summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorCoprDistGit <infra@openeuler.org>2023-05-10 09:00:32 +0000
committerCoprDistGit <infra@openeuler.org>2023-05-10 09:00:32 +0000
commit85b31175fa769255a8a7ab70bf0270e0fa634604 (patch)
tree7cb442a8e6138d4f86cd66f10f1e643ab95a1a19
parente404a990addc49afc86122bf8cbeb622ccd1174a (diff)
automatic import of python-lapdog
-rw-r--r--.gitignore1
-rw-r--r--python-lapdog.spec223
-rw-r--r--sources1
3 files changed, 225 insertions, 0 deletions
diff --git a/.gitignore b/.gitignore
index e69de29..d35489e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1 @@
+/lapdog-0.18.10.tar.gz
diff --git a/python-lapdog.spec b/python-lapdog.spec
new file mode 100644
index 0000000..e3f2e77
--- /dev/null
+++ b/python-lapdog.spec
@@ -0,0 +1,223 @@
+%global _empty_manifest_terminate_build 0
+Name: python-lapdog
+Version: 0.18.10
+Release: 1
+Summary: A relaxed wrapper for FISS and dalmatian
+License: MIT
+URL: https://github.com/broadinstitute/lapdog
+Source0: https://mirrors.nju.edu.cn/pypi/web/packages/e2/4d/6104552f879ea6f2d2f4cdff8c9c9db001b05a2bc0bb6480e2bda08cca15/lapdog-0.18.10.tar.gz
+BuildArch: noarch
+
+Requires: python3-firecloud
+Requires: python3-firecloud-dalmatian
+Requires: python3-hound
+Requires: python3-google-cloud-storage
+Requires: python3-google-cloud-logging
+Requires: python3-googleapis-common-protos
+Requires: python3-google-cloud-core
+Requires: python3-google-auth
+Requires: python3-google-cloud-kms
+Requires: python3-google-api-core[grpc]
+Requires: python3-PyYAML
+Requires: python3-agutil
+Requires: python3-Flask-Cors
+Requires: python3-crayons
+Requires: python3-connexion
+Requires: python3-oauth2client
+Requires: python3-requests
+Requires: python3-cryptography
+Requires: python3-pyOpenSSL
+Requires: python3-protobuf
+Requires: python3-iso8601
+Requires: python3-pandas
+
+%description
+### Roadmap
+See the [milestones page](https://github.com/broadinstitute/lapdog/milestones) to
+read the development roadmap.
+### Pro/Con with Firecloud
+##### Pros
+* Each submission has a dedicated Cromwell instance. Your jobs will never queue, unless you hit a Google usage quota
+* Lapdog supports Requester Pays buckets and GPUs
+* Workspace cache: Lapdog caches most data received from Firecloud.
+ * In the event of a Firecloud error, Lapdog will attempt to keep running by using it's cached data. Any data updates will by pushed back to Firecloud when the workspace is synced
+* Data caches: The Lapdog API caches data sent to the UI and read from Google
+ * These caches greatly improve UI performance by storing results whenever possible
+* Streamlined UI: The Lapdog UI was built with efficiency in mind
+* Quality of life features:
+ * Save time updating methods. Set `methodRepoMethod.methodVersion` to "latest" and let Lapdog figure out what the snapshot ID is
+ * Easy data uploads. Call `prepare_entity_df` on a DataFrame before uploading to Firecloud. Any local filepaths will be uploaded to the workspace's bucket in the background and a new DataFrame will be returned containing the new `gs://` paths
+ * Automatic reference uploads. When you call `update_attributes`, any values which refer to local filepaths will be uploaded in the background (just like `prepare_entity_df`). `update_attributes` now returns a dictionary containing the attributes exactly as uploaded
+##### Cons
+* You pay an additional 5c/hour fee for each submission to run the Cromwell server
+* Submission results must be manually uploaded to Firecloud by clicking the `Upload Results` button in the UI.
+* There are small overhead costs billed to the Lapdog Engine for operation. These costs
+are for calls to the API and for storage of metadata, both of which should be very cheap
+## PyYAML Note
+Often, when installing Lapdog, the installation fails when upgrading PyYAML because
+it is unable to uninstall the current PyYAML version.
