mutts 1.0.3__py3-none-any.whl → 1.0.5__py3-none-any.whl

mutts/cli.py

@@ -107,11 +107,13 @@ def cli(
         # Write the generated data to 'DATA SHEET'
         user_facility_spreadsheet.to_excel(writer, index=False, sheet_name='DATA SHEET')
 
-        # Check if mapper is one of the v15 JGI templates
+        # Check if mapper is one of the v15 or v16 JGI templates
         mapper_basename = os.path.basename(mapper)
         jgi_v15_mappers = ['jgi_mg_header_v15.json', 'jgi_mt_header_v15.json']
+        jgi_v16_mappers = ['jgi_mg_header_v16.json', 'jgi_mt_header_v16.json']
+        jgi_mappers = jgi_v15_mappers + jgi_v16_mappers
 
-        if mapper_basename in jgi_v15_mappers:
+        if mapper_basename in jgi_mappers:
             # Path to static JGI v15 Excel template
             static_excel_path = os.path.join(
                 os.path.dirname(__file__), 'static-excel-tabs', 'JGI.Metagenome.NA.v15.xlsx'

mutts/retriever.py

@@ -120,7 +120,7 @@ class MetadataRetriever:
             all_sample_data_df = pd.concat(sample_data_dfs, ignore_index=True)
             # Merge the combined sample data with df on samp_name
             if not df.empty and not all_sample_data_df.empty:
-                df = pd.merge(df, all_sample_data_df, on="samp_name", how="outer")
+                df = pd.merge(df, all_sample_data_df, on="samp_name", how="left")
 
         # Auto-fill depth with 0 for JGI facilities if no value is provided
         if self.user_facility in ["jgi_mg", "jgi_mt", "jgi_mg_lr"]:
@@ -189,7 +189,7 @@ class MetadataRetriever:
 
         # Address 'Was sample DNAse treated?' col
         # Change from 'yes/no' to 'Y/N'
-        if self.user_facility in ["jgi_mg", "jgi_mt"] and "dnase" in df.columns:
+        if self.user_facility in ["jgi_mg", "jgi_mt", "jgi_mg_lr"] and "dnase" in df.columns:
             df.loc[df["dnase"] == "yes", "dnase"] = "Y"
             df.loc[df["dnase"] == "no", "dnase"] = "N"
 

{mutts-1.0.3.dist-info → mutts-1.0.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mutts
-Version: 1.0.3
+Version: 1.0.5
 Summary: Metadata for User facility Template Transformations
 License: MIT
 Keywords: NMDC,US DOE user facilities,metadata translation
@@ -31,6 +31,7 @@ Description-Content-Type: text/markdown
   - [MUTTs User Documentation](#mutts-user-documentation)
     - [Prerequisites](#prerequisites)
     - [Installation](#installation)
+    - [Updating to the Latest Version](#updating-to-the-latest-version)
     - [Usage](#usage)
       - [Example 1: Generate a JGI Metagenome spreadsheet](#example-1-generate-a-jgi-metagenome-spreadsheet)
       - [Example 2: Generate a JGI Metagenome v15 spreadsheet](#example-2-generate-a-jgi-metagenome-v15-spreadsheet)
@@ -61,9 +62,10 @@ The documentation and setup instructions in this section are meant for any user
 
 This is required for running the examples in the [Usage](#usage) section below (after going through all the [Installation](#installation) steps).
 
-Create a `.env` file in your working directory:
+Create a `.env` file in your working directory with the following environment variables:
 ```bash
 echo "DATA_PORTAL_REFRESH_TOKEN=your_token_here" > .env
+echo "SUBMISSION_PORTAL_BASE_URL=https://data.microbiomedata.org" >> .env
 ```
 
 To get your access token:
@@ -99,6 +101,24 @@ Download the mapper files you need from the [input-files directory](https://gith
 - For JGI Metagenome: `jgi_mg_header.json` or `jgi_mg_header_v15.json`
 - For JGI Metatranscriptome: `jgi_mt_header.json` or `jgi_mt_header_v15.json`
 
