appssubmitter finial version #128

SeverusYixin · 2024-07-19T09:50:43Z

This webapp program contains a form (urls, author, description, license etc) and once the user clicks "submit", all things can be easily uploaded to github.

To protect the security, the Github API key must be updated every 30 days.

This PR closes #94

haesleinhuepf

Hi @SeverusYixin ,

awesome, thanks for sending this! Next time, it would be great if you could write a sentence, what this PR is about. Furthermore, I modified the sentence "closes #94" to your message. This will later close the corresponding issue, once this is merged.

May I also ask you for adding some documentation to our jupyter book? It would be great to have short user guide for your app with some screenshots. See this page as example.

Thank you!

Best,
Robert

SeverusYixin · 2024-07-19T14:26:07Z

Hi @SeverusYixin ,

awesome, thanks for sending this! Next time, it would be great if you could write a sentence, what this PR is about. Furthermore, I modified the sentence "closes #94" to your message. This will later close the corresponding issue, once this is merged.

May I also ask you for adding some documentation to our jupyter book? It would be great to have short user guide for your app with some screenshots. See this page as example.

Thank you!

Best, Robert

Ofc no problem, but which kinds of the documentation did you want me to add to our jupyter book? And I have a screeunshot of the APP, where should I upload it?

haesleinhuepf · 2024-07-19T14:35:46Z

where should I upload it?

As a new page next to this one, certainly in the same folder.

…sponding issue.

haesleinhuepf · 2024-07-23T08:13:54Z

Hey @SeverusYixin ,

ok, this is super super cool!!

May I ask for some minor modifications:

Remove the submitter name
Users should select the license from a list (e.g. the SPDX list)
Users should select the tags from a list (they can select multiple), and there should be an option to add new tags
Users should select the type from a list
Do not create a github issue, the pull-request is enough.
Change the target repository to NFDI4BioImage/training
Test

Big thanks!

SeverusYixin · 2024-07-23T13:20:39Z

Hi @haesleinhuepf, if you can show me the current exact license list, tags list and type list it would be so helpful. Or can I just use the things that show up on the left side of https://nfdi4bioimage.github.io/training/readme.html directly?

haesleinhuepf · 2024-07-23T14:31:28Z

@SeverusYixin

For the license list, let's use the SPDX list you were using in #127 (so we don't reinvent the wheel here) :

training/scripts/data_normalizer.py

Line 7 in f0aa351

SPDX_LICENSE_LIST_URL = "https://spdx.org/licenses/licenses.json"

The current lists of tags and content types can be retrieve as shown in #130 :
https://github.com/NFDI4BIOIMAGE/training/blob/7045d4888217d6b73c53080ba42d020475dd41fd/scripts/tag_statistics.ipynb

Let me know if you need anything else!

SeverusYixin · 2024-07-23T14:47:36Z

@SeverusYixin

For the license list, let's use the SPDX list you were using in #127 (so we don't reinvent the wheel here) :

training/scripts/data_normalizer.py

Line 7 in f0aa351

SPDX_LICENSE_LIST_URL = "https://spdx.org/licenses/licenses.json"

The current lists of tags and content types can be retrieve as shown in #130 : https://github.com/NFDI4BIOIMAGE/training/blob/7045d4888217d6b73c53080ba42d020475dd41fd/scripts/tag_statistics.ipynb

Let me know if you need anything else!

hmmm, that means I need retrieve the license by myself, am I right?

And for https://github.com/NFDI4BIOIMAGE/training/blob/7045d4888217d6b73c53080ba42d020475dd41fd/scripts/tag_statistics.ipynb, it looks like only have the tags list, am I right?

haesleinhuepf · 2024-07-23T19:19:48Z

hmmm, that means I need retrieve the license by myself, am I right?

Yes

it looks like only have the tags list, am I right?

Yes!

