help=( + """ + This tag will be propagated to all dataset's indicators (it will not be assigned to the dataset). + + If you want to use a different tag for a specific indicator you can do it by editing its metadata field `variable.presentation.topic_tags`. + + Exceptionally, and if unsure what to choose, choose tag `Uncategorized`. + """ + ), + key="topic_tags", + options=tag_list, + placeholder="Choose a tag (or multiple)", + default=dummy_values["topic_tags"] if APP_STATE.args.dummy_data else default_last, + on_change=edit_field, + ) + + # Update frequency + today = datetime.today() + APP_STATE.st_widget( + st_widget=st.date_input, + label="When is the next update expected?", + help="Expected date of the next update of this dataset by OWID (typically in a year).", + key="update_period_date", + min_value=today + timedelta(days=1), + default_last=today.replace(year=today.year + 1), + on_change=edit_field, + ) + + if "meadow" in st.session_state.data_steps_to_create: + st.markdown("#### Snapshot") + # Snapshot version + APP_STATE.st_widget( + st.text_input, + label="Snapshot version", + help="Version of the snapshot dataset (by default, the current date, or exceptionally the publication date).", + # placeholder=f"Example: {DATE_TODAY}", + key="snapshot_version", + value=dummy_values["snapshot_version"] if APP_STATE.args.dummy_data else None, + on_change=edit_field, + ) + # File extension + APP_STATE.st_widget( + st.text_input, + label="File extension", + help="File extension (without the '.') of the file to be downloaded.", + placeholder="Example: 'csv', 'xls', 'zip'", + key="file_extension", + value=dummy_values["file_extension"] if APP_STATE.args.dummy_data else None, + on_change=edit_field, + ) + + # Others + st.markdown("#### Other options") + name_mapping = { + "private": ":material/lock: Make dataset private", + "notebook": ":material/skateboarding: Create playground notebook", + # "grapher": ":material/database: Grapher", + } + + st.pills( + label="Select the steps you want to create", + help="Extra options.", + options=["private", "notebook"], + format_func=lambda option: name_mapping[option], + selection_mode="multi", + label_visibility="collapsed", + key="extra_options", + on_change=edit_field, + ) + + # Submit + st.button( + label="Submit", + type="primary", + use_container_width=True, + on_click=submit_form, + ) + + +######################################################### +# MAIN ################################################## +######################################################### +# TITLE +st.title(":material/bolt: Data **:gray[Create steps]**") + +# SELECT MODE +step_selected = render_step_selection() + +# FORM +if step_selected: + form_widget = st.empty() + render_form() + + +######################################################### +# SUBMISSION ############################################ +######################################################### +if st.session_state.submit_form: + # Create form + form = DataForm.from_state() + + if not form.errors: + # Remove form from UI + form_widget.empty() + + # Create files for all steps + generated_files = [] + for channel in ["meadow", "garden", "grapher"]: + generated_files_ = form.create_files(channel) + generated_files.extend(generated_files_) + + # Add lines to DAG + dag_content = form.add_steps_to_dag() + + ####################### + # PREVIEW ############# + ####################### + st.subheader("Generated files") + utils.preview_dag_additions(dag_content, form.dag_path, expanded=True) + + tab_meadow, tab_garden, tab_grapher = st.tabs(["Meadow", "Garden", "Grapher"]) + for f in generated_files: + if f["channel"] == "meadow": + with tab_meadow: + utils.preview_file(f["path"], f["language"]) + elif f["channel"] == "garden": + with tab_garden: + utils.preview_file(f["path"], f["language"]) + elif f["channel"] == "grapher": + with tab_grapher: + utils.preview_file(f["path"], f["language"]) + + ####################### + # NEXT STEPS ########## + ####################### + with tab_meadow: + st.markdown("#### ⏭️ Next") + ## Run step + st.markdown("##### Run ETL meadow step") + st.code( + f"uv run etl run {form.meadow_step_uri} {'--private' if form.is_private else ''}", + language="shellSession", + ) + + with tab_garden: + st.markdown("#### ⏭️ Next") + ## 1/ Harmonize country names + st.markdown("##### Harmonize country names") + st.markdown("Run it in your terminal:") + st.code( + f"uv run etl harmonize data/meadow/{form.base_step_name}/{form.short_name}.feather country etl/steps/data/garden/{form.base_step_name}.countries.json", + "shellSession", + ) + st.markdown("Or run it on Wizard") + utils.st_page_link( + "harmonizer", + use_container_width=True, + help="You will leave this page, and the guideline text will be hidden.", + ) + + # 2/ Run etl step + st.markdown("##### Run ETL step") + st.markdown("After editing the code of your Garden step, run the following command:") + st.code( + f"uv run etl run {form.garden_step_uri} {'--private' if form.is_private else ''}", + "shellSession", + ) + + with tab_grapher: + st.markdown("#### ⏭️ Next") + # 1/ PR + st.markdown("##### Pull request") + st.markdown("Create a pull request in [ETL](https://github.com/owid/etl), get it reviewed and merged.") + + # Prompt user + st.toast("Templates generated. Read the next steps.", icon="✅") + + # Update config + utils.update_wizard_defaults_from_form(form=form) + else: + st.write(form.errors) + st.error("Form not submitted! Check errors!") diff --git a/apps/wizard/home.py b/apps/wizard/home.py index bde6d576242..686319d2d95 100644 --- a/apps/wizard/home.py +++ b/apps/wizard/home.py @@ -106,35 +106,25 @@ def create_card( # 1. Classic: Snapshot -> Meadow -> Garden + Grapher # 2. Fast Track: Fast Track + Grapher - # 1/ First row for [Snapshot, Meadow, Garden, Grapher] - pages = [ - { - "entrypoint": steps[step]["entrypoint"], - "title": steps[step]["title"], - "image_url": steps[step]["image_url"], - # "alias": step, - } - for step in ["snapshot", "meadow", "garden", "grapher"] - if steps[step]["enable"] - ] - if len(pages) > 0: - columns = st.columns(len(pages)) - for i, page in enumerate(pages): - with columns[i]: - create_card(**page, small=True) - - # 2 EXPRESS + # 1/ CLASSIC: Snapshot + Data if steps["fasttrack"]["enable"]: col1, col2 = st.columns([1, 3]) + with col1: + create_card( + entrypoint=steps["snapshot"]["entrypoint"], + title=steps["snapshot"]["title"], + image_url=steps["snapshot"]["image_url"], + custom_styles={"height": "100px"}, + ) with col2: create_card( - entrypoint=steps["express"]["entrypoint"], - title=steps["express"]["title"], - image_url=steps["express"]["image_url"], - custom_styles={"height": "50px"}, + entrypoint=steps["data"]["entrypoint"], + title=steps["data"]["title"], + image_url=steps["data"]["image_url"], + custom_styles={"height": "100px"}, ) - # 3/ FAST TRACK + # 2/ FAST TRACK if steps["fasttrack"]["enable"]: create_card( entrypoint=steps["fasttrack"]["entrypoint"], @@ -169,11 +159,12 @@ def create_card( image_url=app["image_url"], text=text, ) - st.divider() ######################### # Legacy ######################### + st.divider() + if "legacy" in WIZARD_CONFIG: section_legacy = WIZARD_CONFIG["legacy"] apps = [app for app in section_legacy["apps"] if app["enable"]] From f909c263fa83c4b144c5589258f58d41f4615cf6 Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Fri, 13 Dec 2024 14:26:19 +0100 Subject: [PATCH 05/20] move steps to 'legacy' section --- apps/wizard/config/config.yml | 71 ++++++++++++++++++----------------- apps/wizard/etl_steps/data.py | 9 ++++- 2 files changed, 44 insertions(+), 36 deletions(-) diff --git a/apps/wizard/config/config.yml b/apps/wizard/config/config.yml index c28e8ab6d4f..3252ba65f2e 100644 --- a/apps/wizard/config/config.yml +++ b/apps/wizard/config/config.yml @@ -73,41 +73,6 @@ etl: image_url: "https://upload.wikimedia.org/wikipedia/commons/b/be/Alonso_%28Renault%29_qualifying_at_USGP_2005.jpg" sections: - - title: "ETL Steps (legacy)" - description: "Keeping this temporary" - apps: - - alias: express - title: "Express" - description: "Add all data steps." - entrypoint: etl_steps/express.py - icon: ":material/bolt:" - image_url: "https://upload.wikimedia.org/wikipedia/commons/b/b3/Indochinese_leopard.jpg" - disable: - "production": True - - alias: meadow - title: "Meadow" - description: "Add meadow step." - entrypoint: etl_steps/meadow.py - icon: ":material/nature:" - image_url: "https://upload.wikimedia.org/wikipedia/commons/thumb/5/5e/Blumenwiese_bei_Obermaiselstein05.jpg/1024px-Blumenwiese_bei_Obermaiselstein05.jpg" - disable: - "production": True - - alias: garden - title: "Garden" - description: "Add garden step." - entrypoint: etl_steps/garden.py - icon: ":material/deceased:" - image_url: "https://upload.wikimedia.org/wikipedia/commons/2/27/Butchart_gardens.JPG" - disable: - "production": True - - alias: grapher - title: "Grapher" - description: "Add grapher step." - entrypoint: etl_steps/grapher.py - icon: ":material/database:" - image_url: "https://pbs.twimg.com/media/EbHwdjwUcAEfen4?format=jpg&name=large" - disable: - "production": True - title: "Data curation" description: |- Updates, data edits, etc. @@ -261,6 +226,42 @@ sections: disable: "production": True "staging": True + + - title: "ETL Steps (legacy)" + description: "Keeping this temporary" + apps: + - alias: express + title: "Express" + description: "Add all data steps." + entrypoint: etl_steps/express.py + icon: ":material/bolt:" + image_url: "https://upload.wikimedia.org/wikipedia/commons/b/b3/Indochinese_leopard.jpg" + disable: + "production": True + - alias: meadow + title: "Meadow" + description: "Add meadow step." + entrypoint: etl_steps/meadow.py + icon: ":material/nature:" + image_url: "https://upload.wikimedia.org/wikipedia/commons/thumb/5/5e/Blumenwiese_bei_Obermaiselstein05.jpg/1024px-Blumenwiese_bei_Obermaiselstein05.jpg" + disable: + "production": True + - alias: garden + title: "Garden" + description: "Add garden step." + entrypoint: etl_steps/garden.py + icon: ":material/deceased:" + image_url: "https://upload.wikimedia.org/wikipedia/commons/2/27/Butchart_gardens.JPG" + disable: + "production": True + - alias: grapher + title: "Grapher" + description: "Add grapher step." + entrypoint: etl_steps/grapher.py + icon: ":material/database:" + image_url: "https://pbs.twimg.com/media/EbHwdjwUcAEfen4?format=jpg&name=large" + disable: + "production": True # legacy: # description: |- # The pages below are legacy now. They are kept in case the new pages are not working properly. diff --git a/apps/wizard/etl_steps/data.py b/apps/wizard/etl_steps/data.py index 7e44ae62a40..e6814152ff1 100644 --- a/apps/wizard/etl_steps/data.py +++ b/apps/wizard/etl_steps/data.py @@ -13,7 +13,7 @@ from apps.utils.files import add_to_dag, generate_step_to_channel from apps.wizard import utils from apps.wizard.etl_steps.utils import TAGS_DEFAULT, remove_playground_notebook -from apps.wizard.utils import set_states +from apps.wizard.utils import set_states, st_page_link from apps.wizard.utils.components import st_horizontal from etl.config import DB_HOST, DB_NAME from etl.db import get_session @@ -600,3 +600,10 @@ def render_form(): else: st.write(form.errors) st.error("Form not submitted! Check errors!") + + +st.divider() +st.subheader("Legacy") +st_page_link("meadow") +st_page_link("garden") +st_page_link("grapher") From 8084cfa0a4066eb343a5d43ebb5e95ad5bf59240 Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Fri, 13 Dec 2024 14:43:59 +0100 Subject: [PATCH 06/20] future todo --- apps/wizard/app.