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update-meilisearch-index:dev

Passed Started by
Jean CURY
@jcury
This job is archived. Only the complete pipeline can be retried.
1Running with gitlab-runner 16.0.3 (0dc6e706)
2 on k8sdev-01-gitlab-runner 6V_kZ21K, system ID: r_rEwXCBhQlprc
3 Preparing the "kubernetes" executor 00:00
4Using Kubernetes namespace: gitlab-ci
5Using Kubernetes executor with image python:3.11-bullseye ...
6Using attach strategy to execute scripts...
7 Preparing environment 00:04
8Waiting for pod gitlab-ci/runner-6vkz21k-project-5222-concurrent-162p8j to be running, status is Pending
9Running on runner-6vkz21k-project-5222-concurrent-162p8j via gitlab-runner-6c6f994788-26sk7...
10 Getting source from Git repository 00:08
11Fetching changes with git depth set to 20...
12Initialized empty Git repository in /builds/mdm-lab/wiki/.git/
13Created fresh repository.
14Checking out d5380627 as detached HEAD (ref is lpaoli-main-patch-72078)...
15Skipping Git submodules setup
16 Restoring cache 00:15
17Checking cache for default-non_protected...
18Downloading cache.zip from https://s3-dsi.pasteur.fr/gitlab-ci-cache/runner/project/5222/default-non_protected
19Successfully extracted cache
20 Executing "step_script" stage of the job script 00:51
21$ pip install df-wiki-cli --index-url https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.pasteur.fr/api/v4/projects/5222/packages/pypi/simple
22Looking in indexes: https://gitlab-ci-token:****@gitlab.pasteur.fr/api/v4/projects/5222/packages/pypi/simple
23Collecting df-wiki-cli
24 Downloading https://gitlab.pasteur.fr/api/v4/projects/5222/packages/pypi/files/22c18b9ecb20e7eedbc22f34f313f8d1dc185accf10a841c722a7305fccdbb96/df_wiki_cli-0.1.3-py3-none-any.whl (8.4 kB)
25Collecting meilisearch<0.29.0,>=0.28.4 (from df-wiki-cli)
26 Obtaining dependency information for meilisearch<0.29.0,>=0.28.4 from https://files.pythonhosted.org/packages/7c/39/7e15b98609dd2ec77f06729cd2fac931cc54f7942b0e753672e0b7558540/meilisearch-0.28.4-py3-none-any.whl.metadata
27 Downloading meilisearch-0.28.4-py3-none-any.whl.metadata (949 bytes)
28Collecting pandas<3.0.0,>=2.1.2 (from df-wiki-cli)
29 Obtaining dependency information for pandas<3.0.0,>=2.1.2 from https://files.pythonhosted.org/packages/f8/8c/9ad173c5cd2c7178c84075c02ec37b5d1d53fb1d015f51ea3e623ea9c31c/pandas-2.1.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
30 Downloading pandas-2.1.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (18 kB)
31Collecting pydantic<3.0.0,>=2.4.2 (from df-wiki-cli)
32 Obtaining dependency information for pydantic<3.0.0,>=2.4.2 from https://files.pythonhosted.org/packages/0a/2b/64066de1c4cf3d4ed623beeb3bbf3f8d0cc26661f1e7d180ec5eb66b75a5/pydantic-2.5.2-py3-none-any.whl.metadata
33 Downloading pydantic-2.5.2-py3-none-any.whl.metadata (65 kB)
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35Collecting pydantic-yaml<2.0.0,>=1.2.0 (from df-wiki-cli)
36 Obtaining dependency information for pydantic-yaml<2.0.0,>=1.2.0 from https://files.pythonhosted.org/packages/7d/1c/d2418ce20a09e32a7b22a6c8089256a67ddcf4f33a9bf1ff4a3c619392d8/pydantic_yaml-1.2.0-py3-none-any.whl.metadata
37 Downloading pydantic_yaml-1.2.0-py3-none-any.whl.metadata (6.6 kB)
38Collecting python-frontmatter<2.0.0,>=1.0.1 (from df-wiki-cli)
39 Obtaining dependency information for python-frontmatter<2.0.0,>=1.0.1 from https://files.pythonhosted.org/packages/85/07/5a612ff607b44a9540a483c1c159793f6955463d77a323f774b7536b8bfa/python_frontmatter-1.0.1-py3-none-any.whl.metadata
40 Downloading python_frontmatter-1.0.1-py3-none-any.whl.metadata (4.0 kB)