…me Users should select the license from a list (e.g. the SPDX list) Users should select the tags from a list (they can select multiple), and there should be an option to add new tags Users should select the type from a list Do not create a github issue, the pull-request is enough."

SeverusYixin · 2024-07-24T16:13:39Z

Hi @haesleinhuepf, I have a question about URL,Description,Name,Authors. if the users add nothing to these, should they still be allowed to upload, or if they didn't enter the authors, should the submit be denied? For License, Tags and Type, the user chooses at least one, and I add an unknown choice for them. The yaml file also needs to be selected as it can be submitted.

…on. User should select license from a list (e.g. SPDX list) User should select tags from the list (multiple selections are possible) and should be given the option to add new tags The user should select the type from the list Don't create github issues, pull requests are sufficient. Change the target repository to NFDI4BioImage/training Testing” and also add documentation to our jupyter book

SeverusYixin · 2024-07-26T14:32:07Z

Hi @haesleinhuepf, me again :) Could you review this when you have a moment? And enjoy your holiday ：）

haesleinhuepf

Hi @SeverusYixin ,

ok cool, the app looks great! I just tried it and have some minor requests:

It would be great if we could add tags which are not in the list of available tags:
make sure the changes are made on the most recent files. I just submitted a PR using the app (it worked 🥳 ) but it suggests many changes. I could imagine that this happens if my local repository is not up-to-date. Details. But we can pull the most recent file from github, before modifying the file e.g. using this code.
And below some suggestions in the code.

Otherwise, it's looking great!

Best,
Robert

haesleinhuepf · 2024-08-06T11:23:53Z

scripts/appsubmitter.py

+Steps:
+1. Select the YAML file for the type of training material.
+2. Provide the necessary information.
+3. Submit the form to create a pull request.


Suggested change

Steps:

1. Select the YAML file for the type of training material.

2. Provide the necessary information.

3. Submit the form to create a pull request.

Steps:

1. Select the YAML file for the type of training material.

2. Provide the necessary information.

3. Submit the form to create a pull request.

I suggest to remove this. It feels like a duplication of the sentence above and form entries below.

haesleinhuepf · 2024-08-06T11:24:30Z

scripts/appsubmitter.py

+    "AGPL-3.0", "All-rights-reserved", "Apache-2.0", "BSD-2-Clause", "BSD-3-Clause", "BSD-License", "CC0",
+    "CC0-1.0", "CC0-Licence (with some variations noted in dataset attributes)", "CC-BY-4.0", "CC-BY-NC-4.0",
+    "CC-BY-NC-ND-3.0-DEED", "CC-BY-ND-SA-4.0", "CC-BY-SA-4.0", "GPL-2.0", "GPL-3.0", "MIT", "ODC-By-1.0",
+    "Public-domain"


Could we use the fetch_spdx_function from here?

training/scripts/data_normalizer.py

Line 9 in d9146a5

def fetch_spdx_licenses():

haesleinhuepf · 2024-08-06T11:25:36Z

scripts/appsubmitter.py

+    "Arc", "Artificial Intelligence", "Big Data", "Bio-Image Analysis", "Bioimage Analysis", "Bioimage Data",
+    "Bioinformatics", "Cellpose", "Cellprofiler", "Citing", "Clesperanto", "Conda", "Dask", "Data Analysis",
+    "Data Protection", "Data Science", "Data Stewardship", "Dataplant", "Deep Learning", "Deployment", 
+    "Diffusion Models", "Elastix", "Fair", "Fair-Principles", "Fiji", "Flim", "Git", "Github", "Gpu", 
+    "Hackathon", "I3Dbio", "Image Data Management", "Image Registration", "Image Segmentation", "Imagej", 
+    "Imagej Macro", "Itk", "Large Language Models", "Licensing", "Machine Learning", "Mamba", "Meta Data", 
+    "Metadata", "Microscopy Image Analysis", "Napari", "Neubias", "Nfdi4Bioimage", "Notebook", "Notebooks", 
+    "Omero", "Open Access", "Open Science", "Python", "Pytorch", "Quareo-Limi", "R", "Research Data Management", 
+    "Science Communication", "Segmentation", "Sharing", "Teaching", "Tu Dresden", "Workflow", "Workflow Engine", 
+    "Zarr", "Zenodo"
+])