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apps/wizard/app.py b/apps/wizard/app.py index 4b6ea6440f2..04636cc6c8e 100644 --- a/apps/wizard/app.py +++ b/apps/wizard/app.py @@ -89,4 +89,7 @@ # LOGO -st.logo(str(DOCS_DIR / "assets/wizard-logo.png")) +st.logo( + str(DOCS_DIR / "assets/wizard-logo.png"), + # link="https://google.com", # TODO: would be cool if we could link to an internal page (and not only external). Check streamlit issues, and consider creating one. +) From b8f1255f7cf395dfb5a95a6b578b451589105f5e Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Sun, 15 Dec 2024 02:12:45 +0100 Subject: [PATCH 07/20] wip --- apps/wizard/config/config.yml | 9 +- apps/wizard/etl_steps/data.py | 330 +++++++++++++++++++++------------ apps/wizard/utils/__init__.py | 18 +- apps/wizard/utils/step_form.py | 1 - 4 files changed, 223 insertions(+), 135 deletions(-) diff --git a/apps/wizard/config/config.yml b/apps/wizard/config/config.yml index 3252ba65f2e..195e0cabd07 100644 --- a/apps/wizard/config/config.yml +++ b/apps/wizard/config/config.yml @@ -62,7 +62,8 @@ etl: title: "Data step" entrypoint: etl_steps/data.py icon: ":material/table:" - image_url: "https://upload.wikimedia.org/wikipedia/commons/b/b3/Indochinese_leopard.jpg" + image_url: "https://media.gettyimages.com/id/1272610693/es/v%C3%ADdeo/muro-de-perspectiva-del-fondo-del-patr%C3%B3n-digital-del-c%C3%B3digo-binario.jpg?s=640x640&k=20&c=Pb4m4UbGiVZEuQ8egLm2IYtLLmQxncBFFa1zR87-St4%3D" + description: "Meadow, Garden, Grapher." disable: "production": True fasttrack: @@ -132,7 +133,7 @@ sections: image_url: "https://upload.wikimedia.org/wikipedia/commons/c/c3/NGC_4414_%28NASA-med%29.jpg" - title: "Producer analytics" alias: producer-analytics - description: "Extract analytics to share with data producers" + description: "Share analytics with data producers" maintainer: "@pablo" entrypoint: app_pages/producer_analytics.py icon: ":material/analytics:" @@ -163,7 +164,7 @@ sections: apps: - title: "Insight search" alias: insight_search - description: "Browse data insights by their semantic similarity" + description: "Smart-browse DIs" maintainer: "@pablo" entrypoint: app_pages/insight_search.py icon: ":material/search:" @@ -196,7 +197,7 @@ sections: image_url: "https://t3.ftcdn.net/jpg/06/26/23/36/360_F_626233679_tesiSRP9Jinq5wS0ZgbdJ6k5adupmgKl.jpg" - title: "Chart animation" alias: chart-animation - description: "Create an animated GIF or a video from a chart" + description: "Animate charts (GIF/video)" maintainer: "@pablo" entrypoint: app_pages/chart_animation.py icon: ":material/animated_images:" diff --git a/apps/wizard/etl_steps/data.py b/apps/wizard/etl_steps/data.py index e6814152ff1..7b283c77bd0 100644 --- a/apps/wizard/etl_steps/data.py +++ b/apps/wizard/etl_steps/data.py @@ -2,7 +2,7 @@ from datetime import date, datetime, timedelta from pathlib import Path -from typing import Any, Dict, List +from typing import Any, Dict, List, Optional import streamlit as st from rapidfuzz import fuzz @@ -27,8 +27,8 @@ page_icon="🪄", ) st.session_state.submit_form = st.session_state.get("submit_form", False) -st.session_state.data_steps_to_create = st.session_state.get("data_steps_to_create", []) -st.session_state.data_express_mode = st.session_state.get("data_express_mode") +st.session_state["data.steps_to_create"] = st.session_state.get("data.steps_to_create", []) +st.session_state["data_steps_to_create"] = st.session_state.get("data_steps_to_create") st.session_state.update_steps_selection = st.session_state.get("update_steps_selection", False) # Available namespaces @@ -38,7 +38,7 @@ # Get current directory CURRENT_DIR = Path(__file__).parent # FIELDS FROM OTHER STEPS -st.session_state["step_name"] = "express" +st.session_state["step_name"] = "data" APP_STATE = utils.AppState() APP_STATE._previous_step = "snapshot" # Config style @@ -65,6 +65,12 @@ # TODO: Remove following lines, uncomment lines above USING_TAGS_DEFAULT = True tag_list = TAGS_DEFAULT +# Step names +STEP_NAME_PRESENT = { + "meadow": ":material/nature: Meadow", + "garden": ":material/deceased: Garden", + "grapher": ":material/database: Grapher", +} ######################################################### @@ -73,26 +79,28 @@ class DataForm(utils.StepForm): """express step form.""" - step_name: str = "express" + step_name: str = "data" + # List of steps + steps_to_create: List[str] + # Common namespace: str + namespace_custom: Optional[str] = None # Custom short_name: str version: str - update_period_days: int - topic_tags: List[str] add_to_dag: bool dag_file: str - # Others is_private: bool - # Snapshot - snapshot_version: str - file_extension: str - - # Others - namespace_custom: str | None = None - update_period_date: date - - def __init__(self: Self, **data: str | date | bool | int) -> None: # type: ignore[reportInvalidTypeVarUse] + # Only in Garden + snapshot_version: Optional[str] = None + file_extension: Optional[str] = None + notebook: Optional[bool] = None + # Only in Garden + update_period_days: Optional[int] = None + topic_tags: Optional[List[str]] = None + update_period_date: Optional[date] = None # Custom + + def __init__(self: Self, **data: Any) -> None: # type: ignore[reportInvalidTypeVarUse] """Construct class.""" data["add_to_dag"] = data["dag_file"] != utils.ADD_DAG_OPTIONS[0] @@ -107,6 +115,11 @@ def __init__(self: Self, **data: str | date | bool | int) -> None: # type: igno data["update_period_days"] = update_period_days + # Extra options + data["is_private"] = True if "private" in data["extra_options"] else False + data["notebook"] = True if "notebook" in data["extra_options"] else False + + # st.write(data) super().__init__(**data) # type: ignore def validate(self: Self) -> None: @@ -115,18 +128,27 @@ def validate(self: Self) -> None: - Add error message for each field (to be displayed in the form). - Return True if all fields are valid, False otherwise. """ - # Check other fields (non meta) - fields_required = ["namespace", "short_name", "version", "topic_tags", "snapshot_version", "file_extension"] + # Default common checks + fields_required = ["namespace", "short_name", "version"] fields_snake = ["namespace", "short_name"] - fields_version = ["version", "snapshot_version"] + fields_version = ["version"] + + # Extra checks for particular steps + if "meadow" in self.steps_to_create: + fields_required += ["snapshot_version", "file_extension"] + fields_version += ["snapshot_version"] + if "garden" in self.steps_to_create: + fields_required += ["topic_tags"] self.check_required(fields_required) self.check_snake(fields_snake) self.check_is_version(fields_version) # Check tags - if (len(self.topic_tags) > 1) and ("Uncategorized" in self.topic_tags): - self.errors["topic_tags"] = "If you choose multiple tags, you cannot choose `Uncategorized`." + if "garden" in self.steps_to_create: + assert isinstance(self.topic_tags, list), "topic_tags must be a list! Should have been ensured actually!" + if (len(self.topic_tags) > 1) and ("Uncategorized" in self.topic_tags): + self.errors["topic_tags"] = "If you choose multiple tags, you cannot choose `Uncategorized`." @property def base_step_name(self) -> str: @@ -230,14 +252,16 @@ def create_files(self, channel: str) -> List[Dict[str, Any]]: DATASET_DIR = generate_step_to_channel( cookiecutter_path=utils.COOKIE_STEPS[channel], data=self.to_dict(channel) ) - # Remove playground (by default it is created, we no longer want it) - remove_playground_notebook(DATASET_DIR) + # Remove playground notebook if not needed + if channel != "garden" or not self.notebook: + remove_playground_notebook(DATASET_DIR) + # Add to generated files generated_files = [ { "path": DATASET_DIR / (self.short_name + ".py"), "language": "python", - "channel": "meadow", + "channel": channel, } ] if channel == "garden": @@ -253,17 +277,7 @@ def create_files(self, channel: str) -> List[Dict[str, Any]]: def add_steps_to_dag(self) -> str: if form.add_to_dag: dag_content = add_to_dag( - dag={ - self.meadow_step_uri: [ - self.snapshot_step_uri, - ], - self.garden_step_uri: [ - self.meadow_step_uri, - ], - self.grapher_step_uri: [ - self.garden_step_uri, - ], - }, + dag=self.dag(), dag_path=self.dag_path, ) else: @@ -271,6 +285,16 @@ def add_steps_to_dag(self) -> str: return dag_content + def dag(self) -> Dict[str, Any]: + dag = {} + if "meadow" in self.steps_to_create: + dag[self.meadow_step_uri] = [self.snapshot_step_uri] + if "garden" in self.steps_to_create: + dag[self.garden_step_uri] = [self.meadow_step_uri] + if "grapher" in self.steps_to_create: + dag[self.grapher_step_uri] = [self.garden_step_uri] + return dag + def submit_form() -> None: """Submit form.""" @@ -290,34 +314,31 @@ def edit_field() -> None: def render_step_selection(): """Render step selection.""" - name_mapping = { - "meadow": ":material/nature: Meadow", - "garden": ":material/deceased: Garden", - "grapher": ":material/database: Grapher", - } - # st.write(st.session_state) with st_horizontal("center"): # Multi-select (data steps) with st.container(): - if (st.session_state.update_steps_selection) and (st.session_state.data_express_mode is not None): - st.session_state.data_steps_to_create = ["meadow", "garden", "grapher"] + if (st.session_state.update_steps_selection) and (st.session_state["data_steps_to_create"] is not None): + st.session_state["data.steps_to_create"] = ["meadow", "garden", "grapher"] st.session_state.update_steps_selection = False st.segmented_control( label="Select the steps you want to create", options=["meadow", "garden", "grapher"], - format_func=lambda option: name_mapping[option], + format_func=lambda option: STEP_NAME_PRESENT[option], selection_mode="multi", help="You can select multiple steps to create.", - key="data_steps_to_create", + key="data.steps_to_create", + on_change=edit_field, ) # Express mode with st.container(): - if (st.session_state.data_express_mode is not None) and (len(st.session_state.data_steps_to_create) != 3): - st.session_state.data_express_mode = None + if (st.session_state["data_steps_to_create"] is not None) and ( + len(st.session_state["data.steps_to_create"]) != 3 + ): + st.session_state["data_steps_to_create"] = None - # Set to false if: data_express_mode is "express" & len(st.session_state.data_steps_to_create) is not 3 + # Set to false if: data_steps_to_create is "express" & len(st.session_state["data.steps_to_create"]) is not 3 st.segmented_control( "Express?", ["express"], @@ -325,18 +346,18 @@ def render_step_selection(): label_visibility="hidden", help="Express mode will create all steps at once.", # default=default, - key="data_express_mode", - on_change=lambda: set_states({"update_steps_selection": True}), + key="data_steps_to_create", + on_change=lambda: set_states({"update_steps_selection": True, "submit_form": False}), ) - if len(st.session_state.data_steps_to_create) > 0: + if len(st.session_state["data.steps_to_create"]) > 0: return True return False def render_form(): """Render form.""" - with form_widget.container(border=True): + with st.expander("**Form**", expanded=True): if (default_version := APP_STATE.default_value("version", previous_step="snapshot")) == "": default_version = APP_STATE.default_value("snapshot_version", previous_step="snapshot") @@ -403,7 +424,7 @@ def render_form(): on_change=edit_field, ) - if "garden" in st.session_state.data_steps_to_create: + if "garden" in st.session_state["data.steps_to_create"]: # Indicator tags label = "Indicators tag" if USING_TAGS_DEFAULT: @@ -446,7 +467,7 @@ def render_form(): on_change=edit_field, ) - if "meadow" in st.session_state.data_steps_to_create: + if "meadow" in st.session_state["data.steps_to_create"]: st.markdown("#### Snapshot") # Snapshot version APP_STATE.st_widget( @@ -484,7 +505,7 @@ def render_form(): format_func=lambda option: name_mapping[option], selection_mode="multi", label_visibility="collapsed", - key="extra_options", + key="data.extra_options", on_change=edit_field, ) @@ -497,6 +518,109 @@ def render_form(): ) +def render_instructions(form): + for channel in ["meadow", "garden", "grapher"]: + if channel in form.steps_to_create: + with st.container(border=True): + st.markdown(f"##### **{STEP_NAME_PRESENT.get(channel, channel)}**") + render_instructions_step(channel, form) + + +def render_instructions_step(channel, form=None): + if channel == "meadow": + render_instructions_meadow(form) + elif channel == "garden": + render_instructions_garden(form) + elif channel == "grapher": + render_instructions_grapher(form) + + +def render_instructions_meadow(form=None): + ## Run step + st.markdown("**1) Run