+This is because some older versions of PyYAML were distributed through `distutils`
+which prevents packages from being uninstalled. New versions of PyYAML are distributed
+through `setuptools` which can be successfully uninstalled.
+To resolve this issue, navigate to your Python site-packages directory. The site-packages
+directory usually ends with `.../lib/python{version}/site-packages/`. The exact location
+depends on your platform, environment manager, and python configuration.
+* For anaconda, this path is within anaconda's installation folder: `/{path to anaconda}/envs/{environment}/lib/python{version}/site-packages`
+* For virtualenvs, this path is within the environment's installation folder: `/{path to environment}/lib/python{version}/site-packages`
+* For system python on Unix systems: `/usr/local/lib/python{version}/site-packages`
+An easy way to locate this folder is to open python and then:
+```python
+import yaml
+yaml
+```
+This expression will evaluate and print the path to the `yaml` module, which will be
+within your site-packages directory.
+After locating the site-packages directory, you must remove the following two directories:
+* `.../site-packages/yaml/`
+* `.../site-packages/PyYAML*.egg-info`
+Once removed, you can try the installation command for lapdog again.
+
+%package -n python3-lapdog
+Summary: A relaxed wrapper for FISS and dalmatian
+Provides: python-lapdog
+BuildRequires: python3-devel
+BuildRequires: python3-setuptools
+BuildRequires: python3-pip
+%description -n python3-lapdog
+### Roadmap
+See the [milestones page](https://github.com/broadinstitute/lapdog/milestones) to
+read the development roadmap.
+### Pro/Con with Firecloud
+##### Pros
+* Each submission has a dedicated Cromwell instance. Your jobs will never queue, unless you hit a Google usage quota
+* Lapdog supports Requester Pays buckets and GPUs
+* Workspace cache: Lapdog caches most data received from Firecloud.
+ * In the event of a Firecloud error, Lapdog will attempt to keep running by using it's cached data. Any data updates will by pushed back to Firecloud when the workspace is synced
+* Data caches: The Lapdog API caches data sent to the UI and read from Google
+ * These caches greatly improve UI performance by storing results whenever possible
+* Streamlined UI: The Lapdog UI was built with efficiency in mind
+* Quality of life features:
+ * Save time updating methods. Set `methodRepoMethod.methodVersion` to "latest" and let Lapdog figure out what the snapshot ID is
+ * Easy data uploads. Call `prepare_entity_df` on a DataFrame before uploading to Firecloud. Any local filepaths will be uploaded to the workspace's bucket in the background and a new DataFrame will be returned containing the new `gs://` paths
+ * Automatic reference uploads. When you call `update_attributes`, any values which refer to local filepaths will be uploaded in the background (just like `prepare_entity_df`). `update_attributes` now returns a dictionary containing the attributes exactly as uploaded
+##### Cons
+* You pay an additional 5c/hour fee for each submission to run the Cromwell server
+* Submission results must be manually uploaded to Firecloud by clicking the `Upload Results` button in the UI.
+* There are small overhead costs billed to the Lapdog Engine for operation. These costs
+are for calls to the API and for storage of metadata, both of which should be very cheap
+## PyYAML Note
+Often, when installing Lapdog, the installation fails when upgrading PyYAML because
+it is unable to uninstall the current PyYAML version.
+This is because some older versions of PyYAML were distributed through `distutils`
+which prevents packages from being uninstalled. New versions of PyYAML are distributed
+through `setuptools` which can be successfully uninstalled.
+To resolve this issue, navigate to your Python site-packages directory. The site-packages
+directory usually ends with `.../lib/python{version}/site-packages/`. The exact location
+depends on your platform, environment manager, and python configuration.
+* For anaconda, this path is within anaconda's installation folder: `/{path to anaconda}/envs/{environment}/lib/python{version}/site-packages`
+* For virtualenvs, this path is within the environment's installation folder: `/{path to environment}/lib/python{version}/site-packages`
+* For system python on Unix systems: `/usr/local/lib/python{version}/site-packages`
+An easy way to locate this folder is to open python and then:
+```python
+import yaml
+yaml
+```
+This expression will evaluate and print the path to the `yaml` module, which will be
+within your site-packages directory.
