From c8a8c2ba4d618f19cb98b1fc777c289e7109823f Mon Sep 17 00:00:00 2001 From: aschroed Date: Thu, 3 Oct 2024 16:52:17 -0400 Subject: [PATCH 1/6] refactored patch_states action --- .../checks/wrangler_checks.py | 52 ++++++++++++------- 1 file changed, 32 insertions(+), 20 deletions(-) diff --git a/chalicelib_fourfront/checks/wrangler_checks.py b/chalicelib_fourfront/checks/wrangler_checks.py index f5b59a3c..82e0c845 100644 --- a/chalicelib_fourfront/checks/wrangler_checks.py +++ b/chalicelib_fourfront/checks/wrangler_checks.py @@ -1,5 +1,5 @@ from dcicutils import ff_utils -from dcicutils.env_utils import prod_bucket_env_for_app +from dcicutils.s3_utils import s3Utils import boto3 import re import requests @@ -1729,7 +1729,7 @@ def states_files_without_higlass_defaults(connection, **kwargs): updates[uid]['add_tag'] = a_res.get('tags', []).append(valid_tags[0]) if not has_higlass_defaults: updates[uid]['update_defaults'] = True - + if updates: check.status = 'WARN' check.summary = 'Ready to patch higlass_defaults and/or add tag' @@ -1750,29 +1750,41 @@ def patch_states_files_higlass_defaults(connection, **kwargs): action_logs = {'patch_success': [], 'patch_failure': [], 'missing_ref_file': []} updates = check_res.get('full_output').get('updates', {}) + ''' + this action has been refactored to look for a specific single reference file to obtain states based on a tag + the way that the s3 bucket is obtained was updated (previously used a now deprecated function) + an optional kwarg for the tag has been added in case a different one should be used + ''' + + # this is to get the wanted reference file and generate state_colors + s3info = s3Utils() + bucket = s3info.raw_file_bucket + states_ref_file_tag = 'SPIN_states_v1' + if kwargs.get('tag', None): + states_ref_file_tag = kwargs.get('tag') + query = '/search/?type=FileReference&status=released&tags={}'.format(states_ref_file_tag) + search_res = ff_utils.search_metadata(query, key=connection.ff_keys) + if not search_res: + action.status = 'WARN' + action.output = 'Failed to retrieve row_info reference file' + return action + elif len(search_res) > 1: + msg = "WARNING - more than one row_info file found with tag {}\nUsing first one found".format(states_ref_file_tag) + action_logs.setdefault('ref_file_problem', msg) + action.status = 'WARN' + row_info_file_meta = search_res[0] + buck_obj = row_info_file_meta.get('uuid') + '/' + row_info_file_meta.get('display_title') + obj = bucket.Object(buck_obj) + body = obj.get()['Body'].read().decode('utf8') + lines = body.split() + states_colors = [item for num, item in enumerate(lines) if num % 2 != 0] + for uid, needed_updates in updates.items(): patch = {} if 'add_tag' in needed_updates: patch.update({'tags': needed_updates.get('add_tag')}) if needed_updates.get('update_defaults'): - s3 = boto3.resource('s3') - bucket = s3.Bucket('elasticbeanstalk-%s-files' % prod_bucket_env_for_app()) - query = '/search/?type=FileReference' - all_ref_files = ff_utils.search_metadata(query, key=connection.ff_keys) - ref_files_tags = {} - for ref_file in all_ref_files: - if ref_file.get('tags'): - for ref_file_tag in ref_file.get('tags'): - if 'states' in ref_file_tag: - ref_files_tags[ref_file_tag] = {'uuid': ref_file['uuid'], 'accession': ref_file['accession']} - - for ref_files_tag, info in ref_files_tags.items(): - buck_obj = info.get('uuid') + '/' + ref_files_tag['accession'] + '.txt' - obj = bucket.Object(buck_obj) - body = obj.get()['Body'].read().decode('utf8') - lines = body.split() - states_colors = [item for num, item in enumerate(lines) if num % 2 != 0] - patch.update({'higlass_defaults': {'colorScale': states_colors}}) + patch.update({'higlass_defaults': {'colorScale': states_colors}}) # now have all the updates for this uid if patch: From 1925b10b0019db3d11210ef7c3c2cb5913b23f28 Mon Sep 17 00:00:00 2001 From: aschroed Date: Thu, 3 Oct 2024 17:39:34 -0400 Subject: [PATCH 2/6] refactor of the state_file action to simplify --- .../checks/wrangler_checks.py | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/chalicelib_fourfront/checks/wrangler_checks.py b/chalicelib_fourfront/checks/wrangler_checks.py index 82e0c845..e04c7af7 100644 --- a/chalicelib_fourfront/checks/wrangler_checks.py +++ b/chalicelib_fourfront/checks/wrangler_checks.py @@ -1703,7 +1703,10 @@ def states_files_without_higlass_defaults(connection, **kwargs): # add random wait wait = round(random.uniform(0.1, random_wait), 1) time.sleep(wait) - valid_tags = ['SPIN_states_v1'] # only 1 at the moment but make the current tag the first in the list + valid_tag = 'SPIN_states_v1' # only 1 at the moment - have kwargs to pass different tag + # important - the tag added to files MUST match the tag on the reference file to use!!! + if kwargs.get('tag', None): + valid_tag = kwargs.get('tag') query = '/search/?file_type=chromatin states&type=File' res = ff_utils.search_metadata(query, key=connection.ff_keys) updates = {} @@ -1719,14 +1722,14 @@ def states_files_without_higlass_defaults(connection, **kwargs): else: tags = a_res.get('tags') for t in tags: - if t in valid_tags: + if t == valid_tag: has_tag = True break if not has_tag or not has_higlass_defaults: updates.setdefault(uid, {}) updates[uid]['accession'] = acc if not has_tag: - updates[uid]['add_tag'] = a_res.get('tags', []).append(valid_tags[0]) + updates[uid]['add_tag'] = a_res.get('tags', []).append(valid_tag) if not has_higlass_defaults: updates[uid]['update_defaults'] = True @@ -1736,6 +1739,7 @@ def states_files_without_higlass_defaults(connection, **kwargs): check.description = 'Ready to patch higlass_defaults for visualization and add missing tags to file' check.allow_action = True check.action_message = 'Will update {} files'.format(len(updates)) + check.full_output['valid_tag'] = valid_tag check.full_output['updates'] = updates else: check.status = 'PASS' @@ -1749,6 +1753,7 @@ def patch_states_files_higlass_defaults(connection, **kwargs): check_res = action.get_associated_check_result(kwargs) action_logs = {'patch_success': [], 'patch_failure': [], 'missing_ref_file': []} updates = check_res.get('full_output').get('updates', {}) + valid_tag = check_res.get('full_output').get('valid_tag') ''' this action has been refactored to look for a specific single reference file to obtain states based on a tag @@ -1759,17 +1764,15 @@ def patch_states_files_higlass_defaults(connection, **kwargs): # this is to get the wanted reference file and generate state_colors s3info = s3Utils() bucket = s3info.raw_file_bucket - states_ref_file_tag = 'SPIN_states_v1' - if kwargs.get('tag', None): - states_ref_file_tag = kwargs.get('tag') - query = '/search/?type=FileReference&status=released&tags={}'.format(states_ref_file_tag) + + query = '/search/?type=FileReference&status=released&tags={}'.format(valid_tag) search_res = ff_utils.search_metadata(query, key=connection.ff_keys) if not search_res: action.status = 'WARN' action.output = 'Failed to retrieve row_info reference file' return action elif len(search_res) > 1: - msg = "WARNING - more than one row_info file found with tag {}\nUsing first one found".format(states_ref_file_tag) + msg = "WARNING - more than one row_info file found with tag {}\nUsing first one found".format(valid_tag) action_logs.setdefault('ref_file_problem', msg) action.status = 'WARN' row_info_file_meta = search_res[0] From 0d461ad5270fb7c7835411e78be2b230b3454e8d Mon Sep 17 00:00:00 2001 From: aschroed Date: Fri, 4 Oct 2024 10:05:31 -0400 Subject: [PATCH 3/6] updated calls to s3 bucket in states files check and using beta version of dcicutils to allow this --- .../checks/wrangler_checks.py | 14 +- poetry.lock | 579 +++++++++--------- pyproject.toml | 5 +- 3 files changed, 306 insertions(+), 292 deletions(-) diff --git a/chalicelib_fourfront/checks/wrangler_checks.py