Meadow step**") + if form is None: + st.code( + "uv run etl run data://meadow/namespace/version/short_name", + language="shellSession", + wrap_lines=True, + line_numbers=True, + ) + st.markdown("Use `--private` if the dataset is private.") + else: + st.code( + f"uv run etl run {form.meadow_step_uri} {'--private' if form.is_private else ''}", + language="shellSession", + wrap_lines=True, + line_numbers=True, + ) + + +def render_instructions_garden(form=None): + ## 1/ Harmonize country names + st.markdown("**1) Harmonize country names**") + st.markdown("Run it in your terminal:") + if form is None: + st.code( + "uv run etl harmonize data/meadow/version/short_name/table_name.feather country etl/steps/data/garden/version/short_name.countries.json", + "shellSession", + wrap_lines=True, + line_numbers=True, + ) + else: + st.code( + f"uv run etl harmonize data/meadow/{form.base_step_name}/{form.short_name}.feather country etl/steps/data/garden/{form.base_step_name}.countries.json", + "shellSession", + wrap_lines=True, + line_numbers=True, + ) + st.markdown("Or run it on Wizard") + utils.st_page_link( + "harmonizer", + use_container_width=True, + help="You will leave this page, and the guideline text will be hidden.", + ) + + # 2/ Run etl step + st.markdown("**2) Run Garden step**") + st.markdown("After editing the code of your Garden step, run the following command:") + if form is None: + st.code( + "uv run etl run data://garden/namespace/version/short_name", + "shellSession", + wrap_lines=True, + line_numbers=True, + ) + st.markdown("Use `--private` if the dataset is private.") + else: + st.code( + f"uv run etl run {form.garden_step_uri} {'--private' if form.is_private else ''}", + "shellSession", + wrap_lines=True, + line_numbers=True, + ) + + +def render_instructions_grapher(form=None): + st.markdown("**1) Run Grapher step**") + if form is None: + st.code( + "uv run etl run data://meadow/namespace/version/short_name", + language="shellSession", + wrap_lines=True, + line_numbers=True, + ) + st.markdown("Use `--private` if the dataset is private.") + else: + st.code( + f"uv run etl run {form.grapher_step_uri} {'--private' if form.is_private else ''}", + language="shellSession", + wrap_lines=True, + line_numbers=True, + ) + st.markdown("**2) Pull request**") + st.markdown("Create a pull request in [ETL](https://github.com/owid/etl), get it reviewed and merged.") + + ######################################################### # MAIN ################################################## ######################################################### @@ -508,9 +632,10 @@ def render_form(): # FORM if step_selected: - form_widget = st.empty() + # form_widget = st.empty() render_form() - +else: + st.warning("Select at least one step to create.") ######################################################### # SUBMISSION ############################################ @@ -519,78 +644,37 @@ def render_form(): # Create form form = DataForm.from_state() + # st.write(form.model_dump()) if not form.errors: # Remove form from UI - form_widget.empty() + # form_widget.empty() # Create files for all steps - generated_files = [] - for channel in ["meadow", "garden", "grapher"]: + generated_files = {} + for channel in form.steps_to_create: generated_files_ = form.create_files(channel) - generated_files.extend(generated_files_) + generated_files[channel] = generated_files_ # Add lines to DAG dag_content = form.add_steps_to_dag() - ####################### - # PREVIEW ############# - ####################### - st.subheader("Generated files") - utils.preview_dag_additions(dag_content, form.dag_path, expanded=True) - - tab_meadow, tab_garden, tab_grapher = st.tabs(["Meadow", "Garden", "Grapher"]) - for f in generated_files: - if f["channel"] == "meadow": - with tab_meadow: - utils.preview_file(f["path"], f["language"]) - elif f["channel"] == "garden": - with tab_garden: - utils.preview_file(f["path"], f["language"]) - elif f["channel"] == "grapher": - with tab_grapher: - utils.preview_file(f["path"], f["language"]) - - ####################### - # NEXT STEPS ########## - ####################### - with tab_meadow: - st.markdown("#### ⏭️ Next") - ## Run step - st.markdown("##### Run ETL meadow step") - st.code( - f"uv run etl run {form.meadow_step_uri} {'--private' if form.is_private else ''}", - language="shellSession", - ) + ######################## + # PREVIEW & NEXT STEPS # + ######################## + utils.preview_dag_additions(dag_content, form.dag_path, prefix="**DAG**", expanded=True) - with tab_garden: - st.markdown("#### ⏭️ Next") - ## 1/ Harmonize country names - st.markdown("##### Harmonize country names") - st.markdown("Run it in your terminal:") - st.code( - f"uv run etl harmonize data/meadow/{form.base_step_name}/{form.short_name}.feather country etl/steps/data/garden/{form.base_step_name}.countries.json", - "shellSession", - ) - st.markdown("Or run it on Wizard") - utils.st_page_link( - "harmonizer", - use_container_width=True, - help="You will leave this page, and the guideline text will be hidden.", - ) + # st.write(generated_files) + tab_instructions, tab_files = st.tabs(["Instructions", "Files"]) - # 2/ Run etl step - st.markdown("##### Run ETL step") - st.markdown("After editing the code of your Garden step, run the following command:") - st.code( - f"uv run etl run {form.garden_step_uri} {'--private' if form.is_private else ''}", - "shellSession", - ) + with tab_files: + for channel in ["meadow", "garden", "grapher"]: + if channel in generated_files: + # st.markdown(f"**{channel.title()}**") + for f in generated_files[channel]: + utils.preview_file(f["path"], f"**{STEP_NAME_PRESENT.get(channel)}**", f["language"]) - with tab_grapher: - st.markdown("#### ⏭️ Next") - # 1/ PR - st.markdown("##### Pull request") - st.markdown("Create a pull request in [ETL](https://github.com/owid/etl), get it reviewed and merged.") + with tab_instructions: + render_instructions(form) # Prompt user st.toast("Templates generated. Read the next steps.", icon="✅") @@ -602,8 +686,8 @@ def render_form(): st.error("Form not submitted! Check errors!") -st.divider() -st.subheader("Legacy") -st_page_link("meadow") -st_page_link("garden") -st_page_link("grapher") +# st.divider() +# st.subheader("Legacy") +# st_page_link("meadow") +# st_page_link("garden") +# st_page_link("grapher") diff --git a/apps/wizard/utils/__init__.py b/apps/wizard/utils/__init__.py index 82cf0de820b..b3f445dc1c2 100644 --- a/apps/wizard/utils/__init__.py +++ b/apps/wizard/utils/__init__.py @@ -166,13 +166,14 @@ def __get__(self, owner_self: Self, owner_cls: Self): # type: ignore[reportInco class AppState: """Management of state variables shared across different apps.""" - steps: List[str] = ["snapshot", "meadow", "garden", "grapher", "explorers", "express"] + steps: List[str] = ["snapshot", "meadow", "garden", "grapher", "explorers", "express", "data"] dataset_edit: Dict[str, Dataset | None] = { "snapshot": None, "meadow": None, "garden": None, "grapher": None, "express": None, + "data": None, } _previous_step: str | None = None @@ -200,6 +201,9 @@ def _init_steps(self: "AppState") -> None: self.default_steps["express"]["snapshot_version"] = DATE_TODAY self.default_steps["express"]["version"] = DATE_TODAY + self.default_steps["data"]["snapshot_version"] = DATE_TODAY + self.default_steps["data"]["version"] = DATE_TODAY + self.default_steps["meadow"]["version"] = DATE_TODAY self.default_steps["meadow"]["snapshot_version"] = DATE_TODAY self.default_steps["meadow"]["generate_notebook"] = defaults["template"]["meadow"]["generate_notebook"] @@ -315,10 +319,10 @@ def previous_step(self: "AppState") -> str | None: """ if self._previous_step is None: self._check_step() - if self.step not in {"explorer", "express"}: + if self.step not in {"explorer", "express", "data"}: idx = max(self.steps.index(self.step) - 1, 0) self._previous_step = self.steps[idx] - elif self.step == "express": + elif self.step in {"express", "data"}: self._previous_step = "snapshot" return self._previous_step @@ -440,18 +444,18 @@ def config_style_html() -> None: ) -def preview_file(file_path: str | Path, language: str = "python") -> None: +def preview_file(file_path: str | Path, prefix: str = "File", language: str = "python") -> None: """Preview file in streamlit.""" with open(file_path, "r") as f: code = f.read() - with st.expander(f"File: `{file_path}`", expanded=False): + with st.expander(f"{prefix}: `{file_path}`", expanded=False): st.code(code, language=language) -def preview_dag_additions(dag_content: str, dag_path: str | Path, expanded: bool = False) -> None: +def preview_dag_additions(dag_content: str, dag_path: str | Path, prefix: str = "File", expanded: bool = False) -> None: """Preview DAG additions.""" if dag_content: - with st.expander(f"File: `{dag_path}`", expanded=expanded): + with st.expander(f"{prefix}: `{dag_path}`", expanded=expanded): st.code(dag_content, "yaml") diff --git a/apps/wizard/utils/step_form.py b/apps/wizard/utils/step_form.py index 1d0a4ecea94..03f45feb943 100644 --- a/apps/wizard/utils/step_form.py +++ b/apps/wizard/utils/step_form.py @@ -33,7 +33,6 @@ def from_state(cls: Type[Self]) -> Self: """Build object from session_state variables.""" session_state = cast(Dict[str, Any], dict(st.session_state)) data = cls.filter_relevant_fields(step_name=st.session_state["step_name"], data=session_state) - # st.write(data) return cls(**data) def validate(self: Self) -> None: # type: ignore[reportIncompatibleMethodOverride] From b598127bb8d91dc147609acf6588673264823a5d Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Sun, 15 Dec 2024 02:23:04 +0100 Subject: [PATCH 08/20] modularize harmonizer --- apps/wizard/app_pages/harmonizer/__init__.py | 0 apps/wizard/app_pages/harmonizer/app.py | 11 + apps/wizard/app_pages/harmonizer/utils.py | 300 +++++++++++++++++++ apps/wizard/config/config.yml | 2 +- 4 files changed, 312 insertions(+), 1 deletion(-) create mode 100644 apps/wizard/app_pages/harmonizer/__init__.py create mode 100644 apps/wizard/app_pages/harmonizer/app.py create mode 100644 apps/wizard/app_pages/harmonizer/utils.py diff --git a/apps/wizard/app_pages/harmonizer/__init__.py b/apps/wizard/app_pages/harmonizer/__init__.py new file mode 100644 index 00000000000..e69de29bb2d diff --git a/apps/wizard/app_pages/harmonizer/app.py b/apps/wizard/app_pages/harmonizer/app.py new file mode 100644 index 00000000000..f3ea21098ac --- /dev/null +++ b/apps/wizard/app_pages/harmonizer/app.py @@ -0,0 +1,11 @@ +import streamlit as st + +from .utils import render + +# PAGE CONFIG +st.set_page_config( + page_title="Wizard: Entity Harmonizer", + page_icon="🪄", +) + +render() diff --git a/apps/wizard/app_pages/harmonizer/utils.py b/apps/wizard/app_pages/harmonizer/utils.py new file mode 100644 index 00000000000..9ab8759ad33 --- /dev/null +++ b/apps/wizard/app_pages/harmonizer/utils.py @@ -0,0 +1,300 @@ +"""Harmonize entities.""" + +import json +from operator import itemgetter +from pathlib import Path +from typing import List, cast + +import streamlit as st +from owid.catalog import Dataset + +from apps.wizard.utils import get_datasets_in_etl, set_states +from etl.config import ENV_IS_REMOTE +from etl.harmonize import Harmonizer +from etl.paths import STEP_DIR +from etl.steps import load_from_uri + +# Get session state +path = None +if ("steps" in st.session_state) and ("garden" in st.session_state.steps): + garden_vars = st.session_state["steps"]["garden"] + if ("namespace" in garden_vars) and ("meadow_version" in garden_vars) and ("short_name" in garden_vars): + path = f"data://meadow/{garden_vars['namespace']}/{garden_vars['meadow_version']}/{garden_vars['short_name']}" + +# RANK OF PREFERED TABLE NAMES +TABLE_NAME_PRIORITIES = ["main", "core"] +# RANK OF PREFERED COLUMN NAMES (for country) +COLUMN_NAME_PRIORITIES = ["country", "state", "location", "region", "iso"] + + +#################################################################################################### +# FUNCTIONS & other configs +#################################################################################################### +def