Could we determine this list dynamically from the yml files? E.g. as shown in the notebook here:

https://github.com/NFDI4BIOIMAGE/training/blob/7045d4888217d6b73c53080ba42d020475dd41fd/scripts/tag_statistics.ipynb

haesleinhuepf · 2024-08-06T11:25:53Z

scripts/appsubmitter.py

+    "Big Data", "Bioimage Analysis", "Blog", "Book", "Code", "Collection", "Conference Abstract", "Data", 
+    "Dataset", "Document", "Documentation", "Event", "Forum Post", "Github Repository", "Jupyter Book", 
+    "Notebook", "Online Course", "Online Tutorial", "Poster", "Practicals", "Preprint", "Presentation", 
+    "Publication", "Publiction", "Python", "Slide", "Slides", "Tutorial", "Video", "Videos", "Workshop"


Same here. This list should be determined dynamically from the yml files.

haesleinhuepf · 2024-08-06T11:26:13Z

scripts/appsubmitter.py

+
+# List of YAML files
+yaml_list = sorted([
+    'blog_posts.yml', 'events.yml', 'materials.yml', 'nfdi4bioimage.yml', 'papers.yml', 'workflow-tools.yml', 'youtube_channels.yml'


Could we determine this list using os.listdir?

SeverusYixin · 2024-08-19T11:37:12Z

Hi @haesleinhuepf , me again :). If you have a moment, you can run this code for me to see if it works. Especially if the yml files are merged, does it still work on your side, so far no problem on mine.

Also:
"normalisation_mapping = {}" function, will be removed after I update data_normalizer.py.

One question:
Since we have merged all the yml files, do we still need the 'YAML file selecter'? I think we can export it directly to the specified folder or file.

SeverusYixin · 2024-08-19T14:05:19Z

It seems I don't have permission to change the data source? Would you mind changing it for me?

haesleinhuepf · 2024-08-23T05:12:38Z

I'm not sure what you mean with "data source". Please let me know what exactly should be changed. Consider using http-links to point at code pecisely...

SeverusYixin · 2024-08-26T07:18:22Z

I'm not sure what you mean with "data source". Please let me know what exactly should be changed. Consider using http-links to point at code pecisely...

I mean for this:
"This branch has conflicts that must be resolved
Use the web editor or the to resolve conflicts.
Conflicting files
resources/nfdi4bioimage.yml".

It seems I'm not allowed to update it.

haesleinhuepf · 2024-08-26T12:22:05Z

ok, done

SeverusYixin · 2024-08-26T13:30:05Z

ok, done

Thank you :)

…MAGE/training into app_for_adding_entries

SeverusYixin · 2024-08-27T11:28:19Z

Hi @haesleinhuepf, I have already updated it with the docstring. Take your time and check it out.

haesleinhuepf

Hi @SeverusYixin ,

thanks for working on this! It would be great if you could reduce code-duplication, before we merge this. Instead of repeating similar functionality, consider re-using functions. This will result in much shorter code, which is easier to maintain obviously.

Thanks!