+After locating the site-packages directory, you must remove the following two directories:
+* `.../site-packages/yaml/`
+* `.../site-packages/PyYAML*.egg-info`
+Once removed, you can try the installation command for lapdog again.
+
+%package help
+Summary: Development documents and examples for lapdog
+Provides: python3-lapdog-doc
+%description help
+### Roadmap
+See the [milestones page](https://github.com/broadinstitute/lapdog/milestones) to
+read the development roadmap.
+### Pro/Con with Firecloud
+##### Pros
+* Each submission has a dedicated Cromwell instance. Your jobs will never queue, unless you hit a Google usage quota
+* Lapdog supports Requester Pays buckets and GPUs
+* Workspace cache: Lapdog caches most data received from Firecloud.
+ * In the event of a Firecloud error, Lapdog will attempt to keep running by using it's cached data. Any data updates will by pushed back to Firecloud when the workspace is synced
+* Data caches: The Lapdog API caches data sent to the UI and read from Google
+ * These caches greatly improve UI performance by storing results whenever possible
+* Streamlined UI: The Lapdog UI was built with efficiency in mind
+* Quality of life features:
+ * Save time updating methods. Set `methodRepoMethod.methodVersion` to "latest" and let Lapdog figure out what the snapshot ID is
+ * Easy data uploads. Call `prepare_entity_df` on a DataFrame before uploading to Firecloud. Any local filepaths will be uploaded to the workspace's bucket in the background and a new DataFrame will be returned containing the new `gs://` paths
+ * Automatic reference uploads. When you call `update_attributes`, any values which refer to local filepaths will be uploaded in the background (just like `prepare_entity_df`). `update_attributes` now returns a dictionary containing the attributes exactly as uploaded
+##### Cons
+* You pay an additional 5c/hour fee for each submission to run the Cromwell server
+* Submission results must be manually uploaded to Firecloud by clicking the `Upload Results` button in the UI.
+* There are small overhead costs billed to the Lapdog Engine for operation. These costs
+are for calls to the API and for storage of metadata, both of which should be very cheap
+## PyYAML Note
+Often, when installing Lapdog, the installation fails when upgrading PyYAML because
+it is unable to uninstall the current PyYAML version.
+This is because some older versions of PyYAML were distributed through `distutils`
+which prevents packages from being uninstalled. New versions of PyYAML are distributed
+through `setuptools` which can be successfully uninstalled.
+To resolve this issue, navigate to your Python site-packages directory. The site-packages
+directory usually ends with `.../lib/python{version}/site-packages/`. The exact location
+depends on your platform, environment manager, and python configuration.
+* For anaconda, this path is within anaconda's installation folder: `/{path to anaconda}/envs/{environment}/lib/python{version}/site-packages`
+* For virtualenvs, this path is within the environment's installation folder: `/{path to environment}/lib/python{version}/site-packages`
+* For system python on Unix systems: `/usr/local/lib/python{version}/site-packages`
+An easy way to locate this folder is to open python and then:
+```python
+import yaml
+yaml
+```
+This expression will evaluate and print the path to the `yaml` module, which will be
+within your site-packages directory.
+After locating the site-packages directory, you must remove the following two directories:
+* `.../site-packages/yaml/`
+* `.../site-packages/PyYAML*.egg-info`
+Once removed, you can try the installation command for lapdog again.
+
+%prep
+%autosetup -n lapdog-0.18.10
+
+%build
+%py3_build
+
+%install
+%py3_install
+install -d -m755 %{buildroot}/%{_pkgdocdir}
+if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
+if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
+if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
+if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
+pushd %{buildroot}
+if [ -d usr/lib ]; then
+ find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/lib64 ]; then
+ find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/bin ]; then
+ find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/sbin ]; then
+ find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+touch doclist.lst
+if [ -d usr/share/man ]; then
+ find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
+fi
+popd
+mv %{buildroot}/filelist.lst .
+mv %{buildroot}/doclist.lst .
+
+%files -n python3-lapdog -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Wed May 10 2023 Python_Bot <Python_Bot@openeuler.org> - 0.18.10-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..0fcf516
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+beccbfef697c35154ac76b5b225f340d lapdog-0.18.10.tar.gz