sort_values(values: List[str], values_priority: List[str]) -> List[str]: + """Sort values based on priorities. + + For instance, we want column 'country' to be shown first. The top prefered values are in `values_priority`. + The rest is sorted alphabetically. + """ + # Build score list + ## [(value_1, score_1), (value_2, score_2), ...] + ## score 0 means no priority at all, score X (integer) means it fully matched a priority value, score X.5 means it partially matched a priority value + values_with_priority = [] + for value in values[:]: + added = False + for score, value_priority in enumerate(values_priority, start=1): + if value == value_priority: + values_with_priority.append((value, -score)) + added = True + break + elif value in value_priority: + values_with_priority.append((value, -score - 0.5)) + added = True + break + else: + continue + if not added: + values_with_priority.append((value, 0)) + + # Sort values + values_with_priority = sorted(values_with_priority, key=itemgetter(1)) + values_top = [v[0] for v in values_with_priority if v[1] != 0] + values_bottom = sorted([v[0] for v in values_with_priority if v[1] == 0]) + values = values_top + values_bottom + return values + + +def sort_table_names(dataset: Dataset) -> List[str]: + """Sort table names based on priorities. + + For instance, we want table 'location' to be shown first. The top prefered values are in `values_priority`. + The rest is sorted alphabetically. + """ + # Init + if dataset.metadata.short_name is not None: + priorities = [dataset.metadata.short_name] + TABLE_NAME_PRIORITIES + else: + priorities = TABLE_NAME_PRIORITIES + table_names = sort_values(dataset.table_names, priorities) + + return table_names + + +def sort_indicators(indicators: List[str]) -> List[str]: + """Sort indicators based on priorities. + + For instance, we want column 'country' to be shown first. The top prefered values are in `values_priority`. + The rest is sorted alphabetically. + """ + # Init + indicators = sort_values(indicators, COLUMN_NAME_PRIORITIES) + return indicators + + +def render(): + # Page config + st.title(":material/music_note: Entity Harmonizer") + + # Set states + st.session_state["show_all"] = st.session_state.get("show_all", False) + st.session_state["entity_mapping"] = st.session_state.get("entity_mapping", {}) + + # OTHER PARAMS + NUM_SUGGESTIONS = 1000 + + # INTRO + st.markdown( + "Harmonize entity names with this tool. Start by loading an indicator from a dataset below. If you find any problem, remember you can still run `etl harmonize` in the terminal." + ) + #################################################################################################### + # SELECT DATASET, TABLE and INDICATOR + #################################################################################################### + # 1/ DATASET + # show_all = False + options = get_datasets_in_etl( + snapshots=False, + prefixes=None if st.session_state.show_all else ["data://meadow"], + ) + option = st.selectbox( + label="Select a dataset", + placeholder="Select a dataset", + options=options, + index=options.index(path) if path in options else None, + help="By default, only meadow datasets are shown in the dataset search bar.", + ) + st.toggle( + "Show all datasets", + help="By default, only meadow datasets are shown in the dataset search bar.", + on_change=lambda: set_states({"show_all": not st.session_state.show_all}), + ) + + if option: + # Load dataset + try: + dataset = cast(Dataset, load_from_uri(option)) + except FileNotFoundError as e: + st.error(e) + st.stop() + + # 2/ TABLE + table_names = sort_table_names(dataset) + table_name = st.selectbox( + "Select a table", + options=table_names, + placeholder="Choose a table", + index=None if len(table_names) != 1 else 0, + ) + + if table_name: + tb = dataset[table_name].reset_index() + + # 3/ INDICATOR + columns = sort_indicators(tb.columns) + column_name = st.selectbox( + label="Select the entity column", + options=columns, + placeholder="Choose an indicator", + index=0 if set(COLUMN_NAME_PRIORITIES).intersection(set(columns)) else None, + ) + + #################################################################################################### + # HARMONIZATION (generation) + #################################################################################################### + if column_name: + # Transform to string if category + if tb[column_name].apply(type).eq("category").all(): + tb[column_name] = tb[column_name].astype(str) + + # Raise error if nan + if tb[column_name].isna().any(): + st.error( + f"Column '{column_name}' contains missing values. Please clean the data before harmonizing." + ) + st.stop() + + # Sanity check on typing: only support for indicators of type string + if not tb[column_name].apply(type).eq(str).all(): + # if tb[column_name].dtype not in ["object", "category"]: + st.error( + f"Column '{column_name}' is of type `{tb[column_name].dtype}` but 'string' is expected. Harmonization for non-string columns is not supported yet." + ) + st.stop() + + harmonizer = Harmonizer( + tb=tb, + colname=column_name, + output_file=f"{STEP_DIR}/data/garden/{dataset.m.namespace}/{dataset.m.version}/{dataset.m.short_name}.countries.json", + ) + harmonizer.run_automatic() + + ambiguous = cast(List, harmonizer.ambiguous) + mapping = harmonizer.mapping + + st.divider() + + ## 1/ AUTOMATIC + st.session_state.entity_mapping = mapping + if mapping: + with st.expander("Automatically mapped entities", expanded=False): + st.dataframe(mapping) + + ## 2/ MANUAL (user input needed) + with st.container(border=True): + # with st.form("form"): + # Title + st.markdown("#### Manual entity mapping needed") + st.markdown(f"{len(ambiguous)} ambiguous regions") + + # Create a container for each region with: + # - three columns: original entity name, suggestions (as a selectbox), and free text input for custom name + # - a toggle to ignore the region (no mapping) + for i, region in enumerate(ambiguous, 1): + # no exact match, get nearby matches + suggestions = harmonizer.get_suggestions( + region, institution=None, num_suggestions=NUM_SUGGESTIONS + ) + with st.container(border=True): + # Original name + st.markdown(f"**{region}**") + col1, col2 = st.columns(2) + + # New name, custom (useful if no suggestion is good enough) + with col2: + value_custom = st.text_input( + label="Enter custom name", + key=f"region_custom_{i}", + # placeholder="Enter custom name", + # label_visibility="collapsed", + help="Use this when no suggestion is good enough", + ) + # New name, from selectbox + with col1: + value_selected = st.selectbox( + label="Select a region", + options=suggestions, + index=0, + # label_visibility="collapsed", + key=f"region_suggestion_{i}", + disabled=value_custom != "", + ) + value_ignore = st.toggle( + label="Ignore", + key=f"region_ignore_{i}", + ) + # Add defined mapping (only if not ignored) + if not value_ignore: + st.session_state.entity_mapping[region] = cast( + str, value_custom if value_custom not in ("", None) else value_selected + ) + # 3/ PATH to export & export button + path_export = cast(str, harmonizer.output_file) + if ENV_IS_REMOTE: + # Submit button + export_btn = st.form_submit_button( + label="Generate mapping", + type="primary", + ) + + else: + path_export = st.text_input( + label="Export to...", + value=path_export, + ) + # Submit button + export_btn = st.button( + label="Export mapping", + type="primary", + ) + + #################################################################################################### + # EXPORT + #################################################################################################### + if export_btn: + if ENV_IS_REMOTE: + path_export = Path(path_export).name + json_string = json.dumps(st.session_state.entity_mapping) + st.download_button( + label="Download the mapping", + data=json_string, + key="mapping", + file_name=path_export, + help="This file will be downloaded to your computer.", + ) + else: + path_export = Path(path_export) + # Sanity checks + if not path_export.parent.exists(): + st.error(f"Directory {path_export.parent} does not exist!") + st.stop() + if not (suf := path_export.suffix) == ".json": + st.error( + f"Please provide a valid extension of the file. Should be a JSON file, but instead '{suf}' was given." + ) + st.stop() + + # Export + st.json(st.session_state.entity_mapping, expanded=False) + with open(path_export, "w") as ostream: + json.dump(st.session_state.entity_mapping, ostream, indent=2) + + st.success(f"Harmonization mapping exported to {path_export}") diff --git a/apps/wizard/config/config.yml b/apps/wizard/config/config.yml index 195e0cabd07..70bc6d01f24 100644 --- a/apps/wizard/config/config.yml +++ b/apps/wizard/config/config.yml @@ -109,7 +109,7 @@ sections: alias: harmonizer description: "Harmonize a column of a table" maintainer: "@lucas" - entrypoint: app_pages/harmonizer.py + entrypoint: app_pages/harmonizer/app.py icon: ":material/music_note:" image_url: "https://www.shutterstock.com/image-vector/abstract-vector-musical-background-music-260nw-485443810.jpg" From de9289813d10935bdd9ea2e2b5e1f2560bb901bb Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Sun, 15 Dec 2024 02:23:08 +0100 Subject: [PATCH 09/20] tweaks --- apps/wizard/etl_steps/data.py | 32 ++++++++++++++------------------ 1 file changed, 14 insertions(+), 18 deletions(-) diff --git a/apps/wizard/etl_steps/data.py b/apps/wizard/etl_steps/data.py index 7b283c77bd0..2a1d2146cbf 100644 --- a/apps/wizard/etl_steps/data.py +++ b/apps/wizard/etl_steps/data.py @@ -6,17 +6,14 @@ import streamlit as st from rapidfuzz import fuzz -from sqlalchemy.exc import OperationalError from typing_extensions import Self -import etl.grapher_model as gm from apps.utils.files import add_to_dag, generate_step_to_channel from apps.wizard import utils +from apps.wizard.app_pages.harmonizer.utils import render from apps.wizard.etl_steps.utils import TAGS_DEFAULT, remove_playground_notebook -from apps.wizard.utils import set_states, st_page_link from apps.wizard.utils.components import st_horizontal from etl.config import DB_HOST, DB_NAME -from etl.db import get_session from etl.paths import DAG_DIR ######################################################### @@ -518,6 +515,11 @@ def render_form(): ) +@st.dialog("Harmonize country names", width="large") +def render_harm(): + render() + + def render_instructions(form): for channel in ["meadow", "garden", "grapher"]: if channel in form.steps_to_create: @@ -554,11 +556,9 @@ def render_instructions_meadow(form=None): line_numbers=True, ) - -def render_instructions_garden(form=None): - ## 1/ Harmonize country names - st.markdown("**1) Harmonize country names**") - st.markdown("Run it in your terminal:") + st.markdown("**2) Harmonize country names**") + st.button("Harmonize", on_click=render_harm) + st.markdown("You can also run it in your terminal:") if form is None: st.code( "uv run etl harmonize data/meadow/version/short_name/table_name.feather country etl/steps/data/garden/version/short_name.countries.json", @@ -573,15 +573,11 @@ def render_instructions_garden(form=None): wrap_lines=True, line_numbers=True, ) - st.markdown("Or run it on Wizard") - utils.st_page_link( - "harmonizer", - use_container_width=True, - help="You will leave this page, and the guideline text will be hidden.", - ) - - # 2/ Run etl step - st.markdown("**2) Run Garden step**") + + +def render_instructions_garden(form=None): + ## 1/ Run etl step + st.markdown("**1) Run Garden step**") st.markdown("After editing the code of your Garden step, run the following command:") if form is None: st.code( From 543bfbff764a21b77df5e15cc17c64235541defd Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Sun, 15 Dec 2024 02:28:18 +0100 Subject: [PATCH 10/20] tests --- apps/wizard/app_pages/expert/app.py | 1 - apps/wizard/etl_steps/data.py | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/apps/wizard/app_pages/expert/app.py b/apps/wizard/app_pages/expert/app.py index f1fa89f1abf..38be94b2e38 100644 --- a/apps/wizard/app_pages/expert/app.py +++ b/apps/wizard/app_pages/expert/app.py @@ -20,7 +20,6 @@ SYSTEM_PROMPT_START, ) from apps.wizard.utils import set_states -from apps.wizard.utils.components import st_horizontal from apps.wizard.utils.db import DB_IS_SET_UP, WizardDB from etl.config import load_env diff --git a/apps/wizard/etl_steps/data.py b/apps/wizard/etl_steps/data.py index 2a1d2146cbf..293709baea0 100644 --- a/apps/wizard/etl_steps/data.py +++ b/apps/wizard/etl_steps/data.py @@ -344,7 +344,7 @@ def render_step_selection(): help="Express mode will create all steps at once.", # default=default, key="data_steps_to_create", - on_change=lambda: set_states({"update_steps_selection": True, "submit_form": False}), + on_change=lambda: utils.set_states({"update_steps_selection": True, "submit_form": False}), ) if len(st.session_state["data.steps_to_create"]) > 0: From 911a9b54ae7f7fa58854c82518c23986ea0ec870 Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Sun, 15 Dec 2024 02:39:18 +0100 Subject: [PATCH 11/20] ci/cd --- apps/backport/fasttrack_backport.py | 4 ++-- apps/wizard/app_pages/map_brackets.py | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/apps/backport/fasttrack_backport.py b/apps/backport/fasttrack_backport.py index 190362e5aca..7e4d0785507 100644 --- a/apps/backport/fasttrack_backport.py +++ b/apps/backport/fasttrack_backport.py @@ -88,7 +88,7 @@ def _create_client(): # Add your service account file creds = Credentials.from_service_account_file(os.environ["GOOGLE_APPLICATION_CREDENTIALS"], scopes=scope) - return gspread.authorize(creds) + return gspread.authorize(creds) # type: ignore def _create_temp_dataset(pb: PotentialBackport, short_name): @@ -174,7 +174,7 @@ def _fill_variables_meta(spreadsheet, meta, short_name): vars_df = vars_df.reindex(columns=wks.row_values(1)).fillna("") # update values - values = [vars_df.columns.values.tolist()] + vars_df.values.tolist() + values = [vars_df.columns.values.tolist()] + vars_df.values.tolist() # type: ignore wks.update("A1", values) diff --git a/apps/wizard/app_pages/map_brackets.py b/apps/wizard/app_pages/map_brackets.py index 78763bd229e..dfa57e37301 100644 --- a/apps/wizard/app_pages/map_brackets.py +++ b/apps/wizard/app_pages/map_brackets.py @@ -282,7 +282,7 @@ def run( self.brackets_selected = self.brackets_all[self.bracket_type].tolist() # Define the grapher version of the selected brackets, which needs a minimum value and a list of brackets. self.brackets_selected_grapher_min_value = None - self.brackets_selected_grapher_values = self.brackets_selected.copy() + self.brackets_selected_grapher_values = self.brackets_selected.copy() # type: ignore @property def brackets(self): @@ -582,7 +582,7 @@ def update_brackets_selected(self, min_selected: float, max_selected: float) -> self._update_grapher_brackets() def _update_grapher_brackets(self): - self.brackets_selected_grapher_values = self.brackets_selected.copy() + self.brackets_selected_grapher_values = self.brackets_selected.copy() # type: ignore if self.lower_bracket_open: # To ensure the lower bracket is open, use a large value of "customNumericMinValue". self.brackets_selected_grapher_min_value = self.max_value From bbab3d681b6f8eceac86edc79c9c6b567e0e131f Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Sun, 15 Dec 2024 16:00:22 +0100 Subject: [PATCH 12/20] ci/cd --- etl/data_helpers/geo.py | 2 +- etl/datadiff.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/etl/data_helpers/geo.py b/etl/data_helpers/geo.py index e9a85671b63..2b32c759072 100644 --- a/etl/data_helpers/geo.py +++ b/etl/data_helpers/geo.py @@ -1057,7 +1057,7 @@ def detect_overlapping_regions( # List all variables in data (ignoring index columns). variables = [column for column in df.columns if column not in index_columns] # List all country names found in data. - countries_in_data = df[country_col].unique().tolist() # type: ignore + countries_in_data = set(df[country_col].unique().tolist()) # type: ignore # List all regions found in data. # TODO: Possible overlaps in custom regions are not considered here. I think it would be simple enough to include # here custom regions and check for overlaps. diff --git a/etl/datadiff.py b/etl/datadiff.py index cbe37ae3fb1..7a986daa483 100644 --- a/etl/datadiff.py +++ b/etl/datadiff.py @@ -646,7 +646,7 @@ def _data_diff( def _is_datetime(dtype: Any) -> bool: try: - return np.issubdtype(dtype, np.datetime64) + return np.issubdtype(dtype, np.datetime64) # type: ignore except Exception: return False From cbd9e3fc973850c37e44e85652e6219d291d7be7 Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Sun, 15 Dec 2024 17:15:38 +0100 Subject: [PATCH 13/20] minor tweaks to fast-track --- apps/wizard/app_pages/fasttrack/app.py | 484 +++++++++++++------------ 1 file changed, 252 insertions(+), 232 deletions(-) diff --git a/apps/wizard/app_pages/fasttrack/app.py b/apps/wizard/app_pages/fasttrack/app.py index d561191ef83..c1f58e788e7 100644 --- a/apps/wizard/app_pages/fasttrack/app.py +++ b/apps/wizard/app_pages/fasttrack/app.py @@ -106,268 +106,288 @@ def reset_states() -> None: }, } # Choose import method -import_method = st.radio( +# import_method = st.radio( +# label="How do you want to import the dataset?", +# options=IMPORT_OPTIONS.keys(), +# captions=[IMPORT_OPTIONS[x]["description"] for x in IMPORT_OPTIONS], +# format_func=lambda x: IMPORT_OPTIONS[x]["title"], +# help="Select the source of your data.", +# horizontal=True, +# ) + +import_method = st.segmented_control( label="How do you want to import the dataset?", options=IMPORT_OPTIONS.keys(), - captions=[IMPORT_OPTIONS[x]["description"] for x in IMPORT_OPTIONS], + # captions=[IMPORT_OPTIONS[x]["description"] for x in IMPORT_OPTIONS], format_func=lambda x: IMPORT_OPTIONS[x]["title"], - help="Select the source of your data.", - horizontal=True, + help="""Select the source of your data. + +- **New Google sheet**: Import data from a Google sheet. +- **Existing Google sheet**: Update from a Google sheet (already imported in the database). +- **Local CSV**: Import from a local CSV. +""", + default=[IMPORT_GSHEET], ) -# Show brief guidelines for each import method -for option, option_params in IMPORT_OPTIONS.items(): - if import_method == option: - with st.expander(f"More info: {option_params['guidelines']['heading']}", expanded=False): - with open(option_params["guidelines"]["file_path"], "r") as f: - st.markdown(f.read()) +# Show brief guidelines for each import method +if import_method is not None: + with st.popover("Instructions"): + assert import_method in IMPORT_OPTIONS, "import_method not found in IMPORT_OPTIONS!" + with open(IMPORT_OPTIONS[import_method]["guidelines"]["file_path"], "r") as f: + st.markdown(f.read()) ########################################################## # CREATE AND SHOW THE FORM ########################################################## -with st.form("fasttrack-form"): - existing_google_sheet = None - placeholder_for_existing_google_sheet = None - - # Import field - if import_method == IMPORT_GSHEET: - st.text_input( - label="New Google Sheets URL", - help="In the Google spreadsheet, click on `File -> Share -> Publish to Web` and share the entire document as csv.", - key="sheets_url", - ) - elif import_method == UPDATE_GSHEET: - options = load_existing_sheets_from_snapshots() - placeholder_for_existing_google_sheet = st.empty() - else: - st.file_uploader( - label="Upload Local CSV", - type=["csv"], - help="Upload a local CSV file to import data.", - key="uploaded_file", - ) - # Other parameters - st.checkbox( - label="Infer missing metadata (instead of raising an error)", - value=True, - key="infer_metadata", - ) - - placeholder_for_private = st.empty() - - submitted = st.form_submit_button( - "Submit", - type="primary", - use_container_width=True, - on_click=lambda: set_states( - { - "to_be_submitted": True, - "to_be_submitted_confirmed_1": False, - "to_be_submitted_confirmed_2": False, - } - ), - ) - -# These need to be defined outside of the form to be able to make the `is_public` checkbox dependent -# on the `existing_google_sheet` value -if import_method == UPDATE_GSHEET: - if placeholder_for_existing_google_sheet is None: - raise ValueError("placeholder_for_existing_google_sheet is None. This was not expected.") - else: - with placeholder_for_existing_google_sheet: - existing_google_sheet = st.selectbox( - label="Existing Google Sheets", - options=options, # type: ignore - format_func=lambda x: x["label"], - help="Selected sheet will be used if you don't specify Google Sheets URL.", - key="existing_sheet", - on_change=reset_states, +if import_method is None: + st.warning("Select an import method to proceed.") +else: + with st.form("fasttrack-form"): + existing_google_sheet = None + placeholder_for_existing_google_sheet = None + placeholder_for_private = None + + # Import field + if import_method == IMPORT_GSHEET: + st.text_input( + label="New Google Sheets URL", + help="In the Google spreadsheet, click on `File -> Share -> Publish to Web` and share the entire document as csv.", + key="sheets_url", ) + elif import_method == UPDATE_GSHEET: + options = load_existing_sheets_from_snapshots() + placeholder_for_existing_google_sheet = st.empty() + elif import_method == LOCAL_CSV: + st.file_uploader( + label="Upload Local CSV", + type=["csv"], + help="Upload a local CSV file to import data.", + key="uploaded_file", + ) + else: + st.error("Unexpected import method. Please report.") -with placeholder_for_private: - if existing_google_sheet: - default_is_public = existing_google_sheet["is_public"] - else: - default_is_public = True - - st.checkbox( - label="Make dataset private (your metadata will be still public!)", - value=not default_is_public, - key="fasttrack_is_private", - on_change=reset_states, - ) - -if (FERNET_KEY is None) and (st.session_state.fasttrack_is_private): - if import_method == UPDATE_GSHEET: - st.error( - "FASTTRACK_SECRET_KEY not found in environment variables. Not using encryption. Therefore, won't be able to decrypt the existing Google Sheets URL for private datasets!" + # Other parameters + st.checkbox( + label="Infer missing metadata (instead of raising an error)", + value=True, + key="infer_metadata", ) - st.stop() - else: - st.warning("FASTTRACK_SECRET_KEY not found in environment variables. Not using encryption.") -########################################################## -# USER CLICKS ON SUBMIT -########################################################## -if st.session_state.to_be_submitted: - # Sanity check - if ( - not st.session_state.get("existing_sheet") - and not st.session_state.get("uploaded_file") - and st.session_state.get("sheets_url") in (None, "") - ): - st.error("Please provide a valid dataset URI.") - st.stop() - - ##################################################### - # IMPORT & PROCESS DATA - ##################################################### - # expand it first and collapse if successful - status_main = st.status("Importing data from Google Sheets...", expanded=True) - with status_main: - data, dataset_meta, variables_meta_dict, origin, unknown_countries, dataset_uri = processing_part_1( - import_method=import_method, - dataset_uris={ - k: v - for k, v in st.session_state.to_dict().items() - if k in ("uploaded_file", "sheets_url", "existing_sheet") - }, - infer_metadata=st.session_state["infer_metadata"], - is_private=st.session_state["fasttrack_is_private"], - _status=status_main, + placeholder_for_private = st.empty() + + submitted = st.form_submit_button( + "Submit", + type="primary", + use_container_width=True, + on_click=lambda: set_states( + { + "to_be_submitted": True, + "to_be_submitted_confirmed_1": False, + "to_be_submitted_confirmed_2": False, + } + ), ) - status_main.update(expanded=False) - - # If all countries are known, proceed without alterations - if unknown_countries in ([], None): - # continue with submission - st.session_state["fast_import"] = processing_part_2( - data=data, - dataset_meta=dataset_meta, - variables_meta_dict=variables_meta_dict, - origin=origin, - dataset_uri=dataset_uri, - status=status_main, - import_method=import_method, + + # These