Best,
Robert

haesleinhuepf · 2024-08-27T11:32:29Z

docs/contributing/index_2.md

+# How to contribute
+
+This repository contains lists of training materials. It is extensible using GitHub pull requests. You can find a how-to guide at the bottom of this page. The format for entries in the repository is documented on the next page.
+
+## Quick contributing shortcut:
+
+If you're too busy to enter everything in detail yourself, please create a [GitHub issue](https://github.com/NFDI4BIOIMAGE/training/issues) with a link to the materials you want to include in our list. We can take care of all the details.
+
+## What to contribute
+
+Consider adding your favorite training materials and resources. If you know a collection of resources, add it, but do not add all individual entries of the collection. We are working on collecting them automatically ([more information](https://github.com/NFDI4BIOIMAGE/training/issues/2)). However, if there are specific entries in such a collection that you think are particularly valuable, feel free to add them now.
+
+## Inclusion criteria
+
+We will consider merging links to all educative materials related to research data management, especially in the bio-imaging context, and bio-image analysis.
+
+We would like to collect links to resources in various formats/content types, including slides, posters, publications, blog posts, example data, collections (of links to other materials), and more.
+
+## Exclusion criteria
+
+We will only merge links to materials behind a paywall in exceptional cases. We will also not merge links to materials that primarily advertise commercial products. However, if there are openly accessible training resources for commercial software, we welcome links to these resources.
+
+## Maintenance of contributions
+
+We reserve the right to remove and modify entries in this collection at any time.


This duplicated text from the page before. Please only document your AppSubmitter in this page.

haesleinhuepf · 2024-08-27T11:34:20Z

scripts/appsubmitter.py

+def load_yaml_data(file_path):
+    """
+    Load YAML data from a file.
+
+    Args:
+        file_path (str): Path to the YAML file.
+
+    Returns:
+        dict: Parsed YAML data.
+    """
+    with open(file_path, 'r') as file:
+        return yaml.safe_load(file)


Why are you not using this function?

training/scripts/generate_link_lists.py

Line 117 in e19da86

def read_yaml_file(filename):

haesleinhuepf · 2024-08-27T11:35:55Z

scripts/appsubmitter.py

+    return sorted(unique_tags), sorted(unique_types), sorted(unique_licenses)
+
+
+def get_yaml_files(resources_dir):


Why are you not using this function?

training/scripts/generate_link_lists.py

Line 97 in e19da86

def load_dataframe(directory_path):

It gives you a DataFrame with all contents, which you can filter for unique entries in specific columns: df["license"].unique()

haesleinhuepf · 2024-08-27T11:36:29Z

scripts/appsubmitter.py

+def authenticate_with_github():
+    """
+    Authenticate with GitHub using the API key from environment variables.
+
+    Returns:
+        tuple: Authenticated GitHub instance and repository object.
+
+    Raises:
+        Exception: If authentication fails.
+    """
+    GITHUB_API_KEY = os.getenv('GITHUB_API_KEY')
+    if not GITHUB_API_KEY:
+        st.error("GitHub API Key is not set in the environment variables.")
+        st.stop()
+
+    try:
+        g = Github(GITHUB_API_KEY)
+        repo = g.get_repo("NFDI4BIOIMAGE/training")
+    except Exception as e:
+        st.error(f"Failed to authenticate with GitHub: {e}")
+        st.stop()


Consider using this function instead:

training/scripts/_github_utilities.py

Line 8 in e19da86

def get_github_repository(repository):

I do not see your changes here until you commit and push them

I'll push it after I'm done: "It gives you a DataFrame with all content, which you can filter for unique entries in specific columns: df["license"].unique()"

I do not see your changes here until you commit and push them

I marked it to told myself this is finished XD

haesleinhuepf · 2024-08-27T11:37:17Z

scripts/tags_type_licence_retrieve.py

+import yaml
+import os
+
+def load_yaml(file_path):


As mentioned above, consider using pre-existing functions instead of duplicating code.

haesleinhuepf · 2024-08-27T11:38:14Z

scripts/tags_type_licence_retrieve.py

+def extract_tags(yaml_content):
+    tags = set()
+    for item in yaml_content.get('resources', []):
+        if 'tags' in item:
+            tags.update(item['tags'])
+    return tags
+
+def extract_licenses(yaml_content):
+    licenses = set()
+    for item in yaml_content.get('resources', []):
+        if 'license' in item:
+            license_field = item['license']
+            if isinstance(license_field, list):
+                licenses.update(license_field)
+            else:
+                licenses.add(license_field)
+    return licenses
+
+def extract_types(yaml_content):
+    types = set()
+    for item in yaml_content.get('resources', []):
+        if 'type' in item:
+            types.update(item['type'])
+    return types


