Sign upLogin

KarrLab/datanator

View on GitHub
Star
datanator/data_source/protein_localization/victoria_insert_experimental_protein.py

Summary

Maintainability
D
3 days
Test Coverage

Function process_docs has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
Open

    def process_docs(self, skip=0):
        #read .tsv file
        data=pd.read_csv('Experimental-PSORTdb-v4.00.tsv',delimiter="\t")
        data = data.where(pd.notnull(data), None)
Severity: Minor
Found in datanator/data_source/protein_localization/victoria_insert_experimental_protein.py - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function __init__ has 8 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def __init__(self,
Severity: Major
Found in datanator/data_source/protein_localization/victoria_insert_experimental_protein.py - About 1 hr to fix

    Identical blocks of code found in 4 locations. Consider refactoring.
    Open

        def __init__(self,
                 MongoDB=None,
                 db=None,
                 collection=None,
                 max_entries=float('inf'),
    Severity: Major
    Found in datanator/data_source/protein_localization/victoria_insert_experimental_protein.py and 3 other locations - About 7 hrs to fix
    datanator/data_source/protein_localization/victoria_insert_archaea.py on lines 8..26
    datanator/data_source/protein_localization/victoria_insert_neg_wo_outer_membrane.py on lines 7..25
    datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 10..28

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 114.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Similar blocks of code found in 11 locations. Consider refactoring.
    Open

            if doc!=None:
            for j in range(len(doc["canon_anc_names"])):
                d={}
                d["ncbi_taxonomy_id"]=doc["canon_anc_ids"][j]
                d["name"]=doc["canon_anc_names"][j]
    Severity: Major
    Found in datanator/data_source/protein_localization/victoria_insert_experimental_protein.py and 10 other locations - About 6 hrs to fix
    datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py on lines 121..126
    datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py on lines 195..200
    datanator/data_source/protein_half_lives/victoria_parse_mouse_global_quantification.py on lines 225..230
    datanator/data_source/protein_half_lives/victoria_parse_proteome_half_lives.py on lines 126..131
    datanator/data_source/protein_half_lives/victoria_parse_proteome_half_lives.py on lines 257..262
    datanator/data_source/protein_half_lives/victoria_parse_quantification_budding_yeast_proteome.py on lines 98..103
    datanator/data_source/protein_half_lives/victoria_parse_yeast_global_proteome_turnover.py on lines 139..144
    datanator/data_source/protein_half_lives/victoria_parse_yeast_global_proteome_turnover.py on lines 223..228
    datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 198..203
    datanator/data_source/rna_localization/victoria_parse_LncAtlas.py on lines 130..135

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 102.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Similar blocks of code found in 11 locations. Consider refactoring.
    Open

    def main():
    conf=config.Victoria()
    conf_main = config.Config()
    username = conf.USERNAME
    password = conf.PASSWORD
    Severity: Major
    Found in datanator/data_source/protein_localization/victoria_insert_experimental_protein.py and 10 other locations - About 3 hrs to fix
    datanator/data_source/protein_half_lives/victoria_parse_mouse_global_quantification.py on lines 314..327
    datanator/data_source/protein_half_lives/victoria_parse_proteome_half_lives.py on lines 376..389
    datanator/data_source/protein_half_lives/victoria_parse_quantification_budding_yeast_proteome.py on lines 158..170
    datanator/data_source/protein_half_lives/victoria_parse_yeast_global_proteome_turnover.py on lines 316..329
    datanator/data_source/protein_localization/experimental.py on lines 63..74
    datanator/data_source/protein_localization/victoria_insert_archaea.py on lines 148..159
    datanator/data_source/protein_localization/victoria_insert_neg_wo_outer_membrane.py on lines 148..159
    datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 272..283
    datanator/data_source/rna_localization/victoria_parse_LncAtlas.py on lines 224..236
    datanator/parse_metabolite_concentration.py on lines 44..55

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 73.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Similar blocks of code found in 3 locations. Consider refactoring.
    Open

                if obs["entity"]["identifiers"][0]["value"]!="None":
                id_name="uniprot_id"
                value=obs["entity"]["identifiers"][0]["value"]
    Severity: Major
    Found in datanator/data_source/protein_localization/victoria_insert_experimental_protein.py and 2 other locations - About 45 mins to fix
    datanator/data_source/protein_localization/victoria_insert_experimental_protein.py on lines 151..153
    datanator/data_source/protein_localization/victoria_insert_experimental_protein.py on lines 154..156

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 35.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Similar blocks of code found in 3 locations. Consider refactoring.
    Open

                    if obs["entity"]["identifiers"][1]["value"]!="None":
                    id_name="Refseq_Accession"
                    value=obs["entity"]["identifiers"][1]["value"]
    Severity: Major
    Found in datanator/data_source/protein_localization/victoria_insert_experimental_protein.py and 2 other locations - About 45 mins to fix
    datanator/data_source/protein_localization/victoria_insert_experimental_protein.py on lines 147..149
    datanator/data_source/protein_localization/victoria_insert_experimental_protein.py on lines 154..156

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 35.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Similar blocks of code found in 3 locations. Consider refactoring.
    Open

                    elif obs["entity"]["identifiers"][2]["value"]!="None":
                    id_name="Other_Accession"
                    value=obs["entity"]["identifiers"][2]["value"]
    Severity: Major
    Found in datanator/data_source/protein_localization/victoria_insert_experimental_protein.py and 2 other locations - About 45 mins to fix
    datanator/data_source/protein_localization/victoria_insert_experimental_protein.py on lines 147..149
    datanator/data_source/protein_localization/victoria_insert_experimental_protein.py on lines 151..153

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 35.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Similar blocks of code found in 3 locations. Consider refactoring.
    Open

                elif data.iloc[i,1]!="None":
                con_0 = {"identifiers":{"$elemMatch":{"namespace": "Refseq_Accession",
                "value":str(data.iloc[i,1])}}}
    Severity: Major
    Found in datanator/data_source/protein_localization/victoria_insert_experimental_protein.py and 2 other locations - About 40 mins to fix
    datanator/data_source/protein_localization/victoria_insert_experimental_protein.py on lines 127..128
    datanator/data_source/protein_localization/victoria_insert_experimental_protein.py on lines 132..133

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 34.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Similar blocks of code found in 3 locations. Consider refactoring.
    Open

                elif data.iloc[i,2]!="None":
                con_0 = {"identifiers":{"$elemMatch":{"namespace":"Other_Accession","value":str(data.iloc[i,2])}}}
    Severity: Major
    Found in datanator/data_source/protein_localization/victoria_insert_experimental_protein.py and 2 other locations - About 40 mins to fix
    datanator/data_source/protein_localization/victoria_insert_experimental_protein.py on lines 127..128
    datanator/data_source/protein_localization/victoria_insert_experimental_protein.py on lines 129..131

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 34.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Similar blocks of code found in 3 locations. Consider refactoring.
    Open

                if data.iloc[i,0]!="None":
                con_0={"identifiers":{"$elemMatch":{"namespace":"uniprot_id","value":str(data.iloc[i,0])}}}
    Severity: Major
    Found in datanator/data_source/protein_localization/victoria_insert_experimental_protein.py and 2 other locations - About 40 mins to fix
    datanator/data_source/protein_localization/victoria_insert_experimental_protein.py on lines 129..131
    datanator/data_source/protein_localization/victoria_insert_experimental_protein.py on lines 132..133

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 34.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    There are no issues that match your filters.

    Category
    Status