need to be defined outside of the form to be able to make the `is_public` checkbox dependent + # on the `existing_google_sheet` value + if import_method == UPDATE_GSHEET: + if placeholder_for_existing_google_sheet is None: + raise ValueError("placeholder_for_existing_google_sheet is None. This was not expected.") + else: + with placeholder_for_existing_google_sheet: + existing_google_sheet = st.selectbox( + label="Existing Google Sheets", + options=options, # type: ignore + format_func=lambda x: x["label"], + help="Selected sheet will be used if you don't specify Google Sheets URL.", + key="existing_sheet", + on_change=reset_states, + ) + + with placeholder_for_private: + if existing_google_sheet: + default_is_public = existing_google_sheet["is_public"] + else: + default_is_public = True + + st.checkbox( + label="Make dataset private (your metadata will be still public!)", + value=not default_is_public, + key="fasttrack_is_private", + on_change=reset_states, ) - # If there are unknown countries, do something about it - else: - # 1/ Ask what to do - with st.form("unknown_countries_form"): - st.radio( - label="⚠️ There are unknown countries. What do you want to do?", - options=["Keep unknown entities", "Drop unknown entities"], - key="unknown_countries_action", + if (FERNET_KEY is None) and (st.session_state.fasttrack_is_private): + if import_method == UPDATE_GSHEET: + st.error( + "FASTTRACK_SECRET_KEY not found in environment variables. Not using encryption. Therefore, won't be able to decrypt the existing Google Sheets URL for private datasets!" ) - with st.expander(f"See list of {len(unknown_countries)} unknown entities", expanded=False): - df_countries = pd.DataFrame(unknown_countries, columns=["entity"]).sort_values(by="entity") - st.dataframe(df_countries, hide_index=True) - proceed_1 = st.form_submit_button( - "Proceed", - type="primary", - use_container_width=True, - on_click=lambda: set_states( - { - "to_be_submitted_confirmed_1": True, - "to_be_submitted_confirmed_2": False, - } - ), + st.stop() + else: + st.warning("FASTTRACK_SECRET_KEY not found in environment variables. Not using encryption.") + + ########################################################## + # USER CLICKS ON SUBMIT + ########################################################## + if st.session_state.to_be_submitted: + # Sanity check + if ( + not st.session_state.get("existing_sheet") + and not st.session_state.get("uploaded_file") + and st.session_state.get("sheets_url") in (None, "") + ): + st.error("Please provide a valid dataset URI.") + st.stop() + + ##################################################### + # IMPORT & PROCESS DATA + ##################################################### + # expand it first and collapse if successful + status_main = st.status("Importing data from Google Sheets...", expanded=True) + with status_main: + data, dataset_meta, variables_meta_dict, origin, unknown_countries, dataset_uri = processing_part_1( + import_method=import_method, + dataset_uris={ + k: v + for k, v in st.session_state.to_dict().items() + if k in ("uploaded_file", "sheets_url", "existing_sheet") + }, + infer_metadata=st.session_state["infer_metadata"], + is_private=st.session_state["fasttrack_is_private"], + _status=status_main, ) + status_main.update(expanded=False) - if st.session_state.to_be_submitted_confirmed_1: - # 2/ Do something - status_second = st.status("Processing unknown countries...", expanded=False) - with status_second: - if (unknown_countries not in ([], None)) & ( - st.session_state["unknown_countries_action"] == "Drop unknown entities" - ): - st.write("Dropping unknown entities...") - data = data.loc[~data.index.get_level_values("country").isin(unknown_countries)] - - # 3/ Proceed + # If all countries are known, proceed without alterations + if unknown_countries in ([], None): + # continue with submission st.session_state["fast_import"] = processing_part_2( data=data, dataset_meta=dataset_meta, variables_meta_dict=variables_meta_dict, origin=origin, dataset_uri=dataset_uri, - status=status_second, + status=status_main, import_method=import_method, ) + # If there are unknown countries, do something about it + else: + # 1/ Ask what to do + with st.form("unknown_countries_form"): + st.radio( + label="⚠️ There are unknown countries. What do you want to do?", + options=["Keep unknown entities", "Drop unknown entities"], + key="unknown_countries_action", + ) + with st.expander(f"See list of {len(unknown_countries)} unknown entities", expanded=False): + df_countries = pd.DataFrame(unknown_countries, columns=["entity"]).sort_values(by="entity") + st.dataframe(df_countries, hide_index=True) + proceed_1 = st.form_submit_button( + "Proceed", + type="primary", + use_container_width=True, + on_click=lambda: set_states( + { + "to_be_submitted_confirmed_1": True, + "to_be_submitted_confirmed_2": False, + } + ), + ) + + if st.session_state.to_be_submitted_confirmed_1: + # 2/ Do something + status_second = st.status("Processing unknown countries...", expanded=False) + with status_second: + if (unknown_countries not in ([], None)) & ( + st.session_state["unknown_countries_action"] == "Drop unknown entities" + ): + st.write("Dropping unknown entities...") + data = data.loc[~data.index.get_level_values("country").isin(unknown_countries)] + + # 3/ Proceed + st.session_state["fast_import"] = processing_part_2( + data=data, + dataset_meta=dataset_meta, + variables_meta_dict=variables_meta_dict, + origin=origin, + dataset_uri=dataset_uri, + status=status_second, + import_method=import_method, + ) + + ########################################################## + # DATA HAS BEEN PROCESSED + ########################################################## + if st.session_state.to_be_submitted_confirmed_2: + if st.session_state.fast_import: + with st.status("Uploading to Grapher...", expanded=True): + fast_import = st.session_state.fast_import + # add dataset to dag + st.write("Adding dataset to the DAG...") + dag_content = fast_import.add_to_dag() + + # create step and metadata file + st.write("Creating step and metadata files...") + generate_step_to_channel(CURRENT_DIR / "cookiecutter/", fast_import.meta.to_dict()) + fast_import.save_metadata() + + # Uploading snapshot + st.write("Uploading snapshot...") + snapshot_path = fast_import.upload_snapshot() + st.success("Upload successful!") + + # Running ETL and upserting to GrapherDB... + st.write("Running ETL and upserting to GrapherDB...") + step = f"{fast_import.dataset.metadata.uri}" + etl_main( + dag_path=DAG_FASTTRACK_PATH, + steps=[step], + grapher=True, + private=not fast_import.dataset.metadata.is_public, + workers=1, + # NOTE: force is necessary because we are caching checksums with files.CACHE_CHECKSUM_FILE + # we could have cleared the cache, but this is cleaner + force=True, + ) + st.success("Import to MySQL successful!") + + # Others + if config.FASTTRACK_COMMIT: + # Commiting and pushing to Github... + st.write("Commiting and pushing to Github...") + github_link = fast_import.commit_and_push() + st.success("Changes commited and pushed successfully!") + else: + github_link = "" + + # Show final success messages + if config.DB_HOST == "localhost": + url = f"http://localhost:3030/admin/datasets/{fast_import.dataset_id}" + else: + url = f"{config.ADMIN_HOST}/admin/datasets/{fast_import.dataset_id}" + st.success(f"The dataset was imported to the [database]({url})!") + if config.FASTTRACK_COMMIT: + st.success(f"See commit in [ETL repository]({github_link})") -########################################################## -# DATA HAS BEEN PROCESSED -########################################################## -if st.session_state.to_be_submitted_confirmed_2: - if st.session_state.fast_import: - with st.status("Uploading to Grapher...", expanded=True): - fast_import = st.session_state.fast_import - # add dataset to dag - st.write("Adding dataset to the DAG...") - dag_content = fast_import.add_to_dag() - - # create step and metadata file - st.write("Creating step and metadata files...") - generate_step_to_channel(CURRENT_DIR / "cookiecutter/", fast_import.meta.to_dict()) - fast_import.save_metadata() - - # Uploading snapshot - st.write("Uploading snapshot...") - snapshot_path = fast_import.upload_snapshot() - st.success("Upload successful!") - - # Running ETL and upserting to GrapherDB... - st.write("Running ETL and upserting to GrapherDB...") - step = f"{fast_import.dataset.metadata.uri}" - etl_main( + # Show generated files + wizard_utils.preview_dag_additions( + dag_content=dag_content, dag_path=DAG_FASTTRACK_PATH, - steps=[step], - grapher=True, - private=not fast_import.dataset.metadata.is_public, - workers=1, - # NOTE: force is necessary because we are caching checksums with files.CACHE_CHECKSUM_FILE - # we could have cleared the cache, but this is cleaner - force=True, ) - st.success("Import to MySQL successful!") - - # Others - if config.FASTTRACK_COMMIT: - # Commiting and pushing to Github... - st.write("Commiting and pushing to Github...") - github_link = fast_import.commit_and_push() - st.success("Changes commited and pushed successfully!") - else: - github_link = "" + wizard_utils.preview_file( + snapshot_path, + language="yaml", + ) + wizard_utils.preview_file( + fast_import.step_path, + language="python", + ) + wizard_utils.preview_file( + fast_import.metadata_path, + "yaml", + ) - # Show final success messages - if config.DB_HOST == "localhost": - url = f"http://localhost:3030/admin/datasets/{fast_import.dataset_id}" else: - url = f"{config.ADMIN_HOST}/admin/datasets/{fast_import.dataset_id}" - st.success(f"The dataset was imported to the [database]({url})!") - if config.FASTTRACK_COMMIT: - st.success(f"See commit in [ETL repository]({github_link})") - - # Show generated files - wizard_utils.preview_dag_additions( - dag_content=dag_content, - dag_path=DAG_FASTTRACK_PATH, - ) - wizard_utils.preview_file( - snapshot_path, - language="yaml", - ) - wizard_utils.preview_file( - fast_import.step_path, - language="python", - ) - wizard_utils.preview_file( - fast_import.metadata_path, - "yaml", - ) - - else: - st.error("ERROR 100: No fast_import object found. Please report.") + st.error("ERROR 100: No fast_import object found. Please report.") From 53527fb60e30af31f1c828a5475d1339706115e0 Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Sun, 15 Dec 2024 17:58:47 +0100 Subject: [PATCH 14/20] include private steps in harmonizer --- apps/wizard/app_pages/harmonizer.