b/chalicelib_fourfront/checks/wrangler_checks.py index e04c7af7..78bf73d1 100644 --- a/chalicelib_fourfront/checks/wrangler_checks.py +++ b/chalicelib_fourfront/checks/wrangler_checks.py @@ -1762,9 +1762,8 @@ def patch_states_files_higlass_defaults(connection, **kwargs): ''' # this is to get the wanted reference file and generate state_colors - s3info = s3Utils() - bucket = s3info.raw_file_bucket - + s3_util_obj = s3Utils(env=connection.ff_env) + bucketname = s3_util_obj.raw_file_bucket query = '/search/?type=FileReference&status=released&tags={}'.format(valid_tag) search_res = ff_utils.search_metadata(query, key=connection.ff_keys) if not search_res: @@ -1776,9 +1775,10 @@ def patch_states_files_higlass_defaults(connection, **kwargs): action_logs.setdefault('ref_file_problem', msg) action.status = 'WARN' row_info_file_meta = search_res[0] - buck_obj = row_info_file_meta.get('uuid') + '/' + row_info_file_meta.get('display_title') - obj = bucket.Object(buck_obj) - body = obj.get()['Body'].read().decode('utf8') + file_key = row_info_file_meta.get('uuid') + '/' + row_info_file_meta.get('display_title') + #obj = bucket.Object(buck_obj) + #body = obj.get()['Body'].read().decode('utf8') + body = s3_util_obj.read_s3(file_key, bucket=bucketname).decode('utf8') lines = body.split() states_colors = [item for num, item in enumerate(lines) if num % 2 != 0] @@ -1788,7 +1788,7 @@ def patch_states_files_higlass_defaults(connection, **kwargs): patch.update({'tags': needed_updates.get('add_tag')}) if needed_updates.get('update_defaults'): patch.update({'higlass_defaults': {'colorScale': states_colors}}) - + # now have all the updates for this uid if patch: try: diff --git a/poetry.lock b/poetry.lock index 1a4df69e..f717ba30 100644 --- a/poetry.lock +++ b/poetry.lock @@ -168,18 +168,18 @@ wcwidth = ">=0.1.4" [[package]] name = "boto3" -version = "1.35.7" +version = "1.35.33" description = "The AWS SDK for Python" category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "boto3-1.35.7-py3-none-any.whl", hash = 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python-versions = ">=3.8.1,<3.13" -content-hash = "05089abf2114b1754a05db8c74fb68958809d518f5f3c80da222690413b41ddf" +content-hash = "a4a61a5d0f57d714b29b5dc0cd705a551b7a816fe87ba277ac3906b995ceb744" diff --git a/pyproject.toml b/pyproject.toml index c6063f6b..a1a19de9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "foursight" -version = "4.9.3.1b1" +version = "4.9.4" description = "Serverless Chalice Application for Monitoring" authors = ["4DN-DCIC Team "] license = "MIT" @@ -13,7 +13,7 @@ python = ">=3.8.1,<3.13" cron-descriptor = "^1.4.0" click = "^7.1.2" # dcicutils = "^8.13.3" -dcicutils = "8.14.3.2b1" +dcicutils = "8.15.0" docutils = ">=0.10,<0.17" PyJWT = "^2.5.0" Jinja2 = "^3.1.2" From 4e26dfae8f6995fc7b7d3afe0a778e1e231c7994 Mon Sep 17 00:00:00 2001 From: aschroed Date: Mon, 7 Oct 2024 09:54:50 -0400 Subject: [PATCH 5/6] removed commented out line --- pyproject.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index a1a19de9..a5ada40c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,6 @@ packages = [ python = ">=3.8.1,<3.13" cron-descriptor = "^1.4.0" click = "^7.1.2" -# dcicutils = "^8.13.3" dcicutils = "8.15.0" docutils = ">=0.10,<0.17" PyJWT = "^2.5.0" From e2285566dbccb1922d2e0da053fefd51efece403 Mon Sep 17 00:00:00 2001 From: aschroed Date: Mon, 7 Oct 2024 12:48:59 -0400 Subject: [PATCH 6/6] update changelog --- CHANGELOG.rst | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 09546e3c..d515778c 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -7,6 +7,16 @@ foursight Change Log ---------- + +4.9.4 +===== + +`PR 582: Refactor and bug fix for states file action `_ + +* refactor states file action once it was clear bug fix in previous PR was insufficient +* make use of s3Utils s3 access with update to read_s3 method in dcicutils 8.15.0 + + 4.9.3 =====