41Collecting pyzotero<2.0.0,>=1.5.18 (from df-wiki-cli)
42 Obtaining dependency information for pyzotero<2.0.0,>=1.5.18 from https://files.pythonhosted.org/packages/76/e5/cad40df812381ffef3d3bcfb3f54a6d5c74d9ad1775dce8e5feabfb470ff/pyzotero-1.5.18-py3-none-any.whl.metadata
43 Downloading pyzotero-1.5.18-py3-none-any.whl.metadata (6.6 kB)
44Collecting requests<3.0.0,>=2.31.0 (from df-wiki-cli)
45 Obtaining dependency information for requests<3.0.0,>=2.31.0 from https://files.pythonhosted.org/packages/70/8e/0e2d847013cb52cd35b38c009bb167a1a26b2ce6cd6965bf26b47bc0bf44/requests-2.31.0-py3-none-any.whl.metadata
46 Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
47Collecting typer[all]<0.10.0,>=0.9.0 (from df-wiki-cli)
48 Downloading typer-0.9.0-py3-none-any.whl (45 kB)
49 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 45.9/45.9 kB 18.0 MB/s eta 0:00:00
50Collecting typing-extensions<5.0.0,>=4.8.0 (from df-wiki-cli)
51 Obtaining dependency information for typing-extensions<5.0.0,>=4.8.0 from https://files.pythonhosted.org/packages/b7/f4/6a90020cd2d93349b442bfcb657d0dc91eee65491600b2cb1d388bc98e6b/typing_extensions-4.9.0-py3-none-any.whl.metadata
52 Downloading typing_extensions-4.9.0-py3-none-any.whl.metadata (3.0 kB)
53Collecting camel-converter[pydantic] (from meilisearch<0.29.0,>=0.28.4->df-wiki-cli)
54 Obtaining dependency information for camel-converter[pydantic] from https://files.pythonhosted.org/packages/55/fd/065986b2e7d609f57ad94c3b6f883d375235a68ccf1adfa4976d31f67614/camel_converter-3.1.1-py3-none-any.whl.metadata
55 Downloading camel_converter-3.1.1-py3-none-any.whl.metadata (5.4 kB)
56Collecting numpy<2,>=1.23.2 (from pandas<3.0.0,>=2.1.2->df-wiki-cli)
57 Obtaining dependency information for numpy<2,>=1.23.2 from https://files.pythonhosted.org/packages/b6/ab/5b893944b1602a366893559bfb227fdfb3ad7c7629b2a80d039bb5924367/numpy-1.26.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
58 Downloading numpy-1.26.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
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60Collecting python-dateutil>=2.8.2 (from pandas<3.0.0,>=2.1.2->df-wiki-cli)
61 Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
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63Collecting pytz>=2020.1 (from pandas<3.0.0,>=2.1.2->df-wiki-cli)
64 Obtaining dependency information for pytz>=2020.1 from https://files.pythonhosted.org/packages/32/4d/aaf7eff5deb402fd9a24a1449a8119f00d74ae9c2efa79f8ef9994261fc2/pytz-2023.3.post1-py2.py3-none-any.whl.metadata
65 Downloading pytz-2023.3.post1-py2.py3-none-any.whl.metadata (22 kB)
66Collecting tzdata>=2022.1 (from pandas<3.0.0,>=2.1.2->df-wiki-cli)
67 Downloading tzdata-2023.3-py2.py3-none-any.whl (341 kB)
68 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 341.8/341.8 kB 71.9 MB/s eta 0:00:00
69Collecting annotated-types>=0.4.0 (from pydantic<3.0.0,>=2.4.2->df-wiki-cli)
70 Obtaining dependency information for annotated-types>=0.4.0 from https://files.pythonhosted.org/packages/28/78/d31230046e58c207284c6b2c4e8d96e6d3cb4e52354721b944d3e1ee4aa5/annotated_types-0.6.0-py3-none-any.whl.metadata
71 Downloading annotated_types-0.6.0-py3-none-any.whl.metadata (12 kB)
72Collecting pydantic-core==2.14.5 (from pydantic<3.0.0,>=2.4.2->df-wiki-cli)
73 Obtaining dependency information for pydantic-core==2.14.5 from https://files.pythonhosted.org/packages/bf/ed/ee221482b51f368884ea6453f3784eeaeb17f5b737589d39d68a89bffde7/pydantic_core-2.14.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
74 Downloading pydantic_core-2.14.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.5 kB)