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/apps/wizard/app_pages/harmonizer.py b/apps/wizard/app_pages/harmonizer.py index eea2c69bb57..eea11a36bcf 100644 --- a/apps/wizard/app_pages/harmonizer.py +++ b/apps/wizard/app_pages/harmonizer.py @@ -118,7 +118,7 @@ def sort_indicators(indicators: List[str]) -> List[str]: # show_all = False options = get_datasets_in_etl( snapshots=False, - prefixes=None if st.session_state.show_all else ["data://meadow"], + prefixes=None if st.session_state.show_all else ["data://meadow", "data-private://meadow"], ) option = st.selectbox( label="Select a dataset", From e1afa7437ed60fc651abf917c4601482e7f3b2b0 Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Sun, 15 Dec 2024 18:53:34 +0100 Subject: [PATCH 15/20] add customisation for dependencies --- apps/wizard/etl_steps/data.py | 356 ++++++++++++++++++++-------------- apps/wizard/utils/__init__.py | 5 +- 2 files changed, 210 insertions(+), 151 deletions(-) diff --git a/apps/wizard/etl_steps/data.py b/apps/wizard/etl_steps/data.py index 293709baea0..4734201f678 100644 --- a/apps/wizard/etl_steps/data.py +++ b/apps/wizard/etl_steps/data.py @@ -1,5 +1,6 @@ """Garden phase.""" +import re from datetime import date, datetime, timedelta from pathlib import Path from typing import Any, Dict, List, Optional @@ -12,7 +13,8 @@ from apps.wizard import utils from apps.wizard.app_pages.harmonizer.utils import render from apps.wizard.etl_steps.utils import TAGS_DEFAULT, remove_playground_notebook -from apps.wizard.utils.components import st_horizontal +from apps.wizard.utils import get_datasets_in_etl +from apps.wizard.utils.components import st_horizontal, st_multiselect_wider from etl.config import DB_HOST, DB_NAME from etl.paths import DAG_DIR @@ -63,11 +65,41 @@ USING_TAGS_DEFAULT = True tag_list = TAGS_DEFAULT # Step names -STEP_NAME_PRESENT = { - "meadow": ":material/nature: Meadow", - "garden": ":material/deceased: Garden", - "grapher": ":material/database: Grapher", +STEP_ICONS = { + "meadow": ":material/nature:", + "garden": ":material/deceased:", + "grapher": ":material/database:", } +STEP_NAME_PRESENT = {k: f"{v} {k.capitalize()}" for k, v in STEP_ICONS.items()} + +# GET STEP URIS +st.session_state["data_step_uris"] = st.session_state.get( + "data_step_uris", + get_datasets_in_etl( + snapshots=False, + prefixes=["data://", "data-private://"], + ), +) + + +# @st.cache_data +def get_steps_per_channel(): + steps_all = get_datasets_in_etl( + snapshots=True, + ) + steps = {"meadow": [], "garden": [], "grapher": []} + for s in steps_all: + if re.match(r"^(data(-private)?://meadow|snapshot(-private)?://)", s): + steps["meadow"].append(s) + if re.match(r"^(data(-private)?://(meadow|garden))", s): + steps["garden"].append(s) + if re.match(r"^(data(-private)?://(garden|grapher))", s): + steps["grapher"].append(s) + + return steps + + +STEPS_URI = get_steps_per_channel() ######################################################### @@ -354,165 +386,184 @@ def render_step_selection(): def render_form(): """Render form.""" - with st.expander("**Form**", expanded=True): - if (default_version := APP_STATE.default_value("version", previous_step="snapshot")) == "": - default_version = APP_STATE.default_value("snapshot_version", previous_step="snapshot") - - # Namespace - custom_label = "Custom namespace..." - APP_STATE.st_selectbox_responsive( - st_widget=st.selectbox, - custom_label=custom_label, - key="namespace", - label="Namespace", - help="Institution or topic name", - options=OPTIONS_NAMESPACES, - default_last=dummy_values["namespace"] if APP_STATE.args.dummy_data else OPTIONS_NAMESPACES[0], + if (default_version := APP_STATE.default_value("version", previous_step="snapshot")) == "": + default_version = APP_STATE.default_value("snapshot_version", previous_step="snapshot") + + # Namespace + custom_label = "Custom namespace..." + APP_STATE.st_selectbox_responsive( + st_widget=st.selectbox, + custom_label=custom_label, + key="namespace", + label="Namespace", + help="Institution or topic name", + options=OPTIONS_NAMESPACES, + default_last=dummy_values["namespace"] if APP_STATE.args.dummy_data else OPTIONS_NAMESPACES[0], + on_change=edit_field, + ) + if APP_STATE.vars.get("namespace") == custom_label: + namespace_key = "namespace_custom" + else: + namespace_key = "namespace" + + # Short name (meadow, garden, grapher) + APP_STATE.st_widget( + st_widget=st.text_input, + key="short_name", + label="short name", + help="Dataset short name using [snake case](https://en.wikipedia.org/wiki/Snake_case). Example: natural_disasters", + placeholder="Example: 'cherry_blossom'", + value=dummy_values["short_name"] if APP_STATE.args.dummy_data else None, + on_change=edit_field, + ) + + # Version (meadow, garden, grapher) + APP_STATE.st_widget( + st_widget=st.text_input, + label="version", + help="Version of the dataset (by default, the current date, or exceptionally the publication date).", + key="version", + default_last=default_version, + value=dummy_values["version"] if APP_STATE.args.dummy_data else default_version, + on_change=edit_field, + ) + + # Add to DAG + sorted_dag = sorted( + utils.dag_files, + key=lambda file_name: fuzz.ratio(file_name.replace(".yml", ""), APP_STATE.vars[namespace_key]), + reverse=True, + ) + sorted_dag = [ + utils.dag_not_add_option, + *sorted_dag, + ] + if sorted_dag[1].replace(".yml", "") == APP_STATE.vars[namespace_key]: + default_value = sorted_dag[1] + else: + default_value = "" + APP_STATE.st_widget( + st.selectbox, + label="Add to DAG", + options=sorted_dag, + key="dag_file", + help="Add ETL step to a DAG file. This will allow it to be tracked and executed by the `etl` command.", + default_value=default_value, + on_change=edit_field, + ) + + # Customize dependencies + with st.popover( + "Customize dependencies", + use_container_width=True, + help="Use this optionally if you want to add more dependencies to your steps.", + ): + st.markdown("Add other dependencies to your steps in the DAG!") + for channel in ["meadow", "garden", "grapher"]: + if channel in st.session_state["data.steps_to_create"]: + APP_STATE.st_widget( + st_widget=st.multiselect, + label=STEP_NAME_PRESENT.get(channel), + help=("Customize the dependency channel in the DAG."), + key=f"data.dependenies_{channel}", + options=STEPS_URI[channel], + placeholder="Add dependency steps", + default=None, + on_change=edit_field, + ) + + if "garden" in st.session_state["data.steps_to_create"]: + # Indicator tags + label = "Indicators tag" + if USING_TAGS_DEFAULT: + label += f"\n\n:red[Using a 2024 March snapshot of the tags. Couldn't connect to database `{DB_NAME}` in host `{DB_HOST}`.]" + + namespace = APP_STATE.vars[namespace_key].replace("_", " ") + default_last = None + for tag in tag_list: + if namespace.lower() == tag.lower(): + default_last = tag + break + APP_STATE.st_widget( + st_widget=st.multiselect, + label=label, + help=( + """ + This tag will be propagated to all dataset's indicators (it will not be assigned to the dataset). + + If you want to use a different tag for a specific indicator you can do it by editing its metadata field `variable.presentation.topic_tags`. + + Exceptionally, and if unsure what to choose, choose tag `Uncategorized`. + """ + ), + key="topic_tags", + options=tag_list, + placeholder="Choose a tag (or multiple)", + default=dummy_values["topic_tags"] if APP_STATE.args.dummy_data else default_last, on_change=edit_field, ) - if APP_STATE.vars.get("namespace") == custom_label: - namespace_key = "namespace_custom" - else: - namespace_key = "namespace" - # Short name (meadow, garden, grapher) + # Update frequency + today = datetime.today() APP_STATE.st_widget( - st_widget=st.text_input, - key="short_name", - label="short name", - help="Dataset short name using [snake case](https://en.wikipedia.org/wiki/Snake_case). Example: natural_disasters", - placeholder="Example: 'cherry_blossom'", - value=dummy_values["short_name"] if APP_STATE.args.dummy_data else None, + st_widget=st.date_input, + label="When is the next update expected?", + help="Expected date of the next update of this dataset by OWID (typically in a year).", + key="update_period_date", + min_value=today + timedelta(days=1), + default_last=today.replace(year=today.year + 1), on_change=edit_field, ) - # Version (meadow, garden, grapher) + if "meadow" in st.session_state["data.steps_to_create"]: + st.markdown("#### Snapshot") + # Snapshot version APP_STATE.st_widget( - st_widget=st.text_input, - label="version", - help="Version of the dataset (by default, the current date, or exceptionally the publication date).", - key="version", - default_last=default_version, - value=dummy_values["version"] if APP_STATE.args.dummy_data else default_version, + st.text_input, + label="Snapshot version", + help="Version of the snapshot dataset (by default, the current date, or exceptionally the publication date).", + # placeholder=f"Example: {DATE_TODAY}", + key="snapshot_version", + value=dummy_values["snapshot_version"] if APP_STATE.args.dummy_data else None, on_change=edit_field, ) - - # Add to DAG - sorted_dag = sorted( - utils.dag_files, - key=lambda file_name: fuzz.ratio(file_name.replace(".yml", ""), APP_STATE.vars[namespace_key]), - reverse=True, - ) - sorted_dag = [ - utils.dag_not_add_option, - *sorted_dag, - ] - if sorted_dag[1].replace(".yml", "") == APP_STATE.vars[namespace_key]: - default_value = sorted_dag[1] - else: - default_value = "" + # File extension APP_STATE.st_widget( - st.selectbox, - label="Add to DAG", - options=sorted_dag, - key="dag_file", - help="Add ETL step to a DAG file. This will allow it to be tracked and executed by the `etl` command.", - default_value=default_value, + st.text_input, + label="File extension", + help="File extension (without the '.') of the file to be downloaded.", + placeholder="Example: 'csv', 'xls', 'zip'", + key="file_extension", + value=dummy_values["file_extension"] if APP_STATE.args.dummy_data else None, on_change=edit_field, ) - if "garden" in st.session_state["data.steps_to_create"]: - # Indicator tags - label = "Indicators tag" - if USING_TAGS_DEFAULT: - label += f"\n\n:red[Using a 2024 March snapshot of the tags. Couldn't connect to database `{DB_NAME}` in host `{DB_HOST}`.]" - - namespace = APP_STATE.vars[namespace_key].replace("_", " ") - default_last = None - for tag in tag_list: - if namespace.lower() == tag.lower(): - default_last = tag - break - APP_STATE.st_widget( - st_widget=st.multiselect, - label=label, - help=( - """ - This tag will be propagated to all dataset's indicators (it will not be assigned to the dataset). - - If you want to use a different tag for a specific indicator you can do it by editing its metadata field `variable.presentation.topic_tags`. - - Exceptionally, and if unsure what to choose, choose tag `Uncategorized`. - """ - ), - key="topic_tags", - options=tag_list, - placeholder="Choose a tag (or multiple)", - default=dummy_values["topic_tags"] if APP_STATE.args.dummy_data else default_last, - on_change=edit_field, - ) + # Others + st.markdown("#### Other options") + name_mapping = { + "private": ":material/lock: Make dataset private", + "notebook": ":material/skateboarding: Create playground notebook", + # "grapher": ":material/database: Grapher", + } + + st.pills( + label="Select the steps you want to create", + help="Extra options.", + options=["private", "notebook"], + format_func=lambda option: name_mapping[option], + selection_mode="multi", + label_visibility="collapsed", + key="data.extra_options", + on_change=edit_field, + ) - # Update frequency - today = datetime.today() - APP_STATE.st_widget( - st_widget=st.date_input, - label="When is the next update expected?", - help="Expected date of the next update of this dataset by OWID (typically in a year).", - key="update_period_date", - min_value=today + timedelta(days=1), - default_last=today.replace(year=today.year + 1), - on_change=edit_field, - ) - - if "meadow" in st.session_state["data.steps_to_create"]: - st.markdown("#### Snapshot") - # Snapshot version - APP_STATE.st_widget( - st.text_input, - label="Snapshot version", - help="Version of the snapshot dataset (by default, the current date, or exceptionally the publication date).", - # placeholder=f"Example: {DATE_TODAY}", - key="snapshot_version", - value=dummy_values["snapshot_version"] if APP_STATE.args.dummy_data else None, - on_change=edit_field, - ) - # File extension - APP_STATE.st_widget( - st.text_input, - label="File extension", - help="File extension (without the '.') of the file to be downloaded.", - placeholder="Example: 'csv', 'xls', 'zip'", - key="file_extension", - value=dummy_values["file_extension"] if APP_STATE.args.dummy_data else None, - on_change=edit_field, - ) - - # Others - st.markdown("#### Other options") - name_mapping = { - "private": ":material/lock: Make dataset private", - "notebook": ":material/skateboarding: Create playground notebook", - # "grapher": ":material/database: Grapher", - } - - st.pills( - label="Select the steps you want to create", - help="Extra options.", - options=["private", "notebook"], - format_func=lambda option: name_mapping[option], - selection_mode="multi", - label_visibility="collapsed", - key="data.extra_options", - on_change=edit_field, - ) - - # Submit - st.button( - label="Submit", - type="primary", - use_container_width=True, - on_click=submit_form, - ) + # Submit + st.button( + label="Submit", + type="primary", + use_container_width=True, + on_click=submit_form, + ) @st.dialog("Harmonize country names", width="large") @@ -620,6 +671,7 @@ def render_instructions_grapher(form=None): ######################################################### # MAIN ################################################## ######################################################### +st_multiselect_wider() # TITLE st.title(":material/bolt: Data **:gray[Create steps]**") @@ -629,7 +681,11 @@ def render_instructions_grapher(form=None): # FORM if step_selected: # form_widget = st.empty() - render_form() + form_title = " ".join( + [STEP_ICONS[s] for s in ["meadow", "garden", "grapher"] if s in st.session_state["data.steps_to_create"]] + ) + with st.expander(f"**Steps: {form_title}**", expanded=True): + render_form() else: st.warning("Select at least one step to create.") diff --git a/apps/wizard/utils/__init__.py b/apps/wizard/utils/__init__.py index b3f445dc1c2..bc8d29db440 100644 --- a/apps/wizard/utils/__init__.py +++ b/apps/wizard/utils/__init__.py @@ -571,7 +571,10 @@ def get_datasets_in_etl( dag = load_dag() # Define list with options - options = sorted(list(dag.keys())) + if snapshots: + options = sorted(list(set(dag.keys()) | set([dd for d in dag.values() for dd in d]))) + else: + options = sorted(list(dag.keys())) ## Optional: Show some options first based on their prefix. E.g. Show those that are Meadow (i.e. start with 'data://meadow') first. if prefix_priorities: options, options_left = [], options From d3faf3973c7e92485cefcb10ccd93af28e94bb02 Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Sun, 15 Dec 2024 18:53:41 +0100 Subject: [PATCH 16/20] add emojis --- apps/wizard/app_pages/fasttrack/app.