As mentioned above, consider re-using pre-existing functions, e.g. for retrieving a dataframe and then determine unique items in columns.

haesleinhuepf · 2024-08-27T11:38:39Z

scripts/tags_type_licence_retrieve.py

+def collect_tags_licenses_and_types_from_files(directory):
+    all_tags = set()
+    all_licenses = set()
+    all_types = set()
+    if os.path.exists(directory):
+        for file_name in os.listdir(directory):
+            if file_name.endswith('.yaml') or file_name.endswith('.yml'):
+                file_path = os.path.join(directory, file_name)
+                yaml_content = load_yaml(file_path)
+                all_tags.update(extract_tags(yaml_content))
+                all_licenses.update(extract_licenses(yaml_content))
+                all_types.update(extract_types(yaml_content))


As mentioned above, reuse code instead of implementing the same thing multiple times.

ahhh, you can delete this script, or I delete it. We don't need it anymore, I mean the scripts tags_type_licence_retrieve.py, I have already integrated it into the appsubmitter

Please delete it. It's your branch.

haesleinhuepf · 2024-08-27T11:39:42Z

scripts/tags_type_licence_retrieve.py

+    tags_output_file = os.path.abspath(os.path.join(os.path.dirname(__file__), 'tags.txt'))
+    licenses_output_file = os.path.abspath(os.path.join(os.path.dirname(__file__), 'licenses.txt'))
+    types_output_file = os.path.abspath(os.path.join(os.path.dirname(__file__), 'types.txt'))


These three text files, what do we need them for?

… "def load_dataframe(directory_path):" and "def read_yaml_file(filename): "

SeverusYixin · 2024-08-28T10:03:54Z

I have updated them all, so you can check them out now if you have time. :)

SeverusYixin · 2024-09-04T11:29:27Z

This PR also close #193

SeverusYixin · 2024-09-06T07:56:07Z

Hi@haesleinhuepf, you can check it here, I have finished it

… change everything Result example here: https://github.com/NFDI4BIOIMAGE/training/pull/198/files

haesleinhuepf

Hey @SeverusYixin ,

thanks for working on this! I left some comments below. Note: I will do these final modifications before merging this.

Thanks again!

haesleinhuepf · 2024-09-09T12:20:54Z

docs/_toc.yml

@@ -7,6 +7,7 @@ parts:
  - caption: Contributing
    chapters:
    - file: contributing/index
+    - file: contributing/index_2


I'm going to rename this file. "index_2" is not meaningful.

haesleinhuepf · 2024-09-09T12:27:28Z

scripts/generate_link_lists.py

@@ -89,11 +89,11 @@ def all_content(directory_path):
    for filename in os.listdir(directory_path):
        if filename.endswith('.yml'):
            print("Adding", filename)
-            new_content = read_yaml_file(directory_path + filename)
+            new_content = read_yaml_file(os.path.join(directory_path, filename))  # Corrected line


Why is there a comment "# Corrected line" ?

That time, I tried this code to solve the problem, and write a comment to tell you. With this update, it will work again.

Please do not spread such comments in the code, they will accumulate over time and it will be hard to read. Consider using permalinks instead, like this one:

https://github.com/NFDI4BIOIMAGE/training/blob/04cd328841d9b251e7eaf79f3b3b78ff94329687/scripts/generate_link_lists.py#L92

Views like this:

training/scripts/generate_link_lists.py

Line 92 in 04cd328

new_content = read_yaml_file(os.path.join(directory_path, filename)) # Corrected line

And is made by clicking here:

Ok, I will create a branch to delete this comment

haesleinhuepf · 2024-09-09T12:29:34Z

scripts/appsubmitter.py

+def all_content(directory_path):
+    """
+    Load all YAML data from a directory into a list of dictionaries.
+
+    Args:
+        directory_path (str): Path to the directory containing YAML files.
+
+    Returns:
+        dict: Dictionary with a key 'resources' containing a list of all resources from YAML files.
+    """
+    resources = []
+    for yaml_file in os.listdir(directory_path):
+        if yaml_file.endswith('.yml'):
+            yaml_data = read_yaml_file(os.path.join(directory_path, yaml_file))
+            if 'resources' in yaml_data:
+                resources.extend(yaml_data['resources'])
+    return {'resources': resources}


This function is not used. I will remove it.

haesleinhuepf · 2024-09-09T12:35:36Z

scripts/appsubmitter.py

+from _github_utilities import get_github_repository  
+
+# Correct the directory path for resources
+directory_path = os.path.join('..', 'resources')


This will only work if you call the script from within the path "scripts/". You can determine the path, where appsubmitter.py is located using __file__. I will implement this for you.

I got it, thank you:)

appssubmitter finial version

9beb1e2

haesleinhuepf requested changes Jul 19, 2024

View reviewed changes

SeverusYixin added 2 commits July 22, 2024 14:20

File Selection Function Update

87323f1

In this version, after the PR is merged, it will also close the corre…

078174b

…sponding issue.

haesleinhuepf requested changes Aug 6, 2024

View reviewed changes

SeverusYixin added 2 commits August 12, 2024 11:49

update for add a "tags/types/.." retriever

603e579

update for adding tags which are not in the tags select list

849e37d

Delete the specific mapping in the application and renew our data source

a17af85

Merge branch 'main' into app_for_adding_entries

2596d75

SeverusYixin added 2 commits August 27, 2024 13:22

update with Docstring

2ea918d

Merge branch 'app_for_adding_entries' of https://github.com/NFDI4BIOI…

738d248

…MAGE/training into app_for_adding_entries

haesleinhuepf requested changes Aug 27, 2024

View reviewed changes

SeverusYixin added 3 commits August 28, 2024 11:15

Update the function with "def get_github_repository(repository):" and…

58df5a7

… "def load_dataframe(directory_path):" and "def read_yaml_file(filename): "

Update the index_2 to make sure it is only about the app submitter.

2f49b88

Update the introduction with the latest version

019ec5e

SeverusYixin mentioned this pull request Aug 28, 2024

Try integrating Appsubmitter into our website! NFDI4BIOIMAGE/search_engine#30

Open

Update index_2.md

94c66c8

SeverusYixin added 2 commits September 5, 2024 13:10

update for the import function and removal of the yml file selector

93ce49f

make sure all the read and write is "utf-8"

7506ec6

haesleinhuepf added 6 commits September 9, 2024 14:10

renamed documentation page to reasonable filename

25ea9ce

make the app-submitter just append a new entry by the end, stop it to…

4639311

… change everything Result example here: https://github.com/NFDI4BIOIMAGE/training/pull/198/files

minor documentation update

329c52f

change order of fields in form

7d488db

remove unused code

0224804

clean up code, add comments, removed unused imports

6e093bd

haesleinhuepf reviewed Sep 9, 2024

View reviewed changes

renamed app in documentation to be consistent

327a342

haesleinhuepf merged commit 074effd into main Sep 9, 2024
1 check passed

haesleinhuepf deleted the app_for_adding_entries branch September 9, 2024 12:49

haesleinhuepf mentioned this pull request Sep 10, 2024

import function bug #193

Closed

		return sorted(unique_tags), sorted(unique_types), sorted(unique_licenses)


		def get_yaml_files(resources_dir):

appssubmitter finial version #128

appssubmitter finial version #128

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haesleinhuepf commented Jul 23, 2024 •

edited by SeverusYixin

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haesleinhuepf left a comment •

edited by SeverusYixin

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haesleinhuepf Sep 9, 2024 •

edited

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