75Collecting ruamel.yaml<0.18.0,>=0.16.0 (from pydantic-yaml<2.0.0,>=1.2.0->df-wiki-cli)
76 Obtaining dependency information for ruamel.yaml<0.18.0,>=0.16.0 from https://files.pythonhosted.org/packages/35/79/5e2cffa1c77432f11cd93a5351f30732c997a239d3a3090856a72d6d8ba7/ruamel.yaml-0.17.40-py3-none-any.whl.metadata
77 Downloading ruamel.yaml-0.17.40-py3-none-any.whl.metadata (19 kB)
78Collecting importlib-metadata (from pydantic-yaml<2.0.0,>=1.2.0->df-wiki-cli)
79 Obtaining dependency information for importlib-metadata from https://files.pythonhosted.org/packages/73/26/9777cfe0cdc8181a32eaf542f4a2a435e5aba5dd38f41cfc0a532dc51027/importlib_metadata-7.0.0-py3-none-any.whl.metadata
80 Downloading importlib_metadata-7.0.0-py3-none-any.whl.metadata (4.9 kB)
81Collecting PyYAML (from python-frontmatter<2.0.0,>=1.0.1->df-wiki-cli)
82 Obtaining dependency information for PyYAML from https://files.pythonhosted.org/packages/7b/5e/efd033ab7199a0b2044dab3b9f7a4f6670e6a52c089de572e928d2873b06/PyYAML-6.0.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
83 Downloading PyYAML-6.0.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
84Collecting feedparser>=6 (from pyzotero<2.0.0,>=1.5.18->df-wiki-cli)
85 Obtaining dependency information for feedparser>=6 from https://files.pythonhosted.org/packages/7c/d4/8c31aad9cc18f451c49f7f9cfb5799dadffc88177f7917bc90a66459b1d7/feedparser-6.0.11-py3-none-any.whl.metadata
86 Downloading feedparser-6.0.11-py3-none-any.whl.metadata (2.4 kB)
87Collecting bibtexparser (from pyzotero<2.0.0,>=1.5.18->df-wiki-cli)
88 Downloading bibtexparser-1.4.1.tar.gz (55 kB)
89 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 55.1/55.1 kB 10.1 MB/s eta 0:00:00
90 Preparing metadata (setup.py): started
91 Preparing metadata (setup.py): finished with status 'done'
92Collecting charset-normalizer<4,>=2 (from requests<3.0.0,>=2.31.0->df-wiki-cli)
93 Obtaining dependency information for charset-normalizer<4,>=2 from https://files.pythonhosted.org/packages/40/26/f35951c45070edc957ba40a5b1db3cf60a9dbb1b350c2d5bef03e01e61de/charset_normalizer-3.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
94 Downloading charset_normalizer-3.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)
95Collecting idna<4,>=2.5 (from requests<3.0.0,>=2.31.0->df-wiki-cli)
96 Obtaining dependency information for idna<4,>=2.5 from https://files.pythonhosted.org/packages/c2/e7/a82b05cf63a603df6e68d59ae6a68bf5064484a0718ea5033660af4b54a9/idna-3.6-py3-none-any.whl.metadata
97 Downloading idna-3.6-py3-none-any.whl.metadata (9.9 kB)
98Collecting urllib3<3,>=1.21.1 (from requests<3.0.0,>=2.31.0->df-wiki-cli)
99 Obtaining dependency information for urllib3<3,>=1.21.1 from https://files.pythonhosted.org/packages/96/94/c31f58c7a7f470d5665935262ebd7455c7e4c7782eb525658d3dbf4b9403/urllib3-2.1.0-py3-none-any.whl.metadata
100 Downloading urllib3-2.1.0-py3-none-any.whl.metadata (6.4 kB)
101Collecting certifi>=2017.4.17 (from requests<3.0.0,>=2.31.0->df-wiki-cli)
102 Obtaining dependency information for certifi>=2017.4.17 from https://files.pythonhosted.org/packages/64/62/428ef076be88fa93716b576e4a01f919d25968913e817077a386fcbe4f42/certifi-2023.11.17-py3-none-any.whl.metadata
103 Downloading certifi-2023.11.17-py3-none-any.whl.metadata (2.2 kB)
104Collecting click<9.0.0,>=7.1.1 (from typer[all]<0.10.0,>=0.9.0->df-wiki-cli)
105 Obtaining dependency information for click<9.0.0,>=7.1.1 from https://files.pythonhosted.org/packages/00/2e/d53fa4befbf2cfa713304affc7ca780ce4fc1fd8710527771b58311a3229/click-8.1.7-py3-none-any.whl.metadata