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/apps/wizard/app_pages/fasttrack/app.py b/apps/wizard/app_pages/fasttrack/app.py index c1f58e788e7..7e7e0aaba56 100644 --- a/apps/wizard/app_pages/fasttrack/app.py +++ b/apps/wizard/app_pages/fasttrack/app.py @@ -81,7 +81,7 @@ def reset_states() -> None: ########################################################## IMPORT_OPTIONS = { IMPORT_GSHEET: { - "title": "New Google sheet", + "title": ":material/cloud: :material/add: New Google sheet", "description": "Import data from a Google sheet", "guidelines": { "heading": "**How to import from a Google sheet**", @@ -89,7 +89,7 @@ def reset_states() -> None: }, }, UPDATE_GSHEET: { - "title": "Existing Google sheet", + "title": ":material/cloud: :material/sync: Existing Google sheet", "description": "Update from a Google sheet (already imported in the database)", "guidelines": { "heading": "**How to update from an existing sheet**", @@ -97,7 +97,7 @@ def reset_states() -> None: }, }, LOCAL_CSV: { - "title": "Local CSV", + "title": ":material/attach_file: Local CSV", "description": "Import from a local CSV", "guidelines": { "heading": "**How to import a local CSV**", From 5e34ab5d4f2173e6a8c28e6aa3b4cdde8c098311 Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Sun, 15 Dec 2024 18:58:05 +0100 Subject: [PATCH 17/20] cache --- apps/wizard/etl_steps/data.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/apps/wizard/etl_steps/data.py b/apps/wizard/etl_steps/data.py index 4734201f678..efc5dab6bf8 100644 --- a/apps/wizard/etl_steps/data.py +++ b/apps/wizard/etl_steps/data.py @@ -82,7 +82,7 @@ ) -# @st.cache_data +@st.cache_data def get_steps_per_channel(): steps_all = get_datasets_in_etl( snapshots=True, From d64b2aba8396a7c4af4cf24add104b34487c5db6 Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Sun, 15 Dec 2024 19:26:38 +0100 Subject: [PATCH 18/20] fix warning message --- etl/steps/__init__.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/etl/steps/__init__.py b/etl/steps/__init__.py index a3d2ed5aa6b..de7649cf9b2 100644 --- a/etl/steps/__init__.py +++ b/etl/steps/__init__.py @@ -353,14 +353,14 @@ def load_from_uri(uri: str) -> catalog.Dataset | Snapshot | WaldenDataset: try: dataset = Snapshot(path) except FileNotFoundError: - raise FileNotFoundError(f"Snapshot not found for URI '{uri}'. You may want to run `python {path}` first") + raise FileNotFoundError(f"Snapshot not found for URI '{uri}'. Please run `python snapshot {path}` first") # Data else: path = f"{attributes['channel']}/{attributes['namespace']}/{attributes['version']}/{attributes['name']}" try: dataset = catalog.Dataset(paths.DATA_DIR / path) except FileNotFoundError: - raise FileNotFoundError(f"Dataset not found for URI '{uri}'. You may want to run `etl {uri}` first") + raise FileNotFoundError(f"Dataset not found for URI '{uri}'. Please run `etlr {uri}` first") return dataset From 4567a95dbd78889030396873a0985e75414df52c Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Sun, 15 Dec 2024 19:27:23 +0100 Subject: [PATCH 19/20] custom dependencies, harmonizer --- apps/wizard/app_pages/harmonizer/app.py | 10 ++++- apps/wizard/app_pages/harmonizer/utils.py | 11 +---- apps/wizard/etl_steps/data.py | 55 ++++++++++++++++------- 3 files changed, 49 insertions(+), 27 deletions(-) diff --git a/apps/wizard/app_pages/harmonizer/app.py b/apps/wizard/app_pages/harmonizer/app.py index f3ea21098ac..a2369fee6b9 100644 --- a/apps/wizard/app_pages/harmonizer/app.py +++ b/apps/wizard/app_pages/harmonizer/app.py @@ -2,10 +2,18 @@ from .utils import render +# Get session state +path = None +if ("steps" in st.session_state) and ("garden" in st.session_state.steps): + garden_vars = st.session_state["steps"]["garden"] + if ("namespace" in garden_vars) and ("meadow_version" in garden_vars) and ("short_name" in garden_vars): + path = f"data://meadow/{garden_vars['namespace']}/{garden_vars['meadow_version']}/{garden_vars['short_name']}" + + # PAGE CONFIG st.set_page_config( page_title="Wizard: Entity Harmonizer", page_icon="🪄", ) -render() +render(path) diff --git a/apps/wizard/app_pages/harmonizer/utils.py b/apps/wizard/app_pages/harmonizer/utils.py index 9ab8759ad33..22d5f4a950f 100644 --- a/apps/wizard/app_pages/harmonizer/utils.py +++ b/apps/wizard/app_pages/harmonizer/utils.py @@ -14,13 +14,6 @@ from etl.paths import STEP_DIR from etl.steps import load_from_uri -# Get session state -path = None -if ("steps" in st.session_state) and ("garden" in st.session_state.steps): - garden_vars = st.session_state["steps"]["garden"] - if ("namespace" in garden_vars) and ("meadow_version" in garden_vars) and ("short_name" in garden_vars): - path = f"data://meadow/{garden_vars['namespace']}/{garden_vars['meadow_version']}/{garden_vars['short_name']}" - # RANK OF PREFERED TABLE NAMES TABLE_NAME_PRIORITIES = ["main", "core"] # RANK OF PREFERED COLUMN NAMES (for country) @@ -91,7 +84,7 @@ def sort_indicators(indicators: List[str]) -> List[str]: return indicators -def render(): +def render(step_uri): # Page config st.title(":material/music_note: Entity Harmonizer") @@ -119,7 +112,7 @@ def render(): label="Select a dataset", placeholder="Select a dataset", options=options, - index=options.index(path) if path in options else None, + index=options.index(step_uri) if step_uri in options else None, help="By default, only meadow datasets are shown in the dataset search bar.", ) st.toggle( diff --git a/apps/wizard/etl_steps/data.py b/apps/wizard/etl_steps/data.py index efc5dab6bf8..80f737445c5 100644 --- a/apps/wizard/etl_steps/data.py +++ b/apps/wizard/etl_steps/data.py @@ -11,7 +11,7 @@ from apps.utils.files import add_to_dag, generate_step_to_channel from apps.wizard import utils -from apps.wizard.app_pages.harmonizer.utils import render +from apps.wizard.app_pages.harmonizer.utils import render as render_harmonizer from apps.wizard.etl_steps.utils import TAGS_DEFAULT, remove_playground_notebook from apps.wizard.utils import get_datasets_in_etl from apps.wizard.utils.components import st_horizontal, st_multiselect_wider @@ -128,6 +128,8 @@ class DataForm(utils.StepForm): update_period_days: Optional[int] = None topic_tags: Optional[List[str]] = None update_period_date: Optional[date] = None # Custom + # Extra steps + dependencies_extra: Dict[str, Any] def __init__(self: Self, **data: Any) -> None: # type: ignore[reportInvalidTypeVarUse] """Construct class.""" @@ -148,6 +150,11 @@ def __init__(self: Self, **data: Any) -> None: # type: ignore[reportInvalidType data["is_private"] = True if "private" in data["extra_options"] else False data["notebook"] = True if "notebook" in data["extra_options"] else False + data["dependencies_extra"] = { + "meadow": data.get("dependencies_extra_meadow"), + "garden": data.get("dependencies_extra_garden"), + "grapher": data.get("dependencies_extra_grapher"), + } # st.write(data) super().__init__(**data) # type: ignore @@ -184,6 +191,20 @@ def base_step_name(self) -> str: """namespace/version/short_name""" return f"{form.namespace}/{form.version}/{form.short_name}" + def step_uri(self, channel: str) -> str: + """Get step URI.""" + match channel: + case "snapshot": + return f"snapshot{self.private_suffix}://{self.namespace}/{self.snapshot_version}/{self.short_name}.{self.file_extension}" + case "meadow": + return f"data{self.private_suffix}://meadow/{self.base_step_name}" + case "garden": + return f"data{self.private_suffix}://garden/{self.base_step_name}" + case "grapher": + return f"data{self.private_suffix}://grapher/{self.base_step_name}" + case _: + raise ValueError(f"Channel `{channel}` not recognized.") + @property def snapshot_step_uri(self) -> str: """Get snapshot step URI.""" @@ -316,12 +337,12 @@ def add_steps_to_dag(self) -> str: def dag(self) -> Dict[str, Any]: dag = {} - if "meadow" in self.steps_to_create: - dag[self.meadow_step_uri] = [self.snapshot_step_uri] - if "garden" in self.steps_to_create: - dag[self.garden_step_uri] = [self.meadow_step_uri] - if "grapher" in self.steps_to_create: - dag[self.grapher_step_uri] = [self.garden_step_uri] + channels_all = ["snapshot", "meadow", "garden", "grapher"] + for i, channel in enumerate(channels_all[1:]): + if channel in self.steps_to_create: + dag[self.step_uri(channel)] = [self.step_uri(channels_all[i])] + if self.dependencies_extra[channel] is not None: + dag[self.step_uri(channel)] += self.dependencies_extra[channel] return dag @@ -465,7 +486,7 @@ def render_form(): st_widget=st.multiselect, label=STEP_NAME_PRESENT.get(channel), help=("Customize the dependency channel in the DAG."), - key=f"data.dependenies_{channel}", + key=f"data.dependencies_extra_{channel}", options=STEPS_URI[channel], placeholder="Add dependency steps", default=None, @@ -567,8 +588,9 @@ def render_form(): @st.dialog("Harmonize country names", width="large") -def render_harm(): - render() +def render_harm(form): + meadow_step = form.step_uri("meadow") + render_harmonizer(meadow_step) def render_instructions(form): @@ -607,8 +629,11 @@ def render_instructions_meadow(form=None): line_numbers=True, ) - st.markdown("**2) Harmonize country names**") - st.button("Harmonize", on_click=render_harm) + +def render_instructions_garden(form=None): + ## 1/ Run etl step + st.markdown("**1) Harmonize country names**") + st.button("Harmonize", on_click=lambda form=form: render_harm(form)) st.markdown("You can also run it in your terminal:") if form is None: st.code( @@ -624,11 +649,7 @@ def render_instructions_meadow(form=None): wrap_lines=True, line_numbers=True, ) - - -def render_instructions_garden(form=None): - ## 1/ Run etl step - st.markdown("**1) Run Garden step**") + st.markdown("**2) Run Garden step**") st.markdown("After editing the code of your Garden step, run the following command:") if form is None: st.code( From edc93dc6daaff5456fa885b7fe52a84e8bc02a61 Mon Sep 17 00:00:00 2001 From: lucasrodes Date: Sun, 15 Dec 2024 19:47:11 +0100 Subject: [PATCH 20/20] adapt tests --- tests/apps/wizard/app_pages/test_apps.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tests/apps/wizard/app_pages/test_apps.py b/tests/apps/wizard/app_pages/test_apps.py index 70b3affb7b6..d4d3214999d 100644 --- a/tests/apps/wizard/app_pages/test_apps.py +++ b/tests/apps/wizard/app_pages/test_apps.py @@ -101,7 +101,8 @@ def test_app_fasttrack(): assert not at.exception # Try to reimport the latest uploaded sheet - at.radio[0].set_value("update_gsheet") + at.button_group[0].set_value(["update_gsheet"]) + # at.radio[0].set_value("update_gsheet") _pick_button_by_label(at, "Submit").click().run() assert not at.exception