+### Updating to the Latest Version
+
+To ensure you have the latest features and bug fixes, you can upgrade the MUTTs package from PyPI:
+
+```bash
+pip install --upgrade mutts
+```
+
+To check your currently installed version:
+```bash
+pip show mutts
+```
+
+You can also install a specific version if needed:
+```bash
+pip install mutts==<version>
+```
+
 ### Usage
 
 Run the `mutts` command with the required options:
@@ -168,7 +188,7 @@ The software consists of two main components:
 - The `sub_port_mapping` keyword specifies mappings between Submission Portal columns/slots (as dictated by the [NMDC submission schema](https://microbiomedata.github.io/submission-schema/)) and user facility template columns
 - Examples available in [input-files/](input-files/)
 
-1. **`mutts` CLI**
+2. **`mutts` CLI**
 - Command-line application that performs the metadata conversion
 - Consumes mapper files and submission data as inputs
 
@@ -196,9 +216,10 @@ This installs the `mutts` package in development mode and creates the `mutts` co
 cp .env.example .env  # if available, or create a new .env file
 ```
 
-Add your NMDC API token:
+Add your NMDC API token and submission portal base URL:
 ```
 DATA_PORTAL_REFRESH_TOKEN=your_token_here
+SUBMISSION_PORTAL_BASE_URL=https://data.microbiomedata.org
 ```
 
 Get your token from: https://data.microbiomedata.org/user

mutts-1.0.5.dist-info/RECORD

@@ -0,0 +1,9 @@
+mutts/__init__.py,sha256=iTcKOq5Id9qudNWyTGPJyJGuS19yG-FhPlmSfuJM7jU,217
+mutts/cli.py,sha256=vCojLl4wNhZz-5qfKnB1NwfDfJoumqK722qZJBU88SM,5050
+mutts/retriever.py,sha256=Ex62c18tTVPSeIAoGJnRlPj17XC2gBF-V7WNE8ap_lw,8345
+mutts/spreadsheet.py,sha256=hSEEkTcTmkEFsktGG1_s4gAPuDys9Dnzbdk9cfJKwcY,5053
+mutts/static-excel-tabs/JGI.Metagenome.NA.v15.xlsx,sha256=tYlYX5QZVjiiCrsCsxfL73O0BdvlqttBjUyqXsv8s7s,22099
+mutts-1.0.5.dist-info/METADATA,sha256=06SUccJph-r0iO26ptjIm_i5QkSiLpe1_TJ-_TQ-f8w,9546
+mutts-1.0.5.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
+mutts-1.0.5.dist-info/entry_points.txt,sha256=rDp08H4MnNWGYHFE6ZAqOocRyTp68IPJsjXTcQppi8s,39
+mutts-1.0.5.dist-info/RECORD,,

{mutts-1.0.3.dist-info → mutts-1.0.5.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.2.1
+Generator: poetry-core 2.3.0
 Root-Is-Purelib: true
 Tag: py3-none-any

mutts-1.0.3.dist-info/RECORD

@@ -1,9 +0,0 @@
-mutts/__init__.py,sha256=iTcKOq5Id9qudNWyTGPJyJGuS19yG-FhPlmSfuJM7jU,217
-mutts/cli.py,sha256=YzRnMLEtbFc2yuAYqWoljvk0Z9IEHDw3XefjTZE8Rbg,4912
-mutts/retriever.py,sha256=B9cShEaeOY4BN1nWaML_UzMTR971X4rn1XfqyvZhAno,8333
-mutts/spreadsheet.py,sha256=hSEEkTcTmkEFsktGG1_s4gAPuDys9Dnzbdk9cfJKwcY,5053
-mutts/static-excel-tabs/JGI.Metagenome.NA.v15.xlsx,sha256=tYlYX5QZVjiiCrsCsxfL73O0BdvlqttBjUyqXsv8s7s,22099
-mutts-1.0.3.dist-info/METADATA,sha256=JU9879qBfZ0iLTHWHCR1J6XUyUSXPq1sSOm7wW0b0Zg,8928
-mutts-1.0.3.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-mutts-1.0.3.dist-info/entry_points.txt,sha256=rDp08H4MnNWGYHFE6ZAqOocRyTp68IPJsjXTcQppi8s,39
-mutts-1.0.3.dist-info/RECORD,,