106 Downloading click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
107Collecting colorama<0.5.0,>=0.4.3 (from typer[all]<0.10.0,>=0.9.0->df-wiki-cli)
108 Downloading colorama-0.4.6-py2.py3-none-any.whl (25 kB)
109Collecting shellingham<2.0.0,>=1.3.0 (from typer[all]<0.10.0,>=0.9.0->df-wiki-cli)
110 Obtaining dependency information for shellingham<2.0.0,>=1.3.0 from https://files.pythonhosted.org/packages/e0/f9/0595336914c5619e5f28a1fb793285925a8cd4b432c9da0a987836c7f822/shellingham-1.5.4-py2.py3-none-any.whl.metadata
111 Downloading shellingham-1.5.4-py2.py3-none-any.whl.metadata (3.5 kB)
112Collecting rich<14.0.0,>=10.11.0 (from typer[all]<0.10.0,>=0.9.0->df-wiki-cli)
113 Obtaining dependency information for rich<14.0.0,>=10.11.0 from https://files.pythonhosted.org/packages/be/be/1520178fa01eabe014b16e72a952b9f900631142ccd03dc36cf93e30c1ce/rich-13.7.0-py3-none-any.whl.metadata
114 Downloading rich-13.7.0-py3-none-any.whl.metadata (18 kB)
115Collecting sgmllib3k (from feedparser>=6->pyzotero<2.0.0,>=1.5.18->df-wiki-cli)
116 Downloading sgmllib3k-1.0.0.tar.gz (5.8 kB)
117 Preparing metadata (setup.py): started
118 Preparing metadata (setup.py): finished with status 'done'
119Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas<3.0.0,>=2.1.2->df-wiki-cli)
120 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
121Collecting markdown-it-py>=2.2.0 (from rich<14.0.0,>=10.11.0->typer[all]<0.10.0,>=0.9.0->df-wiki-cli)
122 Obtaining dependency information for markdown-it-py>=2.2.0 from https://files.pythonhosted.org/packages/42/d7/1ec15b46af6af88f19b8e5ffea08fa375d433c998b8a7639e76935c14f1f/markdown_it_py-3.0.0-py3-none-any.whl.metadata
123 Downloading markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB)
124Collecting pygments<3.0.0,>=2.13.0 (from rich<14.0.0,>=10.11.0->typer[all]<0.10.0,>=0.9.0->df-wiki-cli)
125 Obtaining dependency information for pygments<3.0.0,>=2.13.0 from https://files.pythonhosted.org/packages/97/9c/372fef8377a6e340b1704768d20daaded98bf13282b5327beb2e2fe2c7ef/pygments-2.17.2-py3-none-any.whl.metadata
126 Downloading pygments-2.17.2-py3-none-any.whl.metadata (2.6 kB)
127Collecting ruamel.yaml.clib>=0.2.7 (from ruamel.yaml<0.18.0,>=0.16.0->pydantic-yaml<2.0.0,>=1.2.0->df-wiki-cli)
128 Obtaining dependency information for ruamel.yaml.clib>=0.2.7 from https://files.pythonhosted.org/packages/a4/f7/22d6b620ed895a05d40802d8281eff924dc6190f682d933d4efff60db3b5/ruamel.yaml.clib-0.2.8-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl.metadata
129 Downloading ruamel.yaml.clib-0.2.8-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl.metadata (2.2 kB)
130Collecting pyparsing>=2.0.3 (from bibtexparser->pyzotero<2.0.0,>=1.5.18->df-wiki-cli)
131 Obtaining dependency information for pyparsing>=2.0.3 from https://files.pythonhosted.org/packages/39/92/8486ede85fcc088f1b3dba4ce92dd29d126fd96b0008ea213167940a2475/pyparsing-3.1.1-py3-none-any.whl.metadata
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133Collecting zipp>=0.5 (from importlib-metadata->pydantic-yaml<2.0.0,>=1.2.0->df-wiki-cli)
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139Downloading pandas-2.1.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.2 MB)
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143Downloading pydantic_core-2.14.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.1 MB)
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182Downloading ruamel.yaml.clib-0.2.8-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (544 kB)
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184Downloading zipp-3.17.0-py3-none-any.whl (7.4 kB)
185Downloading camel_converter-3.1.1-py3-none-any.whl (5.7 kB)
186Building wheels for collected packages: bibtexparser, sgmllib3k
187 Building wheel for bibtexparser (setup.py): started
188 Building wheel for bibtexparser (setup.py): finished with status 'done'
189 Created wheel for bibtexparser: filename=bibtexparser-1.4.1-py3-none-any.whl size=43252 sha256=3150a81ed910ec1b5c4849fd2cf2877ce21a2d5cb5c301544dcb8996b4560649
190 Stored in directory: /root/.cache/pip/wheels/d6/93/c0/58e9981a8f55db19a654503072b50ede34bbcc8e7db5908a84
191 Building wheel for sgmllib3k (setup.py): started
192 Building wheel for sgmllib3k (setup.py): finished with status 'done'
193 Created wheel for sgmllib3k: filename=sgmllib3k-1.0.0-py3-none-any.whl size=6048 sha256=fce9794183e7c0712f62ff7048a12a5d24c8ed6abd5c2c546c3dc654aad1be07
194 Stored in directory: /root/.cache/pip/wheels/3b/25/2a/105d6a15df6914f4d15047691c6c28f9052cc1173e40285d03
195Successfully built bibtexparser sgmllib3k
196Installing collected packages: sgmllib3k, pytz, zipp, urllib3, tzdata, typing-extensions, six, shellingham, ruamel.yaml.clib, PyYAML, pyparsing, pygments, numpy, mdurl, idna, feedparser, colorama, click, charset-normalizer, certifi, camel-converter, annotated-types, typer, ruamel.yaml, requests, python-frontmatter, python-dateutil, pydantic-core, markdown-it-py, importlib-metadata, bibtexparser, rich, pyzotero, pydantic, pandas, pydantic-yaml, meilisearch, df-wiki-cli
197Successfully installed PyYAML-6.0.1 annotated-types-0.6.0 bibtexparser-1.4.1 camel-converter-3.1.1 certifi-2023.11.17 charset-normalizer-3.3.2 click-8.1.7 colorama-0.4.6 df-wiki-cli-0.1.3 feedparser-6.0.11 idna-3.6 importlib-metadata-7.0.0 markdown-it-py-3.0.0 mdurl-0.1.2 meilisearch-0.28.4 numpy-1.26.2 pandas-2.1.4 pydantic-2.5.2 pydantic-core-2.14.5 pydantic-yaml-1.2.0 pygments-2.17.2 pyparsing-3.1.1 python-dateutil-2.8.2 python-frontmatter-1.0.1 pytz-2023.3.post1 pyzotero-1.5.18 requests-2.31.0 rich-13.7.0 ruamel.yaml-0.17.40 ruamel.yaml.clib-0.2.8 sgmllib3k-1.0.0 shellingham-1.5.4 six-1.16.0 typer-0.9.0 typing-extensions-4.9.0 tzdata-2023.3 urllib3-2.1.0 zipp-3.17.0
198WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
199[notice] A new release of pip is available: 23.2.1 -> 23.3.2
200[notice] To update, run: pip install --upgrade pip
201$ df-wiki-cli meilisearch --host ${MEILI_HOST} --key ${MEILI_MASTER_KEY} update --file data/refseq_res.csv --document refseq
202$ df-wiki-cli meilisearch --host ${MEILI_HOST} --key ${MEILI_MASTER_KEY} update --file data/all_predictions_statistics.csv --document structure
203task_uid=523 index_uid='structure' status='enqueued' type='documentAdditionOrUpdate' enqueued_at=datetime.datetime(2023, 12, 20, 15, 36, 31, 892651)
204task_uid=527 index_uid='structure' status='enqueued' type='documentAdditionOrUpdate' enqueued_at=datetime.datetime(2023, 12, 20, 15, 36, 32, 4069)
205task_uid=530 index_uid='structure' status='enqueued' type='settingsUpdate' enqueued_at=datetime.datetime(2023, 12, 20, 15, 36, 32, 84673)
206task_uid=531 index_uid='structure' status='enqueued' type='settingsUpdate' enqueued_at=datetime.datetime(2023, 12, 20, 15, 36, 32, 123050)
207 Saving cache for successful job 00:43
208Creating cache default-non_protected...
209node_modules/: found 32268 matching artifact files and directories
210.output/public: found 2088 matching artifact files and directories
211Uploading cache.zip to https://s3-dsi.pasteur.fr/gitlab-ci-cache/runner/project/5222/default-non_protected
212Created cache
213 Cleaning up project directory and file based variables 00:01
214Job succeeded